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Brouillette M. Gene length could be a critical factor in the aging of the genome. Proc Natl Acad Sci U S A 2024; 121:e2416630121. [PMID: 39236237 DOI: 10.1073/pnas.2416630121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024] Open
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2
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Vermeij WP, Alyodawi K, van Galen I, von der Heide JL, Birkisdóttir MB, Van't Sant LJ, Ozinga RA, Komninos DSJ, Smit K, Rijksen YMA, Brandt RMC, Barnhoorn S, Jaarsma D, Vaiyapuri S, Ritvos O, Huber TB, Kretz O, Patel K. Improved health by combining dietary restriction and promoting muscle growth in DNA repair-deficient progeroid mice. J Cachexia Sarcopenia Muscle 2024. [PMID: 39245994 DOI: 10.1002/jcsm.13570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 06/19/2024] [Accepted: 07/23/2024] [Indexed: 09/10/2024] Open
Abstract
BACKGROUND Ageing is a complex multifactorial process, impacting all organs and tissues, with DNA damage accumulation serving as a common underlying cause. To decelerate ageing, various strategies have been applied to model organisms and evaluated for health and lifespan benefits. Dietary restriction (DR, also known as caloric restriction) is a well-established long-term intervention recognized for its universal anti-ageing effects. DR temporarily suppresses growth, and when applied to progeroid DNA repair-deficient mice doubles lifespan with systemic health benefits. Counterintuitively, attenuation of myostatin/activin signalling by soluble activin receptor (sActRIIB), boosts the growth of muscle and, in these animals, prevents muscle wasting, improves kidney functioning, and compresses morbidity. METHODS Here, we investigated a combined approach, applying an anabolic regime (sActRIIB) at the same time as DR to Ercc1Δ/- progeroid mice. Following both single treatments and combined, we monitored global effects on body weight, lifespan and behaviour, and local effects on muscle and tissue weight, muscle morphology and function, and ultrastructural and transcriptomic changes in muscle and kidney. RESULTS Lifespan was mostly influenced by DR (extended from approximately 20 to 40 weeks; P < 0.001), with sActRIIB clearly increasing muscle mass (35-65%) and tetanic force (P < 0.001). The combined regime yielded a stable uniform body weight, but increased compared with DR alone, synergistically improved motor coordination and further delayed the onset and development of balance problems. sActRIIB significantly increased muscle fibre size (P < 0.05) in mice subjected to DR and lowered all signs of muscle damage. Ercc1Δ/- mice showed abnormal neuromuscular junctions. Single interventions by sActRIIB treatment or DR only partially rescued this phenotype, while in the double intervention group, the regularly shaped junctional foldings were maintained. In kidney of Ercc1Δ/- mice, we observed a mild but significant foot process effacement, which was restored by either intervention. Transcriptome analysis also pointed towards reduced levels of DNA damage in muscle and kidney by DR, but not sActRIIB, while these levels retained lower in the double intervention. CONCLUSIONS In muscle, we found synergistic effects of combining sActRIIB with DR, but not in kidney, with an overall better health in the double intervention group. Crucially, the benefits of each single intervention are not lost when administered in combination, but rather strengthened, even when sActRIIB was applied late in life, opening opportunities for translation to human.
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Affiliation(s)
- Wilbert P Vermeij
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Khalid Alyodawi
- School of Biological Sciences, University of Reading, Reading, UK
- College of Medicine, Wasit University, Kut, Iraq
| | - Ivar van Galen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Jennie L von der Heide
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), Hamburg, Germany
| | - María B Birkisdóttir
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Lisanne J Van't Sant
- Department of Neuroscience, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Rutger A Ozinga
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Daphne S J Komninos
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Kimberly Smit
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Yvonne M A Rijksen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Dick Jaarsma
- Department of Neuroscience, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | | | - Olli Ritvos
- Department of Physiology, University of Helsinki, Helsinki, Finland
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), Hamburg, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), Hamburg, Germany
| | - Ketan Patel
- School of Biological Sciences, University of Reading, Reading, UK
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Abdelmageed M, Palanisamy P, Vernail V, Silberman Y, Paul S, Paul A. An altered cell-specific subcellular distribution of translesion synthesis DNA polymerase kappa (POLK) in aging neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.27.559771. [PMID: 39026788 PMCID: PMC11257472 DOI: 10.1101/2023.09.27.559771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Genomic stability is critical for cellular function, however, in the central nervous system highly metabolically active differentiated neurons are challenged to maintain their genome over the organismal lifespan without replication. DNA damage in neurons increases with chronological age and accelerates in neurodegenerative disorders, resulting in cellular and systemic dysregulation. Distinct DNA damage response strategies have evolved with a host of polymerases. The Y-family translesion synthesis (TLS) polymerases are well known for bypassing and repairing damaged DNA in dividing cells. However, their expression, dynamics, and role if any, in enduring postmitotic differentiated neurons of the brain are completely unknown. We show through systematic longitudinal studies for the first time that DNA polymerase kappa (POLK), a member of the Y-family polymerases, is highly expressed in neurons. With chronological age, there is a progressive and significant reduction of nuclear POLK with a concomitant accumulation in the cytoplasm that is predictive of brain tissue age. The reduction of nuclear POLK in old brains is congruent with an increase in DNA damage markers. The nuclear POLK colocalizes with damaged sites and DNA repair proteins. The cytoplasmic POLK accumulates with stress granules and endo/lysosomal markers. Nuclear POLK expression is significantly higher in GABAergic interneurons compared to excitatory pyramidal neurons and lowest in non-neurons, possibly reflective of the inherent biological differences such as firing rates and neuronal activity. Interneurons associated with microglia have significantly higher levels of cytoplasmic POLK in old age. Finally, we show that neuronal activity itself can lead to an increase in nuclear POLK levels and a reduction of the cytoplasmic fraction. Our findings open a new avenue in understanding how different classes of postmitotic neurons deploy TLS polymerase(s) to maintain their genomic integrity over time, which will help design strategies for longevity, healthspan, and prevention of neurodegeneration.
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Ahmad A, Braden A, Khan S, Xiao J, Khan MM. Crosstalk between the DNA damage response and cellular senescence drives aging and age-related diseases. Semin Immunopathol 2024; 46:10. [PMID: 39095660 DOI: 10.1007/s00281-024-01016-7] [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: 03/13/2024] [Accepted: 05/21/2024] [Indexed: 08/04/2024]
Abstract
Cellular senescence is a crucial process of irreversible cell-cycle arrest, in which cells remain alive, but permanently unable to proliferate in response to distinct types of stressors. Accumulating evidence suggests that DNA damage builds over time and triggers DNA damage response signaling, leading to cellular senescence. Cellular senescence serves as a platform for the perpetuation of inflammatory responses and is central to numerous age-related diseases. Defects in DNA repair genes or senescence can cause premature aging disease. Therapeutic approaches limiting DNA damage or senescence contribute to a rescued phenotype of longevity and neuroprotection, thus suggesting a mechanistic interaction between DNA damage and senescence. Here, we offer a unique perspective on the crosstalk between the DNA damage response pathway and senescence as well as their contribution to age-related diseases. We further summarize recent progress on the mechanisms and therapeutics of senescence, address existing challenges, and offering new insights and future directions in the senescence field.
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Affiliation(s)
- Ajmal Ahmad
- Department of Ophthalmology, College of Medicine, King Saud University Riyadh, Riyadh, Saudi Arabia
| | - Anneliesse Braden
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sazzad Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
| | - Jianfeng Xiao
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA.
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, USA.
- Center for Muscle, Metabolism and Neuropathology, Division of Regenerative and Rehabilitation Sciences, Department of Physical Therapy, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN, USA.
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van Thiel BS, de Boer M, Ridwan Y, de Kleijnen MGJ, van Vliet N, van der Linden J, de Beer I, van Heijningen PM, Vermeij WP, Hoeijmakers JHJ, Danser AHJ, Kanaar R, Duncker DJ, van der Pluijm I, Essers J. Hybrid Molecular and Functional Micro-CT Imaging Reveals Increased Myocardial Apoptosis Preceding Cardiac Failure in Progeroid Ercc1 Mice. Mol Imaging Biol 2024; 26:628-637. [PMID: 38498063 PMCID: PMC11281969 DOI: 10.1007/s11307-024-01902-4] [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: 11/20/2023] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/19/2024]
Abstract
PURPOSE In this study, we explored the role of apoptosis as a potential biomarker for cardiac failure using functional micro-CT and fluorescence molecular tomography (FMT) imaging techniques in Ercc1 mutant mice. Ercc1 is involved in multiple DNA repair pathways, and its mutations contribute to accelerated aging phenotypes in both humans and mice, due to the accumulation of DNA lesions that impair vital DNA functions. We previously found that systemic mutations and cardiomyocyte-restricted deletion of Ercc1 in mice results in left ventricular (LV) dysfunction at older age. PROCEDURES AND RESULTS Here we report that combined functional micro-CT and FMT imaging allowed us to detect apoptosis in systemic Ercc1 mutant mice prior to the development of overt LV dysfunction, suggesting its potential as an early indicator and contributing factor of cardiac impairment. The detection of apoptosis in vivo was feasible as early as 12 weeks of age, even when global LV function appeared normal, underscoring the potential of apoptosis as an early predictor of LV dysfunction, which subsequently manifested at 24 weeks. CONCLUSIONS This study highlights the utility of combined functional micro-CT and FMT imaging in assessing cardiac function and detecting apoptosis, providing valuable insights into the potential of apoptosis as an early biomarker for cardiac failure.
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Affiliation(s)
- Bibi S van Thiel
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus MC Cardiovascular Institute, Erasmus University Medical Center, Room 702A, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Martine de Boer
- Division of Experimental Cardiology, Department of Cardiology, Erasmus MC Cardiovascular Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yanto Ridwan
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiotherapy, Erasmus University Medical Center, Room 702A, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - Marion G J de Kleijnen
- Division of Experimental Cardiology, Department of Cardiology, Erasmus MC Cardiovascular Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Nicole van Vliet
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Janette van der Linden
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Division of Experimental Cardiology, Department of Cardiology, Erasmus MC Cardiovascular Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Isa de Beer
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Paula M van Heijningen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wilbert P Vermeij
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Institute for Genome Stability in Aging and Disease, Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - A H Jan Danser
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Dirk J Duncker
- Division of Experimental Cardiology, Department of Cardiology, Erasmus MC Cardiovascular Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Department of Vascular Surgery, Erasmus MC Cardiovascular Institute, Erasmus University Medical Center, Room 702A, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - Jeroen Essers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
- Department of Vascular Surgery, Erasmus MC Cardiovascular Institute, Erasmus University Medical Center, Room 702A, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
- Department of Radiotherapy, Erasmus University Medical Center, Room 702A, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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Oudmaijer CAJ, Komninos DSJ, Hoeijmakers JHJ, IJzermans JNM, Vermeij WP. Clinical implications of nutritional interventions reducing calories, a systematic scoping review. Clin Nutr ESPEN 2024; 63:427-439. [PMID: 38986906 DOI: 10.1016/j.clnesp.2024.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024]
Abstract
BACKGROUND & AIMS Caloric restriction (CR) constitutes a dietary approach of (temporarily) reducing calorie intake thereby inducing resilience and resistance mechanisms and promoting health. While CR's feasibility and safety have been proven in human trials, its full benefits and translation to different study populations warrants further exploration. METHODS We here conducted a systematic scoping review adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. RESULTS Our search resulted in 3745 individual records, of which 40 were included. We showed that all studies consistently demonstrated the feasibility and safety of CR-like interventions. The specific effects of nutritional preconditioning vary, further underscoring the need for carefully crafted strategies, according to the intended effect, patient population, and logistical limitations. CONCLUSIONS CR-like interventions (long-term CR or short-term fasting) are feasible in a broad range of patient populations. Whether it has clinical benefit, f.i. reducing treatment-induced side effects and enhancing therapy efficacy, has to be investigated further.
