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Herr LM, Schaffer ED, Fuchs KF, Datta A, Brosh RM. Replication stress as a driver of cellular senescence and aging. Commun Biol 2024; 7:616. [PMID: 38777831 PMCID: PMC11111458 DOI: 10.1038/s42003-024-06263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying of the genome. While long considered a nexus for DNA damage, the role of replication stress in aging is under-appreciated. The consequential role of replication stress in promotion of organismal aging phenotypes is evidenced by an extensive list of hereditary accelerated aging disorders marked by molecular defects in factors that promote replication fork progression and operate uniquely in the replication stress response. Additionally, recent studies have revealed cellular pathways and phenotypes elicited by replication stress that align with designated hallmarks of aging. Here we review recent advances demonstrating the role of replication stress as an ultimate driver of cellular senescence and aging. We discuss clinical implications of the intriguing links between cellular senescence and aging including application of senotherapeutic approaches in the context of replication stress.
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Affiliation(s)
- Lauren M Herr
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ethan D Schaffer
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kathleen F Fuchs
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Arindam Datta
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
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2
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Youssef R, Maniar R, Khan J, Mesa H. Metabolic Interplay in the Tumor Microenvironment: Implications for Immune Function and Anticancer Response. Curr Issues Mol Biol 2023; 45:9753-9767. [PMID: 38132455 PMCID: PMC10742411 DOI: 10.3390/cimb45120609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/26/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Malignant tumors exhibit rapid growth and high metabolic rates, similar to embryonic stem cells, and depend on aerobic glycolysis, known as the "Warburg effect". This understanding has enabled the use of radiolabeled glucose analogs in tumor staging and therapeutic response assessment via PET scans. Traditional treatments like chemotherapy and radiotherapy target rapidly dividing cells, causing significant toxicity. Despite immunotherapy's impact on solid tumor treatment, gaps remain, leading to research on cancer cell evasion of immune response and immune tolerance induction via interactions with the tumor microenvironment (TME). The TME, consisting of immune cells, fibroblasts, vessels, and the extracellular matrix, regulates tumor progression and therapy responses. TME-targeted therapies aim to transform this environment from supporting tumor growth to impeding it and fostering an effective immune response. This review examines the metabolic disparities between immune cells and cancer cells, their impact on immune function and therapeutic targeting, the TME components, and the complex interplay between cancer cells and nontumoral cells. The success of TME-targeted therapies highlights their potential to achieve better cancer control or even a cure.
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Affiliation(s)
- Reem Youssef
- Department of Laboratory Medicine and Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rohan Maniar
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jaffar Khan
- Department of Laboratory Medicine and Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hector Mesa
- Department of Laboratory Medicine and Pathology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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3
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Zhang Y, Li X, Liu Z, Zhao X, Chen L, Hao G, Ye X, Meng S, Xiao G, Mu J, Mu X, Qiu J, Qian Y. The neurobehavioral impacts of typical antibiotics toward zebrafish larvae. CHEMOSPHERE 2023; 340:139829. [PMID: 37598953 DOI: 10.1016/j.chemosphere.2023.139829] [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: 05/22/2023] [Revised: 07/26/2023] [Accepted: 08/13/2023] [Indexed: 08/22/2023]
Abstract
Due to the widely usage in livestock, aquaculture and clinics, antibiotic residues are existed in aqueous environments and their potential toxicity to aquatic organisms is concerning. Here, we used zebrafish as the model to investigate the neurotoxicity and involved mechanism of seven antibiotics that were frequently detected in surface waters. The results revealed that the short-term exposure to clarithromycin (CLA), chlortetracycline (CTC) and roxithromycin (ROX) induced behavioral effects, with effective concentration of 1 μg/L (CTC and ROX) and 100 μg/L (CLA, CTC and ROX) respectively. A significant decrease in the travel distance and velocity as well as an increase in turn angle was measured. TUNEL assay identified increased cell apoptosis in brain sections of larvae exposed to three neurotoxic antibiotics, which raised the possibility that the behavioral symptoms were associated with neural damage. Transcriptome sequencing showed that the three antibiotics could affect the nervous system of zebrafish including the alteration of synaptogenesis and neurotransmission. Additionally, ROX and CTC affected pathways involved in mitochondrial stress response and endocrine system in zebrafish larvae. Besides, BDNF, ASCL1, and CREBBP are potential upstream regulatory factors that mediated these impacts. These findings indicated that exposure of CTC, ROX and CLA may cause abnormal behavior toward zebrafish larvae under environmental relevant concentration and revealed the potential role of neural cell apoptosis and synaptogenesis signaling in mediating this effect.
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Affiliation(s)
- Yining Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Li
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China; Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin, China
| | - Zaiteng Liu
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyu Zhao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lu Chen
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guijie Hao
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fish Health and Nutrition of Zhejiang Province; Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Xueping Ye
- Key Laboratory of Healthy Freshwater Aquaculture, Ministry of Agriculture and Rural Affairs; Key Laboratory of Fish Health and Nutrition of Zhejiang Province; Zhejiang Institute of Freshwater Fisheries, Huzhou, China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Jiangsu Province, China.
| | - Guohua Xiao
- Hebei Ocean and Fisheries Science Research Institute, Qinhuangdao, China; Hebei Marine Living Resources and Environment Key Laboratory, Qinhuangdao, China
| | - Jiandong Mu
- Hebei Ocean and Fisheries Science Research Institute, Qinhuangdao, China; Hebei Marine Living Resources and Environment Key Laboratory, Qinhuangdao, China
| | - Xiyan Mu
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Jing Qiu
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhong Qian
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, China
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Rhee K, Choi H, Kim KP, Joo JH. A Method for Physical Analysis of Recombination Intermediates in Saccharomyces cerevisiae. J Microbiol 2023; 61:939-951. [PMID: 38082069 DOI: 10.1007/s12275-023-00094-w] [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: 10/09/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 12/19/2023]
Abstract
Meiosis is a process through which diploid cells divide into haploid cells, thus promoting genetic diversity. This diversity arises from the formation of genetic crossovers (COs) that repair DNA double-strand breaks (DSBs), through homologous recombination (HR). Deficiencies in HR can lead to chromosomal abnormality resulting from chromosomal nondisjunction, and genetic disorders. Therefore, investigating the mechanisms underlying effective HR is crucial for reducing genome instability. Budding yeast serves as an ideal model for studying HR mechanisms due to its amenability to gene modifications and the ease of inducing synchronized meiosis to yield four spores. During meiosis, at the DNA level, programmed DSBs are repaired as COs or non-crossovers (NCOs) through structural alterations in the nascent D-loop, involving single-end invasions (SEIs) and double-Holliday junctions (dHJs). This repair occurs using homologous templates rather than sister templates. This protocol, using Southern blotting, allows for the analysis and monitoring of changes in DNA structures in the recombination process. One-dimensional (1D) gel electrophoresis is employed to detect DSBs, COs, and NCOs, while two-dimensional (2D) gel electrophoresis is utilized to identify joint molecules (JMs). Therefore, physical analysis is considered the most effective method for investigating the HR mechanism. Our protocol provides more comprehensive information than previous reports by introducing conditions for obtaining a greater number of cells from synchronized yeast and a method that can analyze not only meiotic/mitotic recombination but also mitotic replication.
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Affiliation(s)
- Kiwon Rhee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyungseok Choi
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Keun P Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Jeong H Joo
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Nepalia A, Fernandes SE, Singh H, Rana S, Saini DK. Anti-microbial resistance and aging-A design for evolution. WIREs Mech Dis 2023; 15:e1626. [PMID: 37553220 DOI: 10.1002/wsbm.1626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/10/2023]
Abstract
The emergence of resistance to anti-infective agents poses a significant threat to successfully treating infections caused by bacteria. Bacteria acquire random mutations due to exposure to environmental stresses, which may increase their fitness to other selection pressures. Interestingly, for bacteria, the frequency of anti-microbial resistance (AMR) seems to be increasing in tandem with the human lifespan. Based on evidence from previous literature, we speculate that increased levels of free radicals (Reactive Oxygen Species-ROS and Reactive Nitrosative Species-RNS), elevated inflammation, and the altered tissue microenvironment in aged individuals may drive pathogen mutagenesis. If these mutations result in the hyperactivation of efflux pumps or alteration in drug target binding sites, it could confer AMR, thus rendering antibiotic therapy ineffective while leading to the selection of novel drug-resistant variants. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Infectious Diseases > Environmental Factors Metabolic Diseases > Environmental Factors.
