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Ahmad A, Braden A, Khan S, Xiao J, Khan MM. Crosstalk between the DNA damage response and cellular senescence drives aging and age-related diseases. Semin Immunopathol 2024; 46:10. [PMID: 39095660 DOI: 10.1007/s00281-024-01016-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/21/2024] [Indexed: 08/04/2024]
Abstract
Cellular senescence is a crucial process of irreversible cell-cycle arrest, in which cells remain alive, but permanently unable to proliferate in response to distinct types of stressors. Accumulating evidence suggests that DNA damage builds over time and triggers DNA damage response signaling, leading to cellular senescence. Cellular senescence serves as a platform for the perpetuation of inflammatory responses and is central to numerous age-related diseases. Defects in DNA repair genes or senescence can cause premature aging disease. Therapeutic approaches limiting DNA damage or senescence contribute to a rescued phenotype of longevity and neuroprotection, thus suggesting a mechanistic interaction between DNA damage and senescence. Here, we offer a unique perspective on the crosstalk between the DNA damage response pathway and senescence as well as their contribution to age-related diseases. We further summarize recent progress on the mechanisms and therapeutics of senescence, address existing challenges, and offering new insights and future directions in the senescence field.
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Affiliation(s)
- Ajmal Ahmad
- Department of Ophthalmology, College of Medicine, King Saud University Riyadh, Riyadh, Saudi Arabia
| | - Anneliesse Braden
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sazzad Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
| | - Jianfeng Xiao
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, 855 Monroe Avenue, Suite 415 Link Building, Memphis, TN, 38163, USA.
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN, USA.
- Center for Muscle, Metabolism and Neuropathology, Division of Regenerative and Rehabilitation Sciences, Department of Physical Therapy, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN, USA.
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2
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Moses E, Atlan T, Sun X, Franěk R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. NATURE AGING 2024; 4:791-813. [PMID: 38750187 DOI: 10.1038/s43587-024-00632-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. In this study, we used the turquoise killifish (Nothobranchius furzeri) to genetically arrest germline development at discrete stages and examine how different modes of infertility impact life history. We first constructed a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. We show here that germline depletion-but not arresting germline differentiation-enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted Caenorhabditis elegans. Our results, therefore, demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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Affiliation(s)
- Eitan Moses
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Tehila Atlan
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Xue Sun
- Department of Biochemistry, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Roman Franěk
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Atif Siddiqui
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | | | - Sagiv Shifman
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - David M Zucker
- Department of Statistics and Data Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Oron-Gottesman
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | - Oren Ram
- Department of Biochemistry, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Itamar Harel
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel.
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Moses E, Atlan T, Sun X, Franek R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572041. [PMID: 38187630 PMCID: PMC10769255 DOI: 10.1101/2023.12.18.572041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Classical evolutionary theories propose tradeoffs between reproduction, damage repair, and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. Here, we use the turquoise killifish ( N. furzeri ) to genetically arrest germline development at discrete stages, and examine how different modes of infertility impact life-history. We first construct a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. Next, we show that germline depletion - but not arresting germline differentiation - enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted C. elegans . Our results therefore demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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Panier S, Wang S, Schumacher B. Genome Instability and DNA Repair in Somatic and Reproductive Aging. ANNUAL REVIEW OF PATHOLOGY 2024; 19:261-290. [PMID: 37832947 DOI: 10.1146/annurev-pathmechdis-051122-093128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Genetic material is constantly subjected to genotoxic insults and is critically dependent on DNA repair. Genome maintenance mechanisms differ in somatic and germ cells as the soma only requires maintenance during an individual's lifespan, while the germline indefinitely perpetuates its genetic information. DNA lesions are recognized and repaired by mechanistically highly diverse repair machineries. The DNA damage response impinges on a vast array of homeostatic processes and can ultimately result in cell fate changes such as apoptosis or cellular senescence. DNA damage causally contributes to the aging process and aging-associated diseases, most prominently cancer. By causing mutations, DNA damage in germ cells can lead to genetic diseases and impact the evolutionary trajectory of a species. The mechanisms ensuring tight control of germline DNA repair could be highly instructive in defining strategies for improved somatic DNA repair. They may provide future interventions to maintain health and prevent disease during aging.
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Affiliation(s)
- Stephanie Panier
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Siyao Wang
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease and Cluster of Excellence: Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne and University Hospital of Cologne, Cologne, Germany;
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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Betti MJ, Aldrich MC, Gamazon ER. Minimum entropy framework identifies a novel class of genomic functional elements and reveals regulatory mechanisms at human disease loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544507. [PMID: 37398170 PMCID: PMC10312628 DOI: 10.1101/2023.06.11.544507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We introduce CoRE-BED, a framework trained using 19 epigenomic features in 33 major cell and tissue types to predict cell-type-specific regulatory function. CoRE-BED identifies nine functional classes de-novo, capturing both known and new regulatory categories. Notably, we describe a previously undercharacterized class that we term Development Associated Elements (DAEs), which are highly enriched in cell types with elevated regenerative potential and distinguished by the dual presence of either H3K4me2 and H3K9ac (an epigenetic signature associated with kinetochore assembly) or H3K79me3 and H4K20me1 (a signature associated with transcriptional pause release). Unlike bivalent promoters, which represent a transitory state between active and silenced promoters, DAEs transition directly to or from a non-functional state during stem cell differentiation and are proximal to highly expressed genes. CoRE-BED's interpretability facilitates causal inference and functional prioritization. Across 70 complex traits, distal insulators account for the largest mean proportion of SNP heritability (~49%) captured by the GWAS. Collectively, our results demonstrate the value of exploring non-conventional ways of regulatory classification that enrich for trait heritability, to complement existing approaches for cis-regulatory prediction.
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Affiliation(s)
| | | | - Eric R Gamazon
- Vanderbilt University Medical Center, Nashville, TN
- Clare Hall, University of Cambridge, Cambridge, England
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van der Woude M, Davó-Martínez C, Thijssen K, Vermeulen W, Lans H. Recovery of protein synthesis to assay DNA repair activity in transcribed genes in living cells and tissues. Nucleic Acids Res 2023; 51:e93. [PMID: 37522336 PMCID: PMC10570043 DOI: 10.1093/nar/gkad642] [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: 01/24/2023] [Revised: 06/19/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023] Open
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that protects against the negative effects of transcription-blocking DNA lesions. Hereditary TC-NER deficiencies cause pleiotropic and often severe neurodegenerative and progeroid symptoms. While multiple assays have been developed to determine TC-NER activity for clinical and research purposes, monitoring TC-NER is hampered by the low frequency of repair events occurring in transcribed DNA. 'Recovery of RNA Synthesis' is widely used as indirect TC-NER assay based on the notion that lesion-blocked transcription only resumes after successful TC-NER. Here, we show that measuring novel synthesis of a protein after its compound-induced degradation prior to DNA damage induction is an equally effective but more versatile manner to indirectly monitor DNA repair activity in transcribed genes. This 'Recovery of Protein Synthesis' (RPS) assay can be adapted to various degradable proteins and readouts, including imaging and immunoblotting. Moreover, RPS allows real-time monitoring of TC-NER activity in various living cells types and even in differentiated tissues of living organisms. To illustrate its utility, we show that DNA repair in transcribed genes declines in aging muscle tissue of C. elegans. Therefore, the RPS assay constitutes an important novel clinical and research tool to investigate transcription-coupled DNA repair.