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Affiliation(s)
- C A J Oudmaijer
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands; Erasmus MC Transplant Institute, Division of Hepatobiliary and Transplantation Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
| | - D S J Komninos
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
| | - J H J Hoeijmakers
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands; Oncode Institute, Utrecht, The Netherlands; Erasmus MC Cancer Institute, Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, The Netherlands; Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Centre for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - J N M IJzermans
- Erasmus MC Transplant Institute, Division of Hepatobiliary and Transplantation Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - W P Vermeij
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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Liharska L, Charney A. Transcriptomics : Approaches to Quantifying Gene Expression and Their Application to Studying the Human Brain. Curr Top Behav Neurosci 2024. [PMID: 38972894 DOI: 10.1007/7854_2024_466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
To date, the field of transcriptomics has been characterized by rapid methods development and technological advancement, with new technologies continuously rendering older ones obsolete.This chapter traces the evolution of approaches to quantifying gene expression and provides an overall view of the current state of the field of transcriptomics, its applications to the study of the human brain, and its place in the broader emerging multiomics landscape.
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Affiliation(s)
- Lora Liharska
- Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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8
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Swer PB, Kharbuli B, Syiem D, Sharma R. Age-related decline in the expression of BRG1, ATM and ATR are partially reversed by dietary restriction in the livers of female mice. Biogerontology 2024:10.1007/s10522-024-10117-7. [PMID: 38970714 DOI: 10.1007/s10522-024-10117-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 06/26/2024] [Indexed: 07/08/2024]
Abstract
BRG1 (Brahma-related gene 1) is a member of the SWI/SNF (switch/sucrose nonfermentable) chromatin remodeling complex which utilizes the energy from ATP hydrolysis for its activity. In addition to its role of regulating the expression of a vast array of genes, BRG1 mediates DNA repair upon genotoxic stress and regulates senescence. During organismal ageing, there is accumulation of unrepaired/unrepairable DNA damage due to progressive breakdown of the DNA repair machinery. The present study investigates the expression level of BRG1 as a function of age in the liver of 5- and 21-month-old female mice. It also explores the impact of dietary restriction on BRG1 expression in the old (21-month) mice. Salient findings of the study are: Real-time PCR and Western blot analyses reveal that BRG1 levels are higher in 5-month-old mice but decrease significantly with age. Dietary restriction increases BRG1 expression in the 21-month-old mice, nearly restoring it to the level observed in the younger group. Similar expression patterns are observed for DNA damage response genes ATM (Ataxia Telangiectasia Mutated) and ATR (Ataxia Telangiectasia and Rad3-related) with the advancement in age and which appears to be modulated by dietary restriction. BRG1 transcriptionally regulates ATM as a function of age and dietary restriction. These results suggest that BRG1, ATM and ATR are downregulated as mice age, and dietary restriction can restore their expression. This implies that dietary restriction may play a crucial role in regulating BRG1 and related gene expression, potentially maintaining liver repair and metabolic processes as mice age.
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Affiliation(s)
- Pynskhem Bok Swer
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | | | - Donkupar Syiem
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Ramesh Sharma
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
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Badja C, Momen S, Koh GCC, Boushaki S, Roumeliotis TI, Kozik Z, Jones I, Bousgouni V, Dias JML, Krokidis MG, Young J, Chen H, Yang M, Docquier F, Memari Y, Valcarcel-Zimenez L, Gupta K, Kong LR, Fawcett H, Robert F, Zhao S, Degasperi A, Kumar Y, Davies H, Harris R, Frezza C, Chatgilialoglu C, Sarkany R, Lehmann A, Bakal C, Choudhary J, Fassihi H, Nik-Zainal S. Insights from multi-omic modeling of neurodegeneration in xeroderma pigmentosum using an induced pluripotent stem cell system. Cell Rep 2024; 43:114243. [PMID: 38805398 DOI: 10.1016/j.celrep.2024.114243] [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: 07/27/2023] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Xeroderma pigmentosum (XP) is caused by defective nucleotide excision repair of DNA damage. This results in hypersensitivity to ultraviolet light and increased skin cancer risk, as sunlight-induced photoproducts remain unrepaired. However, many XP patients also display early-onset neurodegeneration, which leads to premature death. The mechanism of neurodegeneration is unknown. Here, we investigate XP neurodegeneration using pluripotent stem cells derived from XP patients and healthy relatives, performing functional multi-omics on samples during neuronal differentiation. We show substantially increased levels of 5',8-cyclopurine and 8-oxopurine in XP neuronal DNA secondary to marked oxidative stress. Furthermore, we find that the endoplasmic reticulum stress response is upregulated and reversal of the mutant genotype is associated with phenotypic rescue. Critically, XP neurons exhibit inappropriate downregulation of the protein clearance ubiquitin-proteasome system (UPS). Chemical enhancement of UPS activity in XP neuronal models improves phenotypes, albeit inadequately. Although more work is required, this study presents insights with intervention potential.
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Affiliation(s)
- Cherif Badja
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK.
| | - Sophie Momen
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Gene Ching Chiek Koh
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Soraya Boushaki
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Zuza Kozik
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Ian Jones
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Vicky Bousgouni
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - João M L Dias
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Marios G Krokidis
- Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", Agia Paraskevi Attikis, 15310 Athens, Greece; Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece
| | - Jamie Young
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Hongwei Chen
- Wellcome Sanger Institute, Hinxton CB10 1RQ, UK; Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Ming Yang
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - France Docquier
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK
| | - Yasin Memari
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Lorea Valcarcel-Zimenez
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Komal Gupta
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Li Ren Kong
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; NUS Centre for Cancer Research, N2CR, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Heather Fawcett
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Florian Robert
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Salome Zhao
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Andrea Degasperi
- Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Yogesh Kumar
- Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Helen Davies
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Rebecca Harris
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Robert Sarkany
- National Xeroderma Pigmentosum Service, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London SE1 7EH, UK
| | - Alan Lehmann
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Chris Bakal
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Jyoti Choudhary
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London SE1 7EH, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK.
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10
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Gutta G, Mehta J, Kingston R, Xie J, Brenner E, Ma F, Herrup K. DNA Damage and Senescence in the Aging and Alzheimer's Disease Cortex Are Not Uniformly Distributed. Biomedicines 2024; 12:1327. [PMID: 38927534 PMCID: PMC11201767 DOI: 10.3390/biomedicines12061327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative illness with a typical age of onset exceeding 65 years of age. The age dependency of the condition led us to track the appearance of DNA damage in the frontal cortex of individuals who died with a diagnosis of AD. The focus on DNA damage was motivated by evidence that increasing levels of irreparable DNA damage are a major driver of the aging process. The connection between aging and the loss of genomic integrity is compelling because DNA damage has also been identified as a possible cause of cellular senescence. The number of senescent cells has been reported to increase with age, and their senescence-associated secreted products are likely contributing factors to age-related illnesses. We tracked DNA damage with 53BP1 and cellular senescence with p16 immunostaining of human post-mortem brain samples. We found that DNA damage was significantly increased in the BA9 region of the AD cortex compared with the same region in unaffected controls (UCs). In the AD but not UC cases, the density of cells with DNA damage increased with distance from the pia mater up to approximately layer V and then decreased in deeper areas. This pattern of DNA damage was overlaid with the pattern of cellular senescence, which also increased with cortical depth. On a cell-by-cell basis, we found that the intensities of the two markers were tightly linked in the AD but not the UC brain. To test whether DNA damage was a causal factor in the emergence of the senescence program, we used etoposide treatment to damage the DNA of cultured mouse primary neurons. While DNA damage increased after treatment, after 24 h, no change in the expression of senescence-associated markers was observed. Our work suggests that DNA damage and cellular senescence are both increased in the AD brain and increasingly coupled. We propose that in vivo, the relationship between the two age-related processes is more complex than previously thought.
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Affiliation(s)
- Gnanesh Gutta
- School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (G.G.)
| | - Jay Mehta
- School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15260, USA;
| | - Rody Kingston
- School of Medicine, Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.K.); (K.H.)
| | - Jiaan Xie
- School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (G.G.)
| | - Eliana Brenner
- School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA; (G.G.)
| | - Fulin Ma
- School of Medicine, Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.K.); (K.H.)
| | - Karl Herrup
- School of Medicine, Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15260, USA; (R.K.); (K.H.)
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11
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He Y, Yang W, Huang L, Mever MA, Ramautar R, Harms A, Rijksen Y, Brandt RM, Barnhoorn S, Smit K, Jaarsma D, Lindenburg P, Hoeijmakers JHJ, Vermeij WP, Hankemeier T. Metabolomic analysis of dietary-restriction-induced attenuation of sarcopenia in prematurely aging DNA repair-deficient mice. J Cachexia Sarcopenia Muscle 2024; 15:868-882. [PMID: 38689513 PMCID: PMC11154776 DOI: 10.1002/jcsm.13433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 12/17/2023] [Accepted: 12/20/2023] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Sarcopenia is characterized by loss of skeletal muscle mass and function, and is a major risk factor for disability and independence in the elderly. Effective medication is not available. Dietary restriction (DR) has been found to attenuate aging and aging-related diseases, including sarcopenia, but the mechanism of both DR and sarcopenia are incompletely understood. METHODS In this study, mice body weight, fore and all limb grip strength, and motor learning and coordination performance were first analysed to evaluate the DR effects on muscle functioning. Liquid chromatography-mass spectrometry (LC-MS) was utilized for the metabolomics study of the DR effects on sarcopenia in progeroid DNA repair-deficient Ercc1∆/- and Xpg-/- mice, to identify potential biomarkers for attenuation of sarcopenia. RESULTS Muscle mass was significantly (P < 0.05) decreased (13-20%) by DR; however, the muscle quality was improved with retained fore limbs and all limbs grip strength in Ercc1∆/- and Xpg-/- mice. The LC-MS results revealed that metabolites and pathways related to oxidative-stress, that is, GSSG/GSH (P < 0.01); inflammation, that is, 9-HODE, 11-HETE (P < 0.05), PGE2, PGD2, and TXB2 (P < 0.01); and muscle growth (PGF2α) (P < 0.01) and regeneration stimulation (PGE2) (P < 0.05) are significantly downregulated by DR. On the other hand, anti-inflammatory indicator and several related metabolites, that is, β-hydroxybutyrate (P < 0.01), 14,15-DiHETE (P < 0.0001), 8,9-EET, 12,13-DiHODE, and PGF1 (P < 0.05); consumption of sources of energy (i.e., muscle and liver glycogen); and energy production pathways, that is, glycolysis (glucose, glucose-6-P, fructose-6-P) (P < 0.01), tricarboxylic acid cycle (succinyl-CoA, malate) (P < 0.001), and gluconeogenesis-related metabolite, alanine (P < 0.01), are significantly upregulated by DR. The notably (P < 0.01) down-modulated muscle growth (PGF2α) and regeneration (PGE2) stimulation metabolite and the increased consumption of glycogen in muscle and liver may be related to the significantly (P < 0.01) lower body weight and muscle mass by DR. The downregulated oxidative stress, pro-inflammatory mediators, and upregulated anti-inflammatory metabolites resulted in a lower energy expenditure, which contributed to enhanced muscle quality together with upregulated energy production pathways by DR. The improved muscle quality may explain why grip strength is maintained and motor coordination and learning performance are improved by DR in Ercc1∆/- and Xpg-/- mice. CONCLUSIONS This study provides fundamental supporting information on biomarkers and pathways related to the attenuation of sarcopenia, which might facilitate its diagnosis, prevention, and clinical therapy.