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Affiliation(s)
- Amrita Nepalia
- Department of Developmental Biology and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Sheryl Erica Fernandes
- Department of Developmental Biology and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Harpreet Singh
- Division of Biomedical Informatics, ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, India
| | - Shweta Rana
- Division of Biomedical Informatics, ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, India
| | - Deepak Kumar Saini
- Department of Developmental Biology and Genetics, and Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
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Gao M, Liu W, Li T, Song Z, Wang X, Zhang X. Identifying Genetic Signatures Associated with Oncogene-Induced Replication Stress in Osteosarcoma and Screening for Potential Targeted Drugs. Biochem Genet 2023:10.1007/s10528-023-10497-4. [PMID: 37672187 DOI: 10.1007/s10528-023-10497-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 08/07/2023] [Indexed: 09/07/2023]
Abstract
Osteosarcoma is the most common type of primary malignant bone tumor. Due to the lack of selectivity and sensitivity of chemotherapy drugs to tumor cells, coupled with the use of large doses, chemotherapy drugs often have systemic toxicity. The use of modern sequencing technology to screen tumor markers in a large number of tumor samples is a common method for screening highly specific and selective anti-tumor drugs. This study aims to identify potential biomarkers using the latest reported gene expression signatures of oncogene-induced replication stress (ORS) in aggressive cancers, and potential anti-osteosarcoma drugs were screened in different drug databases. In this study, we obtained 89 osteosarcoma-related samples in the TARGET database, all of which included survival information. According to the median expression of each of six reported ORS gene markers (NAT10/DDX27/ZNF48/C8ORF33/MOCS3/MPP6), we divided 89 osteosarcoma gene expression datasets into a high expression group and a low expression group and then performed a differentially expressed gene (DEG) analysis. The coexisting genes of 6 groups of DEGs were used as replication stress-related genes (RSGs) of osteosarcoma. Then, key RSGs were screened using LASSO regression, a Cox risk proportional regression prognostic model and a tenfold cross-validation test. GSE21257 datasets collected from the Gene Expression Omnibus (GEO) database were used to verify the prognostic model. The final key RSGs selected were used in the L1000PWD and DGIdb databases to mine potential drugs. After further validation by the prognostic model, we identified seven genes associated with ORS in osteosarcoma as key RSGs, including transcription factor 7 like 2 (TCF7L2), solute carrier family 27 member 4 (SLC27A4), proprotein convertase subtilisin/kexin type 5 (PCSK5), nucleolar protein 6 (NOL6), coiled-coil-coil-coil-coil-helix domain containing 4 (CHCHD4), eukaryotic translation initiation factor 3 subunit B (EIF3B), and synthesis of cytochrome C oxidase 1 (SCO1). Then, we screened the seven key RSGs in two drug databases and found six potential anti-osteosarcoma drugs (D GIdb database: repaglinide, tacrolimus, sirolimus, cyclosporine, and hydrochlorothiazide; L1000PWD database: the small molecule VU-0365117-1). Seven RSGs (TCF7L2, SLC27A4, PCSK5, NOL6, CHCHD4, EIF3B, and SCO1) may be associated with the ORS gene signatures in osteosarcoma. Repaglinide, tacrolimus, sirolimus, cyclosporine, hydrochlorothiazide and the small molecule VU-0365117-1 are potential therapeutic drugs for osteosarcoma.
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Affiliation(s)
- Meng Gao
- School of Medicine, Nankai University, Tianjin, China
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China
| | - Weibo Liu
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China
| | - Teng Li
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China
| | - ZeLong Song
- School of Medicine, Nankai University, Tianjin, China
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China
| | - XiangYu Wang
- Department of Pain Medicine, First Medical Center, PLA General Hospital, Beijing, 100000, China.
| | - XueSong Zhang
- School of Medicine, Nankai University, Tianjin, China.
- Department of Orthopaedics, The Fourth Medical Centre, Chinese PLA General Hospital, Haidian District, 51 Fucheng Road, Beijing, 100048, China.
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Ogunleye AO, Nimmakayala RK, Batra SK, Ponnusamy MP. Metabolic Rewiring and Stemness: A Critical Attribute of Pancreatic Cancer Progression. Stem Cells 2023; 41:417-430. [PMID: 36869789 PMCID: PMC10183971 DOI: 10.1093/stmcls/sxad017] [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: 11/11/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive diseases with a poor 5-year survival rate. PDAC cells rely on various metabolic pathways to fuel their unlimited proliferation and metastasis. Reprogramming glucose, fatty acid, amino acid, and nucleic acid metabolisms contributes to PDAC cell growth. Cancer stem cells are the primary cell types that play a critical role in the progression and aggressiveness of PDAC. Emerging studies indicate that the cancer stem cells in PDAC tumors are heterogeneous and show specific metabolic dependencies. In addition, understanding specific metabolic signatures and factors that regulate these metabolic alterations in the cancer stem cells of PDAC paves the way for developing novel therapeutic strategies targeting CSCs. In this review, we discuss the current understanding of PDAC metabolism by specifically exploring the metabolic dependencies of cancer stem cells. We also review the current knowledge of targeting these metabolic factors that regulate CSC maintenance and PDAC progression.
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Affiliation(s)
- Ayoola O Ogunleye
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Rama Krishna Nimmakayala
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Moorthy P Ponnusamy
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
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8
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Ruprecht NA, Singhal S, Schaefer K, Gill JS, Bansal B, Sens D, Singhal SK. Establishing a genomic radiation-age association for space exploration supplements lung disease differentiation. Front Public Health 2023; 11:1161124. [PMID: 37250098 PMCID: PMC10213902 DOI: 10.3389/fpubh.2023.1161124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/07/2023] [Indexed: 05/31/2023] Open
Abstract
Purpose One possible way to quantify each individual's response or damage from ionizing radiation is to estimate their accelerated biological age following exposure. Since there is currently no definitive way to know if biological age estimations are accurate, we aim to establish a rad-age association using genomics as its foundation. Methods Two datasets were combined and used to empirically find the age cutoff between young and old patients. With age as both a categorical and continuous variable, two other datasets that included radiation exposure are used to test the interaction between radiation and age. The gene lists are oriented in preranked lists for both pathway and diseases analysis. Finally, these genes are used to evaluate another dataset on the clinical relevance in differentiating lung disease given ethnicity and sex using both pairwise t-tests and linear models. Results Using 12 well-known genes associated with aging, a threshold of 29-years-old was found to be the difference between young and old patients. The two interaction tests yielded 234 unique genes such that pathway analysis flagged IL-1 signaling and PRPP biosynthesis as significant with high cell proliferation diseases and carcinomas being a common trend. LAPTM4B was the only gene with significant interaction among lung disease, ethnicity, and sex, with fold change greater than two. Conclusion The results corroborate an initial association between radiation and age, given inflammation and metabolic pathways and multiple genes emphasizing mitochondrial function, oxidation, and histone modification. Being able to tie rad-age genes to lung disease supplements future work for risk assessment following radiation exposure.
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Affiliation(s)
- Nathan A. Ruprecht
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND, United States
| | - Sonalika Singhal
- Department of Pathology, University of North Dakota, Grand Forks, ND, United States
| | - Kalli Schaefer
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND, United States
| | - Jappreet S. Gill
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND, United States
| | - Benu Bansal
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND, United States
| | - Donald Sens
- Department of Pathology, University of North Dakota, Grand Forks, ND, United States
| | - Sandeep K. Singhal
- Department of Biomedical Engineering, University of North Dakota, Grand Forks, ND, United States
- Department of Pathology, University of North Dakota, Grand Forks, ND, United States
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Sahinyan K, Lazure F, Blackburn DM, Soleimani VD. Decline of regenerative potential of old muscle stem cells: contribution to muscle aging. FEBS J 2023; 290:1267-1289. [PMID: 35029021 DOI: 10.1111/febs.16352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/23/2021] [Accepted: 01/11/2022] [Indexed: 01/01/2023]
Abstract
Muscle stem cells (MuSCs) are required for life-long muscle regeneration. In general, aging has been linked to a decline in the numbers and the regenerative potential of MuSCs. Muscle regeneration depends on the proper functioning of MuSCs, which is itself dependent on intricate interactions with its niche components. Aging is associated with both cell-intrinsic and niche-mediated changes, which can be the result of transcriptional, posttranscriptional, or posttranslational alterations in MuSCs or in the components of their niche. The interplay between cell intrinsic alterations in MuSCs and changes in the stem cell niche environment during aging and its impact on the number and the function of MuSCs is an important emerging area of research. In this review, we discuss whether the decline in the regenerative potential of MuSCs with age is the cause or the consequence of aging skeletal muscle. Understanding the effect of aging on MuSCs and the individual components of their niche is critical to develop effective therapeutic approaches to diminish or reverse the age-related defects in muscle regeneration.
