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Andrawus M, David GB, Terziyska I, Sharvit L, Bergman A, Barzilai N, Raj SM, Govindaraju DR, Atzmon G. Genome integrity as a potential index of longevity in Ashkenazi Centenarian's families. GeroScience 2024; 46:4147-4162. [PMID: 38724875 PMCID: PMC11335978 DOI: 10.1007/s11357-024-01178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/24/2024] [Indexed: 06/19/2024] Open
Abstract
The aging process, or senescence, is characterized by age-specific decline in physical and physiological function, and increased frailty and genomic changes, including mutation accumulation. However, the mechanisms through which changes in genomic architecture influence human longevity have remained obscure. Copy number variants (CNVs), an abundant class of genomic variants, offer unique opportunities for understanding age-related genomic changes. Here we report the spectrum of CNVs in a cohort of 670 Ashkenazi Jewish centenarians, their progeny, and unrelated controls. The average ages of these groups were 97.4 ± 2.8, 69.2 ± 9.2, and 66.5 ± 7.0 respectively. For the first time, we compared different size classes of CNVs, from 1 kB to 100 MB in size. Using a high-resolution custom Affymetrix array, targeting 44,639 genomic regions, we identified a total of 12,166, 22,188, and 10,285 CNVs in centenarians, their progeny, and control groups, respectively. Interestingly, the offspring group showed the highest number of unique CNVs, followed by control and centenarians. While both gains and losses were found in all three groups, centenarians showed a significantly higher average number of both total gains and losses relative to their controls (p < 0.0327, 0.0182, respectively). Moreover, centenarians showed a lower total length of genomic material lost, suggesting that they may maintain superior genomic integrity over time. We also observe a significance fold increase of CNVs among the offspring, implying greater genomic integrity and a putative mechanism for longevity preservation. Genomic regions that experienced loss or gains appear to be distributed across many sites in the genome and contain genes involved in DNA transcription, cellular transport, developmental pathways, and metabolic functions. Our findings suggest that the exceptional longevity observed in centenarians may be attributed to the prolonged maintenance of functionally important genes. These genes are intrinsic to specific genomic regions as well as to the overall integrity of the genomic architecture. Additionally, a strong association between longer CNVs and differential gene expression observed in this study supports the notion that genomic integrity could positively influence longevity.
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Affiliation(s)
| | - Gil Ben David
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Ave., 3498838, Mount Carmel, Haifa, Israel
| | | | - Lital Sharvit
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Nir Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Srilakshmi M Raj
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | | | - Gil Atzmon
- Faculty of Natural Sciences, University of Haifa, Haifa, Israel.
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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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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3
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Xiao Y, Chen X, Chen Z, Dai W, Hu X, Zhang S, Zhong J, Chen J, Liu X, Liang L, Hu Y. Comparative single-cell transcriptomic analysis across tissues of aging primates reveals specific autologous activation of ZNF281 to mitigate oxidative stress in cornea. Aging Cell 2024:e14319. [PMID: 39254179 DOI: 10.1111/acel.14319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/23/2024] [Accepted: 08/09/2024] [Indexed: 09/11/2024] Open
Abstract
Reactive oxygen species (ROS) and oxidative stress accelerate cellular aging, but their impact on different tissues varies. The cornea, known for its robust antioxidant defense systems, is relatively resistant to age-related diseases like cancer. However, the precise mechanisms by which the cornea maintains ROS homeostasis during aging remain unclear. Through comparative single-cell transcriptomic analysis of the cornea and other tissues in young and old nonhuman primates, we identified that a ZNF281 coding transcriptomic program is specifically activated in cornea during aging. Further investigation revealed that ZNF281 forms a positive feedback loop with FOXO3 to sense elevated levels of ROS and mitigate their effects potentially by regulating the mitochondrial respiratory chain and superoxide dismutase (SOD) expression. Importantly, we observed that overexpression of ZNF281 in MSCs prevented cellular senescence. In summary, these findings open up possibilities for understanding tissue-specific aging and developing new therapies targeting ROS damage.
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Affiliation(s)
- Yuhua Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Xu Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Zheyao Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Wangxuan Dai
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Xing Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Shuyao Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Jiawei Zhong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Jia Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Xu Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Lingyi Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
| | - Youjin Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology Visual Science, Guangzhou, China
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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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5
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Gao D, Zhao B, Yu J, Li X, Yang D, Luo Y, Xia Y, Cai X, Guo Y. Deletion of stimulator of interferons genes aggravated cardiac dysfunction in physiological aged mice. Mech Ageing Dev 2024; 222:111978. [PMID: 39233064 DOI: 10.1016/j.mad.2024.111978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 08/15/2024] [Accepted: 08/31/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Stimulator of interferons genes (STING) is crucial for innate immune response. It has been demonstrated that cGAS-STING pathway was the driver of aging-related inflammation. However, whether STING is involved in cardiac dysfunction during the physiological aging process remains unclear. METHODS Gene expression profiles were obtained from the Gene Expression Omnibus database, followed by weighted gene co-expression network analysis, gene ontology analysis and protein network interaction analysis to identify key pathway and genes associated with aging. The effects of STING on cardiac function, glucose homeostasis, inflammation, and autophagy in physiological aging were investigated with STING knockout mice. RESULTS Bioinformatics analysis revealed STING emerged as a hub gene of interest. Subsequent experiments demonstrated the activation of STING pathway in the heart of aged mice. Knockout of STING alleviated the inflammation in aged mice. However, Knockout of STING impaired glucose tolerance, inhibited autophagy, enhanced oxidative stress and aggravated cardiac dysfunction in aged mice. CONCLUSION Although reducing inflammation, long-term STING inhibition by genetic ablation exacerbated cardiac dysfunction in aged mice. Given the multifaceted nature of aging and the diverse cellular functions of STING beyond immune regulation, the negative effects of targeting STING as a strategy to mitigate aging phenotype should be fully considered.