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Affiliation(s)
- Yupeng He
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Wei Yang
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Luojiao Huang
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Marlien Admiraal‐van Mever
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Amy Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
| | - Yvonne Rijksen
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Renata M.C. Brandt
- Department of Molecular Genetics, Erasmus MC Cancer InstituteErasmus University Medical Center RotterdamRotterdamThe Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC Cancer InstituteErasmus University Medical Center RotterdamRotterdamThe Netherlands
| | - Kimberly Smit
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Dick Jaarsma
- Department of NeuroscienceErasmus University Medical Center RotterdamRotterdamThe Netherlands
| | - Peter Lindenburg
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
- Research Group Metabolomics, Leiden Center for Applied BioscienceUniversity of Applied Sciences LeidenLeidenThe Netherlands
| | - Jan H. J. Hoeijmakers
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
- Department of Molecular Genetics, Erasmus MC Cancer InstituteErasmus University Medical Center RotterdamRotterdamThe Netherlands
- Institute for Genome Stability in Aging and Disease, Cologne Excellence Cluster for Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug ResearchLeiden UniversityLeidenThe Netherlands
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12
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Sember E, Chennakesavula R, Beard B, Opoola M, Hwangbo DS. Dietary restriction fails to extend lifespan of Drosophila model of Werner syndrome. G3 (BETHESDA, MD.) 2024; 14:jkae056. [PMID: 38491858 PMCID: PMC11075538 DOI: 10.1093/g3journal/jkae056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
Werner syndrome (WS) is a rare genetic disease in humans, caused by mutations in the WRN gene that encodes a protein containing helicase and exonuclease domains. WS is characterized by symptoms of accelerated aging in multiple tissues and organs, involving increased risk of cancer, heart failure, and metabolic dysfunction. These conditions ultimately lead to the premature mortality of patients with WS. In this study, using the null mutant flies (WRNexoΔ) for the gene WRNexo (CG7670), homologous to the exonuclease domain of WRN in humans, we examined how diets affect the lifespan, stress resistance, and sleep/wake patterns of a Drosophila model of WS. We observed that dietary restriction (DR), one of the most robust nongenetic interventions to extend lifespan in animal models, failed to extend the lifespan of WRNexoΔ mutant flies and even had a detrimental effect in females. Interestingly, the mean lifespan of WRNexoΔ mutant flies was not reduced on a protein-rich diet compared to that of wild-type (WT) flies. Compared to WT control flies, the mutant flies also exhibited altered responses to DR in their resistance to starvation and oxidative stress, as well as changes in sleep/wake patterns. These findings show that the WRN protein is necessary for mediating the effects of DR and suggest that the exonuclease domain of WRN plays an important role in metabolism in addition to its primary role in DNA-repair and genome stability.
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Affiliation(s)
- Eileen Sember
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | | | - Breanna Beard
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Mubaraq Opoola
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Dae-Sung Hwangbo
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
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13
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Chen Q, Wu M, Tang Q, Yan P, Zhu L. Age-Related Alterations in Immune Function and Inflammation: Focus on Ischemic Stroke. Aging Dis 2024; 15:1046-1074. [PMID: 37728582 PMCID: PMC11081165 DOI: 10.14336/ad.2023.0721-1] [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: 05/03/2023] [Accepted: 07/21/2023] [Indexed: 09/21/2023] Open
Abstract
The aging of the global population poses significant scientific challenges. Moreover, the biological process of aging is the most significant risk factor for most chronic illnesses; therefore, understanding the molecular and cellular mechanisms underlying these aging-related challenges is crucial for extending the healthy lifespan of older individuals. Preventing brain aging remains a priority public health goal, and integrative and comprehensive aging analyses have revealed that immunosenescence is a potential cause of age-related brain damage and disease (e.g., stroke). Importantly, the neuroinflammatory and immune systems present two-way contact and thus can affect each other. Emerging evidence supports the numerous effects of immunosenescence- and inflammation-mediated immunity in neurologically injured brains. In this study, we briefly outline how aging alters the pathophysiology and transcriptional amplitude in patients who experienced stroke and then discuss how the immune system and its cellular components and molecular mechanisms are affected by age after stroke. Finally, we highlight emerging interventions with the potential to slow down or reduce aging and prevent stroke onset.
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Affiliation(s)
- Qiuxin Chen
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150000, China
| | - Minmin Wu
- Heilongjiang University of Chinese Medicine, Harbin 150000, China
| | - Qiang Tang
- The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150000, China
| | - Peiyu Yan
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau 999078, China
| | - Luwen Zhu
- The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin 150000, China
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14
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van der Linden J, Stefens SJM, Heredia‐Genestar JM, Ridwan Y, Brandt RMC, van Vliet N, de Beer I, van Thiel BS, Steen H, Cheng C, Roks AJM, Danser AHJ, Essers J, van der Pluijm I. Ercc1 DNA repair deficiency results in vascular aging characterized by VSMC phenotype switching, ECM remodeling, and an increased stress response. Aging Cell 2024; 23:e14126. [PMID: 38451018 PMCID: PMC11113264 DOI: 10.1111/acel.14126] [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: 01/11/2024] [Accepted: 02/05/2024] [Indexed: 03/08/2024] Open
Abstract
Cardiovascular diseases are the number one cause of death globally. The most important determinant of cardiovascular health is a person's age. Aging results in structural changes and functional decline of the cardiovascular system. DNA damage is an important contributor to the aging process, and mice with a DNA repair defect caused by Ercc1 deficiency display hypertension, vascular stiffening, and loss of vasomotor control. To determine the underlying cause, we compared important hallmarks of vascular aging in aortas of both Ercc1Δ/- and age-matched wildtype mice. Additionally, we investigated vascular aging in 104 week old wildtype mice. Ercc1Δ/- aortas displayed arterial thickening, a loss of cells, and a discontinuous endothelial layer. Aortas of 24 week old Ercc1Δ/- mice showed phenotypical switching of vascular smooth muscle cells (VSMCs), characterized by a decrease in contractile markers and a decrease in synthetic markers at the RNA level. As well as an increase in osteogenic markers, microcalcification, and an increase in markers for damage induced stress response. This suggests that Ercc1Δ/- VSMCs undergo a stress-induced contractile-to-osteogenic phenotype switch. Ercc1Δ/- aortas showed increased MMP activity, elastin fragmentation, and proteoglycan deposition, characteristic of vascular aging and indicative of age-related extracellular matrix remodeling. The 104 week old WT mice showed loss of cells, VSMC dedifferentiation, and senescence. In conclusion, Ercc1Δ/- aortas rapidly display many characteristics of vascular aging, and thus the Ercc1Δ/- mouse is an excellent model to evaluate drugs that prevent vascular aging in a short time span at the functional, histological, and cellular level.
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Affiliation(s)
- Janette van der Linden
- Division of Vascular Medicine and Pharmacology, Department of Internal MedicineErasmus University Medical CenterRotterdamThe Netherlands
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | - Sanne J. M. Stefens
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | - José María Heredia‐Genestar
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | - Yanto Ridwan
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
- AMIE Core facilityErasmus University Medical CenterRotterdamThe Netherlands
| | - Renata M. C. Brandt
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | - Nicole van Vliet
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | - Isa de Beer
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | - Bibi S. van Thiel
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | | | - Caroline Cheng
- Division of Experimental Cardiology, Department of CardiologyMC UtrechtUtrechtThe Netherlands
- Division of Internal Medicine and Dermatology, Department of Nephrology and HypertensionMC UtrechtUtrechtThe Netherlands
| | - Anton J. M. Roks
- Division of Vascular Medicine and Pharmacology, Department of Internal MedicineErasmus University Medical CenterRotterdamThe Netherlands
| | - A. H. Jan Danser
- Division of Vascular Medicine and Pharmacology, Department of Internal MedicineErasmus University Medical CenterRotterdamThe Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
- Department of Vascular SurgeryCardiovascular Institute, Erasmus University Medical CenterRotterdamThe Netherlands
- Department of RadiotherapyErasmus University Medical CenterRotterdamThe Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Cancer Genomics CenterErasmus University Medical CenterRotterdamThe Netherlands
- Department of Vascular SurgeryCardiovascular Institute, Erasmus University Medical CenterRotterdamThe Netherlands
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15
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Pfeifer GP. DNA Damage and Parkinson's Disease. Int J Mol Sci 2024; 25:4187. [PMID: 38673772 PMCID: PMC11050701 DOI: 10.3390/ijms25084187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 03/20/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
The etiology underlying most sporadic Parkinson's' disease (PD) cases is unknown. Environmental exposures have been suggested as putative causes of the disease. In cell models and in animal studies, certain chemicals can destroy dopaminergic neurons. However, the mechanisms of how these chemicals cause the death of neurons is not understood. Several of these agents are mitochondrial toxins that inhibit the mitochondrial complex I of the electron transport chain. Familial PD genes also encode proteins with important functions in mitochondria. Mitochondrial dysfunction of the respiratory chain, in combination with the presence of redox active dopamine molecules in these cells, will lead to the accumulation of reactive oxygen species (ROS) in dopaminergic neurons. Here, I propose a mechanism regarding how ROS may lead to cell killing with a specificity for neurons. One rarely considered hypothesis is that ROS produced by defective mitochondria will lead to the formation of oxidative DNA damage in nuclear DNA. Many genes that encode proteins with neuron-specific functions are extraordinary long, ranging in size from several hundred kilobases to well over a megabase. It is predictable that such long genes will contain large numbers of damaged DNA bases, for example in the form of 8-oxoguanine (8-oxoG), which is a major DNA damage type produced by ROS. These DNA lesions will slow down or stall the progression of RNA polymerase II, which is a term referred to as transcription stress. Furthermore, ROS-induced DNA damage may cause mutations, even in postmitotic cells such as neurons. I propose that the impaired transcription and mutagenesis of long, neuron-specific genes will lead to a loss of neuronal integrity, eventually leading to the death of these cells during a human lifetime.
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Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
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16
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Song X, Wei J, Li Y, Zhu W, Cai Z, Li K, Wei J, Lu J, Pan W, Li M. An integrative pan-cancer analysis of the molecular characteristics of dietary restriction in tumour microenvironment. EBioMedicine 2024; 102:105078. [PMID: 38507875 PMCID: PMC10965464 DOI: 10.1016/j.ebiom.2024.105078] [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: 11/14/2023] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Dietary restriction (DR), a general term for dieting, has been demonstrated as an effective intervention in reducing the occurrence of cancers. Molecular activities associated with DR are crucial in mediating its anti-cancer effects, yet a comprehensive exploration of the landscape of these activities at the pan-cancer level is still lacking. METHODS We proposed a computational approach for quantifying DR-related molecular activities and delineating the landscape of these activities across 33 cancer types and 30 normal tissues within 27,320 samples. We thoroughly examined the associations between DR-related molecular activities and various factors, including the tumour microenvironment, immunological phenotypes, genomic features, and clinical prognosis. Meanwhile, we identified two DR genes that show potential as prognostic predictors in hepatocellular carcinoma and verified them by immunohistochemical assays in 90 patients. FINDINGS We found that DR-related molecular activities showed a close association with tumour immunity and hold potential for predicting immunotherapy responses in various cancers. Importantly, a higher level of DR-related molecular activities is associated with improved overall survival and cancer-specific survival. FZD1 and G6PD are two DR genes that serve as biomarkers for predicting the prognosis of patients with hepatocellular carcinoma. INTERPRETATION This study presents a robust link between DR-related molecular activities and tumour immunity across multiple cancer types. Our research could open the path for further investigation of DR-related molecular processes in cancer treatment. FUNDING National Natural Science Foundation of China (Grant No. 82000628) and the Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine Foundation of Guangdong Province (Grant No. 2023LSYS001).
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Affiliation(s)
- Xiaoyi Song
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jiaxing Wei
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Yang Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Wen Zhu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Zhiyuan Cai
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Kunwei Li
- Department of Radiology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jingyue Wei
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Jieyu Lu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Wanping Pan
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Man Li
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Biobank, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China; Department of Information Technology and Data Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China.
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17
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Soheili-Nezhad S, Ibáñez-Solé O, Izeta A, Hoeijmakers JHJ, Stoeger T. Time is ticking faster for long genes in aging. Trends Genet 2024; 40:299-312. [PMID: 38519330 PMCID: PMC11003850 DOI: 10.1016/j.tig.2024.01.009] [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: 11/21/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 03/24/2024]
Abstract
Recent studies of aging organisms have identified a systematic phenomenon, characterized by a negative correlation between gene length and their expression in various cell types, species, and diseases. We term this phenomenon gene-length-dependent transcription decline (GLTD) and suggest that it may represent a bottleneck in the transcription machinery and thereby significantly contribute to aging as an etiological factor. We review potential links between GLTD and key aging processes such as DNA damage and explore their potential in identifying disease modification targets. Notably, in Alzheimer's disease, GLTD spotlights extremely long synaptic genes at chromosomal fragile sites (CFSs) and their vulnerability to postmitotic DNA damage. We suggest that GLTD is an integral element of biological aging.