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Affiliation(s)
- Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
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Li TH, Qin XH, Wang LQ, Qin C, Zhao BB, Cao HT, Yang XY, Wang YY, Li ZR, Zhou XT, Wang WB. Prognostic value and immune infiltration of ARMC10 in pancreatic adenocarcinoma via integrated bioinformatics analyses. Heliyon 2023; 9:e20464. [PMID: 37842592 PMCID: PMC10569960 DOI: 10.1016/j.heliyon.2023.e20464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 09/16/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
Background Armadillo repeat-containing 10 (ARMC10) is involved in the progression of multiple types of tumors. Pancreatic adenocarcinoma (PAAD) is a lethal disease with poor survival and prognosis. Methods We acquired the data of ARMC10 in PAAD patients from the cancer genome atlas (TCGA) and gene expression omnibus (GEO) datasets and compared the expression level with normal pancreatic tissues. We evaluated the relevance between ARMC10 expression and clinicopathological factors, immune infiltration degree and prognosis in PAAD. Results High expression of ARMC10 was relevant to T stage, M stage, pathologic stage, histologic grade, residual tumor, primary therapy outcome (P < 0.05) and related to lower Overall-Survival (OS), Disease-Specific Survival (DSS), and Progression-Free Interval (PFI). Gene set enrichment analysis showed that ARMC10 was related to methylation in neural precursor cells (NPC), G alpha (i) signaling events, APC targets, energy metabolism, potassium channels and IL10 synthesis. The expression level of ARMC10 was positively related to the abundance of T helper cells and negatively to that of plasmacytoid dendritic cells (pDCs). Knocking down of ARMC10 could lead to lower proliferation, invasion, migration ability and colony formation rate of PAAD cells in vitro. Conclusions Our research firstly discovered ARMC10 as a novel prognostic biomarker for PAAD patients and played a crucial role in immune regulation in PAAD.
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Affiliation(s)
- Tian-Hao Li
- Department of Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiao-Han Qin
- Department of Cardiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li-Quan Wang
- Department of Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Cheng Qin
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Bang-Bo Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hong-Tao Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xiao-Ying Yang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yuan-Yang Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Ze-Ru Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Xing-Tong Zhou
- Department of Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Wei-Bin Wang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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López-Gil L, Pascual-Ahuir A, Proft M. Genomic Instability and Epigenetic Changes during Aging. Int J Mol Sci 2023; 24:14279. [PMID: 37762580 PMCID: PMC10531692 DOI: 10.3390/ijms241814279] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
Aging is considered the deterioration of physiological functions along with an increased mortality rate. This scientific review focuses on the central importance of genomic instability during the aging process, encompassing a range of cellular and molecular changes that occur with advancing age. In particular, this revision addresses the genetic and epigenetic alterations that contribute to genomic instability, such as telomere shortening, DNA damage accumulation, and decreased DNA repair capacity. Furthermore, the review explores the epigenetic changes that occur with aging, including modifications to histones, DNA methylation patterns, and the role of non-coding RNAs. Finally, the review discusses the organization of chromatin and its contribution to genomic instability, including heterochromatin loss, chromatin remodeling, and changes in nucleosome and histone abundance. In conclusion, this review highlights the fundamental role that genomic instability plays in the aging process and underscores the need for continued research into these complex biological mechanisms.
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Affiliation(s)
- Lucía López-Gil
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
| | - Amparo Pascual-Ahuir
- Department of Biotechnology, Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain;
| | - Markus Proft
- Department of Molecular and Cellular Pathology and Therapy, Instituto de Biomedicina de Valencia IBV-CSIC, Consejo Superior de Investigaciones Científicas CSIC, Jaime Roig 11, 46010 Valencia, Spain
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Freeman TF, Zhao Q, Surya A, Rothe R, Cenik ES. Ribosome biogenesis disruption mediated chromatin structure changes revealed by SRAtac, a customizable end to end analysis pipeline for ATAC-seq. BMC Genomics 2023; 24:512. [PMID: 37658321 PMCID: PMC10472662 DOI: 10.1186/s12864-023-09576-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 08/11/2023] [Indexed: 09/03/2023] Open
Abstract
The nucleolus is a large nuclear body that serves as the primary site for ribosome biogenesis. Recent studies have suggested that it also plays an important role in organizing chromatin architecture. However, to establish a causal relationship between nucleolar ribosome assembly and chromatin architecture, genetic tools are required to disrupt nucleolar ribosome biogenesis. In this study, we used ATAC-seq to investigate changes in chromatin accessibility upon specific depletion of two ribosome biogenesis components, RPOA-2 and GRWD-1, in the model organism Caenorhabditis elegans. To facilitate the analysis of ATAC-seq data, we introduced two tools: SRAlign, an extensible NGS data processing workflow, and SRAtac, a customizable end-to-end ATAC-seq analysis pipeline. Our results revealed highly comparable changes in chromatin accessibility following both RPOA-2 and GRWD-1 perturbations. However, we observed a weak correlation between changes in chromatin accessibility and gene expression. While our findings corroborate the idea of a feedback mechanism between ribosomal RNA synthesis, nucleolar ribosome large subunit biogenesis, and chromatin structure during the L1 stage of C. elegans development, they also prompt questions regarding the functional impact of these alterations on gene expression.
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Affiliation(s)
- Trevor F Freeman
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Agustian Surya
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Reed Rothe
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA.
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Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e292. [PMID: 37220590 PMCID: PMC10200003 DOI: 10.1002/mco2.292] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Histones are DNA-binding basic proteins found in chromosomes. After the histone translation, its amino tail undergoes various modifications, such as methylation, acetylation, phosphorylation, ubiquitination, malonylation, propionylation, butyrylation, crotonylation, and lactylation, which together constitute the "histone code." The relationship between their combination and biological function can be used as an important epigenetic marker. Methylation and demethylation of the same histone residue, acetylation and deacetylation, phosphorylation and dephosphorylation, and even methylation and acetylation between different histone residues cooperate or antagonize with each other, forming a complex network. Histone-modifying enzymes, which cause numerous histone codes, have become a hot topic in the research on cancer therapeutic targets. Therefore, a thorough understanding of the role of histone post-translational modifications (PTMs) in cell life activities is very important for preventing and treating human diseases. In this review, several most thoroughly studied and newly discovered histone PTMs are introduced. Furthermore, we focus on the histone-modifying enzymes with carcinogenic potential, their abnormal modification sites in various tumors, and multiple essential molecular regulation mechanism. Finally, we summarize the missing areas of the current research and point out the direction of future research. We hope to provide a comprehensive understanding and promote further research in this field.