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Affiliation(s)
- Korin Sahinyan
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Felicia Lazure
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Darren M Blackburn
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
| | - Vahab D Soleimani
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC, Canada
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He Z, Shou C, Han Z. Transcriptome Analysis of Marbled Rockfish Sebastiscus marmoratus under Salinity Stress. Animals (Basel) 2023; 13:ani13030400. [PMID: 36766289 PMCID: PMC9913653 DOI: 10.3390/ani13030400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/12/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023] Open
Abstract
The marbled rockfish, Sebastiscus marmoratus, belongs to the euryhaline fish and is an oviparous scleractinian fish. There are few studies on the adaptation mechanism, functional genes, and related pathways of S. marmoratus and salinity. The results showed that a total of 72.1 GB of clean reads were obtained and all clean reads annotated a total of 25,278 Unigenes, of which 2,160 were novel genes. Compared to 20‱, 479 and 520 differential genes were obtained for 35‱ and 10‱, respectively. Gene ontology (GO) enrichment analysis revealed significant enrichment in protein binding, ion binding, ATP binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that differentially expressed genes significantly expressed under salinity stress were mainly involved in the pathways of the cytochrome P450 metabolism of xenobiotics, tryptophan metabolism, cellular senescence, and calcium signaling pathways. Among them, pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups, and they were associated with apoptosis, inflammation, DNA damage, immune regulation, and other physiological processes. Six differentially expressed genes were randomly selected for qRT-PCR validation, and the results showed that the transcriptomic data were of high confidence.
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Lee SY, Kim JJ, Miller KM. Single-Cell Analysis of Histone Acetylation Dynamics at Replication Forks Using PLA and SIRF. Methods Mol Biol 2023; 2589:345-360. [PMID: 36255636 DOI: 10.1007/978-1-0716-2788-4_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Genome integrity is constantly challenged by various processes including DNA damage, structured DNA, transcription, and DNA-protein crosslinks. During DNA replication, active replication forks that encounter these obstacles can result in their stalling and collapse. Accurate DNA replication requires the ability of forks to navigate these threats, which is aided by DNA repair proteins. Histone acetylation participates in this process through an ability to signal and recruit proteins to regions of replicating DNA. For example, the histone acetyltransferase PCAF promotes the recruitment of the DNA repair factors MRE11 and EXO1 to stalled forks by acetylating histone H4 at lysine 8 (H4K8ac). These highly dynamic processes can be detected and analyzed using a modified proximity ligation assay (PLA) method, known as SIRF (in situ protein interactions with nascent DNA replication forks). This single-cell assay combines PLA with EdU-coupled Click-iT chemistry reactions and fluorescence microscopy to detect these interactions at sites of replicating DNA. Here we provide a detailed protocol utilizing SIRF that detects the HAT PCAF and histone acetylation at replication forks. This technique provides a robust methodology to determine protein recruitment and modifications at the replication fork with single-cell resolution.
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Affiliation(s)
- Seo Yun Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jae Jin Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
- Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
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12
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Hunter JE, Campbell AE, Kerridge S, Fraser C, Hannaway NL, Luli S, Ivanova I, Brownridge PJ, Coxhead J, Taylor L, Leary P, Hasoon MSR, Eyers CE, Perkins ND. Up-regulation of the PI3K/AKT and RHO/RAC/PAK signalling pathways in CHK1 inhibitor resistant Eµ-Myc lymphoma cells. Biochem J 2022; 479:2131-2151. [PMID: 36240067 PMCID: PMC9704644 DOI: 10.1042/bcj20220103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/14/2022]
Abstract
The development of resistance and the activation of bypass pathway signalling represents a major problem for the clinical application of protein kinase inhibitors. While investigating the effect of either a c-Rel deletion or RelAT505A phosphosite knockin on the Eµ-Myc mouse model of B-cell lymphoma, we discovered that both NF-κB subunit mutations resulted in CHK1 inhibitor resistance, arising from either loss or alteration of CHK1 activity, respectively. However, since Eµ-Myc lymphomas depend on CHK1 activity to cope with high levels of DNA replication stress and consequent genomic instability, it was not clear how these mutant NF-κB subunit lymphomas were able to survive. To understand these survival mechanisms and to identify potential compensatory bypass signalling pathways in these lymphomas, we applied a multi-omics strategy. With c-Rel-/- Eµ-Myc lymphomas we observed high levels of Phosphatidyl-inositol 3-kinase (PI3K) and AKT pathway activation. Moreover, treatment with the PI3K inhibitor Pictilisib (GDC-0941) selectively inhibited the growth of reimplanted c-Rel-/- and RelAT505A, but not wild type (WT) Eµ-Myc lymphomas. We also observed up-regulation of a RHO/RAC pathway gene expression signature in both Eµ-Myc NF-κB subunit mutation models. Further investigation demonstrated activation of the RHO/RAC effector p21-activated kinase (PAK) 2. Here, the PAK inhibitor, PF-3758309 successfully overcame resistance of RelAT505A but not WT lymphomas. These findings demonstrate that up-regulation of multiple bypass pathways occurs in CHK1 inhibitor resistant Eµ-Myc lymphomas. Consequently, drugs targeting these pathways could potentially be used as either second line or combinatorial therapies to aid the successful clinical application of CHK1 inhibitors.
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Affiliation(s)
- Jill E. Hunter
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Amy E. Campbell
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Scott Kerridge
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Callum Fraser
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Nicola L. Hannaway
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Saimir Luli
- Newcastle University Clinical and Translational Research Institute, Preclinical In Vivo Imaging (PIVI), Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Iglika Ivanova
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Philip J. Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Jonathan Coxhead
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Leigh Taylor
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Peter Leary
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Megan S. R. Hasoon
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Neil D. Perkins
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Newcastle University, Level 6, Herschel Building, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
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13
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Madgwick S, Luli S, Sellier H, Butterworth JA, Leslie J, Moore AJ, Corbin EK, Yemm AI, Chiremba RT, Tiniakos D, Oakley F, Perkins ND, Hunter JE. Claspin haploinsufficiency leads to defects in fertility, hyperplasia and an increased oncogenic potential. Biochem J 2022; 479:2115-2130. [PMID: 36240068 PMCID: PMC9704638 DOI: 10.1042/bcj20220101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
Claspin is an adaptor protein required for ATR-dependent phosphorylation of CHK1 during S-phase following DNA replication stress. Claspin expression is highly variable in cancer, with low levels frequently correlating with poor patient survival. To learn more about the biological consequences of reduced Claspin expression and its effects on tumorigenesis, we investigated mice with a heterozygous knockout of the Clspn gene. Claspin haploinsufficiency resulted in reduced female fertility and a maternally inherited defect in oocyte meiosis I cell cycle progression. Furthermore, aged Clspn+/- mice developed spontaneous lymphoid hyperplasia and increased susceptibility to non-alcoholic fatty liver disease. Importantly, we demonstrate a tumour suppressor role for Claspin. Reduced Claspin levels result in increased liver damage and tumourigenesis in the DEN model of hepatocellular carcinoma. These data reveal that Clspn haploinsufficiency has widespread unanticipated biological effects and establishes the importance of Claspin as a regulatory node controlling tumorigenesis and multiple disease aetiologies.
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Affiliation(s)
- Suzanne Madgwick
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Saimir Luli
- Preclinical In Vivo Imaging Facility, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Helene Sellier
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Jacqueline A. Butterworth
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Jack Leslie
- Newcastle Fibrosis Research Group, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Adam J. Moore
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Emma K. Corbin
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Adrian I. Yemm
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Robson T. Chiremba
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Dina Tiniakos
- Newcastle Fibrosis Research Group, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Neil D. Perkins
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
| | - Jill E. Hunter
- Newcastle University Biosciences Institute, Wolfson Childhood Cancer Research Centre, Level 6, Herschel Building, Newcastle University, Brewery Lane, Newcastle upon Tyne NE1 7RU, U.K
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14
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Hunter JE, Campbell AE, Hannaway NL, Kerridge S, Luli S, Butterworth JA, Sellier H, Mukherjee R, Dhillon N, Sudhindar PD, Shukla R, Brownridge PJ, Bell HL, Coxhead J, Taylor L, Leary P, Hasoon MS, Collins I, Garrett MD, Eyers CE, Perkins ND. Regulation of CHK1 inhibitor resistance by a c-Rel and USP1 dependent pathway. Biochem J 2022; 479:2063-2086. [PMID: 36240066 PMCID: PMC9704646 DOI: 10.1042/bcj20220102] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/12/2022] [Accepted: 08/23/2022] [Indexed: 12/19/2022]
Abstract
Previously, we discovered that deletion of c-Rel in the Eµ-Myc mouse model of lymphoma results in earlier onset of disease, a finding that contrasted with the expected function of this NF-κB subunit in B-cell malignancies. Here we report that Eµ-Myc/cRel-/- cells have an unexpected and major defect in the CHK1 pathway. Total and phospho proteomic analysis revealed that Eµ-Myc/cRel-/- lymphomas highly resemble wild-type (WT) Eµ-Myc lymphomas treated with an acute dose of the CHK1 inhibitor (CHK1i) CCT244747. Further analysis demonstrated that this is a consequence of Eµ-Myc/cRel-/- lymphomas having lost expression of CHK1 protein itself, an effect that also results in resistance to CCT244747 treatment in vivo. Similar down-regulation of CHK1 protein levels was also seen in CHK1i resistant U2OS osteosarcoma and Huh7 hepatocellular carcinoma cells. Further investigation revealed that the deubiquitinase USP1 regulates CHK1 proteolytic degradation and that its down-regulation in our model systems is responsible, at least in part, for these effects. We demonstrate that treating WT Eµ-Myc lymphoma cells with the USP1 inhibitor ML323 was highly effective at reducing tumour burden in vivo. Targeting USP1 activity may thus be an alternative therapeutic strategy in MYC-driven tumours.