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Affiliation(s)
- Sourena Soheili-Nezhad
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Olga Ibáñez-Solé
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Institute for Genome Stability in Aging and Disease, Medical Faculty, University and University Hospital of Cologne, Joseph-Stelzmann-Strasse 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-Strasse 26, 50931 Cologne, Germany
| | - Ander Izeta
- Stem Cells & Aging Group, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Tecnun-University of Navarra, 20018 Donostia-San Sebastian, Spain.
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands; University of Cologne, Faculty of Medicine, Cluster of Excellence for Aging Research, Institute for Genome Stability in Ageing and Disease, Cologne, Germany; Princess Maxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands.
| | - Thomas Stoeger
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, IL, USA; Potocsnak Longevity Institute, Northwestern University, Chicago, IL, USA; Simpson Querrey Lung Institute for Translational Science, Chicago, IL, USA.
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18
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Hill RJ, Bona N, Smink J, Webb HK, Crisp A, Garaycoechea JI, Crossan GP. p53 regulates diverse tissue-specific outcomes to endogenous DNA damage in mice. Nat Commun 2024; 15:2518. [PMID: 38514641 PMCID: PMC10957910 DOI: 10.1038/s41467-024-46844-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
DNA repair deficiency can lead to segmental phenotypes in humans and mice, in which certain tissues lose homeostasis while others remain seemingly unaffected. This may be due to different tissues facing varying levels of damage or having different reliance on specific DNA repair pathways. However, we find that the cellular response to DNA damage determines different tissue-specific outcomes. Here, we use a mouse model of the human XPF-ERCC1 progeroid syndrome (XFE) caused by loss of DNA repair. We find that p53, a central regulator of the cellular response to DNA damage, regulates tissue dysfunction in Ercc1-/- mice in different ways. We show that ablation of p53 rescues the loss of hematopoietic stem cells, and has no effect on kidney, germ cell or brain dysfunction, but exacerbates liver pathology and polyploidisation. Mechanistically, we find that p53 ablation led to the loss of cell-cycle regulation in the liver, with reduced p21 expression. Eventually, p16/Cdkn2a expression is induced, serving as a fail-safe brake to proliferation in the absence of the p53-p21 axis. Taken together, our data show that distinct and tissue-specific functions of p53, in response to DNA damage, play a crucial role in regulating tissue-specific phenotypes.
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Affiliation(s)
- Ross J Hill
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Nazareno Bona
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Job Smink
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Hannah K Webb
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Alastair Crisp
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Juan I Garaycoechea
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands.
| | - Gerry P Crossan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK.
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19
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Shi R, Wang S, Jiang Y, Zhong G, Li M, Sun Y. ERCC4: a potential regulatory factor in inflammatory bowel disease and inflammation-associated colorectal cancer. Front Endocrinol (Lausanne) 2024; 15:1348216. [PMID: 38516408 PMCID: PMC10954797 DOI: 10.3389/fendo.2024.1348216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Abstract
The pathogenesis of inflammatory bowel disease (IBD) remains unclear and is associated with an increased risk of developing colitis-associated cancer (CAC). Under sustained inflammatory stimulation in the intestines, loss of early DNA damage response genes can lead to tumor formation. Many proteins are involved in the pathways of DNA damage response and play critical roles in protecting genes from various potential damages that DNA may undergo. ERCC4 is a structure-specific endonuclease that participates in the nucleotide excision repair (NER) pathway. The catalytic site of ERCC4 determines the activity of NER and is an indispensable gene in the NER pathway. ERCC4 may be involved in the imbalanced process of DNA damage and repair in IBD-related inflammation and CAC. This article primarily reviews the function of ERCC4 in the DNA repair pathway and discusses its potential role in the processes of IBD-related inflammation and carcinogenesis. Finally, we explore how this knowledge may open novel avenues for the treatment of IBD and IBD-related cancer.
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Affiliation(s)
| | | | | | | | | | - Yan Sun
- *Correspondence: Yan Sun, ; Mingsong Li,
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20
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Benfato ID, Quintanilha ACS, Henrique JS, Souza MA, Dos Anjos Rosário B, Beserra-Filho JIA, Ribeiro AM, Le Sueur Maluf L, de Oliveira CAM. Long-term calorie restriction prevented memory impairment in middle-aged male mice and increased a marker of DNA oxidative stress in hippocampal dentate gyrus. Neurobiol Learn Mem 2024; 209:107902. [PMID: 38336097 DOI: 10.1016/j.nlm.2024.107902] [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: 05/05/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Calorie restriction (CR) is a non-invasive and economic approachknown to increase healthspan and life expectancy, through a decrease in oxidative stress, an increase in neurotrophins, among other benefits. However, it is not clear whether its benefit could be noted earlier, as at the beginning of middle-age. Hence, weaimed to determine whether six months of long-term CR, from early adulthood to the beginning of middle age (10 months of age) could positively affect cognitive, neurochemical, and behavioral parameters. Male C57BL6/J mice were randomly distributed into Young Control (YC, ad libitum food), Old Control (OC, ad libitum food), and Old Restricted (OR, 30 % of caloric restriction) groups. To analyze the cognitive and behavioral aspects, the novel object recognition task (NOR), open field, and elevated plus maze tests were performed. In addition, immunohistochemistry targetingΔFosB (neuronal activity), brain-derived neurotrophic factor (BDNF) and the DNA oxidative damage (8OHdG) in hippocampal subfields CA1, CA2, CA3, and dentate gyrus (DG), and in basolateral amygdala and striatum were performed. Our results showed that long-term CR prevented short-term memory impairment related to aging and increased 8OHdG in hippocampal DG. BDNF was not involved in the effects of either age or CR on memory at middle-age, as it increased in CA3 of the OC group but was not altered in OR. Regarding anxiety-type behavior, no parameter showed differences between the groups. In conclusion, while the effects of long-term CR on anxiety-type behavior were inconclusive, it mitigated the memory deficit related to aging, which was accompanied by an increase in hippocampal 8OHdG in DG. Future studies should investigate whether the benefits of CR would remain if the restriction were interrupted after this long-term protocol.
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Affiliation(s)
- Izabelle Dias Benfato
- Programa de Pós-Graduação Interdisciplinar em Ciências da Saúde, Universidade Federal de São Paulo (UNIFESP), Brasil
| | | | - Jessica Salles Henrique
- Programa de Pós-Graduação em Neurologia e Neurociências, Universidade Federal de São Paulo (UNIFESP), Brasil
| | - Melyssa Alves Souza
- Programa de Pós-Graduação Interdisciplinar em Ciências da Saúde, Universidade Federal de São Paulo (UNIFESP), Brasil
| | | | | | - Alessandra Mussi Ribeiro
- Departamento de Biociências, Instituto de Saúde e Sociedade, Universidade Federal de São Paulo (UNIFESP), Brasil
| | - Luciana Le Sueur Maluf
- Departamento de Biociências, Instituto de Saúde e Sociedade, Universidade Federal de São Paulo (UNIFESP), Brasil
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21
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Jaarsma D, Birkisdóttir MB, van Vossen R, Oomen DWGD, Akhiyat O, Vermeij WP, Koekkoek SKE, De Zeeuw CI, Bosman LWJ. Different Purkinje cell pathologies cause specific patterns of progressive gait ataxia in mice. Neurobiol Dis 2024; 192:106422. [PMID: 38286390 DOI: 10.1016/j.nbd.2024.106422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 01/31/2024] Open
Abstract
Gait ataxia is one of the most common and impactful consequences of cerebellar dysfunction. Purkinje cells, the sole output neurons of the cerebellar cortex, are often involved in the underlying pathology, but their specific functions during locomotor control in health and disease remain obfuscated. We aimed to describe the effect of gradual adult-onset Purkinje cell degeneration on gaiting patterns in mice, and to determine whether two different mechanisms that both lead to Purkinje cell degeneration cause different patterns in the development of gait ataxia. Using the ErasmusLadder together with a newly developed limb detection algorithm and machine learning-based classification, we subjected mice to a challenging locomotor task with detailed analysis of single limb parameters, intralimb coordination and whole-body movement. We tested two Purkinje cell-specific mouse models, one involving stochastic cell death due to impaired DNA repair mechanisms (Pcp2-Ercc1-/-), the other carrying the mutation that causes spinocerebellar ataxia type 1 (Pcp2-ATXN1[82Q]). Both mouse models showed progressive gaiting deficits, but the sequence with which gaiting parameters deteriorated was different between mouse lines. Our longitudinal approach revealed that gradual loss of Purkinje cell function can lead to a complex pattern of loss of function over time, and that this pattern depends on the specifics of the pathological mechanisms involved. We hypothesize that this variability will also be present in disease progression in patients, and that our findings will facilitate the study of therapeutic interventions in mice, as subtle changes in locomotor abilities can be quantified by our methods.
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Affiliation(s)
- Dick Jaarsma
- Department of Neuroscience, Erasmus MC, 3015 CA, Rotterdam, the Netherlands.
| | - Maria B Birkisdóttir
- Department of Neuroscience, Erasmus MC, 3015 CA, Rotterdam, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands
| | - Randy van Vossen
- Department of Neuroscience, Erasmus MC, 3015 CA, Rotterdam, the Netherlands
| | - Demi W G D Oomen
- Department of Neuroscience, Erasmus MC, 3015 CA, Rotterdam, the Netherlands
| | - Oussama Akhiyat
- Department of Neuroscience, Erasmus MC, 3015 CA, Rotterdam, the Netherlands
| | - Wilbert P Vermeij
- Princess Máxima Center for Pediatric Oncology, 3584 CS, Utrecht, the Netherlands; Oncode Institute, 3521 AL, Utrecht, the Netherlands
| | | | - Chris I De Zeeuw
- Department of Neuroscience, Erasmus MC, 3015 CA, Rotterdam, the Netherlands; Netherlands Institute for Neuroscience, Royal Dutch Academy of Arts & Science, 1105 BA, Amsterdam, the Netherlands
| | - Laurens W J Bosman
- Department of Neuroscience, Erasmus MC, 3015 CA, Rotterdam, the Netherlands.
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22
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Voshart DC, Oshima T, Jiang Y, van der Linden GP, Ainslie AP, Reali Nazario L, van Buuren-Broek F, Scholma AC, van Weering HRJ, Brouwer N, Sewdihal J, Brouwer U, Coppes RP, Holtman IR, Eggen BJL, Kooistra SM, Barazzuol L. Radiotherapy induces persistent innate immune reprogramming of microglia into a primed state. Cell Rep 2024; 43:113764. [PMID: 38358885 DOI: 10.1016/j.celrep.2024.113764] [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: 05/16/2023] [Revised: 12/06/2023] [Accepted: 01/25/2024] [Indexed: 02/17/2024] Open
Abstract
Over half of patients with brain tumors experience debilitating and often progressive cognitive decline after radiotherapy treatment. Microglia, the resident macrophages in the brain, have been implicated in this decline. In response to various insults, microglia can develop innate immune memory (IIM), which can either enhance (priming or training) or repress (tolerance) the response to subsequent inflammatory challenges. Here, we investigate whether radiation affects the IIM of microglia by irradiating the brains of rats and later exposing them to a secondary inflammatory stimulus. Comparative transcriptomic profiling and protein validation of microglia isolated from irradiated rats show a stronger immune response to a secondary inflammatory insult, demonstrating that radiation can lead to long-lasting molecular reprogramming of microglia. Transcriptomic analysis of postmortem normal-appearing non-tumor brain tissue of patients with glioblastoma indicates that radiation-induced microglial priming is likely conserved in humans. Targeting microglial priming or avoiding further inflammatory insults could decrease radiotherapy-induced neurotoxicity.