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Affiliation(s)
- Ruiqi Liu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jiajun Wu
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Haiwei Guo
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Weiping Yao
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Shuang Li
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentJinzhou Medical UniversityJinzhouLiaoningChina
| | - Yanwei Lu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Yongshi Jia
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiaodong Liang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jianming Tang
- Department of Radiation OncologyThe First Hospital of Lanzhou UniversityLanzhou UniversityLanzhouGansuChina
| | - Haibo Zhang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
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Vijg J, Schumacher B, Abakir A, Antonov M, Bradley C, Cagan A, Church G, Gladyshev VN, Gorbunova V, Maslov AY, Reik W, Sharifi S, Suh Y, Walsh K. Mitigating age-related somatic mutation burden. Trends Mol Med 2023:S1471-4914(23)00072-2. [PMID: 37121869 DOI: 10.1016/j.molmed.2023.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023]
Abstract
Genomes are inherently unstable and require constant DNA repair to maintain their genetic information. However, selective pressure has optimized repair mechanisms in somatic cells only to allow transmitting genetic information to the next generation, not to maximize sequence integrity long beyond the reproductive age. Recent studies have confirmed that somatic mutations, due to errors during genome repair and replication, accumulate in tissues and organs of humans and model organisms. Here, we describe recent advances in the quantitative analysis of somatic mutations in vivo. We also review evidence for or against a possible causal role of somatic mutations in aging. Finally, we discuss options to prevent, delay or eliminate de novo, random somatic mutations as a cause of aging.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Center for Single-Cell Omics, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, University and University Hospital of Cologne, Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Abdulkadir Abakir
- Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK
| | | | | | - Alex Cagan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - George Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wolf Reik
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK; Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK; Altos Labs Cambridge Institute of Science, Granta Park, Cambridge, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | | | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY, USA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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12
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Koyauchi T, Niida H, Motegi A, Sakai S, Uchida C, Ohhata T, Iijima K, Yokoyama A, Suda T, Kitagawa M. Chromatin-remodeling factor BAZ1A/ACF1 targets UV damage sites in an MLL1-dependent manner to facilitate nucleotide excision repair. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119332. [PMID: 35940372 DOI: 10.1016/j.bbamcr.2022.119332] [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: 04/03/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Ultraviolet (UV) light irradiation generates pyrimidine dimers on DNA, such as cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts. Such dimers distort the high-order DNA structure and prevent transcription and replication. The nucleotide excision repair (NER) system contributes to resolving this type of DNA lesion. There are two pathways that recognize pyrimidine dimers. One acts on transcribed strands of DNA (transcription-coupled NER), and the other acts on the whole genome (global genome-NER; GG-NER). In the latter case, DNA damage-binding protein 2 (DDB2) senses pyrimidine dimers with several histone modification enzymes. We previously reported that histone acetyltransferase binding to ORC1 (HBO1) interacts with DDB2 and facilitates recruitment of the imitation switch chromatin remodeler at UV-irradiated sites via an unknown methyltransferase. Here, we found that the phosphorylated histone methyltransferase mixed lineage leukemia 1 (MLL1) was maintained at UV-irradiated sites in an HBO1-dependent manner. Furthermore, MLL1 catalyzed histone H3K4 methylation and recruited the chromatin remodeler bromodomain adjacent to zinc finger domain 1A (BAZ1A)/ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1). Depletion of MLL1 suppressed BAZ1A accumulation at UV-irradiated sites and inhibited the removal of CPDs. These data indicate that the DDB2-HBO1-MLL1 axis is essential for the recruitment of BAZ1A to facilitate GG-NER.
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Affiliation(s)
- Takafumi Koyauchi
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan.
| | - Akira Motegi
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Chiharu Uchida
- Advanced Research Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kenta Iijima
- Laboratory Animal Facilities and Services, Preeminent Medical Photonics Education and Research Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata 997-0052, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-Ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
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13
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Ren X, Tian S, Meng Q, Kim HM. Histone Demethylase AMX-1 Regulates Fertility in a p53/CEP-1 Dependent Manner. Front Genet 2022; 13:929716. [PMID: 35846143 PMCID: PMC9280695 DOI: 10.3389/fgene.2022.929716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022] Open
Abstract
Histone methylation shapes the epigenetic configuration and adjusts multiple fundamental nuclear processes, including transcription, cell cycle control and DNA repair. The absence of histone demethylase LSD1/SPR-5 leads to progressive fertility defects as well as a reduction in brood size. Similarly, C. elegans LSD2 homolog AMX-1 has been implicated in regulating H3K4me2 and maintaining interstrand crosslinks (ICL) susceptibility. However, the mechanisms of how lack of AMX-1 induces sterility have not been addressed so far. This study investigated the histone demethylase AMX-1 in C. elegans and uncovered how amx-1 contributes to sterility in a p53/CEP-1 dependent manner. We show that while sterility in spr-5 mutants exhibited progressive over generations, amx-1 mutants displayed non-transgenerational fertility defects. Also, amx-1 mutants exhibited a reduced number of sperms and produced low brood size (LBS) or sterile worms that retain neither sperms nor germline nuclei, suggesting that fertility defects originated from germline development failure. Surprisingly, sterility exhibited in amx-1 was mediated by p53/CEP-1 function. Consistent with this result, upregulation of Piwi expression in amx-1 mutants suggested that AMX-1 is essential for germline development by regulating Piwi gene expressions. We propose that AMX-1 is required for proper Piwi expression and transposon silencing in a p53/CEP-1 dependent manner; thus, the absence of AMX-1 expression leads to defective meiotic development and sterility. This study elucidates how LSD2/AMX-1 contributes to sterility, therefore, expanding the boundaries of histone demethylase function.
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Affiliation(s)
- Xiaojing Ren
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Sisi Tian
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Qinghao Meng
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Hyun-Min Kim
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Division of Natural and Applied Sciences, Duke Kunshan University, Kunshan, China
- *Correspondence: Hyun-Min Kim,
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14
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Song H, Shen R, Liu X, Yang X, Xie K, Guo Z, Wang D. Histone post-translational modification and the DNA damage response. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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15
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Fenclová T, Řimnáčová H, Chemek M, Havránková J, Klein P, Králíčková M, Nevoral J. Nursing Exposure to Bisphenols as a Cause of Male Idiopathic Infertility. Front Physiol 2022; 13:725442. [PMID: 35283775 PMCID: PMC8908107 DOI: 10.3389/fphys.2022.725442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Idiopathic infertility is a serious problem, which can be caused and explained by exposure to endocrine disruptors, such as bisphenols. In our study, we studied transactional exposure to bisphenol and its effects on newborn male mice throughout their reproductive life. Newborn male mice were exposed to bisphenol S and bisphenol F through maternal milk from post-natal day 0 to post-natal day 15 at concentrations of 0.1 ng.g/bw/day and 10 ng.g/bw/day, respectively. Although there were minimal differences between the control and experimental groups in testicular tissue quality and spermatozoa quality, we discovered an interesting influence on early embryonic development. Moderate doses of bisphenol negatively affected cleavage of the early embryo and subsequently, the blastocyst rate, as well as the number of blastomeres per blastocyst. In our study, we focused on correlations between particular stages from spermatogenesis to blastocyst development. We followed epigenetic changes such as dimethylation of histone H3 and phosphorylation of histone H2 from germ cells to blastocysts; we discovered the transfer of DNA double-strand breaks through the paternal pronucleus from spermatozoa to blastomeres in the blastocyst. We elucidated the impact of sperm DNA damage on early embryonic development, and our results indicate that idiopathic infertility in adulthood may have causes related to the perinatal period.