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Affiliation(s)
- Jill E. Hunter
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Amy E. Campbell
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Nicola L. Hannaway
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Scott Kerridge
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Saimir Luli
- Newcastle University Clinical and Translational Research Institute, Preclinical In Vivo Imaging (PIVI), Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Jacqueline A. Butterworth
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Helene Sellier
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Reshmi Mukherjee
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Nikita Dhillon
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Praveen D. Sudhindar
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Ruchi Shukla
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Philip J. Brownridge
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Hayden L. Bell
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Jonathan Coxhead
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Leigh Taylor
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Peter Leary
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Megan S.R. Hasoon
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
| | - Ian Collins
- Division of Cancer Therapeutics, The Institute of Cancer Research, Sutton SM2 5NG, U.K
| | - Michelle D. Garrett
- School of Biosciences, Stacey Building, University of Kent, Canterbury, Kent CT2 7NJ, U.K
| | - Claire E. Eyers
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K
| | - Neil D. Perkins
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, U.K
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15
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Lu C, Lv Y, Kou G, Liu Y, Liu Y, Chen Y, Wu X, Yang F, Luo J, Yang X. Silver nanoparticles induce developmental toxicity via oxidative stress and mitochondrial dysfunction in zebrafish (Danio rerio). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 243:113993. [PMID: 35994909 DOI: 10.1016/j.ecoenv.2022.113993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 06/28/2022] [Accepted: 08/16/2022] [Indexed: 02/05/2023]
Abstract
Sliver nanoparticles (AgNPs) are widely used in industry, agriculture, and medicine, potentially resulting in adverse effects on human health and aquatic environments. Here, we investigated the developmental toxicity of zebrafish embryos with acute exposure to AgNPs. Our results demonstrated developmental defects in 4 hpf zebrafish embryos after exposure to different concentrations of AgNPs for 72 h. In addition, RNA-seq profiling of zebrafish embryos after AgNPs treatment. Further Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the differentially expressed genes (DEGs) were enriched in DNA replication initiation, oxidoreductase activity, DNA replication, cellular senescence, and oxidative phosphorylation signaling pathways in the AgNPs-treated group. Notably, we also found that AgNPs exposure could result in the accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), the inhibition of superoxide dismutase (SOD), catalase (CAT), and mitochondrial complex I-V activities, and the downregulated expression of SOD, CAT, and mitochondrial complex I-IV chain-related genes. Moreover, the expression of mitochondrion-mediated apoptosis signaling pathway-related genes, such as bax, bcl2, caspase-3, and caspase-9, was significantly regulated after AgNPs exposure in zebrafish. Therefore, these findings demonstrated that AgNPs exposure could cause oxidative stress, induce mitochondrial dysfunction, and ultimately lead to developmental toxicity.
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Affiliation(s)
- Chunjiao Lu
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Yuhang Lv
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Guanhua Kou
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Yao Liu
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Yi Liu
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Yang Chen
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Xuewei Wu
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Fan Yang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Juanjuan Luo
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Xiaojun Yang
- Guangdong Provincial Key Laboratory of Infectious Disease and Molecular Immunopathology, Shantou University Medical College, Shantou, China
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16
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P16INK4A—More Than a Senescence Marker. Life (Basel) 2022; 12:life12091332. [PMID: 36143369 PMCID: PMC9501954 DOI: 10.3390/life12091332] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Aging is a biological feature that is characterized by gradual degeneration of function in cells, tissues, organs, or an intact organism due to the accumulation of environmental factors and stresses with time. Several factors have been attributed to aging such as oxidative stress and augmented production or exposure to reactive oxygen species, inflammatory cytokines production, telomere shortening, DNA damage, and, importantly, the deposit of senescent cells. These are irreversibly mitotically inactive, yet metabolically active cells. The reason underlying their senescence lies within the extrinsic and the intrinsic arms. The extrinsic arm is mainly characterized by the expression and the secretory profile known as the senescence-associated secretory phenotype (SASP). The intrinsic arm results from the impact of several genes meant to regulate the cell cycle, such as tumor suppressor genes. P16INK4A is a tumor suppressor and cell cycle regulator that has been linked to aging and senescence. Extensive research has revealed that p16 expression is significantly increased in senescent cells, as well as during natural aging or age-related pathologies. Based on this fact, p16 is considered as a specific biomarker for detecting senescent cells and aging. Other studies have found that p16 is not only a senescence marker, but also a protein with many functions outside of senescence and aging. In this paper, we discuss and shed light on several studies that show the different functions of p16 and provide insights in its role in several biological processes besides senescence and aging.
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17
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Targeting nucleotide metabolism: a promising approach to enhance cancer immunotherapy. J Hematol Oncol 2022; 15:45. [PMID: 35477416 PMCID: PMC9044757 DOI: 10.1186/s13045-022-01263-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/18/2022] [Indexed: 12/12/2022] Open
Abstract
Targeting nucleotide metabolism can not only inhibit tumor initiation and progression but also exert serious side effects. With in-depth studies of nucleotide metabolism, our understanding of nucleotide metabolism in tumors has revealed their non-proliferative effects on immune escape, indicating the potential effectiveness of nucleotide antimetabolites for enhancing immunotherapy. A growing body of evidence now supports the concept that targeting nucleotide metabolism can increase the antitumor immune response by (1) activating host immune systems via maintaining the concentrations of several important metabolites, such as adenosine and ATP, (2) promoting immunogenicity caused by increased mutability and genomic instability by disrupting the purine and pyrimidine pool, and (3) releasing nucleoside analogs via microbes to regulate immunity. Therapeutic approaches targeting nucleotide metabolism combined with immunotherapy have achieved exciting success in preclinical animal models. Here, we review how dysregulated nucleotide metabolism can promote tumor growth and interact with the host immune system, and we provide future insights into targeting nucleotide metabolism for immunotherapeutic treatment of various malignancies.
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18
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Dynamic Spatiotemporal Expression Pattern of the Senescence-Associated Factor p16Ink4a in Development and Aging. Cells 2022; 11:cells11030541. [PMID: 35159350 PMCID: PMC8833900 DOI: 10.3390/cells11030541] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 02/01/2023] Open
Abstract
A plethora of factors have been attributed to underly aging, including oxidative stress, telomere shortening and cellular senescence. Several studies have shown a significant role of the cyclin-dependent kinase inhibitor p16ink4a in senescence and aging. However, its expression in development has been less well documented. Therefore, to further clarify a potential role of p16 in development and aging, we conducted a developmental expression study of p16, as well as of p19ARF and p21, and investigated their expression on the RNA level in brain, heart, liver, and kidney of mice at embryonic, postnatal, adult, and old ages. P16 expression was further assessed on the protein level by immunohistochemistry. Expression of p16 was highly dynamic in all organs in embryonic and postnatal stages and increased dramatically in old mice. Expression of p19 and p21 was less variable and increased to a moderate extent at old age. In addition, we observed a predominant expression of p16 mRNA and protein in liver endothelial cells versus non-endothelial cells of old mice, which suggests a functional role specifically in liver endothelium of old subjects. Thus, p16 dynamic spatiotemporal expression might implicate p16 in developmental and physiological processes in addition to its well-known function in the build-up of senescence.
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19
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Kawahata I, Fukunaga K. Impact of fatty acid-binding proteins and dopamine receptors on α-synucleinopathy. J Pharmacol Sci 2022; 148:248-254. [DOI: 10.1016/j.jphs.2021.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/29/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
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20
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Phosphorothioate-DNA bacterial diet reduces the ROS levels in C. elegans while improving locomotion and longevity. Commun Biol 2021; 4:1335. [PMID: 34824369 PMCID: PMC8617147 DOI: 10.1038/s42003-021-02863-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 11/05/2021] [Indexed: 11/20/2022] Open
Abstract
DNA phosphorothioation (PT) is widely distributed in the human gut microbiome. In this work, PT-diet effect on nematodes was studied with PT-bioengineering bacteria. We found that the ROS level decreased by about 20–50% and the age-related lipofuscin accumulation was reduced by 15–25%. Moreover, the PT-feeding worms were more active at all life periods, and more resistant to acute stressors. Intriguingly, their lifespans were prolonged by ~21.7%. Comparative RNA-seq analysis indicated that many gene expressions were dramatically regulated by PT-diet, such as cysteine-rich protein (scl-11/12/13), sulfur-related enzyme (cpr-2), longevity gene (jnk-1) and stress response (sod-3/5, gps-5/6, gst-18/20, hsp-12.6). Both the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that neuroactivity pathways were upregulated, while phosphoryl transfer and DNA-repair pathways were down-regulated in good-appetite young worms. The findings pave the way for pro-longevity of multicellular organisms by PT-bacterial interference. Qiang Huang et al. fed C. elegans with E. coli containing phosphorothioate (PT) DNA or a control strain and evaluated the impact on animal physiology. They observed that worms fed PT( + ) diets exhibited low reactive oxygen species, more active movement, and a longer lifespan compared to controls, suggesting that PT-DNA may have a positive effect on animal health.