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Affiliation(s)
- Diansa Gao
- Division of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Boying Zhao
- Division of Cardiothoracic Surgery, The Center Hospital of Chongqing University, Chongqing 400016, China
| | - Jiang Yu
- Division of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaorong Li
- Division of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Ding Yang
- Division of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yuan Luo
- Division of Cardiothoracic Surgery, The Center Hospital of Chongqing University, Chongqing 400016, China
| | - Yong Xia
- Division of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiongwei Cai
- Department of Gynecology, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400037, China.
| | - Yongzheng Guo
- Division of Cardiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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6
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Kuldell JC, Kaplan CD. RNA Polymerase II activity control of gene expression and involvement in disease. J Mol Biol 2024:168770. [PMID: 39214283 DOI: 10.1016/j.jmb.2024.168770] [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: 07/23/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
Abstract
Gene expression is dependent on RNA Polymerase II (Pol II) activity in eukaryotes. In addition to determining the rate of RNA synthesis for all protein coding genes, Pol II serves as a platform for the recruitment of factors and regulation of co-transcriptional events, from RNA processing to chromatin modification and remodeling. The transcriptome can be shaped by changes in Pol II kinetics affecting RNA synthesis itself or because of alterations to co-transcriptional events that are responsive to or coupled with transcription. Genetic, biochemical, and structural approaches to Pol II in model organisms have revealed critical insights into how Pol II works and the types of factors that regulate it. The complexity of Pol II regulation generally increases with organismal complexity. In this review, we describe fundamental aspects of how Pol II activity can shape gene expression, discuss recent advances in how Pol II elongation is regulated on genes, and how altered Pol II function is linked to human disease and aging.
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Affiliation(s)
- James C Kuldell
- Department of Biological Sciences, 202A LSA, Fifth and Ruskin Avenues, University of Pittsburgh, Pittsburgh PA 15260
| | - Craig D Kaplan
- Department of Biological Sciences, 202A LSA, Fifth and Ruskin Avenues, University of Pittsburgh, Pittsburgh PA 15260.
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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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Meyer DH, Schumacher B. Aging clocks based on accumulating stochastic variation. NATURE AGING 2024; 4:871-885. [PMID: 38724736 PMCID: PMC11186771 DOI: 10.1038/s43587-024-00619-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 03/28/2024] [Indexed: 05/15/2024]
Abstract
Aging clocks have provided one of the most important recent breakthroughs in the biology of aging, and may provide indicators for the effectiveness of interventions in the aging process and preventive treatments for age-related diseases. The reproducibility of accurate aging clocks has reinvigorated the debate on whether a programmed process underlies aging. Here we show that accumulating stochastic variation in purely simulated data is sufficient to build aging clocks, and that first-generation and second-generation aging clocks are compatible with the accumulation of stochastic variation in DNA methylation or transcriptomic data. We find that accumulating stochastic variation is sufficient to predict chronological and biological age, indicated by significant prediction differences in smoking, calorie restriction, heterochronic parabiosis and partial reprogramming. Although our simulations may not explicitly rule out a programmed aging process, our results suggest that stochastically accumulating changes in any set of data that have a ground state at age zero are sufficient for generating aging clocks.
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Affiliation(s)
- David H Meyer
- Institute for Genome Stability in Aging and Disease, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, University Hospital and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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Chu LX, Wang WJ, Gu XP, Wu P, Gao C, Zhang Q, Wu J, Jiang DW, Huang JQ, Ying XW, Shen JM, Jiang Y, Luo LH, Xu JP, Ying YB, Chen HM, Fang A, Feng ZY, An SH, Li XK, Wang ZG. Spatiotemporal multi-omics: exploring molecular landscapes in aging and regenerative medicine. Mil Med Res 2024; 11:31. [PMID: 38797843 PMCID: PMC11129507 DOI: 10.1186/s40779-024-00537-4] [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: 12/15/2023] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
Aging and regeneration represent complex biological phenomena that have long captivated the scientific community. To fully comprehend these processes, it is essential to investigate molecular dynamics through a lens that encompasses both spatial and temporal dimensions. Conventional omics methodologies, such as genomics and transcriptomics, have been instrumental in identifying critical molecular facets of aging and regeneration. However, these methods are somewhat limited, constrained by their spatial resolution and their lack of capacity to dynamically represent tissue alterations. The advent of emerging spatiotemporal multi-omics approaches, encompassing transcriptomics, proteomics, metabolomics, and epigenomics, furnishes comprehensive insights into these intricate molecular dynamics. These sophisticated techniques facilitate accurate delineation of molecular patterns across an array of cells, tissues, and organs, thereby offering an in-depth understanding of the fundamental mechanisms at play. This review meticulously examines the significance of spatiotemporal multi-omics in the realms of aging and regeneration research. It underscores how these methodologies augment our comprehension of molecular dynamics, cellular interactions, and signaling pathways. Initially, the review delineates the foundational principles underpinning these methods, followed by an evaluation of their recent applications within the field. The review ultimately concludes by addressing the prevailing challenges and projecting future advancements in the field. Indubitably, spatiotemporal multi-omics are instrumental in deciphering the complexities inherent in aging and regeneration, thus charting a course toward potential therapeutic innovations.
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Affiliation(s)
- Liu-Xi Chu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Wen-Jia Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xin-Pei Gu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 510515, China
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China
| | - Ping Wu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Chen Gao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Quan Zhang
- Integrative Muscle Biology Laboratory, Division of Regenerative and Rehabilitative Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States
| | - Jia Wu
- Key Laboratory for Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Da-Wei Jiang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jun-Qing Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China
| | - Xin-Wang Ying
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jia-Men Shen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi Jiang
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Li-Hua Luo
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, 324025, Zhejiang, China
| | - Jun-Peng Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yi-Bo Ying
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao-Man Chen
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ao Fang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zun-Yong Feng
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Singapore, 138673, Singapore.
| | - Shu-Hong An
- Department of Human Anatomy, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, Shandong, China.
| | - Xiao-Kun Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
| | - Zhou-Guang Wang
- Affiliated Cixi Hospital, Wenzhou Medical University, Ningbo, 315300, Zhejiang, China.