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Affiliation(s)
- Tereza Fenclová
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- *Correspondence: Tereza Fenclová,
| | - Hedvika Řimnáčová
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Marouane Chemek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Jiřina Havránková
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Prague, Czechia
| | - Pavel Klein
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
| | - Milena Králíčková
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Prague, Czechia
| | - Jan Nevoral
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czechia
- Department of Histology and Embryology, Faculty of Medicine in Pilsen, Charles University, Prague, Czechia
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16
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Meron E, Thaysen M, Angeli S, Antebi A, Barzilai N, Baur JA, Bekker-Jensen S, Birkisdottir M, Bischof E, Bruening J, Brunet A, Buchwalter A, Cabreiro F, Cai S, Chen BH, Ermolaeva M, Ewald CY, Ferrucci L, Florian MC, Fortney K, Freund A, Georgievskaya A, Gladyshev VN, Glass D, Golato T, Gorbunova V, Hoejimakers J, Houtkooper RH, Jager S, Jaksch F, Janssens G, Jensen MB, Kaeberlein M, Karsenty G, de Keizer P, Kennedy B, Kirkland JL, Kjaer M, Kroemer G, Lee KF, Lemaitre JM, Liaskos D, Longo VD, Lu YX, MacArthur MR, Maier AB, Manakanatas C, Mitchell SJ, Moskalev A, Niedernhofer L, Ozerov I, Partridge L, Passegué E, Petr MA, Peyer J, Radenkovic D, Rando TA, Rattan S, Riedel CG, Rudolph L, Ai R, Serrano M, Schumacher B, Sinclair DA, Smith R, Suh Y, Taub P, Trapp A, Trendelenburg AU, Valenzano DR, Verburgh K, Verdin E, Vijg J, Westendorp RGJ, Zonari A, Bakula D, Zhavoronkov A, Scheibye-Knudsen M. Meeting Report: Aging Research and Drug Discovery. Aging (Albany NY) 2022. [PMID: 35089871 PMCID: PMC8833115 DOI: 10.18632/aging.203859] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Aging is the single largest risk factor for most chronic diseases, and thus possesses large socioeconomic interest to continuously aging societies. Consequently, the field of aging research is expanding alongside a growing focus from the industry and investors in aging research. This year’s 8th Annual Aging Research and Drug Discovery (ARDD) meeting was organized as a hybrid meeting from August 30th to September 3rd 2021 with more than 130 attendees participating on-site at the Ceremonial Hall at University of Copenhagen, Denmark, and 1800 engaging online. The conference comprised of presentations from 75 speakers focusing on new research in topics including mechanisms of aging and how these can be modulated as well as the use of AI and new standards of practices within aging research. This year, a longevity workshop was included to build stronger connections with the clinical community.
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Affiliation(s)
- Esther Meron
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Maria Thaysen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Suzanne Angeli
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Joseph A Baur
- Smilow Center for Translational Research, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon Bekker-Jensen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Maria Birkisdottir
- Department of Molecular Genetics, Erasmus MC, Rotterdam, Netherlands.,Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
| | - Evelyne Bischof
- Shanghai University of Medicine and Health Sciences, College of Clinical Medicine, Shanghai, China
| | - Jens Bruening
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Anne Brunet
- Department of Genetics, Stanford School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Abigail Buchwalter
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Filipe Cabreiro
- Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK.,CECAD Research Center, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Shiqing Cai
- Institute of Neuroscience, Chinese Academy of Science, Shanghai, China
| | - Brian H Chen
- FOXO Technologies Inc, Minneapolis, MN 55402, USA.,The Herbert Wertheim School of Public Health and Human Longevity Science, UC San Diego, La Jolla, CA 92093, USA
| | | | - Collin Y Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zürich, Schwerzenbach CH-8603, Switzerland
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | | | | | - Adam Freund
- Arda Therapeutics, San Carlos, CA 94070, USA
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David Glass
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | | | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | - Jan Hoejimakers
- Department of Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Sibylle Jager
- L'Oréal Research and Innovation, Aulnay-sous-Bois, France
| | | | - Georges Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Matt Kaeberlein
- Departments of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Gerard Karsenty
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Peter de Keizer
- Department of Molecular Cancer Research, Center for Molecular Medicine, Division of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Brian Kennedy
- Buck Institute for Research on Aging, Novato, CA 94945, USA.,Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University Singapore, Singapore.,Center for Healthy Longevity, National University Health System, Singapore
| | - James L Kirkland
- Division of General Internal Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Michael Kjaer
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Université de Paris, Sorbonne Université, Inserm U1138, Paris, France
| | - Kai-Fu Lee
- Sinovation Ventures and Sinovation AI Institute, Beijing, China
| | - Jean-Marc Lemaitre
- Institute for Regenerative Medicine and Biotherapies, INSERM UMR 1183, Montpellier, France
| | | | - Valter D Longo
- USC Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Yu-Xuan Lu
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Michael R MacArthur
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Andrea B Maier
- Center for Healthy Longevity, National University Health System, Singapore.,Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Amsterdam Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Medicine, Yong Loo Lin School of Medicine, National University Singapore, Singapore
| | | | - Sarah J Mitchell
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Alexey Moskalev
- Institute of Biology of FRC Komi Science Center of Ural Division of RAS, Syktyvkar, Russia.,Russian Clinical and Research Center of Gerontology, Moscow, Russia
| | - Laura Niedernhofer
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ivan Ozerov
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong
| | - Linda Partridge
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | | | - Michael A Petr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.,Tracked.bio, Copenhagen, Denmark
| | | | - Dina Radenkovic
- Hooke London by Health and Longevity Optimisation, London, UK
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences and Paul F. Glenn Center for Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Suresh Rattan
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | | | - Ruixue Ai
- Department of Clinical Molecular Biology
- UiO, University of Oslo and Akershus University Hospital, Norway
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Björn Schumacher
- CECAD Research Center, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - David A Sinclair
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA 94107, USA
| | | | - Yousin Suh
- Departments of Obstetrics and Gynecology, Genetics and Development, Columbia University, New York, NY 10027, USA
| | - Pam Taub
- Division of Cardiovascular Medicine, University of California, San Diego, CA 92093, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Dario Riccardo Valenzano
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Leibniz Institute on Aging, Jena, Germany
| | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | | | - Daniela Bakula
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Alex Zhavoronkov
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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17
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Aguiari G, Crudele F, Taccioli C, Minotti L, Corrà F, Keillor JW, Grassilli S, Cervellati C, Volinia S, Bergamini CM, Bianchi N. Dysregulation of Transglutaminase type 2 through GATA3 defines aggressiveness and Doxorubicin sensitivity in breast cancer. Int J Biol Sci 2022; 18:1-14. [PMID: 34975314 PMCID: PMC8692156 DOI: 10.7150/ijbs.64167] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/30/2021] [Indexed: 11/05/2022] Open
Abstract
The role of transglutaminase type 2 in cell physiology is related to protein transamidation and signal transduction (affecting extracellular, intracellular and nuclear processes) aided by the expression of truncated isoforms and of two lncRNAs with regulatory functions. In breast cancer TG2 is associated with disease progression supporting motility, epithelial-mesenchymal transition, invasion and drug resistance. The aim of his work is to clarify these issues by emphasizing the interconnections among TGM2 variants and transcription factors associated with an aggressive phenotype, in which the truncated TGH isoform correlates with malignancy. TGM2 transcripts are upregulated by several drugs in MCF-7, but only Doxorubicin is effective in MDA-MB-231 cells. These differences reflect the expression of GATA3, as demonstrated by silencing, suggesting a link between this transcription factor and gene dysregulation. Of note, NC9, an irreversible inhibitor of enzymatic TG2 activities, emerges to control NF-ĸB and apoptosis in breast cancer cell lines, showing potential for combination therapies with Doxorubicin.