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21
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Li Y, Luo W, Zhang H, Wang C, Yu C, Jiang Z, Zhang W. Antitumor Mechanism of Hydroxycamptothecin via the Metabolic Perturbation of Ribonucleotide and Deoxyribonucleotide in Human Colorectal Carcinoma Cells. Molecules 2021; 26:4902. [PMID: 34443490 PMCID: PMC8398164 DOI: 10.3390/molecules26164902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Hydroxycamptothecin (SN38) is a natural plant extract isolated from Camptotheca acuminate. It has a broad spectrum of anticancer activity through inhibition of DNA topoisomerase I, which could affect DNA synthesis and lead to DNA damage. Thus, the action of SN38 against cancers could inevitably affect endogenous levels of ribonucleotide (RNs) and deoxyribonucleotide (dRNs) that play critical roles in many biological processes, especially in DNA synthesis and repair. However, the exact impact of SN38 on RNs and dRNs is yet to be fully elucidated. In this study, we evaluated the anticancer effect and associated mechanism of SN38 in human colorectal carcinoma HCT 116 cells. As a result, SN38 could decrease the cell viability and induce DNA damage in a concentration-dependent manner. Furthermore, cell cycle arrest and intracellular nucleotide metabolism were perturbed due to DNA damage response, of which ATP, UTP, dATP, and TTP may be the critical metabolites during the whole process. Combined with the expression of deoxyribonucleoside triphosphates synthesis enzymes, our results demonstrated that the alteration and imbalance of deoxyribonucleoside triphosphates caused by SN38 was mainly due to the de novo nucleotide synthesis at 24 h, and subsequently the salvage pathways at 48 h. The unique features of SN38 suggested that it might be recommended as an effective supplementary drug with an anticancer effect.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Wendi Luo
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Huixia Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Caiyun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Caiyuan Yu
- Faculty of Agroforestry and Medicine, The Open University of China, Beijing 100039, China;
| | - Zhihong Jiang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
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22
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Novo CL. A Tale of Two States: Pluripotency Regulation of Telomeres. Front Cell Dev Biol 2021; 9:703466. [PMID: 34307383 PMCID: PMC8300013 DOI: 10.3389/fcell.2021.703466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/08/2021] [Indexed: 01/01/2023] Open
Abstract
Inside the nucleus, chromatin is functionally organized and maintained as a complex three-dimensional network of structures with different accessibility such as compartments, lamina associated domains, and membraneless bodies. Chromatin is epigenetically and transcriptionally regulated by an intricate and dynamic interplay of molecular processes to ensure genome stability. Phase separation, a process that involves the spontaneous organization of a solution into separate phases, has been proposed as a mechanism for the timely coordination of several cellular processes, including replication, transcription and DNA repair. Telomeres, the repetitive structures at the end of chromosomes, are epigenetically maintained in a repressed heterochromatic state that prevents their recognition as double-strand breaks (DSB), avoiding DNA damage repair and ensuring cell proliferation. In pluripotent embryonic stem cells, telomeres adopt a non-canonical, relaxed epigenetic state, which is characterized by a low density of histone methylation and expression of telomere non-coding transcripts (TERRA). Intriguingly, this telomere non-canonical conformation is usually associated with chromosome instability and aneuploidy in somatic cells, raising the question of how genome stability is maintained in a pluripotent background. In this review, we will explore how emerging technological and conceptual developments in 3D genome architecture can provide novel mechanistic perspectives for the pluripotent epigenetic paradox at telomeres. In particular, as RNA drives the formation of LLPS, we will consider how pluripotency-associated high levels of TERRA could drive and coordinate phase separation of several nuclear processes to ensure genome stability. These conceptual advances will provide a better understanding of telomere regulation and genome stability within the highly dynamic pluripotent background.
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Affiliation(s)
- Clara Lopes Novo
- The Francis Crick Institute, London, United Kingdom
- Imperial College London, London, United Kingdom
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23
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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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Vodnala M, Choi EB, Fong YW. Low complexity domains, condensates, and stem cell pluripotency. World J Stem Cells 2021; 13:416-438. [PMID: 34136073 PMCID: PMC8176841 DOI: 10.4252/wjsc.v13.i5.416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Biological reactions require self-assembly of factors in the complex cellular milieu. Recent evidence indicates that intrinsically disordered, low-complexity sequence domains (LCDs) found in regulatory factors mediate diverse cellular processes from gene expression to DNA repair to signal transduction, by enriching specific biomolecules in membraneless compartments or hubs that may undergo liquid-liquid phase separation (LLPS). In this review, we discuss how embryonic stem cells take advantage of LCD-driven interactions to promote cell-specific transcription, DNA damage response, and DNA repair. We propose that LCD-mediated interactions play key roles in stem cell maintenance and safeguarding genome integrity.
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Affiliation(s)
- Munender Vodnala
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Eun-Bee Choi
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
| | - Yick W Fong
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, United States
- Harvard Stem Cell Institute, Cambridge, MA 02138, United States.
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25
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Hsu YK, Chen HY, Wu CC, Huang YC, Hsieh CP, Su PF, Huang YF. Butein induces cellular senescence through reactive oxygen species-mediated p53 activation in osteosarcoma U-2 OS cells. ENVIRONMENTAL TOXICOLOGY 2021; 36:773-781. [PMID: 33325610 DOI: 10.1002/tox.23079] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Butein is a flavonoid isolated from various medicinal plants. It is known to have different biological activities including anti-inflammation, anti-adipogenesis, and anti-angiogenesis. In the study, we demonstrated the anti-proliferative effect of butein in human osteosarcoma U-2 OS cells. Our data showed that butein significantly suppressed the viability and colony formation ability of U-2 OS cells. Further experiments revealed butein exposure resulted in a cell cycle arrest at S and G2/M phase in U-2 OS cells. Importantly, we found that butein activated the tumor suppressor p53, and trigged a p53-dependent senescence in U-2 OS cells. Knockdown of p53 suppressed the senescence and rescued the viability in butein-treated U-2 OS cells. Furthermore, we observed that butein exposure significantly enhanced reactive oxygen species (ROS) levels in U-2 OS cells. Co-administration of the ROS inhibitor NAC largely abolished the up-regulated p53 protein level, and rescued the suppressed viability and colony formation ability in butein-exposed U-2 OS cells. Taken together, our data proposed the increased ROS by butein exposure activated p53, and the activated p53 was involved in the anti-proliferative effect of butein via inducing senescence in U-2 OS cells. This report suggests that butein is a promising candidate for cancer therapy against osteosarcoma.
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Affiliation(s)
- Yung-Ken Hsu
- Department of Orthopedic Surgery, Changhua Christian Hospital, Changhua, Taiwan
| | - Hsuan-Ying Chen
- Orthopedics and Sports Medicine Laboratory, Changhua Christian Hospital, Changhua, Taiwan
| | - Chia-Chieh Wu
- Department of Orthopedic Surgery, Changhua Christian Hospital, Changhua, Taiwan
- School of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ying-Chih Huang
- Department of Research, Changhua Christian Hospital, Changhua, Taiwan
| | - Cheng-Pu Hsieh
- Department of Orthopedic Surgery, Changhua Christian Hospital, Changhua, Taiwan
- Orthopedics and Sports Medicine Laboratory, Changhua Christian Hospital, Changhua, Taiwan
| | - Po-Feng Su
- Department of Orthopedic Surgery, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Fu Huang
- Orthopedics and Sports Medicine Laboratory, Changhua Christian Hospital, Changhua, Taiwan
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26
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Mehdi MM, Solanki P, Singh P. Oxidative stress, antioxidants, hormesis and calorie restriction: The current perspective in the biology of aging. Arch Gerontol Geriatr 2021; 95:104413. [PMID: 33845417 DOI: 10.1016/j.archger.2021.104413] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 02/25/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022]
Abstract
Aging, in a large measure, has long been defined as the resultant of oxidative stress acting on the cells. The cellular machinery eventually malfunctions at the basic level by the damage from the processes of oxidation and the system starts slowing down because of intrinsic eroding. To understand the initial destruction at the cellular level spreading outward to affect tissues, organs and the organism, the relationship between molecular damage and oxidative stress is required to understand. Retarding the aging process is a matter of cumulatively decreasing the rate of oxidative damage to the cellular machinery. Along with the genetic reasons, the decrease of oxidative stress is somehow a matter of lifestyle and importantly of diet. In the current review, the theories of aging and the understanding of various levels of molecular damage by oxidative stress have been emphasized. A broader understanding of mechanisms of aging have been elaborated in terms of effects of oxidative at molecular, mitochondrial, cellular and organ levels. The antioxidants supplementation, hormesis and calorie restriction as the prominent anti-aging strategies have also been discussed. The relevance and the efficacy of the antiaging strategies at system level have also been presented.