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- National Key Laboratory of Macromolecular Drug Development and Manufacturing, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Institute of Imaging Diagnosis and Minimally Invasive Intervention Research, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui, 323000, Zhejiang, China.
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10
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Hutson M. Software tools identify forgotten genes. Nature 2024:10.1038/d41586-024-01548-w. [PMID: 38789607 DOI: 10.1038/d41586-024-01548-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
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11
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Nicholson MD, Anderson CJ, Odom DT, Aitken SJ, Taylor MS. DNA lesion bypass and the stochastic dynamics of transcription-coupled repair. Proc Natl Acad Sci U S A 2024; 121:e2403871121. [PMID: 38717857 PMCID: PMC11098089 DOI: 10.1073/pnas.2403871121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
DNA base damage is a major source of oncogenic mutations and disruption to gene expression. The stalling of RNA polymerase II (RNAP) at sites of DNA damage and the subsequent triggering of repair processes have major roles in shaping the genome-wide distribution of mutations, clearing barriers to transcription, and minimizing the production of miscoded gene products. Despite its importance for genetic integrity, key mechanistic features of this transcription-coupled repair (TCR) process are controversial or unknown. Here, we exploited a well-powered in vivo mammalian model system to explore the mechanistic properties and parameters of TCR for alkylation damage at fine spatial resolution and with discrimination of the damaged DNA strand. For rigorous interpretation, a generalizable mathematical model of DNA damage and TCR was developed. Fitting experimental data to the model and simulation revealed that RNA polymerases frequently bypass lesions without triggering repair, indicating that small alkylation adducts are unlikely to be an efficient barrier to gene expression. Following a burst of damage, the efficiency of transcription-coupled repair gradually decays through gene bodies with implications for the occurrence and accurate inference of driver mutations in cancer. The reinitation of transcription from the repair site is not a general feature of transcription-coupled repair, and the observed data is consistent with reinitiation never taking place. Collectively, these results reveal how the directional but stochastic activity of TCR shapes the distribution of mutations following DNA damage.
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Affiliation(s)
- Michael D. Nicholson
- Cancer Research United Kingdom Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Craig J. Anderson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
| | - Duncan T. Odom
- Division of Regulatory Genomics and Cancer Evolution (B270), German Cancer Research Center, Heidelberg69120, Germany
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
| | - Sarah J. Aitken
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, CambridgeCB2 0RE, United Kingdom
- Medical Research Council Toxicology Unit, University of Cambridge, CambridgeCB2 1QR, United Kingdom
- Department of Histopathology, Cambridge University Hospitals National Health Service Foundation Trust, CambridgeCB2 0QQ, United Kingdom
| | - Martin S. Taylor
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, EdinburghEH4 2XU, United Kingdom
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12
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Kumar NH, Kluever V, Barth E, Krautwurst S, Furlan M, Pelizzola M, Marz M, Fornasiero EF. Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain. Nucleic Acids Res 2024; 52:2865-2885. [PMID: 38471806 PMCID: PMC11014377 DOI: 10.1093/nar/gkae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/18/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
A comprehensive understanding of molecular changes during brain aging is essential to mitigate cognitive decline and delay neurodegenerative diseases. The interpretation of mRNA alterations during brain aging is influenced by the health and age of the animal cohorts studied. Here, we carefully consider these factors and provide an in-depth investigation of mRNA splicing and dynamics in the aging mouse brain, combining short- and long-read sequencing technologies with extensive bioinformatic analyses. Our findings encompass a spectrum of age-related changes, including differences in isoform usage, decreased mRNA dynamics and a module showing increased expression of neuronal genes. Notably, our results indicate a reduced abundance of mRNA isoforms leading to nonsense-mediated RNA decay and suggest a regulatory role for RNA-binding proteins, indicating that their regulation may be altered leading to the reshaping of the aged brain transcriptome. Collectively, our study highlights the importance of studying mRNA splicing events during brain aging.
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Affiliation(s)
- Nisha Hemandhar Kumar
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Verena Kluever
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Emanuel Barth
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
- Bioinformatics Core Facility, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Sebastian Krautwurst
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Mattia Furlan
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), 20139 Milan, Italy
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126 Milan, Italy
| | - Manja Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, 07743 Jena, Germany
- Leibniz Institute for Age Research, FLI, Beutenbergstraße 11, Jena 07743, Germany
- European Virus Bioinformatics Center, Friedrich Schiller University, Leutragraben 1, Jena 07743, Germany
- German Center for Integrative Biodiversity Research (iDiv), Puschstraße 4, Leipzig 04103, Germany
- Michael Stifel Center Jena, Friedrich Schiller University, Ernst-Abbe-Platz 2, Jena 07743, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fuerstengraben 1, Jena 07743, Germany
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
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13
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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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14
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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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15
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Richardson R, Tejedor Navarro H, Amaral LAN, Stoeger T. Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results. eLife 2024; 12:RP93429. [PMID: 38546716 PMCID: PMC10977968 DOI: 10.7554/elife.93429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2024] Open
Abstract
Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results. Understudied genes remain abandoned by studies that cite these -omics experiments. Conversely, we find that publications on understudied genes may even accrue a greater number of citations. Among 45 biological and experimental factors previously proposed to affect which genes are being studied, we find that 33 are significantly associated with the choice of hit genes presented in titles and abstracts of -omics studies. To promote the investigation of understudied genes, we condense our insights into a tool, find my understudied genes (FMUG), that allows scientists to engage with potential bias during the selection of hits. We demonstrate the utility of FMUG through the identification of genes that remain understudied in vertebrate aging. FMUG is developed in Flutter and is available for download at fmug.amaral.northwestern.edu as a MacOS/Windows app.