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Affiliation(s)
- Gianluca Aguiari
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | - Francesca Crudele
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Cristian Taccioli
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Padua, Italy
| | - Linda Minotti
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Fabio Corrà
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Jeffrey W. Keillor
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Silvia Grassilli
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), Via Fossato di Mortara 70, 44124 Ferrara FE, Italy
| | - Carlo Cervellati
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Stefano Volinia
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Laboratory for Advanced Therapy Technologies (LTTA), Via Fossato di Mortara 70, 44124 Ferrara FE, Italy
| | - Carlo M. Bergamini
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | - Nicoletta Bianchi
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
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18
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Caron M, Gely L, Garvis S, Adrait A, Couté Y, Palladino F, Fabrizio P. Loss of SET1/COMPASS methyltransferase activity reduces lifespan and fertility in Caenorhabditis elegans. Life Sci Alliance 2021; 5:5/3/e202101140. [PMID: 34893559 PMCID: PMC8675910 DOI: 10.26508/lsa.202101140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/06/2023] Open
Abstract
Changes in histone post-translational modifications are associated with aging through poorly defined mechanisms. Histone 3 lysine 4 (H3K4) methylation at promoters is deposited by SET1 family methyltransferases acting within conserved multiprotein complexes known as COMPASS. Previous work yielded conflicting results about the requirement for H3K4 methylation during aging. Here, we reassessed the role of SET1/COMPASS-dependent H3K4 methylation in Caenorhabditis elegans lifespan and fertility by generating set-2(syb2085) mutant animals that express a catalytically inactive form of SET-2, the C. elegans SET1 homolog. We show that set-2(syb2085) animals retain the ability to form COMPASS, but have a marked global loss of H3K4 di- and trimethylation (H3K4me2/3). Reduced H3K4 methylation was accompanied by loss of fertility, as expected; however, in contrast to earlier studies, set-2(syb2085) mutants displayed a significantly shortened, not extended, lifespan and had normal intestinal fat stores. Other commonly used set-2 mutants were also short-lived, as was a cfp-1 mutant that lacks the SET1/COMPASS chromatin-targeting component. These results challenge previously held views and establish that WT H3K4me2/3 levels are essential for normal lifespan in C. elegans.
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Affiliation(s)
- Matthieu Caron
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Loïc Gely
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Steven Garvis
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Annie Adrait
- University of Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Yohann Couté
- University of Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, CNRS, CEA, FR2048, Grenoble, France
| | - Francesca Palladino
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
| | - Paola Fabrizio
- Laboratory of Biology and Modelling of the Cell, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM U1210, Université de Lyon, Lyon, France
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19
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Impact of Chromatin Dynamics and DNA Repair on Genomic Stability and Treatment Resistance in Pediatric High-Grade Gliomas. Cancers (Basel) 2021; 13:cancers13225678. [PMID: 34830833 PMCID: PMC8616465 DOI: 10.3390/cancers13225678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Pediatric high-grade gliomas (pHGGs) are the leading cause of mortality in pediatric neuro-oncology, due in great part to treatment resistance driven by complex DNA repair mechanisms. pHGGs have recently been divided into molecular subtypes based on mutations affecting the N-terminal tail of the histone variant H3.3 and the ATRX/DAXX histone chaperone that deposits H3.3 at repetitive heterochromatin loci that are of paramount importance to the stability of our genome. This review addresses the functions of H3.3 and ATRX/DAXX in chromatin dynamics and DNA repair, as well as the impact of mutations affecting H3.3/ATRX/DAXX on treatment resistance and how the vulnerabilities they expose could foster novel therapeutic strategies. Abstract Despite their low incidence, pediatric high-grade gliomas (pHGGs), including diffuse intrinsic pontine gliomas (DIPGs), are the leading cause of mortality in pediatric neuro-oncology. Recurrent, mutually exclusive mutations affecting K27 (K27M) and G34 (G34R/V) in the N-terminal tail of histones H3.3 and H3.1 act as key biological drivers of pHGGs. Notably, mutations in H3.3 are frequently associated with mutations affecting ATRX and DAXX, which encode a chaperone complex that deposits H3.3 into heterochromatic regions, including telomeres. The K27M and G34R/V mutations lead to distinct epigenetic reprogramming, telomere maintenance mechanisms, and oncogenesis scenarios, resulting in distinct subgroups of patients characterized by differences in tumor localization, clinical outcome, as well as concurrent epigenetic and genetic alterations. Contrasting with our understanding of the molecular biology of pHGGs, there has been little improvement in the treatment of pHGGs, with the current mainstays of therapy—genotoxic chemotherapy and ionizing radiation (IR)—facing the development of tumor resistance driven by complex DNA repair pathways. Chromatin and nucleosome dynamics constitute important modulators of the DNA damage response (DDR). Here, we summarize the major DNA repair pathways that contribute to resistance to current DNA damaging agent-based therapeutic strategies and describe the telomere maintenance mechanisms encountered in pHGGs. We then review the functions of H3.3 and its chaperones in chromatin dynamics and DNA repair, as well as examining the impact of their mutation/alteration on these processes. Finally, we discuss potential strategies targeting DNA repair and epigenetic mechanisms as well as telomere maintenance mechanisms, to improve the treatment of pHGGs.