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Affiliation(s)
- Daniëlle C Voshart
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Takuya Oshima
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Yuting Jiang
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Gideon P van der Linden
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Anna P Ainslie
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands; European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Luiza Reali Nazario
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Fleur van Buuren-Broek
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Ayla C Scholma
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Hilmar R J van Weering
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Nieske Brouwer
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Jeffrey Sewdihal
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Uilke Brouwer
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Rob P Coppes
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands
| | - Inge R Holtman
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Susanne M Kooistra
- Department of Biomedical Sciences, Section of Molecular Neurobiology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Lara Barazzuol
- Department of Biomedical Sciences, Section of Molecular Cell Biology, University Medical Center Groningen, University of Groningen, 9700 AD Groningen, the Netherlands; Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, the Netherlands.
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23
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Mattson MP, Leak RK. The hormesis principle of neuroplasticity and neuroprotection. Cell Metab 2024; 36:315-337. [PMID: 38211591 DOI: 10.1016/j.cmet.2023.12.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/06/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
Animals live in habitats fraught with a range of environmental challenges to their bodies and brains. Accordingly, cells and organ systems have evolved stress-responsive signaling pathways that enable them to not only withstand environmental challenges but also to prepare for future challenges and function more efficiently. These phylogenetically conserved processes are the foundation of the hormesis principle, in which single or repeated exposures to low levels of environmental challenges improve cellular and organismal fitness and raise the probability of survival. Hormetic principles have been most intensively studied in physical exercise but apply to numerous other challenges known to improve human health (e.g., intermittent fasting, cognitive stimulation, and dietary phytochemicals). Here we review the physiological mechanisms underlying hormesis-based neuroplasticity and neuroprotection. Approaching natural resilience from the lens of hormesis may reveal novel methods for optimizing brain function and lowering the burden of neurological disorders.
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Affiliation(s)
- Mark P Mattson
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Rehana K Leak
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, USA
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24
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Shilovsky GA. Calculating Aging: Analysis of Survival Curves in the Norm and Pathology, Fluctuations in Mortality Dynamics, Characteristics of Lifespan Distribution, and Indicators of Lifespan Variation. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:371-376. [PMID: 38622103 DOI: 10.1134/s0006297924020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 11/24/2023] [Accepted: 12/29/2023] [Indexed: 04/17/2024]
Abstract
The article describes the history of studies of survival data carried out at the Research Institute of Physico-Chemical Biology under the leadership of Academician V. P. Skulachev from 1970s until present, with special emphasis on the last decade. The use of accelerated failure time (AFT) model and analysis of coefficient of variation of lifespan (CVLS) in addition to the Gompertz methods of analysis, allows to assess survival curves for the presence of temporal scaling (i.e., manifestation of accelerated aging), without changing the shape of survival curve with the same coefficient of variation. A modification of the AFT model that uses temporal scaling as the null hypothesis made it possible to distinguish between the quantitative and qualitative differences in the dynamics of aging. It was also shown that it is possible to compare the data on the survival of species characterized by the survival curves of the original shape (i.e., "flat" curves without a pronounced increase in the probability of death with age typical of slowly aging species), when considering the distribution of lifespan as a statistical random variable and comparing parameters of such distribution. Thus, it was demonstrated that the higher impact of mortality caused by external factors (background mortality) in addition to the age-dependent mortality, the higher the disorder of mortality values and the greater its difference from the calculated value characteristic of developed countries (15-20%). For comparison, CVLS for the Paraguayan Ache Indians is 100% (57% if we exclude prepuberty individuals as suggested by Jones et al.). According to Skulachev, the next step is considering mortality fluctuations as a measure for the disorder of survival data. Visual evaluation of survival curves can already provide important data for subsequent analysis. Thus, Sokolov and Severin [1] found that mutations have different effects on the shape of survival curves. Type I survival curves generally retains their standard convex rectangular shape, while type II curves demonstrate a sharp increase in the mortality which makes them similar to a concave exponential curve with a stably high mortality rate. It is noteworthy that despite these differences, mutations in groups I and II are of a similar nature. They are associated (i) with "DNA metabolism" (DNA repair, transcription, and replication); (ii) protection against oxidative stress, associated with the activity of the transcription factor Nrf2, and (iii) regulation of proliferation, and (or these categories may overlap). However, these different mutations appear to produce the same result at the organismal level, namely, accelerated aging according to the Gompertz's law. This might be explained by the fact that all these mutations, each in its own unique way, either reduce the lifespan of cells or accelerate their transition to the senescent state, which supports the concept of Skulachev on the existence of multiple pathways of aging (chronic phenoptosis).
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Affiliation(s)
- Gregory A Shilovsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia
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25
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Perez K, Parras A, Picó S, Rechsteiner C, Haghani A, Brooke R, Mrabti C, Schoenfeldt L, Horvath S, Ocampo A. DNA repair-deficient premature aging models display accelerated epigenetic age. Aging Cell 2024; 23:e14058. [PMID: 38140713 PMCID: PMC10861193 DOI: 10.1111/acel.14058] [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: 04/07/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Several premature aging mouse models have been developed to study aging and identify interventions that can delay age-related diseases. Yet, it is still unclear whether these models truly recapitulate natural aging. Here, we analyzed DNA methylation in multiple tissues of four previously reported mouse models of premature aging (Ercc1, LAKI, Polg, and Xpg). We estimated DNA methylation (DNAm) age of these samples using the Horvath clock. The most pronounced increase in DNAm age could be observed in Ercc1 mice, a strain which exhibits a deficit in DNA nucleotide excision repair. Similarly, we detected an increase in epigenetic age in fibroblasts isolated from patients with progeroid syndromes associated with mutations in DNA excision repair genes. These findings highlight that mouse models with deficiencies in DNA repair, unlike other premature aging models, display accelerated epigenetic age, suggesting a strong connection between DNA damage and epigenetic dysregulation during aging.
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Affiliation(s)
- Kevin Perez
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Alberto Parras
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Sara Picó
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Cheyenne Rechsteiner
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | | | - Robert Brooke
- Epigenetic Clock Development FoundationTorranceCaliforniaUSA
| | - Calida Mrabti
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
| | - Lucas Schoenfeldt
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
| | - Steve Horvath
- Altos LabsSan DiegoCaliforniaUSA
- Epigenetic Clock Development FoundationTorranceCaliforniaUSA
- Human Genetics, David Geffen School of MedicineUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Alejandro Ocampo
- Department of Biomedical Sciences, Faculty of Biology and MedicineUniversity of LausanneLausanneSwitzerland
- EPITERNA SAEpalingesSwitzerland
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26
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Sokolov SS, Severin FF. Two Types of Survival Curves of Different Lines of Progeric Mice. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:367-370. [PMID: 38622102 DOI: 10.1134/s0006297924020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/02/2023] [Accepted: 12/29/2023] [Indexed: 04/17/2024]
Abstract
For most of their lifespan, the probability of death for many animal species increases with age. Gompertz law states that this increase is exponential. In this work, we have compared previously published data on the survival kinetics of different lines of progeric mice. Visual analysis showed that in six lines of these rapidly aging mutants, the probability of death did not strictly depend on age. In contrast, ten lines of progeric mice have survival curves similar to those of the control animals, that is, in agreement with Gompertz law, similar to the shape of an exponential curve upside down. Interestingly, these ten mutations cause completely different cell malfunctions. We speculate that what these mutations have in common is a reduction in the lifespan of cells and/or an acceleration of the transition to the state of cell senescence. Thus, our analysis, similar to the conclusions of many previously published works, indicates that the aging of an organism is a consequence of the aging of individual cells.
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Affiliation(s)
- Svyatoslav S Sokolov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Fedor F Severin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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27
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Panier S, Wang S, Schumacher B. Genome Instability and DNA Repair in Somatic and Reproductive Aging. ANNUAL REVIEW OF PATHOLOGY 2024; 19:261-290. [PMID: 37832947 DOI: 10.1146/annurev-pathmechdis-051122-093128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Genetic material is constantly subjected to genotoxic insults and is critically dependent on DNA repair. Genome maintenance mechanisms differ in somatic and germ cells as the soma only requires maintenance during an individual's lifespan, while the germline indefinitely perpetuates its genetic information. DNA lesions are recognized and repaired by mechanistically highly diverse repair machineries. The DNA damage response impinges on a vast array of homeostatic processes and can ultimately result in cell fate changes such as apoptosis or cellular senescence. DNA damage causally contributes to the aging process and aging-associated diseases, most prominently cancer. By causing mutations, DNA damage in germ cells can lead to genetic diseases and impact the evolutionary trajectory of a species. The mechanisms ensuring tight control of germline DNA repair could be highly instructive in defining strategies for improved somatic DNA repair. They may provide future interventions to maintain health and prevent disease during aging.
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Affiliation(s)
- Stephanie Panier
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Siyao Wang
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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28
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Paine PT, Rechsteiner C, Morandini F, Desdín-Micó G, Mrabti C, Parras A, Haghani A, Brooke R, Horvath S, Seluanov A, Gorbunova V, Ocampo A. Initiation phase cellular reprogramming ameliorates DNA damage in the ERCC1 mouse model of premature aging. FRONTIERS IN AGING 2024; 4:1323194. [PMID: 38322248 PMCID: PMC10844398 DOI: 10.3389/fragi.2023.1323194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/04/2023] [Indexed: 02/08/2024]
Abstract
Unlike aged somatic cells, which exhibit a decline in molecular fidelity and eventually reach a state of replicative senescence, pluripotent stem cells can indefinitely replenish themselves while retaining full homeostatic capacity. The conferment of beneficial-pluripotency related traits via in vivo partial cellular reprogramming in vivo partial reprogramming significantly extends lifespan and restores aging phenotypes in mouse models. Although the phases of cellular reprogramming are well characterized, details of the rejuvenation processes are poorly defined. To understand whether cellular reprogramming can ameliorate DNA damage, we created a reprogrammable accelerated aging mouse model with an ERCC1 mutation. Importantly, using enhanced partial reprogramming by combining small molecules with the Yamanaka factors, we observed potent reversion of DNA damage, significant upregulation of multiple DNA damage repair processes, and restoration of the epigenetic clock. In addition, we present evidence that pharmacological inhibition of ALK5 and ALK2 receptors in the TGFb pathway are able to phenocopy some benefits including epigenetic clock restoration suggesting a role in the mechanism of rejuvenation by partial reprogramming.
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Affiliation(s)
- Patrick Treat Paine
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- Center for Virology and Vaccine Research, Harvard Medical School, Boston, MA, United States
| | | | - Francesco Morandini
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Gabriela Desdín-Micó
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Calida Mrabti
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Alberto Parras
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- EPITERNA SA, Vaud, Switzerland
| | | | - Robert Brooke
- Epigenetic Clock Development Foundation, Torrance, CA, United States
| | - Steve Horvath
- Altos Labs, San Diego, CA, United States
- Epigenetic Clock Development Foundation, Torrance, CA, United States
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, United States
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, United States
- Department of Medicine, University of Rochester Medical Center, Rochester, NY, United States
| | - Alejandro Ocampo
- Department of Biomedical Sciences, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
- EPITERNA SA, Vaud, Switzerland
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Mishra A, Giuliani G, Longo VD. Nutrition and dietary restrictions in cancer prevention. Biochim Biophys Acta Rev Cancer 2024; 1879:189063. [PMID: 38147966 DOI: 10.1016/j.bbcan.2023.189063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/15/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023]
Abstract
The composition and pattern of dietary intake have emerged as key factors influencing aging, regeneration, and consequently, healthspan and lifespan. Cancer is one of the major diseases more tightly linked with aging, and age-related mortality. Although the role of nutrition in cancer incidence is generally well established, we are far from a consensus on how diet influences tumour development in different tissues. In this review, we will discuss how diet and dietary restrictions affect cancer risk and the molecular mechanisms potentially responsible for their effects. We will cover calorie restriction, intermittent fasting, prolonged fasting, fasting-mimicking diet, time-restricted eating, ketogenic diet, high protein diet, Mediterranean diet, and the vegan and vegetarian diets.
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Affiliation(s)
- Amrendra Mishra
- Longevity Institute and Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Giacomo Giuliani
- Longevity Institute and Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Valter D Longo
- Longevity Institute and Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; IFOM, FIRC Institute of Molecular Oncology, Via Adamello, 16, 20139 Milano, Italy.