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Affiliation(s)
- Reese Richardson
- Interdisciplinary Biological Sciences, Northwestern UniversityEvanstonUnited States
- Department of Chemical and Biological Engineering, Northwestern UniversityEvanstonUnited States
| | - Heliodoro Tejedor Navarro
- Department of Chemical and Biological Engineering, Northwestern UniversityEvanstonUnited States
- Northwestern Institute on Complex Systems, Northwestern UniversityEvanstonUnited States
| | - Luis A Nunes Amaral
- Department of Chemical and Biological Engineering, Northwestern UniversityEvanstonUnited States
- Northwestern Institute on Complex Systems, Northwestern UniversityEvanstonUnited States
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States
- Department of Physics and Astronomy, Northwestern UniversityEvanstonUnited States
| | - Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern UniversityEvanstonUnited States
- The Potocsnak Longevity Institute, Northwestern UniversityChicagoUnited States
- Simpson Querrey Lung Institute for Translational Science, Northwestern UniversityChicagoUnited States
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16
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Jagaraj CJ, Shadfar S, Kashani SA, Saravanabavan S, Farzana F, Atkin JD. Molecular hallmarks of ageing in amyotrophic lateral sclerosis. Cell Mol Life Sci 2024; 81:111. [PMID: 38430277 PMCID: PMC10908642 DOI: 10.1007/s00018-024-05164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, severely debilitating and rapidly progressing disorder affecting motor neurons in the brain, brainstem, and spinal cord. Unfortunately, there are few effective treatments, thus there remains a critical need to find novel interventions that can mitigate against its effects. Whilst the aetiology of ALS remains unclear, ageing is the major risk factor. Ageing is a slowly progressive process marked by functional decline of an organism over its lifespan. However, it remains unclear how ageing promotes the risk of ALS. At the molecular and cellular level there are specific hallmarks characteristic of normal ageing. These hallmarks are highly inter-related and overlap significantly with each other. Moreover, whilst ageing is a normal process, there are striking similarities at the molecular level between these factors and neurodegeneration in ALS. Nine ageing hallmarks were originally proposed: genomic instability, loss of telomeres, senescence, epigenetic modifications, dysregulated nutrient sensing, loss of proteostasis, mitochondrial dysfunction, stem cell exhaustion, and altered inter-cellular communication. However, these were recently (2023) expanded to include dysregulation of autophagy, inflammation and dysbiosis. Hence, given the latest updates to these hallmarks, and their close association to disease processes in ALS, a new examination of their relationship to pathophysiology is warranted. In this review, we describe possible mechanisms by which normal ageing impacts on neurodegenerative mechanisms implicated in ALS, and new therapeutic interventions that may arise from this.
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Affiliation(s)
- Cyril Jones Jagaraj
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sina Shadfar
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sara Assar Kashani
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Sayanthooran Saravanabavan
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Fabiha Farzana
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- MND Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, 75 Talavera Road, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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17
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Richardson RAK, Tejedor Navarro H, Amaral LAN, Stoeger T. Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.28.530483. [PMID: 36909550 PMCID: PMC10002660 DOI: 10.1101/2023.02.28.530483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Present-day publications on human genes primarily feature genes that already appeared in many publications prior to completion of the Human Genome Project in 2003. These patterns persist despite the subsequent adoption of high-throughput technologies, which routinely identify novel genes associated with biological processes and disease. Although several hypotheses for bias in the selection of genes as research targets have been proposed, their explanatory powers have not yet been compared. Our analysis suggests that understudied genes are systematically abandoned in favor of better-studied genes between the completion of -omics experiments and the reporting of results. Understudied genes remain abandoned by studies that cite these -omics experiments. Conversely, we find that publications on understudied genes may even accrue a greater number of citations. Among 45 biological and experimental factors previously proposed to affect which genes are being studied, we find that 33 are significantly associated with the choice of hit genes presented in titles and abstracts of - omics studies. To promote the investigation of understudied genes we condense our insights into a tool, find my understudied genes (FMUG), that allows scientists to engage with potential bias during the selection of hits. We demonstrate the utility of FMUG through the identification of genes that remain understudied in vertebrate aging. FMUG is developed in Flutter and is available for download at fmug.amaral.northwestern.edu as a MacOS/Windows app.
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Affiliation(s)
- Reese AK Richardson
- Interdisciplinary Biological Sciences, Northwestern University
- Department of Chemical and Biological Engineering, Northwestern University
| | - Heliodoro Tejedor Navarro
- Department of Chemical and Biological Engineering, Northwestern University
- Northwestern Institute on Complex Systems, Northwestern University
| | - Luis A Nunes Amaral
- Department of Chemical and Biological Engineering, Northwestern University
- Northwestern Institute on Complex Systems, Northwestern University
- Department of Physics and Astronomy, Northwestern University
- Department of Molecular Biosciences, Northwestern University
| | - Thomas Stoeger
- Department of Chemical and Biological Engineering, Northwestern University
- The Potocsnak Longevity Institute, Northwestern University
- Simpson Querrey Lung Institute for Translational Science, Northwestern University
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18
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Horvath S, Singh K, Raj K, Khairnar SI, Sanghavi A, Shrivastava A, Zoller JA, Li CZ, Herenu CB, Canatelli-Mallat M, Lehmann M, Habazin S, Novokmet M, Vučković F, Solberg Woods LC, Martinez AG, Wang T, Chiavellini P, Levine AJ, Chen H, Brooke RT, Gordevicius J, Lauc G, Goya RG, Katcher HL. Reversal of biological age in multiple rat organs by young porcine plasma fraction. GeroScience 2024; 46:367-394. [PMID: 37875652 PMCID: PMC10828479 DOI: 10.1007/s11357-023-00980-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
Young blood plasma is known to confer beneficial effects on various organs in mice and rats. However, it was not known whether plasma from young adult pigs rejuvenates old rat tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n = 613 tissue samples. As indicated by their respective names, the rat pan-tissue clock can be applied to DNA methylation profiles from all rat tissues, while the rat brain, liver, and blood clocks apply to the corresponding tissue types. We also developed two epigenetic clocks that apply to both human and rat tissues by adding n = 1366 human tissue samples to the training data. We employed these six rat clocks to investigate the rejuvenation effects of a porcine plasma fraction treatment in different rat tissues. The treatment more than halved the epigenetic ages of blood, heart, and liver tissue. A less pronounced, but statistically significant, rejuvenation effect could be observed in the hypothalamus. The treatment was accompanied by progressive improvement in the function of these organs as ascertained through numerous biochemical/physiological biomarkers, behavioral responses encompassing cognitive functions. An immunoglobulin G (IgG) N-glycosylation pattern shift from pro- to anti-inflammatory also indicated reversal of glycan aging. Overall, this study demonstrates that a young porcine plasma-derived treatment markedly reverses aging in rats according to epigenetic clocks, IgG glycans, and other biomarkers of aging.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA.