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Kupkova K, Shetty SJ, Haque R, Petri WA, Auble DT. Histone H3 lysine 27 acetylation profile undergoes two global shifts in undernourished children and suggests altered one-carbon metabolism. Clin Epigenetics 2021; 13:182. [PMID: 34565452 PMCID: PMC8474848 DOI: 10.1186/s13148-021-01173-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/15/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Stunting is a condition in which a child does not reach their full growth potential due to chronic undernutrition. It arises during the first 2 years of a child's life and is associated with developmental deficiencies and life-long health problems. Current interventions provide some benefit, but new approaches to prevention and treatment grounded in a molecular understanding of stunting are needed. Epigenetic analyses are critical as they can provide insight into how signals from a poor environment lead to changes in cell function. RESULTS Here we profiled histone H3 acetylation on lysine 27 (H3K27ac) in peripheral blood mononuclear cells (PBMCs) of 18-week-old (n = 14) and 1-year-old children (n = 22) living in an urban slum in Dhaka, Bangladesh. We show that 18-week-old children destined to become stunted have elevated levels of H3K27ac overall, functional analysis of which indicates activation of the immune system and stress response pathways as a primary response to a poor environment with high pathogen load. Conversely, overt stunting at 1-year-of age is associated with globally reduced H3K27ac that is indicative of metabolic rewiring and downregulation of the immune system and DNA repair pathways that are likely secondary responses to chronic exposure to a poor environment with limited nutrients. Among processes altered in 1-year-old children, we identified one-carbon metabolism, the significance of which is supported by integrative analysis with results from histone H3 trimethylation on lysine 4 (H3K4me3). Together, these results suggest altered one-carbon metabolism in this population of stunted children. CONCLUSIONS The epigenomes of stunted children undergo two global changes in H3K27ac within their first year of life, which are associated with probable initial hyperactive immune responses followed by reduced metabolic capacity. Limitation of one-carbon metabolites may play a key role in the development of stunting. Trial registration ClinicalTrials.gov NCT01375647. Registered 17 June 2011, retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT01375647 .
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Affiliation(s)
- Kristyna Kupkova
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
- Center for Public Health Genomics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Savera J Shetty
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - Rashidul Haque
- Laboratory Sciences Division, International Centre for Diarrhoeal Disease Research, Dhaka, 1000, Bangladesh
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA, 22908, USA
| | - David T Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA, 22908, USA.
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21
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Rieckher M, Garinis GA, Schumacher B. Molecular pathology of rare progeroid diseases. Trends Mol Med 2021; 27:907-922. [PMID: 34272172 DOI: 10.1016/j.molmed.2021.06.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/21/2022]
Abstract
Progeroid syndromes (PSs) are characterized by the premature onset of age-related pathologies. The genetic mutations underlying PSs are functionally linked to genome maintenance and repair, supporting the causative role of DNA damage accumulation in aging. Recent advances from studies in animal models of PSs have provided new insight into the role of DNA repair mechanisms in human disease and the physiological adaptations to accumulating DNA damage during aging. The molecular pathology of PSs is reminiscent of the natural aging process, highlighting the relevance for a wide range of age-related diseases. Recent progress has led to the development of novel therapeutic strategies against age-related diseases that are relevant to rare diseases as well as the general aging population.
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Affiliation(s)
- Matthias Rieckher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, GR70013, Heraklion, Crete, Greece; Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Björn Schumacher
- Institute for Genome Stability in Aging and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany; Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany.
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22
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Zhang X, Tian S, Beese-Sims SE, Chen J, Shin N, Colaiácovo MP, Kim HM. Histone demethylase AMX-1 is necessary for proper sensitivity to interstrand crosslink DNA damage. PLoS Genet 2021; 17:e1009715. [PMID: 34329293 PMCID: PMC8357103 DOI: 10.1371/journal.pgen.1009715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 08/11/2021] [Accepted: 07/14/2021] [Indexed: 01/02/2023] Open
Abstract
Histone methylation is dynamically regulated to shape the epigenome and adjust central nuclear processes including transcription, cell cycle control and DNA repair. Lysine-specific histone demethylase 2 (LSD2) has been implicated in multiple types of human cancers. However, its functions remain poorly understood. This study investigated the histone demethylase LSD2 homolog AMX-1 in C. elegans and uncovered a potential link between H3K4me2 modulation and DNA interstrand crosslink (ICL) repair. AMX-1 is a histone demethylase and mainly localizes to embryonic cells, the mitotic gut and sheath cells. Lack of AMX-1 expression resulted in embryonic lethality, a decreased brood size and disorganized premeiotic tip germline nuclei. Expression of AMX-1 and of the histone H3K4 demethylase SPR-5 is reciprocally up-regulated upon lack of each other and the mutants show increased H3K4me2 levels in the germline, indicating that AMX-1 and SPR-5 regulate H3K4me2 demethylation. Loss of AMX-1 function activates the CHK-1 kinase acting downstream of ATR and leads to the accumulation of RAD-51 foci and increased DNA damage-dependent apoptosis in the germline. AMX-1 is required for the proper expression of mismatch repair component MutL/MLH-1 and sensitivity against ICLs. Interestingly, formation of ICLs lead to ubiquitination-dependent subcellular relocalization of AMX-1. Taken together, our data suggest that AMX-1 functions in ICL repair in the germline.
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Affiliation(s)
- Xiaojuan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Sisi Tian
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Sara E. Beese-Sims
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jingjie Chen
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Nara Shin
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Monica P. Colaiácovo
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hyun-Min Kim
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
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24
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Entz-Werlé N, Poidevin L, Nazarov PV, Poch O, Lhermitte B, Chenard MP, Burckel H, Guérin E, Fuchs Q, Castel D, Noel G, Choulier L, Dontenwill M, Van Dyck E. A DNA Repair and Cell Cycle Gene Expression Signature in Pediatric High-Grade Gliomas: Prognostic and Therapeutic Value. Cancers (Basel) 2021; 13:cancers13092252. [PMID: 34067180 PMCID: PMC8125831 DOI: 10.3390/cancers13092252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Pediatric high-grade gliomas (pHGGs) are the leading cause of mortality in pediatric neuro-oncology, displaying frequent resistance to standard therapies. Profiling DNA repair and cell cycle gene expression has recently been proposed as a strategy to classify adult glioblastomas. To improve our understanding of the DNA damage response pathways that operate in pHGGs and the vulnerabilities that these pathways might expose, we sought to identify and characterize a specific DNA repair and cell-cycle gene expression signature of pHGGs. METHODS Transcriptomic analyses were performed to identify a DNA repair and cell-cycle gene expression signature able to discriminate pHGGs (n = 6) from low-grade gliomas (n = 10). This signature was compared to related signatures already established. We used the pHGG signature to explore already transcriptomic datasets of DIPGs and sus-tentorial pHGGs. Finally, we examined the expression of key proteins of the pHGG signature in 21 pHGG diagnostic samples and nine paired relapses. Functional inhibition of one DNA repair factor was carried out in four patients who derived H3.3 K27M mutant cell lines. RESULTS We identified a 28-gene expression signature of DNA repair and cell cycle that clustered pHGGs cohorts, in particular sus-tentorial locations, in two groups. Differential protein expression levels of PARP1 and XRCC1 were associated to TP53 mutations and TOP2A amplification and linked significantly to the more radioresistant pHGGs displaying the worst outcome. Using patient-derived cell lines, we showed that the PARP-1/XRCC1 expression balance might be correlated with resistance to PARP1 inhibition. CONCLUSION We provide evidence that PARP1 overexpression, associated to XRCC1 expression, TP53 mutations, and TOP2A amplification, is a new theranostic and potential therapeutic target.