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30
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Cogut V, McNeely TL, Bussian TJ, Graves SI, Baker DJ. Caloric Restriction Improves Spatial Learning Deficits in Tau Mice. J Alzheimers Dis 2024; 98:925-940. [PMID: 38517786 PMCID: PMC11068089 DOI: 10.3233/jad-231117] [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: 03/24/2024]
Abstract
Background Caloric restriction (CR) has been recognized for its benefits in delaying age-related diseases and extending lifespan. While its effects on amyloid pathology in Alzheimer's disease (AD) mouse models are well-documented, its effects on tauopathy, another hallmark of AD, are less explored. Objective To assess the impact of a short-term 30% CR regimen on age-dependent spatial learning deficits and pathological features in a tauopathy mouse model. Methods We subjected male PS19 tau P301S (hereafter PS19) and age-matched wildtype mice from two age cohorts (4.5 and 7.5 months old) to a 6-week 30% CR regimen. Spatial learning performance was assessed using the Barnes Maze test. Tau pathology, neuroinflammation, hippocampal cell proliferation, and neurogenesis were evaluated in the older cohort by immunohistochemical staining and RT-qPCR. Results CR mitigated age-dependent spatial learning deficits in PS19 mice but exhibited limited effects on tau pathology and the associated neuroinflammation. Additionally, we found a decrease in hippocampal cell proliferation, predominantly of Iba1+ cells. Conclusions Our findings reinforce the cognitive benefits conferred by CR despite its limited modulation of disease pathology. Given the pivotal role of microglia in tau-driven pathology, the observed reduction in Iba1+ cells under CR suggests potential therapeutic implications, particularly if CR would be introduced early in disease progression.
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Affiliation(s)
- Valeria Cogut
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
| | - Taylor L. McNeely
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
| | - Tyler J. Bussian
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
| | - Sara I. Graves
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
| | - Darren J. Baker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
- Paul F. Glenn Center for Biology of Aging Research at Mayo Clinic, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA
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31
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Oudmaijer CAJ, Pol RA, Minnee RC, Vermeij WP, IJzermans JNM. Chocolate brownies and calorie restriction: the sweetest paradox? BMJ 2023; 383:2585. [PMID: 38123171 DOI: 10.1136/bmj.p2585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- C A J Oudmaijer
- Erasmus MC Transplant Institute, department of surgery, division of hepatobiliary and transplantation surgery, University Medical Center, Rotterdam, Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - R A Pol
- Department of transplantation surgery, University Medical Center Groningen, Groningen, Netherlands
| | - R C Minnee
- Erasmus MC Transplant Institute, department of surgery, division of hepatobiliary and transplantation surgery, University Medical Center, Rotterdam, Netherlands
| | - W P Vermeij
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - J N M IJzermans
- Erasmus MC Transplant Institute, department of surgery, division of hepatobiliary and transplantation surgery, University Medical Center, Rotterdam, Netherlands
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32
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Jouabadi SM, Ataabadi EA, Golshiri K, Bos D, Stricker BHC, Danser AHJ, Mattace-Raso F, Roks AJM. Clinical Impact and Mechanisms of Nonatherosclerotic Vascular Aging: The New Kid to Be Blocked. Can J Cardiol 2023; 39:1839-1858. [PMID: 37495207 DOI: 10.1016/j.cjca.2023.07.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/07/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Ischemic cardiovascular disease and stroke remain the leading cause of global morbidity and mortality. During aging, protective mechanisms in the body gradually deteriorate, resulting in functional, structural, and morphologic changes that affect the vascular system. Because atherosclerotic plaques are not always present along with these alterations, we refer to this kind of vascular aging as nonatherosclerotic vascular aging (NAVA). To maintain proper vascular function during NAVA, it is important to preserve intracellular signalling, prevent inflammation, and block the development of senescent cells. Pharmacologic interventions targeting these components are potential therapeutic approaches for NAVA, with a particular emphasis on inflammation and senescence. This review provides an overview of the pathophysiology of vascular aging and explores potential pharmacotherapies that can improve the function of aged vasculature, focusing on NAVA.
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Affiliation(s)
- Soroush Mohammadi Jouabadi
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ehsan Ataei Ataabadi
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Keivan Golshiri
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Daniel Bos
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands; Department of Radiology and Nuclear Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Bruno H C Stricker
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - A H Jan Danser
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Francesco Mattace-Raso
- Division of Geriatric Medicine, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Anton J M Roks
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands.
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33
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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34
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Jeffries AM, Yu T, Ziegenfuss JS, Tolles AK, Kim Y, Weng Z, Lodato MA. Single-cell transcriptomic and genomic changes in the aging human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566050. [PMID: 37986960 PMCID: PMC10659272 DOI: 10.1101/2023.11.07.566050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Aging brings dysregulation of various processes across organs and tissues, often stemming from stochastic damage to individual cells over time. Here, we used a combination of single-nucleus RNA-sequencing and single-cell whole-genome sequencing to identify transcriptomic and genomic changes in the prefrontal cortex of the human brain across life span, from infancy to centenarian. We identified infant-specific cell clusters enriched for the expression of neurodevelopmental genes, and a common down-regulation of cell-essential homeostatic genes that function in ribosomes, transport, and metabolism during aging across cell types. Conversely, expression of neuron-specific genes generally remains stable throughout life. We observed a decrease in specific DNA repair genes in aging, including genes implicated in generating brain somatic mutations as indicated by mutation signature analysis. Furthermore, we detected gene-length-specific somatic mutation rates that shape the transcriptomic landscape of the aged human brain. These findings elucidate critical aspects of human brain aging, shedding light on transcriptomic and genomics dynamics.
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Affiliation(s)
- Ailsa M. Jeffries
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Tianxiong Yu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jennifer S. Ziegenfuss
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Allie K. Tolles
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Yerin Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael A. Lodato
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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35
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Ivessa AS, Singh S. The increase in cell death rates in caloric restricted cells of the yeast helicase mutant rrm3 is Sir complex dependent. Sci Rep 2023; 13:17832. [PMID: 37857740 PMCID: PMC10587150 DOI: 10.1038/s41598-023-45125-z] [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: 11/29/2022] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
Calorie restriction (CR), which is a reduction in calorie intake without malnutrition, usually extends lifespan and improves tissue integrity. This report focuses on the relationship between nuclear genomic instability and dietary-restriction and its effect on cell survival. We demonstrate that the cell survival rates of the genomic instability yeast mutant rrm3 change under metabolic restricted conditions. Rrm3 is a DNA helicase, chromosomal replication slows (and potentially stalls) in its absence with increased rates at over 1400 natural pause sites including sites within ribosomal DNA and tRNA genes. Whereas rrm3 mutant cells have lower cell death rates compared to wild type (WT) in growth medium containing normal glucose levels (i.e., 2%), under CR growth conditions cell death rates increase in the rrm3 mutant to levels, which are higher than WT. The silent-information-regulatory (Sir) protein complex and mitochondrial oxidative stress are required for the increase in cell death rates in the rrm3 mutant when cells are transferred from growth medium containing 2% glucose to CR-medium. The Rad53 checkpoint protein is highly phosphorylated in the rrm3 mutant in response to genomic instability in growth medium containing 2% glucose. Under CR, Rad53 phosphorylation is largely reduced in the rrm3 mutant in a Sir-complex dependent manner. Since CR is an adjuvant treatment during chemotherapy, which may target genomic instability in cancer cells, our studies may gain further insight into how these therapy strategies can be improved.
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Affiliation(s)
- Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA.
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ, 07101-1709, USA
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36
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Wang J, Muste Sadurni M, Saponaro M. RNAPII response to transcription-blocking DNA lesions in mammalian cells. FEBS J 2023; 290:4382-4394. [PMID: 35731652 PMCID: PMC10952651 DOI: 10.1111/febs.16561] [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: 11/12/2021] [Revised: 05/15/2022] [Accepted: 06/21/2022] [Indexed: 09/21/2023]
Abstract
RNA polymerase II moves along genes to decode genetic information stored in the mammalian genome into messenger RNA and different forms of non-coding RNA. However, the transcription process is frequently challenged by DNA lesions caused by exogenous and endogenous insults, among which helix-distorting DNA lesions and double-stranded DNA breaks are particularly harmful for cell survival. In response to such DNA damage, RNA polymerase II transcription is regulated both locally and globally by multi-layer mechanisms, whereas transcription-blocking lesions are repaired before transcription can recover. Failure in DNA damage repair will cause genome instability and cell death. Although recent studies have expanded our understanding of RNA polymerase II regulation confronting DNA lesions, it is still not always clear what the direct contribution of RNA polymerase II is in the DNA damage repair processes. In this review, we focus on how RNA polymerase II and transcription are both repressed by transcription stalling lesions such as DNA-adducts and double strand breaks, as well as how they are actively regulated to support the cellular response to DNA damage and favour the repair of lesions.
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Affiliation(s)
- Jianming Wang
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Martina Muste Sadurni
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
| | - Marco Saponaro
- Transcription Associated Genome Instability Laboratory, Institute of Cancer and Genomic SciencesUniversity of BirminghamUK
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37
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van Schaik J, van Roessel IMAA, Bos ID, Claashen-van der Grinten HL, Clement SC, van Iersel L, Bakker B, Meijer L, Kremer L, Schouten-van Meeteren AYN, van Santen HM. Elevated IGF-1 concentrations in children with low grade glioma: A descriptive analysis in a retrospective national cohort. J Neuroendocrinol 2023; 35:e13317. [PMID: 37439273 DOI: 10.1111/jne.13317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/20/2023] [Accepted: 06/02/2023] [Indexed: 07/14/2023]
Abstract
Children with low grade glioma (LGG) may present with, or develop, elevated concentrations of insulin-like growth factor 1 (IGF-1). The prevalence, pathophysiology, or its possible clinical effects are poorly understood. Our aim was to evaluate the prevalence of such elevated IGF-1 concentrations and to describe its association with linear growth, body mass index (BMI), pituitary outcome, and tumor behavior in a large retrospective national cohort. From a nationwide retrospective cohort of pediatric brain tumor survivors diagnosed between 2002 and 2012, tumor, treatment, endocrine, and auxological data of children with LGG were collected (n = 358). Prevalence and risk factors for elevated IGF-1 concentrations, as well as the association between having elevated IGF-1 concentrations and receiving tumor treatment, were explored. IGF-1 concentrations had only been measured in 45.5% of cases (n = 163/358). In 18.4% of 163 children with available IGF-1 measurements, IGF-1 concentrations were found elevated. No association was described between having an elevated IGF-1 concentration and tumor behavior or height SDS at last moment of follow-up. Multivariate logistic regression identified posterior pituitary disorder (OR 6.14 95% CI: 2.21-17.09) and BMI SDS at follow-up (OR 1.56 95% CI: 1.09-2.20) to be significantly associated with elevated IGF-1 concentrations. In this retrospective cohort of children with LGG, IGF-1 was found elevated in 18.4% of children with available IGF-1 measurements. Elevated IGF-1 seems to be related to hypothalamic dysfunction worsening over time. Larger prospective cohort studies are needed.