- Altos Labs, Cambridge, UK.
| | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS University, Mumbai, India
| | | | - Shraddha I Khairnar
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS University, Mumbai, India
| | | | | | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Caesar Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Claudia B Herenu
- Institute for Experimental Pharmacology of Cordoba (IFEC), School of Chemical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Martina Canatelli-Mallat
- Biochemistry Research Institute of La Plata-Histology B, Pathology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Marianne Lehmann
- Biochemistry Research Institute of La Plata-Histology B, Pathology B, School of Medicine, University of La Plata, La Plata, Argentina
| | | | | | | | - Leah C Solberg Woods
- Wake Forest University School of Medicine, Medical Center Drive, Winston Salem, NC, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Priscila Chiavellini
- Biochemistry Research Institute of La Plata-Histology B, Pathology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Andrew J Levine
- Department of Neurology, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | | | | | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Rodolfo G Goya
- Biochemistry Research Institute of La Plata-Histology B, Pathology B, School of Medicine, University of La Plata, La Plata, Argentina
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19
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Szatmári EZ, Csordás A, Kerepesi C. Unique Patterns in Amino Acid Sequences of Aging-Related Proteins. Adv Biol (Weinh) 2024; 8:e2300436. [PMID: 37880927 DOI: 10.1002/adbi.202300436] [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: 08/21/2023] [Revised: 10/14/2023] [Indexed: 10/27/2023]
Abstract
Aging has strong genetic components and the list of genes that may regulate the aging process is collected in the GenAge database. There may be characteristic patterns in the amino acid sequences of aging-related proteins that distinguish them from other proteins and this information will lead to a better understanding of the aging process. To test this hypothesis, human protein sequences are extracted from the UniProt database and the relative frequency of every amino acid residue in aging-related proteins and the remaining proteins is calculated. The main observation is that the mean relative frequency of aspartic acid (D) is consistently higher, while the mean relative frequencies of tryptophan (W) and leucine (L) are consistently lower in aging-related proteins compared to the non-aging-related proteins for the human and four examined model organisms. It is also observed that the mean relative frequency of aspartic acid is higher, while the mean relative frequency of tryptophan is lower in pro-longevity proteins compared to anti-longevity proteins in model organisms. Finally, it is found that aging-related proteins tend to be longer than non-aging-related proteins. It is hoped that this analysis initiates further computational and experimental research to explore the underlying mechanisms of these findings.
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Affiliation(s)
- Eszter Zita Szatmári
- Institute for Computer Science and Control (SZTAKI), Hungarian Research Network (HUN-REN), Budapest, 1111, Hungary
- Department of Applied Analysis and Computational Mathematics, Eötvös Loránd University (ELTE), Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | | | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI), Hungarian Research Network (HUN-REN), Budapest, 1111, Hungary
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20
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Jiménez-Loygorri JI, Villarejo-Zori B, Viedma-Poyatos Á, Zapata-Muñoz J, Benítez-Fernández R, Frutos-Lisón MD, Tomás-Barberán FA, Espín JC, Area-Gómez E, Gomez-Duran A, Boya P. Mitophagy curtails cytosolic mtDNA-dependent activation of cGAS/STING inflammation during aging. Nat Commun 2024; 15:830. [PMID: 38280852 PMCID: PMC10821893 DOI: 10.1038/s41467-024-45044-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/10/2024] [Indexed: 01/29/2024] Open
Abstract
Macroautophagy decreases with age, and this change is considered a hallmark of the aging process. It remains unknown whether mitophagy, the essential selective autophagic degradation of mitochondria, also decreases with age. In our analysis of mitophagy in multiple organs in the mito-QC reporter mouse, mitophagy is either increased or unchanged in old versus young mice. Transcriptomic analysis shows marked upregulation of the type I interferon response in the retina of old mice, which correlates with increased levels of cytosolic mtDNA and activation of the cGAS/STING pathway. Crucially, these same alterations are replicated in primary human fibroblasts from elderly donors. In old mice, pharmacological induction of mitophagy with urolithin A attenuates cGAS/STING activation and ameliorates deterioration of neurological function. These findings point to mitophagy induction as a strategy to decrease age-associated inflammation and increase healthspan.