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Affiliation(s)
- Mohammad Murtaza Mehdi
- Department of Biochemistry, School of Bio-engineering and Biosciences, Lovely Professional University, Phagwara, 144411, Punjab, India.
| | - Preeti Solanki
- Multidisciplinary Research Unit, Pandit Bhagwat Dayal Sharma Post Graduate Institute of Medical Sciences, Rohtak, 124001, Haryana, India
| | - Prabhakar Singh
- Department of Biochemistry, Veer Bahadur Singh Purvanchal University, Jaunpur, 222003, Uttar Pradesh, India
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27
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Replication-stress-associated DSBs induced by ionizing radiation risk genomic destabilization and associated clonal evolution. iScience 2021; 24:102313. [PMID: 33870130 PMCID: PMC8042347 DOI: 10.1016/j.isci.2021.102313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/11/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022] Open
Abstract
Exposure to ionizing radiation is associated with cancer risk. Although multiple types of DNA damage are caused by radiation, it remains unknown how this damage is associated with cancer risk. Here, we show that after repair of double-strand breaks (DSBs) directly caused by radiation (dir-DSBs), irradiated cells enter a state at higher risk of genomic destabilization due to accumulation of replication-stress-associated DSBs (rs-DSBs), ultimately resulting in clonal evolution of cells with abrogated defense systems. These effects were observed over broad ranges of radiation doses (0.25–2 Gy) and dose rates (1.39–909 mGy/min), but not upon high-dose irradiation, which caused permanent cell-cycle arrest. The resultant genomic destabilization also increased the risk of induction of single-nucleotide variants (SNVs), including radiation-associated SNVs, as well as structural alterations in chromosomes. Thus, the radiation-associated risk can be attributed to rs-DSB accumulation and resultant genomic destabilization. Replication-stress-associated DSBs accumulate after exposure to ionizing radiation Such DSBs risk genomic destabilization and associated mutagenesis The resulting genomic rearrangements and mutations lead to clonal evolution The radiation-associated risks arise at wide ranges of radiation doses and dose rates
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28
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Chong SJF, Iskandar K, Lai JXH, Qu J, Raman D, Valentin R, Herbaux C, Collins M, Low ICC, Loh T, Davids M, Pervaiz S. Serine-70 phosphorylated Bcl-2 prevents oxidative stress-induced DNA damage by modulating the mitochondrial redox metabolism. Nucleic Acids Res 2021; 48:12727-12745. [PMID: 33245769 PMCID: PMC7736805 DOI: 10.1093/nar/gkaa1110] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/25/2020] [Accepted: 10/29/2020] [Indexed: 12/16/2022] Open
Abstract
Bcl-2 phosphorylation at serine-70 (S70pBcl2) confers resistance against drug-induced apoptosis. Nevertheless, its specific mechanism in driving drug-resistance remains unclear. We present evidence that S70pBcl2 promotes cancer cell survival by acting as a redox sensor and modulator to prevent oxidative stress-induced DNA damage and execution. Increased S70pBcl2 levels are inversely correlated with DNA damage in chronic lymphocytic leukemia (CLL) and lymphoma patient-derived primary cells as well as in reactive oxygen species (ROS)- or chemotherapeutic drug-treated cell lines. Bioinformatic analyses suggest that S70pBcl2 is associated with lower median overall survival in lymphoma patients. Empirically, sustained expression of the redox-sensitive S70pBcl2 prevents oxidative stress-induced DNA damage and cell death by suppressing mitochondrial ROS production. Using cell lines and lymphoma primary cells, we further demonstrate that S70pBcl2 reduces the interaction of Bcl-2 with the mitochondrial complex-IV subunit-5A, thereby reducing mitochondrial complex-IV activity, respiration and ROS production. Notably, targeting S70pBcl2 with the phosphatase activator, FTY720, is accompanied by an enhanced drug-induced DNA damage and cell death in CLL primary cells. Collectively, we provide a novel facet of the anti-apoptotic Bcl-2 by demonstrating that its phosphorylation at serine-70 functions as a redox sensor to prevent drug-induced oxidative stress-mediated DNA damage and execution with potential therapeutic implications.
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Affiliation(s)
- Stephen Jun Fei Chong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kartini Iskandar
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Jolin Xiao Hui Lai
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Jianhua Qu
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Deepika Raman
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Rebecca Valentin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles Herbaux
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mary Collins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ivan Cherh Chiet Low
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Thomas Loh
- Department of Otolaryngology, National University of Healthcare System (NUHS), Singapore, Singapore
| | - Matthew Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shazib Pervaiz
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore.,NUS Graduate School of Integrative Science and Engineering, NUS, Singapore, Singapore.,National University Cancer Institute, NUHS, Singapore, Singapore.,Faculté de Médecine, Université de Paris, Paris, France
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29
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Tissue-specific Gene Expression Changes Are Associated with Aging in Mice. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:430-442. [PMID: 33309863 PMCID: PMC8242333 DOI: 10.1016/j.gpb.2020.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/13/2019] [Accepted: 04/10/2019] [Indexed: 12/17/2022]
Abstract
Aging is a complex process that can be characterized by functional and cognitive decline in an individual. Aging can be assessed based on the functional capacity of vital organs and their intricate interactions with one another. Thus, the nature of aging can be described by focusing on a specific organ and an individual itself. However, to fully understand the complexity of aging, one must investigate not only a single tissue or biological process but also its complex interplay and interdependencies with other biological processes. Here, using RNA-seq, we monitored changes in the transcriptome during aging in four tissues (including brain, blood, skin and liver) in mice at 9 months, 15 months, and 24 months, with a final evaluation at the very old age of 30 months. We identified several genes and processes that were differentially regulated during aging in both tissue-dependent and tissue-independent manners. Most importantly, we found that the electron transport chain (ETC) of mitochondria was similarly affected at the transcriptome level in the four tissues during the aging process. We also identified the liver as the tissue showing the largest variety of differentially expressed genes (DEGs) over time. Lcn2 (Lipocalin-2) was found to be similarly regulated among all tissues, and its effect on longevity and survival was validated using its orthologue in Caenorhabditis elegans. Our study demonstrated that the molecular processes of aging are relatively subtle in their progress, and the aging process of every tissue depends on the tissue’s specialized function and environment. Hence, individual gene or process alone cannot be described as the key of aging in the whole organism.
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30
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Liu Y, Chen Q. Senescent Mesenchymal Stem Cells: Disease Mechanism and Treatment Strategy. ACTA ACUST UNITED AC 2020; 6:173-182. [PMID: 33816065 DOI: 10.1007/s40610-020-00141-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Purpose of review Mesenchymal stem cells (MSCs) have been extensively studied for therapeutic application in tissue engineering and regenerative medicine. Despite their promise, recent findings suggest that MSC replication during repair process may lead to replicative senescence and stem cell exhaustion. Here, we review the basic mechanisms of MSC senescence, how it leads to degenerative diseases, and potential treatments for such diseases. Recent findings Emerging evidence has shown a link between senescent MSCs and degenerative diseases, especially age-related diseases such as osteoarthritis and idiopathic pulmonary fibrosis. During these disease processes, MSCs undergo cell senescence and mediate Senescence Associated Secretory Phenotypes (SASP) to affect the surrounding microenvironment. Thus, senescent MSCs can accelerate tissue aging by increasing the number of senescent cells and spreading inflammation to neighboring cells. Summary Senescent MSCs not only hamper tissue repair through cell senescence associated stem cell exhaustion, but also mediate tissue degeneration by initiating and spreading senescence-associated inflammation. It suggests new strategies of MSC-based cell therapy to remove, rejuvenate, or replace (3Rs) the senescent MSCs.