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Affiliation(s)
- Natacha Entz-Werlé
- UMR CNRS 7021, Laboratory Bioimaging and Pathologies, Tumoral Signaling and Therapeutic Targets, Faculty of Pharmacy, 67401 Illkirch, France; (Q.F.); (L.C.); (M.D.)
- Pediatric Onco-Hematology Unit, University Hospital of Strasbourg, 67098 Strasbourg, France
- Correspondence: (N.E.-W.); (E.V.D.); Tel.: +33-3-88-12-83-96 (N.E.-W.); +352-26970-239 (E.V.D.)
| | - Laetitia Poidevin
- ICube-UMR7357, CSTB, Centre de Recherche en Biomédecine de Strasbourg, 67084 Strasbourg, France; (L.P.); (O.P.)
| | - Petr V. Nazarov
- Multiomics Data Science Research Group, Quantitative Biology Unit, Department of Oncology and Bioinformatics Platform, Luxembourg Institute of Health, L-1445 Luxembourg, Luxembourg;
| | - Olivier Poch
- ICube-UMR7357, CSTB, Centre de Recherche en Biomédecine de Strasbourg, 67084 Strasbourg, France; (L.P.); (O.P.)
| | - Benoit Lhermitte
- Pathology Department, University Hospital of Strasbourg, 67098 Strasbourg, France; (B.L.); (M.P.C.)
| | - Marie Pierre Chenard
- Pathology Department, University Hospital of Strasbourg, 67098 Strasbourg, France; (B.L.); (M.P.C.)
- Centre de Ressources Biologiques, University Hospital of Strasbourg, 67098 Strasbourg, France
| | - Hélène Burckel
- Paul Strauss Comprehensive Cancer Center, Radiobioly Laboratory, ICANS (Institut de Cancérologie Strasbourg Europe), University of Strasbourg, Unicancer, 67200 Strasbourg, France; (H.B.); (G.N.)
| | - Eric Guérin
- Oncobiology Platform, Laboratory of Biochemistry, University Hospital of Strasbourg, 67098 Strasbourg, France;
| | - Quentin Fuchs
- UMR CNRS 7021, Laboratory Bioimaging and Pathologies, Tumoral Signaling and Therapeutic Targets, Faculty of Pharmacy, 67401 Illkirch, France; (Q.F.); (L.C.); (M.D.)
| | - David Castel
- Team Genomics & Oncogenesis of Pediatric Brain Tumors, Inserm U981, Gustave Roussy Institute, 94805 Villejuif, France;
| | - Georges Noel
- Paul Strauss Comprehensive Cancer Center, Radiobioly Laboratory, ICANS (Institut de Cancérologie Strasbourg Europe), University of Strasbourg, Unicancer, 67200 Strasbourg, France; (H.B.); (G.N.)
| | - Laurence Choulier
- UMR CNRS 7021, Laboratory Bioimaging and Pathologies, Tumoral Signaling and Therapeutic Targets, Faculty of Pharmacy, 67401 Illkirch, France; (Q.F.); (L.C.); (M.D.)
| | - Monique Dontenwill
- UMR CNRS 7021, Laboratory Bioimaging and Pathologies, Tumoral Signaling and Therapeutic Targets, Faculty of Pharmacy, 67401 Illkirch, France; (Q.F.); (L.C.); (M.D.)
| | - Eric Van Dyck
- DNA Repair and Chemoresistance, Department of Oncology, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- Correspondence: (N.E.-W.); (E.V.D.); Tel.: +33-3-88-12-83-96 (N.E.-W.); +352-26970-239 (E.V.D.)
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25
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Schumacher B, Pothof J, Vijg J, Hoeijmakers JH. The central role of DNA damage in the ageing process. Nature 2021; 592:695-703. [PMID: 33911272 PMCID: PMC9844150 DOI: 10.1038/s41586-021-03307-7] [Citation(s) in RCA: 344] [Impact Index Per Article: 114.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 01/28/2021] [Indexed: 01/31/2023]
Abstract
Ageing is a complex, multifaceted process leading to widespread functional decline that affects every organ and tissue, but it remains unknown whether ageing has a unifying causal mechanism or is grounded in multiple sources. Phenotypically, the ageing process is associated with a wide variety of features at the molecular, cellular and physiological level-for example, genomic and epigenomic alterations, loss of proteostasis, declining overall cellular and subcellular function and deregulation of signalling systems. However, the relative importance, mechanistic interrelationships and hierarchical order of these features of ageing have not been clarified. Here we synthesize accumulating evidence that DNA damage affects most, if not all, aspects of the ageing phenotype, making it a potentially unifying cause of ageing. Targeting DNA damage and its mechanistic links with the ageing phenotype will provide a logical rationale for developing unified interventions to counteract age-related dysfunction and disease.
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Affiliation(s)
- Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Cologne, Germany. .,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Joris Pothof
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA,Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jan H.J. Hoeijmakers
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany,Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany,Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands,Princess Máxima Center for Pediatric Oncology, Oncode Institute, Utrecht, The Netherlands
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26
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van den Heuvel D, Spruijt CG, González-Prieto R, Kragten A, Paulsen MT, Zhou D, Wu H, Apelt K, van der Weegen Y, Yang K, Dijk M, Daxinger L, Marteijn JA, Vertegaal ACO, Ljungman M, Vermeulen M, Luijsterburg MS. A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair. Nat Commun 2021; 12:1342. [PMID: 33637760 PMCID: PMC7910549 DOI: 10.1038/s41467-021-21520-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 01/28/2021] [Indexed: 02/06/2023] Open
Abstract
Bulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. Although dispensable for TCR-mediated repair, PAF1C is essential for transcription recovery after UV irradiation. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress. The transcription-coupled repair pathway removes transcription-blocking DNA lesions, but how transcription is restored following DNA repair is not clear. Here the authors reveal that the PAF1 complex, while dispensable for the repair process, restores transcription after DNA damage.
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Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelia G Spruijt
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.,Prinses Maxima Center, Utrecht, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Di Zhou
- Department of Molecular Genetics, Oncode Institute, Rotterdam, The Netherlands
| | - Haoyu Wu
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kevin Yang
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Madelon Dijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Rotterdam, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Michiel Vermeulen
- Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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Gartner A, Engebrecht J. DNA repair, recombination, and damage signaling. Genetics 2021; 220:6522877. [PMID: 35137093 PMCID: PMC9097270 DOI: 10.1093/genetics/iyab178] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/10/2021] [Indexed: 01/09/2023] Open
Abstract
DNA must be accurately copied and propagated from one cell division to the next, and from one generation to the next. To ensure the faithful transmission of the genome, a plethora of distinct as well as overlapping DNA repair and recombination pathways have evolved. These pathways repair a large variety of lesions, including alterations to single nucleotides and DNA single and double-strand breaks, that are generated as a consequence of normal cellular function or by external DNA damaging agents. In addition to the proteins that mediate DNA repair, checkpoint pathways have also evolved to monitor the genome and coordinate the action of various repair pathways. Checkpoints facilitate repair by mediating a transient cell cycle arrest, or through initiation of cell suicide if DNA damage has overwhelmed repair capacity. In this chapter, we describe the attributes of Caenorhabditis elegans that facilitate analyses of DNA repair, recombination, and checkpoint signaling in the context of a whole animal. We review the current knowledge of C. elegans DNA repair, recombination, and DNA damage response pathways, and their role during development, growth, and in the germ line. We also discuss how the analysis of mutational signatures in C. elegans is helping to inform cancer mutational signatures in humans.