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Affiliation(s)
- Juan Ignacio Jiménez-Loygorri
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Beatriz Villarejo-Zori
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Álvaro Viedma-Poyatos
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Juan Zapata-Muñoz
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Rocío Benítez-Fernández
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
- Department of Neuroscience and Movement Science, Section of Medicine, University of Fribourg, Fribourg, Switzerland
| | - María Dolores Frutos-Lisón
- Food & Health Lab, Research Group on Quality, Safety, and Bioactivity of Plant Foods, CEBAS-CSIC, Murcia, Spain
| | - Francisco A Tomás-Barberán
- Food & Health Lab, Research Group on Quality, Safety, and Bioactivity of Plant Foods, CEBAS-CSIC, Murcia, Spain
| | - Juan Carlos Espín
- Food & Health Lab, Research Group on Quality, Safety, and Bioactivity of Plant Foods, CEBAS-CSIC, Murcia, Spain
| | - Estela Area-Gómez
- Department of Biomedicine, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Aurora Gomez-Duran
- Department of Biomedicine, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
- MitoPhenomics Lab, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Patricia Boya
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain.
- Department of Neuroscience and Movement Science, Section of Medicine, University of Fribourg, Fribourg, Switzerland.
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21
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Di Fraia D, Marino A, Lee JH, Kelmer Sacramento E, Baumgart M, Bagnoli S, Tomaz da Silva P, Kumar Sahu A, Siano G, Tiessen M, Terzibasi-Tozzini E, Gagneur J, Frydman J, Cellerino A, Ori A. Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.20.549210. [PMID: 38260253 PMCID: PMC10802395 DOI: 10.1101/2023.07.20.549210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Aging and neurodegeneration entail diverse cellular and molecular hallmarks. Here, we studied the effects of aging on the transcriptome, translatome, and multiple layers of the proteome in the brain of a short-lived killifish. We reveal that aging causes widespread reduction of proteins enriched in basic amino acids that is independent of mRNA regulation, and it is not due to impaired proteasome activity. Instead, we identify a cascade of events where aberrant translation pausing leads to reduced ribosome availability resulting in proteome remodeling independently of transcriptional regulation. Our research uncovers a vulnerable point in the aging brain's biology - the biogenesis of basic DNA/RNA binding proteins. This vulnerability may represent a unifying principle that connects various aging hallmarks, encompassing genome integrity and the biosynthesis of macromolecules.
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Affiliation(s)
- Domenico Di Fraia
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Antonio Marino
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Jae Ho Lee
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Mario Baumgart
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Pedro Tomaz da Silva
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Amit Kumar Sahu
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Max Tiessen
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alessandro Cellerino
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- BIO@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
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22
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Baralle M, Romano M. Age-Related Alternative Splicing: Driver or Passenger in the Aging Process? Cells 2023; 12:2819. [PMID: 38132139 PMCID: PMC10742131 DOI: 10.3390/cells12242819] [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: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy;
| | - Maurizio Romano
- Department of Life Sciences, University of Trieste, Via A. Valerio 28, 34127 Trieste, Italy
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23
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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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24
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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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25
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Abdellatif M, Rainer PP, Sedej S, Kroemer G. Hallmarks of cardiovascular ageing. Nat Rev Cardiol 2023; 20:754-777. [PMID: 37193857 DOI: 10.1038/s41569-023-00881-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/21/2023] [Indexed: 05/18/2023]
Abstract
Normal circulatory function is a key determinant of disease-free life expectancy (healthspan). Indeed, pathologies affecting the cardiovascular system, which are growing in prevalence, are the leading cause of global morbidity, disability and mortality, whereas the maintenance of cardiovascular health is necessary to promote both organismal healthspan and lifespan. Therefore, cardiovascular ageing might precede or even underlie body-wide, age-related health deterioration. In this Review, we posit that eight molecular hallmarks are common denominators in cardiovascular ageing, namely disabled macroautophagy, loss of proteostasis, genomic instability (in particular, clonal haematopoiesis of indeterminate potential), epigenetic alterations, mitochondrial dysfunction, cell senescence, dysregulated neurohormonal signalling and inflammation. We also propose a hierarchical order that distinguishes primary (upstream) from antagonistic and integrative (downstream) hallmarks of cardiovascular ageing. Finally, we discuss how targeting each of the eight hallmarks might be therapeutically exploited to attenuate residual cardiovascular risk in older individuals.
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Affiliation(s)
- Mahmoud Abdellatif
- Department of Cardiology, Medical University of Graz, Graz, Austria.
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.
- BioTechMed Graz, Graz, Austria.
| | - Peter P Rainer
- Department of Cardiology, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Simon Sedej
- Department of Cardiology, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Institute of Physiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France.
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France.
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France.
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26
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Han S, Budinger GS, Gottardi CJ. Alveolar epithelial regeneration in the aging lung. J Clin Invest 2023; 133:e170504. [PMID: 37843280 PMCID: PMC10575730 DOI: 10.1172/jci170504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
Advancing age is the most important risk factor for the development of and mortality from acute and chronic lung diseases, including pneumonia, chronic obstructive pulmonary disease, and pulmonary fibrosis. This risk was manifest during the COVID-19 pandemic, when elderly people were disproportionately affected and died from SARS-CoV-2 pneumonia. However, the recent pandemic also provided lessons on lung resilience. An overwhelming majority of patients with SARS-CoV-2 pneumonia, even those with severe disease, recovered with near-complete restoration of lung architecture and function. These observations are inconsistent with historic views of the lung as a terminally differentiated organ incapable of regeneration. Here, we review emerging hypotheses that explain how the lung repairs itself after injury and why these mechanisms of lung repair fail in some individuals, particularly the elderly.