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Affiliation(s)
- Yajun Liu
- Laboratory of Molecular Biology and Nanomedicine, Department of Orthopaedics, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02903, USA
| | - Qian Chen
- Laboratory of Molecular Biology and Nanomedicine, Department of Orthopaedics, Alpert Medical School of Brown University, Rhode Island Hospital, Providence, RI 02903, USA
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31
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Chicote J, Yuste VJ, Boix J, Ribas J. Cell Death Triggered by the Autophagy Inhibitory Drug 3-Methyladenine in Growing Conditions Proceeds With DNA Damage. Front Pharmacol 2020; 11:580343. [PMID: 33178023 PMCID: PMC7593545 DOI: 10.3389/fphar.2020.580343] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/18/2020] [Indexed: 01/07/2023] Open
Abstract
Macroautophagy (hereafter autophagy) is a multistep intracellular catabolic process with pleiotropic implications in cell fate. Attending to its activation, autophagy can be classified into inducible or constitutive. Constitutive, or basal autophagy, unfolds under nutrient-replete conditions to maintain the cellular homeostasis. Autophagy inhibitory drugs are powerful tools to interrogate the role of autophagy and its consequences on cell fate. However, 3-methyladenine and various of these compounds present an intrinsic capacity to trigger cell death, for instance the broadly-employed 3-methyladenine. To elucidate whether the inhibition of basal autophagy is causative of cell demise, we have employed several representative compounds acting at different phases of the autophagic process: initiation (SBI0206965 and MHY1485), nucleation (3-methyladenine, SAR405, Spautin-1 and Cpd18), and completion (Bafilomycin A1 and Chloroquine). These compounds inhibited the basal autophagy of MEF cultures in growing conditions. Among them, 3-methyladenine, SBI-0206965, Chloroquine, and Bafilomycin A1 triggered BAX- and/or BAK-dependent cytotoxicity and caspase activation. 3-methyladenine was the only compound to induce a consistent and abrupt decrease in cell viability across a series of ontologically unrelated human cell lines. 3-methyladenine-induced cytotoxicity was not driven by the inhibition of the AKT/mTOR axis. Autophagy-deficient Fip200-/- MEFs displayed an increased sensitivity to activate caspases and to undergo cell death in response to 3-methyladenine. The cytotoxicity induced by 3-methyladenine correlated with a massive DNA damage, as shown by γ-H2A.X. This genotoxicity was observed at 10 mM 3-methyladenine, the usual concentration to inhibit autophagy and was maximized in Fip200-/- MEFs. In sum, our results suggest that, in growing conditions, autophagy acts as a protective mechanism to diminish the intrinsic cytotoxicity of 3-methyladenine. However, when the cellular stress exerted by 3-methyladenine surpasses the protective effect of basal autophagy, caspase activation and DNA damage compromise the cell viability.
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Affiliation(s)
- Javier Chicote
- Pharmacology of Cellular Stress Group, Department of Experimental Medicine, School of Medicine, University of Lleida, Lleida, Spain.,Lleida Institute for Biomedical Research (IRBLleida), Lleida, Spain
| | - Víctor J Yuste
- Cell Death, Senescence and Survival Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Autonomous University of Barcelona, Barcelona, Spain.,Institute of Neurosciences, Autonomous University of Barcelona, Barcelona, Spain
| | - Jacint Boix
- Department of Experimental Medicine, Faculty of Medicine, University of Lleida, Lleida, Spain
| | - Judit Ribas
- Pharmacology of Cellular Stress Group, Department of Experimental Medicine, School of Medicine, University of Lleida, Lleida, Spain.,Lleida Institute for Biomedical Research (IRBLleida), Lleida, Spain
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32
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Young TZ, Liu P, Urbonaite G, Acar M. Quantitative Insights into Age-Associated DNA-Repair Inefficiency in Single Cells. Cell Rep 2020; 28:2220-2230.e7. [PMID: 31433994 PMCID: PMC6744837 DOI: 10.1016/j.celrep.2019.07.082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 06/02/2019] [Accepted: 07/23/2019] [Indexed: 01/03/2023] Open
Abstract
Although double-strand break (DSB) repair is essential for a cell's survival, little is known about how DSB repair mechanisms are affected by age. Here we characterize the impact of cellular aging on the efficiency of single-strand annealing (SSA), a DSB repair mechanism. We measure SSA repair efficiency in young and old yeast cells and report a 23.4% decline in repair efficiency. This decline is not due to increased use of non-homologous end joining. Instead, we identify increased G1 phase duration in old cells as a factor responsible for the decreased SSA repair efficiency. Expression of 3xCLN2 leads to higher SSA repair efficiency in old cells compared with expression of 1xCLN2, confirming the involvement of cell-cycle regulation in age-associated repair inefficiency. Examining how SSA repair efficiency is affected by sequence heterology, we find that heteroduplex rejection remains high in old cells. Our work provides insights into the links between single-cell aging and DSB repair efficiency.
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Affiliation(s)
- Thomas Z Young
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Ping Liu
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Guste Urbonaite
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Murat Acar
- Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA.
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33
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Harnessing DNA Replication Stress for Novel Cancer Therapy. Genes (Basel) 2020; 11:genes11090990. [PMID: 32854236 PMCID: PMC7564951 DOI: 10.3390/genes11090990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/03/2020] [Accepted: 08/20/2020] [Indexed: 12/16/2022] Open
Abstract
DNA replication is the fundamental process for accurate duplication and transfer of genetic information. Its fidelity is under constant stress from endogenous and exogenous factors which can cause perturbations that lead to DNA damage and defective replication. This can compromise genomic stability and integrity. Genomic instability is considered as one of the hallmarks of cancer. In normal cells, various checkpoints could either activate DNA repair or induce cell death/senescence. Cancer cells on the other hand potentiate DNA replicative stress, due to defective DNA damage repair mechanism and unchecked growth signaling. Though replicative stress can lead to mutagenesis and tumorigenesis, it can be harnessed paradoxically for cancer treatment. Herein, we review the mechanism and rationale to exploit replication stress for cancer therapy. We discuss both established and new approaches targeting DNA replication stress including chemotherapy, radiation, and small molecule inhibitors targeting pathways including ATR, Chk1, PARP, WEE1, MELK, NAE, TLK etc. Finally, we review combination treatments, biomarkers, and we suggest potential novel methods to target DNA replication stress to treat cancer.
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34
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Kuang H, Duan Y, Li D, Xu Y, Ai W, Li W, Wang Y, Liu S, Li M, Liu X, Shao M. The role of serum inflammatory cytokines and berberine in the insulin signaling pathway among women with polycystic ovary syndrome. PLoS One 2020; 15:e0235404. [PMID: 32785222 PMCID: PMC7423132 DOI: 10.1371/journal.pone.0235404] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE To study the role of selected serum inflammatory cytokines and berberine in the insulin signaling pathway among women with polycystic ovary syndrome (PCOS). METHODS Selected serum inflammatory cytokines were analyzed in the particle cells, which were interfered by berberine, from 78 infertile women who were to be treated with In Vitro Fertilization (IVF) /Intracytoplasmic Sperm Injection-Embryo Transfer (icsi-et). Among them, 49 patients had PCOS infertility, and 29 were non-PCOS patients whose infertility resulted from fallopian tube and male factors. The elisa method was used to detect the changes in the expression levels of inflammatory factors in the cells. The correlations between the serum inflammatory cytokine expression levels and the corresponding clinical hormones were analyzed. The changes in the expression (mRNA and protein) levels of the serum inflammatory cytokines were studied by real-time quantitative PCR and protein printing. Fluorescence microscope and flow cytometry were used to detect the glucose uptake capacity of ovarian granulosa cells in PCOS patients under the action of insulin after berberine. RESULTS In the PCOS group, IL-17a (P = 0.001), IL-1Ra (P<0.0001), and IL-6 (P = 0.035) were significantly higher than those in the non-PCOS group. In the non-PCOS group, AMH level was negatively correlated with inflammatory cytokines IL-17a (r = -0.819;P = 0.004), IL-1a (r = -0.716;P = 0.0.02), IL-1b (r = -0.678;P = 0.031), IL-2 (r = -0.765;P = 0.01), and IL-8 (r = -0.705;P = 0.023). However, in the PCOS group, AMH levels were not significantly correlated with the levels of the examined inflammatory cytokines. Berberine significantly reduced the expression level of mTOR mRNA (P = 0.001), and increased the expression level of IRS-1 mRNA (P = 0.009) in the PCOS granule cells. CONCLUSION In this study, we find that the elevated levels of serum inflammatory factors IL-17a, IL-1Ra, and IL-6 cause women to be in a subclinical inflammatory state for a long time. Abnormal changes in inflammatory factors alter their original negative correlations with AMH levels, thereby weakening the metabolism of glycolipids, promoting insulin resistance, destroying the normal ovulation and fertilization system of women, leading to polycystic ovary syndrome characterized by menstrual thinning and abnormal ovulation. Berberine can improve the sensitivity of insulin by regulating the signal pathway of insulin receptor substrate-1 (IRS-1) and mammalian target of rapamycin (mTOR) in PCOS patients and achieve a therapeutic effect of treating PCOS.