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Affiliation(s)
- Jiska van Schaik
- Division of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Pediatric Oncology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Ichelle M A A van Roessel
- Division of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Pediatric Oncology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Iris D Bos
- Division of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Sarah C Clement
- Division of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Pediatrics, Emma Children's Hospital, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Laura van Iersel
- Division of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Boudewijn Bakker
- Division of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lisethe Meijer
- Department of Pediatric Oncology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Leontien Kremer
- Department of Pediatric Oncology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | | | - Hanneke M van Santen
- Division of Pediatric Endocrinology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Pediatric Oncology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
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Cavalcante MB, Sampaio OGM, Câmara FEA, Schneider A, de Ávila BM, Prosczek J, Masternak MM, Campos AR. Ovarian aging in humans: potential strategies for extending reproductive lifespan. GeroScience 2023; 45:2121-2133. [PMID: 36913129 PMCID: PMC10651588 DOI: 10.1007/s11357-023-00768-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023] Open
Abstract
Ovarian reserve is a term used to estimate the total number of immature follicles present in the ovaries. Between birth and menopause, there is a progressive decrease in the number of ovarian follicles. Ovarian aging is a continuous physiological phenomenon, with menopause being the clinical mark of the end of ovarian function. Genetics, measured as family history for age at the onset of menopause, is the main determinant. However, physical activity, diet, and lifestyle are important factors that can influence the age of menopause. The low estrogen levels after natural or premature menopause increased the risk for several diseases, resulting in increased mortality risk. Besides that, the decreasing ovarian reserve is associated to reduced fertility. In women with infertility undergoing in vitro fertilization, reduced markers of ovarian reserve, including antral follicular count and anti-Mullerian hormone, are the main indicators of reduced chances of becoming pregnant. Therefore, it becomes clear that the ovarian reserve has a central role in women's life, affecting fertility early in life and overall health later in life. Based on this, the ideal strategy for delaying ovarian aging should have the following characteristics: (1) be initiated in the presence of good ovarian reserve; (2) maintained for a long period; (3) have an action on the dynamics of primordial follicles, controlling the rate of activation and atresia; and (4) safe use in pre-conception, pregnancy, and lactation. In this review, we therefore discuss some of these strategies and its feasibility for preventing a decline in the ovarian reserve.
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Affiliation(s)
- Marcelo Borges Cavalcante
- Postgraduate Program in Medical Sciences, University of Fortaleza (UNIFOR), Fortaleza, CE, 60.811-905, Brazil.
| | - Olga Goiana Martins Sampaio
- Postgraduate Program in Medical Sciences, University of Fortaleza (UNIFOR), Fortaleza, CE, 60.811-905, Brazil
| | | | - Augusto Schneider
- Nutrition College, Federal University of Pelotas (UFPel), Pelotas, RS, 96010-610, Brazil
| | | | - Juliane Prosczek
- Nutrition College, Federal University of Pelotas (UFPel), Pelotas, RS, 96010-610, Brazil
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando FL, USA
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, Poznan, Poland
| | - Adriana Rolim Campos
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, Poznan, Poland
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39
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Ghosh Chowdhury S, Ray R, Karmakar P. Relating aging and autophagy: a new perspective towards the welfare of human health. EXCLI JOURNAL 2023; 22:732-748. [PMID: 37662706 PMCID: PMC10471842 DOI: 10.17179/excli2023-6300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023]
Abstract
The most common factor that contributes to aging is the loss of proteostasis, resulting in an excess amount of non-functional/damaged proteins. These proteins lead to various age-associated phenotypes such as cellular senescence and dysfunction in the nutrient-sensing pathways. Despite the various factors that can contribute to aging, it is still a process that can be changed. According to recent advances in the field of biology, the ability to alter the pathways that are involved in aging can improve the lifespan of a person. Autophagy is a process that helps in preserving survival during stressful situations, such as starvation. It is a common component of various anti-aging interventions, including those that target the insulin/IGF-1 and rapamycin signaling pathways. It has been shown that altered autophagy is a common feature of old age and its impaired regulation could have significant effects on the aging process. This review aims to look into the role of autophagy in aging and how it can be used to improve one's health.
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Affiliation(s)
| | - Rachayeeta Ray
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata-700032, India
| | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, Kolkata-700032, India
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40
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Townley BA, Buerer L, Tsao N, Bacolla A, Mansoori F, Rusanov T, Clark N, Goodarzi N, Schmidt N, Srivatsan SN, Sun H, Sample RA, Brickner JR, McDonald D, Tsai MS, Walter MJ, Wozniak DF, Holehouse AS, Pena V, Tainer JA, Fairbrother WG, Mosammaparast N. A functional link between lariat debranching enzyme and the intron-binding complex is defective in non-photosensitive trichothiodystrophy. Mol Cell 2023; 83:2258-2275.e11. [PMID: 37369199 PMCID: PMC10483886 DOI: 10.1016/j.molcel.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 03/25/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
The pre-mRNA life cycle requires intron processing; yet, how intron-processing defects influence splicing and gene expression is unclear. Here, we find that TTDN1/MPLKIP, which is encoded by a gene implicated in non-photosensitive trichothiodystrophy (NP-TTD), functionally links intron lariat processing to spliceosomal function. The conserved TTDN1 C-terminal region directly binds lariat debranching enzyme DBR1, whereas its N-terminal intrinsically disordered region (IDR) binds the intron-binding complex (IBC). TTDN1 loss, or a mutated IDR, causes significant intron lariat accumulation, as well as splicing and gene expression defects, mirroring phenotypes observed in NP-TTD patient cells. A Ttdn1-deficient mouse model recapitulates intron-processing defects and certain neurodevelopmental phenotypes seen in NP-TTD. Fusing DBR1 to the TTDN1 IDR is sufficient to recruit DBR1 to the IBC and circumvents the functional requirement for TTDN1. Collectively, our findings link RNA lariat processing with splicing outcomes by revealing the molecular function of TTDN1.
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Affiliation(s)
- Brittany A Townley
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Luke Buerer
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Ning Tsao
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Fadhel Mansoori
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Timur Rusanov
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathanial Clark
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA
| | - Negar Goodarzi
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - Nicolas Schmidt
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Hua Sun
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Reilly A Sample
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua R Brickner
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Drew McDonald
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Matthew J Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David F Wozniak
- Department of Psychiatry, Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110-1093, USA
| | - Alex S Holehouse
- Department of Biochemistry & Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Vladimir Pena
- Mechanisms and Regulation of Splicing Research Group, The Institute of Cancer Research, London, UK
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - William G Fairbrother
- Center for Computational Molecular Biology, Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912, USA; Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI 02912, USA.
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Kell L, Simon AK, Alsaleh G, Cox LS. The central role of DNA damage in immunosenescence. FRONTIERS IN AGING 2023; 4:1202152. [PMID: 37465119 PMCID: PMC10351018 DOI: 10.3389/fragi.2023.1202152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/22/2023] [Indexed: 07/20/2023]
Abstract
Ageing is the biggest risk factor for the development of multiple chronic diseases as well as increased infection susceptibility and severity of diseases such as influenza and COVID-19. This increased disease risk is linked to changes in immune function during ageing termed immunosenescence. Age-related loss of immune function, particularly in adaptive responses against pathogens and immunosurveillance against cancer, is accompanied by a paradoxical gain of function of some aspects of immunity such as elevated inflammation and increased incidence of autoimmunity. Of the many factors that contribute to immunosenescence, DNA damage is emerging as a key candidate. In this review, we discuss the evidence supporting the hypothesis that DNA damage may be a central driver of immunosenescence through senescence of both immune cells and cells of non-haematopoietic lineages. We explore why DNA damage accumulates during ageing in a major cell type, T cells, and how this may drive age-related immune dysfunction. We further propose that existing immunosenescence interventions may act, at least in part, by mitigating DNA damage and restoring DNA repair processes (which we term "genoprotection"). As such, we propose additional treatments on the basis of their evidence for genoprotection, and further suggest that this approach may provide a viable therapeutic strategy for improving immunity in older people.
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Affiliation(s)
- Loren Kell
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Anna Katharina Simon
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ghada Alsaleh
- Botnar Institute for Musculoskeletal Sciences, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Lynne S. Cox
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Vijay Kumar MJ, Morales R, Tsvetkov AS. G-quadruplexes and associated proteins in aging and Alzheimer's disease. FRONTIERS IN AGING 2023; 4:1164057. [PMID: 37323535 PMCID: PMC10267416 DOI: 10.3389/fragi.2023.1164057] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023]
Abstract
Aging is a prominent risk factor for many neurodegenerative disorders, such as Alzheimer's disease (AD). Alzheimer's disease is characterized by progressive cognitive decline, memory loss, and neuropsychiatric and behavioral symptoms, accounting for most of the reported dementia cases. This disease is now becoming a major challenge and burden on modern society, especially with the aging population. Over the last few decades, a significant understanding of the pathophysiology of AD has been gained by studying amyloid deposition, hyperphosphorylated tau, synaptic dysfunction, oxidative stress, calcium dysregulation, and neuroinflammation. This review focuses on the role of non-canonical secondary structures of DNA/RNA G-quadruplexes (G4s, G4-DNA, and G4-RNA), G4-binding proteins (G4BPs), and helicases, and their roles in aging and AD. Being critically important for cellular function, G4s are involved in the regulation of DNA and RNA processes, such as replication, transcription, translation, RNA localization, and degradation. Recent studies have also highlighted G4-DNA's roles in inducing DNA double-strand breaks that cause genomic instability and G4-RNA's participation in regulating stress granule formation. This review emphasizes the significance of G4s in aging processes and how their homeostatic imbalance may contribute to the pathophysiology of AD.
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Affiliation(s)
- M. J. Vijay Kumar
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
| | - Rodrigo Morales
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- Centro Integrativo de Biologia y Quimica Aplicada (CIBQA), Universidad Bernardo O’Higgins, Santiago, Chile
| | - Andrey S. Tsvetkov
- The Department of Neurology, The University of Texas McGovern Medical School at Houston, Houston, TX, United States
- The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
- UTHealth Consortium on Aging, The University of Texas McGovern Medical School, Houston, TX, United States
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43
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van’t Sant LJ, Birkisdóttir MB, Ozinga RA, Gyenis Á, Hoeijmakers JH, Vermeij WP, Jaarsma D. Gene expression changes in cerebellum induced by dietary restriction. Front Mol Neurosci 2023; 16:1185665. [PMID: 37293544 PMCID: PMC10244750 DOI: 10.3389/fnmol.2023.1185665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Background Dietary restriction (DR) is a well-established universal anti-aging intervention, and is neuroprotective in multiple models of nervous system disease, including models with cerebellar pathology. The beneficial effects of DR are associated with a rearrangement of gene expression that modulate metabolic and cytoprotective pathways. However, the effect of DR on the cerebellar transcriptome remained to be fully defined. Results Here we analyzed the effect of a classical 30% DR protocol on the transcriptome of cerebellar cortex of young-adult male mice using RNAseq. We found that about 5% of expressed genes were differentially expressed in DR cerebellum, the far majority of whom showing subtle expression changes. A large proportion of down-regulated genes are implicated in signaling pathways, in particular pathways associated with neuronal signaling. DR up regulated pathways in large part were associated with cytoprotection and DNA repair. Analysis of the expression of cell-specific gene sets, indicated a strong enrichment of DR down genes in Purkinje cells, while genes specifically associated with granule cells did not show such a preferential down-regulation. Conclusion Our data show that DR may have a clear effect on the cerebellar transcriptome inducing a mild shift from physiology towards maintenance and repair, and having cell-type specific effects.
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Affiliation(s)
| | - María B. Birkisdóttir
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Rutger A. Ozinga
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Ákos Gyenis
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, Institute for Genome Stability in Ageing and Disease, University of Cologne, Cologne, Germany
| | - Jan H.J. Hoeijmakers
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, Institute for Genome Stability in Ageing and Disease, University of Cologne, Cologne, Germany
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Dick Jaarsma
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
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44
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Becker F, Behrends MM, Rudolph KL. Evolution, mechanism and limits of dietary restriction induced health benefits & longevity. Redox Biol 2023; 63:102725. [PMID: 37257276 DOI: 10.1016/j.redox.2023.102725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 06/02/2023] Open
Abstract
Dietary restriction (DR) is the most powerful intervention to enhance health and lifespan across species. However, recent findings indicate that DR started in late life has limited capacity to induce health benefits. Age-dependent changes that impair DR at old age remain to be delineated. This requires a better mechanistic understanding of the different aspects that constitute DR, how they act independently and in concert. Current research efforts aim to tackle these questions: Are fasting periods needed for the induction of DR's health benefits? Does the improvement of cellular and organismal functions depend on the reduction of specific dietary components like proteins or even micronutrients and/or vitamins? How is the aging process intervening with DR-mediated responses? Understanding the evolutionary benefits of nutrient stress responses in driving molecular and cellular adaptation in response to nutrient deprivation is likely providing answers to some of these questions. Cellular memory of early life may lead to post-reproductive distortions of gene regulatory networks and metabolic pathways that inhibit DR-induced stress responses and health benefits when the intervention is started at old age. Inhere we discuss new insights into mechanisms of DR-mediated health benefits and how evolutionary selection for fitness in early life may limit DR-mediated improvements at old age.