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Affiliation(s)
- SeungHye Han
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
| | - G.R. Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA
| | - Cara J. Gottardi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, and
- Cell and Developmental Biology, Northwestern University, Chicago, Illinois, USA
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27
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Popescu I, Deelen J, Illario M, Adams J. Challenges in anti-aging medicine-trends in biomarker discovery and therapeutic interventions for a healthy lifespan. J Cell Mol Med 2023; 27:2643-2650. [PMID: 37610311 PMCID: PMC10494298 DOI: 10.1111/jcmm.17912] [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: 06/07/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023] Open
Abstract
We are facing a growing aging population, along with increasing pressure on health systems, caused by the impact of chronic co-morbidities (i.e. cancer, cardiovascular and neurodegenerative diseases) and functional disabilities as people age. Relatively simple preventive lifestyle interventions, such as dietary restriction and physical exercise, are important contributors to active and healthy aging in the general population. However, as shown in model organisms or in 'in vitro' conditions, lifestyle-independent interventions may have additional health benefits and can even be conceived as possible reversers of the aging process. Thus, pharmaceutical laboratories, research institutes, and universities are putting more and more effort into finding new molecular pathways and druggable targets to develop gerotherapeutics. One approach is to target the driving mechanisms of aging, some of which, like cellular senescence and impaired autophagy, we discussed in an update on the biology of aging at AgingFit 2023 in Lille, France. We underline the importance of carefully and extensively testing senotherapeutics, given the pleiotropism and heterogeneity of targeted senescent cells within different organs, at different time frames. Other druggable targets emerging from new putative mechanisms, like those based on transcriptome imbalance, nucleophagy, protein phosphatase depletion, glutamine metabolism, or seno-antigenicity, have been evidenced by recent preclinical studies in classical models of aging but need to be validated in humans. Finally, we highlight several approaches in the discovery of biomarkers of healthy aging, as well as for the prediction of neurodegenerative diseases and the evaluation of rejuvenation strategies.
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Affiliation(s)
- Iuliana Popescu
- Barnstable Brown Diabetes Research CenterUniversity of Kentucky, College of MedicineLexingtonKentuckyUSA
| | - Joris Deelen
- Max Planck Institute for Biology of AgeingKölnGermany
| | - Maddalena Illario
- Department of Public Health and EDANFederico II University and HospitalNaplesItaly
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28
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Schroader JH, Handley MT, Reddy K. Inosine triphosphate pyrophosphatase: A guardian of the cellular nucleotide pool and potential mediator of RNA function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1790. [PMID: 37092460 DOI: 10.1002/wrna.1790] [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: 11/30/2022] [Revised: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
Inosine triphosphate pyrophosphatase (ITPase), encoded by the ITPA gene in humans, is an important enzyme that preserves the integrity of cellular nucleotide pools by hydrolyzing the noncanonical purine nucleotides (deoxy)inosine and (deoxy)xanthosine triphosphate into monophosphates and pyrophosphate. Variants in the ITPA gene can cause partial or complete ITPase deficiency. Partial ITPase deficiency is benign but clinically relevant as it is linked to altered drug responses. Complete ITPase deficiency causes a severe multisystem disorder characterized by seizures and encephalopathy that is frequently associated with fatal infantile dilated cardiomyopathy. In the absence of ITPase activity, its substrate noncanonical nucleotides have the potential to accumulate and become aberrantly incorporated into DNA and RNA. Hence, the pathophysiology of ITPase deficiency could arise from metabolic imbalance, altered DNA or RNA regulation, or from a combination of these factors. Here, we review the known functions of ITPase and highlight recent work aimed at determining the molecular basis for ITPA-associated pathogenesis which provides evidence for RNA dysfunction. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jacob H Schroader
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Mark T Handley
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Kaalak Reddy
- The RNA Institute, University at Albany, State University of New York, Albany, New York, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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29
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Kurland JV, Cutler AA, Stanley JT, Betta ND, Van Deusen A, Pawlikowski B, Hall M, Antwine T, Russell A, Allen MA, Dowell R, Olwin B. Aging disrupts gene expression timing during muscle regeneration. Stem Cell Reports 2023; 18:1325-1339. [PMID: 37315524 PMCID: PMC10277839 DOI: 10.1016/j.stemcr.2023.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
Skeletal muscle function and regenerative capacity decline during aging, yet factors driving these changes are incompletely understood. Muscle regeneration requires temporally coordinated transcriptional programs to drive myogenic stem cells to activate, proliferate, fuse to form myofibers, and to mature as myonuclei, restoring muscle function after injury. We assessed global changes in myogenic transcription programs distinguishing muscle regeneration in aged mice from young mice by comparing pseudotime trajectories from single-nucleus RNA sequencing of myogenic nuclei. Aging-specific differences in coordinating myogenic transcription programs necessary for restoring muscle function occur following muscle injury, likely contributing to compromised regeneration in aged mice. Differences in pseudotime alignment of myogenic nuclei when comparing aged with young mice via dynamic time warping revealed pseudotemporal differences becoming progressively more severe as regeneration proceeds. Disruptions in timing of myogenic gene expression programs may contribute to incomplete skeletal muscle regeneration and declines in muscle function as organisms age.
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Affiliation(s)
- Jesse V Kurland
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Alicia A Cutler
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Jacob T Stanley
- BioFrontiers Institute, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA
| | - Nicole Dalla Betta
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Ashleigh Van Deusen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Edgewise Therapeutics, 3415 Colorado Avenue, Boulder, CO 80303, USA
| | - Brad Pawlikowski
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Department of Pediatrics Section of Section of Hematology, Oncology, Bone Marrow Transplant, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Monica Hall
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59718, USA
| | - Tiffany Antwine
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Alan Russell
- Edgewise Therapeutics, 3415 Colorado Avenue, Boulder, CO 80303, USA
| | - Mary Ann Allen
- BioFrontiers Institute, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA
| | - Robin Dowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; BioFrontiers Institute, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, CO 80303, USA.
| | - Bradley Olwin
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA.