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Affiliation(s)
- Anton Gartner
- Department for Biological Sciences, IBS Center for Genomic Integrity, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea,Corresponding author: (A.G.); (J.E.)
| | - JoAnne Engebrecht
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, USA,Corresponding author: (A.G.); (J.E.)
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28
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Principles of the Molecular and Cellular Mechanisms of Aging. J Invest Dermatol 2021; 141:951-960. [PMID: 33518357 DOI: 10.1016/j.jid.2020.11.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]
Abstract
Aging can be defined as a state of progressive functional decline accompanied by an increase in mortality. Time-dependent accumulation of cellular damage, namely lesions and mutations in the DNA and misfolded proteins, impair organellar and cellular function. Ensuing cell fate alterations lead to the accumulation of dysfunctional cells and hamper homeostatic processes, thus limiting regenerative potential; trigger low-grade inflammation; and alter intercellular and intertissue communication. The accumulation of molecular damage together with modifications in the epigenetic landscape, dysregulation of gene expression, and altered endocrine communication, drive the aging process and establish age as the main risk factor for age-associated diseases and multimorbidity.
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Mkrtchyan GV, Abdelmohsen K, Andreux P, Bagdonaite I, Barzilai N, Brunak S, Cabreiro F, de Cabo R, Campisi J, Cuervo AM, Demaria M, Ewald CY, Fang EF, Faragher R, Ferrucci L, Freund A, Silva-García CG, Georgievskaya A, Gladyshev VN, Glass DJ, Gorbunova V, de Grey A, He WW, Hoeijmakers J, Hoffmann E, Horvath S, Houtkooper RH, Jensen MK, Jensen MB, Kane A, Kassem M, de Keizer P, Kennedy B, Karsenty G, Lamming DW, Lee KF, MacAulay N, Mamoshina P, Mellon J, Molenaars M, Moskalev A, Mund A, Niedernhofer L, Osborne B, Pak HH, Parkhitko A, Raimundo N, Rando TA, Rasmussen LJ, Reis C, Riedel CG, Franco-Romero A, Schumacher B, Sinclair DA, Suh Y, Taub PR, Toiber D, Treebak JT, Valenzano DR, Verdin E, Vijg J, Young S, Zhang L, Bakula D, Zhavoronkov A, Scheibye-Knudsen M. ARDD 2020: from aging mechanisms to interventions. Aging (Albany NY) 2020; 12:24484-24503. [PMID: 33378272 PMCID: PMC7803558 DOI: 10.18632/aging.202454] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/12/2020] [Indexed: 02/07/2023]
Abstract
Aging is emerging as a druggable target with growing interest from academia, industry and investors. New technologies such as artificial intelligence and advanced screening techniques, as well as a strong influence from the industry sector may lead to novel discoveries to treat age-related diseases. The present review summarizes presentations from the 7th Annual Aging Research and Drug Discovery (ARDD) meeting, held online on the 1st to 4th of September 2020. The meeting covered topics related to new methodologies to study aging, knowledge about basic mechanisms of longevity, latest interventional strategies to target the aging process as well as discussions about the impact of aging research on society and economy. More than 2000 participants and 65 speakers joined the meeting and we already look forward to an even larger meeting next year. Please mark your calendars for the 8th ARDD meeting that is scheduled for the 31st of August to 3rd of September, 2021, at Columbia University, USA.
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Affiliation(s)
- Garik V. Mkrtchyan
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Pénélope Andreux
- Amazentis SA, EPFL Innovation Park, Bâtiment C, Lausanne, Switzerland
| | - Ieva Bagdonaite
- Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Filipe Cabreiro
- Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, London, W12 0NN, UK
| | - Rafael de Cabo
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Judith Campisi
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Marco Demaria
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Collin Y. Ewald
- Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute for Technology Zürich, Switzerland
| | - Evandro Fei Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, 1478 Lørenskog, Norway
| | - Richard Faragher
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, UK
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Adam Freund
- Calico Life Sciences, LLC, South San Francisco, CA 94080, USA
| | - Carlos G. Silva-García
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | | | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David J. Glass
- Regeneron Pharmaceuticals, Inc. Tarrytown, NY 10591, USA
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | | | - Wei-Wu He
- Human Longevity Inc., San Diego, CA 92121, USA
| | - Jan Hoeijmakers
- Department of Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Eva Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Majken K. Jensen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | | | - Alice Kane
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA 94107, USA
| | - Moustapha Kassem
- Molecular Endocrinology Unit, Department of Endocrinology, University Hospital of Odense and University of Southern Denmark, Odense, Denmark
| | - Peter de Keizer
- Department of Molecular Cancer Research, Center for Molecular Medicine, Division of Biomedical Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Brian Kennedy
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University Singapore, Singapore
- Centre for Healthy Ageing, National University Healthy System, Singapore
| | - Gerard Karsenty
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Dudley W. Lamming
- Department of Medicine, University of Wisconsin-Madison and William S. Middleton Memorial Veterans Hospital, Madison, WI 53792, USA
| | - Kai-Fu Lee
- Sinovation Ventures and Sinovation AI Institute, Beijing, China
| | - Nanna MacAulay
- Department of Neuroscience, University of Copenhagen, Denmark
| | - Polina Mamoshina
- Deep Longevity Inc., Hong Kong Science and Technology Park, Hong Kong
| | - Jim Mellon
- Juvenescence Limited, Douglas, Isle of Man, UK
| | - Marte Molenaars
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Alexey Moskalev
- Institute of Biology of FRC Komi Science Center of Ural Division of RAS, Syktyvkar, Russia
| | - Andreas Mund
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Laura Niedernhofer
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brenna Osborne
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Heidi H. Pak
- Department of Medicine, University of Wisconsin-Madison and William S. Middleton Memorial Veterans Hospital, Madison, WI 53792, USA
| | | | - Nuno Raimundo
- Institute of Cellular Biochemistry, University Medical Center Goettingen, Goettingen, Germany
| | - Thomas A. Rando
- Department of Neurology and Neurological Sciences and Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | - Christian G. Riedel
- Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden
| | | | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Medical Faculty, University of Cologne, Cologne, Germany
| | - David A. Sinclair
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA 94107, USA
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Yousin Suh
- Departments of Obstetrics and Gynecology, Genetics and Development, Columbia University, New York, NY 10027, USA
| | - Pam R. Taub
- Division of Cardiovascular Medicine, University of California, San Diego, CA 92093, USA
| | - Debra Toiber
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Jonas T. Treebak
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Lei Zhang
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniela Bakula
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Alex Zhavoronkov
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong
| | - Morten Scheibye-Knudsen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
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