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Affiliation(s)
- Friedrich Becker
- Research Group on Stem Cell and Metabolism Aging, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
| | - Marthe M Behrends
- Research Group on Stem Cell and Metabolism Aging, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
| | - K Lenhard Rudolph
- Research Group on Stem Cell and Metabolism Aging, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
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45
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Xu J, Shao T, Lou J, Zhang J, Xia C. Aging, cell senescence, the pathogenesis and targeted therapies of intervertebral disc degeneration. Front Pharmacol 2023; 14:1172920. [PMID: 37214476 PMCID: PMC10196014 DOI: 10.3389/fphar.2023.1172920] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
Intervertebral disc degeneration (IVDD) refers to the aging and degenerative diseases of intervertebral disc components such as nucleus pulposus, annulus fibrosus, and cartilage endplate, and is the main cause of chronic low back pain. Over the past few years, many researchers around the world concerned that the degeneration of nucleus pulposus (NP) cells plays the main role in IVDD. The degeneration of NP cells is caused by a series of pathological processes, including oxidative stress, inflammatory response, apoptosis, abnormal proliferation, and autophagy. Interestingly, many studies have found a close relationship between the senescence of NP cells and the progression of NP degeneration. The classical aging pathways also have been confirmed to be involved in the pathological process of IVDD. Moreover, several anti-aging drugs have been used to treat IVDD by inhibiting NP cells senescence, such as proanthocyanidins, resveratrol and bone morphogenetic protein 2. Therefore, this article will systematically list and discuss aging, cell senescence, the pathogenesis and targeted therapies of IVDD, in order to provide new ideas for the treatment of IVDD in the future.
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Affiliation(s)
- Jiongnan Xu
- Center for Plastic and Reconstructive Surgery, Department of Orthopedics, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital Hangzhou Medical College, Hangzhou, China
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ting Shao
- Center for Plastic and Reconstructive Surgery, Department of Orthopedics, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital Hangzhou Medical College, Hangzhou, China
| | - Jianfen Lou
- Center for Plastic and Reconstructive Surgery, Department of Orthopedics, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital Hangzhou Medical College, Hangzhou, China
| | - Jun Zhang
- Department of Orthopedics, Zhejiang Provincial People’s Hospital Bijie Hospital, Bijie, Guizhou, China
| | - Chen Xia
- Center for Plastic and Reconstructive Surgery, Department of Orthopedics, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital Hangzhou Medical College, Hangzhou, China
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46
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Rogers RS, Wang H, Durham TJ, Stefely JA, Owiti NA, Markhard AL, Sandler L, To TL, Mootha VK. Hypoxia extends lifespan and neurological function in a mouse model of aging. PLoS Biol 2023; 21:e3002117. [PMID: 37220109 PMCID: PMC10204955 DOI: 10.1371/journal.pbio.3002117] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/07/2023] [Indexed: 05/25/2023] Open
Abstract
There is widespread interest in identifying interventions that extend healthy lifespan. Chronic continuous hypoxia delays the onset of replicative senescence in cultured cells and extends lifespan in yeast, nematodes, and fruit flies. Here, we asked whether chronic continuous hypoxia is beneficial in mammalian aging. We utilized the Ercc1 Δ/- mouse model of accelerated aging given that these mice are born developmentally normal but exhibit anatomic, physiological, and biochemical features of aging across multiple organs. Importantly, they exhibit a shortened lifespan that is extended by dietary restriction, the most potent aging intervention across many organisms. We report that chronic continuous 11% oxygen commenced at 4 weeks of age extends lifespan by 50% and delays the onset of neurological debility in Ercc1 Δ/- mice. Chronic continuous hypoxia did not impact food intake and did not significantly affect markers of DNA damage or senescence, suggesting that hypoxia did not simply alleviate the proximal effects of the Ercc1 mutation, but rather acted downstream via unknown mechanisms. To the best of our knowledge, this is the first study to demonstrate that "oxygen restriction" can extend lifespan in a mammalian model of aging.
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Affiliation(s)
- Robert S Rogers
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hong Wang
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Timothy J Durham
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jonathan A Stefely
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Norah A Owiti
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Andrew L Markhard
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lev Sandler
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tsz-Leung To
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
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Sims AA, Gurkar AU. DNA damage-induced stalling of transcription drives aging through gene expression imbalance. DNA Repair (Amst) 2023; 125:103483. [PMID: 36921370 DOI: 10.1016/j.dnarep.2023.103483] [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: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
Age-related changes in gene expression have long been examined to understand the biology of aging. The hallmarks of aging are biological processes known to be associated with aging, but whether there is a unifying driver of these attributes, is not well understood. With the advent of technology over the last few years, it is quite clear that aging leads to global decline in transcription. In this Perspective, we highlight a new study in Nature Genetics that aimed to determine why global transcription rate reduces with age and how this phenomenon is the driver that interconnects multiple hallmarks of aging. This study recognizes that age-related accumulation of DNA damage, particularly transcription-blocking lesions, stalls RNA polymerase. This phenomenon affects longer genes leading to a gradual loss of transcription and skewing the transcriptome. In order to design a successful aging intervention, future work will be needed to test how some promising therapies in pre-clinical trials target affect transcriptional rate.
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Affiliation(s)
- Austin A Sims
- 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.
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48
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Stoeger T. The Road Less Traveled: Uncovering the Convergence Toward Specific Pleiotropic Phenotypes in Aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534472. [PMID: 37034589 PMCID: PMC10081180 DOI: 10.1101/2023.03.28.534472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Aging is a complex process influenced by a wide range of environmental and molecular factors. Despite this complexity, individuals tend to age in highly similar ways, leading to the question of what drives this convergence. Recent research, including my own discoveries, suggests that the length of transcript molecules plays a crucial role in age-dependent changes to the transcriptome. Drawing inspiration from the road trip analogy of cellular transcription, I propose that a non-linear scaling law drives convergence towards specific pleiotropic phenotypes in biological aging. This scaling law is based on the notion that molecular changes observed during aging may reflect unspecific damage to cellular physiology. By validating this hypothesis, I can improve our understanding of biological aging and identify new candidate compounds for anti-aging interventions, as well as re-identify one known intervention. This work has actionable implications for improving human health and extending lifespans.
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Affiliation(s)
- Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
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49
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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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50
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de Boer M, Te Lintel Hekkert M, Chang J, van Thiel BS, Martens L, Bos MM, de Kleijnen MGJ, Ridwan Y, Octavia Y, van Deel ED, Blonden LA, Brandt RMC, Barnhoorn S, Bautista-Niño PK, Krabbendam-Peters I, Wolswinkel R, Arshi B, Ghanbari M, Kupatt C, de Windt LJ, Danser AHJ, van der Pluijm I, Remme CA, Stoll M, Pothof J, Roks AJM, Kavousi M, Essers J, van der Velden J, Hoeijmakers JHJ, Duncker DJ. DNA repair in cardiomyocytes is critical for maintaining cardiac function in mice. Aging Cell 2023; 22:e13768. [PMID: 36756698 PMCID: PMC10014058 DOI: 10.1111/acel.13768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/30/2022] [Accepted: 12/19/2022] [Indexed: 02/10/2023] Open
Abstract
Heart failure has reached epidemic proportions in a progressively ageing population. The molecular mechanisms underlying heart failure remain elusive, but evidence indicates that DNA damage is enhanced in failing hearts. Here, we tested the hypothesis that endogenous DNA repair in cardiomyocytes is critical for maintaining normal cardiac function, so that perturbed repair of spontaneous DNA damage drives early onset of heart failure. To increase the burden of spontaneous DNA damage, we knocked out the DNA repair endonucleases xeroderma pigmentosum complementation group G (XPG) and excision repair cross-complementation group 1 (ERCC1), either systemically or cardiomyocyte-restricted, and studied the effects on cardiac function and structure. Loss of DNA repair permitted normal heart development but subsequently caused progressive deterioration of cardiac function, resulting in overt congestive heart failure and premature death within 6 months. Cardiac biopsies revealed increased oxidative stress associated with increased fibrosis and apoptosis. Moreover, gene set enrichment analysis showed enrichment of pathways associated with impaired DNA repair and apoptosis, and identified TP53 as one of the top active upstream transcription regulators. In support of the observed cardiac phenotype in mutant mice, several genetic variants in the ERCC1 and XPG gene in human GWAS data were found to be associated with cardiac remodelling and dysfunction. In conclusion, unrepaired spontaneous DNA damage in differentiated cardiomyocytes drives early onset of cardiac failure. These observations implicate DNA damage as a potential novel therapeutic target and highlight systemic and cardiomyocyte-restricted DNA repair-deficient mouse mutants as bona fide models of heart failure.
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Affiliation(s)
- Martine de Boer
- Division of Experimental Cardiology, Department of Cardiology, Thoraxcenter, Erasmus MC, Rotterdam, The Netherlands
| | - Maaike Te Lintel Hekkert
- Division of Experimental Cardiology, Department of Cardiology, Thoraxcenter, Erasmus MC, Rotterdam, The Netherlands
| | - Jiang Chang
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Bibi S van Thiel
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands.,Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands.,Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Leonie Martens
- Department of Genetic Epidemiology, Institute of Human Genetics, University Hospital Münster, Münster, Germany
| | - Maxime M Bos
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Marion G J de Kleijnen
- Division of Experimental Cardiology, Department of Cardiology, Thoraxcenter, Erasmus MC, Rotterdam, The Netherlands
| | - Yanto Ridwan
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands.,Department of Radiotherapy, Erasmus MC, Rotterdam, The Netherlands
| | - Yanti Octavia
- Division of Experimental Cardiology, Department of Cardiology, Thoraxcenter, Erasmus MC, Rotterdam, The Netherlands
| | - Elza D van Deel
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Lau A Blonden
- Division of Experimental Cardiology, Department of Cardiology, Thoraxcenter, Erasmus MC, Rotterdam, The Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Paula K Bautista-Niño
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands.,Centro de Investigaciones, Fundación Cardiovascular de Colombia- FCV, Bucaramanga, Colombia
| | - Ilona Krabbendam-Peters
- Division of Experimental Cardiology, Department of Cardiology, Thoraxcenter, Erasmus MC, Rotterdam, The Netherlands
| | - Rianne Wolswinkel
- Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Banafsheh Arshi
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Christian Kupatt
- I. Medizinische Klinik und Poliklinik, University Clinic Rechts der Isar, Technical University of Munich, Munich, Germany.,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,Walter-Brendel-Centre for Experimental Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Leon J de Windt
- Department of Molecular Genetics, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands.,Faculty of Science and Engineering, Maastricht University, Maastricht, The Netherlands
| | - A H Jan Danser
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Ingrid van der Pluijm
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands.,Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands
| | - Carol Ann Remme
- Department of Clinical and Experimental Cardiology, Heart Center, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Monika Stoll
- Department of Genetic Epidemiology, Institute of Human Genetics, University Hospital Münster, Münster, Germany.,Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Anton J M Roks
- Division of Vascular Medicine and Pharmacology, Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands.,Department of Vascular Surgery, Erasmus MC, Rotterdam, The Netherlands.,Department of Radiotherapy, Erasmus MC, Rotterdam, The Netherlands
| | - Jolanda van der Velden
- Department of Physiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Netherlands Heart Institute, Utrecht, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Molecular Genetics, Erasmus MC, Rotterdam, The Netherlands.,CECAD Forschungszentrum, Universität zu Köln, Köln, Germany.,Princess Máxima Center for Pediatric Oncology, Genome Instability and Nutrition, ONCODE Institute, Utrecht, The Netherlands
| | - Dirk J Duncker
- Division of Experimental Cardiology, Department of Cardiology, Thoraxcenter, Erasmus MC, Rotterdam, The Netherlands
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