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30
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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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31
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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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32
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Mittal BB, Vaughan DE. Inclusion of epigenetic age acceleration in oncological trials. THE LANCET. HEALTHY LONGEVITY 2023; 4:e185-e186. [PMID: 36972716 DOI: 10.1016/s2666-7568(23)00034-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 03/29/2023] Open
Affiliation(s)
- Bharat B Mittal
- Department of Radiation Oncology, Northwestern University, Chicago, IL 60611, USA.
| | - Douglas E Vaughan
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
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33
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Salnikov L, Goldberg S, Rijhwani H, Shi Y, Pinsky E. The RNA-Seq data analysis shows how the ontogenesis defines aging. FRONTIERS IN AGING 2023; 4:1143334. [PMID: 36999000 PMCID: PMC10046809 DOI: 10.3389/fragi.2023.1143334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/03/2023] [Indexed: 03/15/2023]
Abstract
This paper presents a global statistical analysis of the RNA-Seq results of the entire Mus musculus genome. We explain aging by a gradual redistribution of limited resources between two major tasks of the organism: its self-sustenance based on the function of the housekeeping gene group (HG) and functional differentiation provided by the integrative gene group (IntG). All known disorders associated with aging are the result of a deficiency in the repair processes provided by the cellular infrastructure. Understanding exactly how this deficiency arises is our primary goal. Analysis of RNA production data of 35,630 genes, from which 5,101 were identified as HG genes, showed that RNA production levels in the HG and IntG genes had statistically significant differences (p-value <0.0001) throughout the entire observation period. In the reproductive period of life, which has the lowest actual mortality risk for Mus musculus, changes in the age dynamics of RNA production occur. The statistically significant dynamics of the decrease of RNA production in the HG group in contrast to the IntG group was determined (p-value = 0.0045). The trend toward significant shift in the HG/IntG ratio occurs after the end of the reproductive period, coinciding with the beginning of the mortality rate increase in Mus musculus indirectly supports our hypothesis. The results demonstrate a different orientation of the impact of ontogenesis regulatory mechanisms on the groups of genes representing cell infrastructures and their organismal functions, making the chosen direction promising for further research and understanding the mechanisms of aging.
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Affiliation(s)
- Lev Salnikov
- AntiCA Biomed, San Diego, CA, United States
- *Correspondence: Lev Salnikov,
| | - Saveli Goldberg
- Department of Radiation Oncology, Mass General Hospital, Boston, MA, United Kingdom
| | - Heena Rijhwani
- Department of Computer Science, Met College, Boston University, Boston, MA, United Kingdom
| | - Yuran Shi
- Department of Computer Science, Brandeis University, Waltham, MA, United Kingdom
| | - Eugene Pinsky
- Department of Computer Science, Met College, Boston University, Boston, MA, United Kingdom
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34
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Yang BA, Larouche JA, Sabin KM, Fraczek PM, Parker SCJ, Aguilar CA. Three-dimensional chromatin re-organization during muscle stem cell aging. Aging Cell 2023; 22:e13789. [PMID: 36727578 PMCID: PMC10086523 DOI: 10.1111/acel.13789] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/29/2022] [Accepted: 01/11/2023] [Indexed: 02/03/2023] Open
Abstract
Age-related skeletal muscle atrophy or sarcopenia is a significant societal problem that is becoming amplified as the world's population continues to increase. The regeneration of damaged skeletal muscle is mediated by muscle stem cells, but in old age muscle stem cells become functionally attenuated. The molecular mechanisms that govern muscle stem cell aging encompass changes across multiple regulatory layers and are integrated by the three-dimensional organization of the genome. To quantitatively understand how hierarchical chromatin architecture changes during muscle stem cell aging, we generated 3D chromatin conformation maps (Hi-C) and integrated these datasets with multi-omic (chromatin accessibility and transcriptome) profiles from bulk populations and single cells. We observed that muscle stem cells display static behavior at global scales of chromatin organization during aging and extensive rewiring of local contacts at finer scales that were associated with variations in transcription factor binding and aberrant gene expression. These data provide insights into genome topology as a regulator of molecular function in stem cell aging.
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Affiliation(s)
- Benjamin A Yang
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Jacqueline A Larouche
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Kaitlyn M Sabin
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Paula M Fraczek
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephen C J Parker
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, USA
| | - Carlos A Aguilar
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA.,Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA
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35
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Gyenis A, Chang J, Demmers JJPG, Bruens ST, Barnhoorn S, Brandt RMC, Baar MP, Raseta M, Derks KWJ, Hoeijmakers JHJ, Pothof J. Genome-wide RNA polymerase stalling shapes the transcriptome during aging. Nat Genet 2023; 55:268-279. [PMID: 36658433 PMCID: PMC9925383 DOI: 10.1038/s41588-022-01279-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/07/2022] [Indexed: 01/21/2023]
Abstract
Gene expression profiling has identified numerous processes altered in aging, but how these changes arise is largely unknown. Here we combined nascent RNA sequencing and RNA polymerase II chromatin immunoprecipitation followed by sequencing to elucidate the underlying mechanisms triggering gene expression changes in wild-type aged mice. We found that in 2-year-old liver, 40% of elongating RNA polymerases are stalled, lowering productive transcription and skewing transcriptional output in a gene-length-dependent fashion. We demonstrate that this transcriptional stress is caused by endogenous DNA damage and explains the majority of gene expression changes in aging in most mainly postmitotic organs, specifically affecting aging hallmark pathways such as nutrient sensing, autophagy, proteostasis, energy metabolism, immune function and cellular stress resilience. Age-related transcriptional stress is evolutionary conserved from nematodes to humans. Thus, accumulation of stochastic endogenous DNA damage during aging deteriorates basal transcription, which establishes the age-related transcriptome and causes dysfunction of key aging hallmark pathways, disclosing how DNA damage functionally underlies major aspects of normal aging.
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Affiliation(s)
- Akos Gyenis
- 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
| | - Jiang Chang
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joris J P G Demmers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Serena T Bruens
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Renata M C Brandt
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marjolein P Baar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marko Raseta
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Kasper W J Derks
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics and School for Oncology & Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - 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
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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