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Affiliation(s)
- Hongying Kuang
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yuwei Duan
- The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Dan Li
- Department of Acupuncture, the Third Affiliated Hospital, Beijing University Of Chinese Medicine, Beijing, China
| | - Yanwen Xu
- The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Reproductive Medicine, Guangzhou, China
| | - Wenxia Ai
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Wei Li
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ying Wang
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Sha Liu
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Mushan Li
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiaoqiu Liu
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Manqi Shao
- Heilongjiang University of Chinese Medicine, Harbin, China
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35
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Lee M, Rizzo R, Surman F, Zenobi-Wong M. Guiding Lights: Tissue Bioprinting Using Photoactivated Materials. Chem Rev 2020; 120:10950-11027. [DOI: 10.1021/acs.chemrev.0c00077] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mihyun Lee
- Tissue Engineering + Biofabrication HPL J22, ETH Zürich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Riccardo Rizzo
- Tissue Engineering + Biofabrication HPL J22, ETH Zürich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - František Surman
- Tissue Engineering + Biofabrication HPL J22, ETH Zürich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Marcy Zenobi-Wong
- Tissue Engineering + Biofabrication HPL J22, ETH Zürich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
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36
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Kawahata I, Fukunaga K. Degradation of Tyrosine Hydroxylase by the Ubiquitin-Proteasome System in the Pathogenesis of Parkinson's Disease and Dopa-Responsive Dystonia. Int J Mol Sci 2020; 21:ijms21113779. [PMID: 32471089 PMCID: PMC7312529 DOI: 10.3390/ijms21113779] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/19/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
Nigrostriatal dopaminergic systems govern physiological functions related to locomotion, and their dysfunction leads to movement disorders, such as Parkinson’s disease and dopa-responsive dystonia (Segawa disease). Previous studies revealed that expression of the gene encoding nigrostriatal tyrosine hydroxylase (TH), a rate-limiting enzyme of dopamine biosynthesis, is reduced in Parkinson’s disease and dopa-responsive dystonia; however, the mechanism of TH depletion in these disorders remains unclear. In this article, we review the molecular mechanism underlying the neurodegeneration process in dopamine-containing neurons and focus on the novel degradation pathway of TH through the ubiquitin-proteasome system to advance our understanding of the etiology of Parkinson’s disease and dopa-responsive dystonia. We also introduce the relation of α-synuclein propagation with the loss of TH protein in Parkinson’s disease as well as anticipate therapeutic targets and early diagnosis of these diseases.
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Affiliation(s)
- Ichiro Kawahata
- Correspondence: (I.K.); (K.F.); Tel.: +81-22-795-6838 (I.K.); +81-22-795-6836 (K.F.); Fax: +81-22-795-6835 (I.K. & K.F.)
| | - Kohji Fukunaga
- Correspondence: (I.K.); (K.F.); Tel.: +81-22-795-6838 (I.K.); +81-22-795-6836 (K.F.); Fax: +81-22-795-6835 (I.K. & K.F.)
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37
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Albers E, Avram A, Sbroggio M, Fernandez-Capetillo O, Lopez-Contreras AJ. Supraphysiological protection from replication stress does not extend mammalian lifespan. Aging (Albany NY) 2020; 12:5612-5624. [PMID: 32253367 PMCID: PMC7185120 DOI: 10.18632/aging.103039] [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: 01/08/2020] [Accepted: 03/10/2020] [Indexed: 12/05/2022]
Abstract
Replication Stress (RS) is a type of DNA damage generated at the replication fork, characterized by single-stranded DNA (ssDNA) accumulation, and which can be caused by a variety of factors. Previous studies have reported elevated RS levels in aged cells. In addition, mouse models with a deficient RS response show accelerated aging. However, the relevance of endogenous or physiological RS, compared to other sources of genomic instability, for the normal onset of aging is unknown. We have performed long term survival studies of transgenic mice with extra copies of the Chk1 and/or Rrm2 genes, which we previously showed extend the lifespan of a progeroid ATR-hypomorphic model suffering from high levels of RS. In contrast to their effect in the context of progeria, the lifespan of Chk1, Rrm2 and Chk1/Rrm2 transgenic mice was similar to WT littermates in physiological settings. Most mice studied died due to tumors -mainly lymphomas- irrespective of their genetic background. Interestingly, a higher but not statistically significant percentage of transgenic mice developed tumors compared to WT mice. Our results indicate that supraphysiological protection from RS does not extend lifespan, indicating that RS may not be a relevant source of genomic instability on the onset of normal aging.
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Affiliation(s)
- Eliene Albers
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Avram
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Mauro Sbroggio
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | | | - Andres J Lopez-Contreras
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
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38
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Anti-stress, Glial- and Neuro-differentiation Potential of Resveratrol: Characterization by Cellular, Biochemical and Imaging Assays. Nutrients 2020; 12:nu12030671. [PMID: 32121454 PMCID: PMC7146125 DOI: 10.3390/nu12030671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/26/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023] Open
Abstract
Environmental stress, exhaustive industrialization and the use of chemicals in our daily lives contribute to increasing incidence of cancer and other pathologies. Although the cancer treatment has revolutionized in last 2–3 decades, shortcomings such as (i) extremely high cost of treatment, (ii) poor availability of drugs, (iii) severe side effects and (iv) emergence of drug resistance have prioritized the need of developing alternate natural, economic and welfare (NEW) therapeutics reagents. Identification and characterization of such anti-stress NEW drugs that not only limit the growth of cancer cells but also reprogram them to perform their specific functions are highly desired. We recruited rat glioma- and human neuroblastoma-based assays to explore such activities of resveratrol, a naturally occurring stilbenoid. We demonstrate that nontoxic doses of resveratrol protect cells against a variety of stresses that are largely involved in age-related brain pathologies. These included oxidative, DNA damage, metal toxicity, heat, hypoxia, and protein aggregation stresses. Furthermore, it caused differentiation of cells to functional astrocytes and neurons as characterized by the upregulation of their specific protein markers. These findings endorse multiple bioactivities of resveratrol and encourage them to be tested for their benefits in animal models and humans.
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Fumasoni M, Murray AW. The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress. eLife 2020; 9:e51963. [PMID: 32043971 PMCID: PMC7069727 DOI: 10.7554/elife.51963] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/11/2020] [Indexed: 01/22/2023] Open
Abstract
Many biological features are conserved and thus considered to be resistant to evolutionary change. While rapid genetic adaptation following the removal of conserved genes has been observed, we often lack a mechanistic understanding of how adaptation happens. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism, a network of evolutionary conserved modules. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the enzymatic activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, concerted mutations. These mutations altered conserved features of two chromosome metabolism modules, DNA replication and sister chromatid cohesion, and inactivated a third, the DNA damage checkpoint. The selected mutations define a functionally reproducible evolutionary trajectory. We suggest that the evolutionary plasticity of chromosome metabolism has implications for genome evolution in natural populations and cancer.
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Affiliation(s)
- Marco Fumasoni
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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40
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Balliu B, Durrant M, Goede OD, Abell N, Li X, Liu B, Gloudemans MJ, Cook NL, Smith KS, Knowles DA, Pala M, Cucca F, Schlessinger D, Jaiswal S, Sabatti C, Lind L, Ingelsson E, Montgomery SB. Genetic regulation of gene expression and splicing during a 10-year period of human aging. Genome Biol 2019; 20:230. [PMID: 31684996 PMCID: PMC6827221 DOI: 10.1186/s13059-019-1840-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 09/27/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Molecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age. RESULTS We perform RNA sequencing in whole blood from the same individuals at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging at a population and individual level. We observe that individuals are more similar to their own expression profiles later in life than profiles of other individuals their own age. We identify 1291 and 294 genes differentially expressed and alternatively spliced with age, as well as 529 genes with outlying individual trajectories. Further, we observe a strong correlation of genetic effects on expression and splicing between the two ages, with a small subset of tested genes showing a reduction in genetic associations with expression and splicing in older age. CONCLUSIONS These findings demonstrate that, although the transcriptome and its genetic regulation is mostly stable late in life, a small subset of genes is dynamic and is characterized by a reduction in genetic regulation, most likely due to increasing environmental variance with age.
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Affiliation(s)
- Brunilda Balliu
- Department of Pathology, Stanford University School of Medicine, Stanford, USA.
| | - Matthew Durrant
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
| | - Olivia de Goede
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
| | - Nathan Abell
- Department of Genetics, Stanford University School of Medicine, Stanford, USA
| | - Xin Li
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
| | - Boxiang Liu
- Department of Biology, Stanford University School of Medicine, Stanford, USA
| | | | - Naomi L Cook
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Kevin S Smith
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
| | | | - Mauro Pala
- Dipartimento di Scienze Biomediche, Universita di Sassari, Sassari, Italy
| | - Francesco Cucca
- Dipartimento di Scienze Biomediche, Universita di Sassari, Sassari, Italy
| | | | - Siddhartha Jaiswal
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
| | - Chiara Sabatti
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, USA
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, USA.
- Stanford Cardiovascular Institute, Stanford University, Stanford, USA.
- Stanford Diabetes Research Center, Stanford University, Stanford, USA.
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, USA.
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41
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Angelova DM, Brown DR. Microglia and the aging brain: are senescent microglia the key to neurodegeneration? J Neurochem 2019; 151:676-688. [PMID: 31478208 DOI: 10.1111/jnc.14860] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/21/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022]
Abstract
The single largest risk factor for etiology of neurodegenerative diseases like Alzheimer's disease is increased age. Therefore, understanding the changes that occur as a result of aging is central to any possible prevention or cure for such conditions. Microglia, the resident brain glial population most associated with both protection of neurons in health and their destruction is disease, could be a significant player in age related changes. Microglia can adopt an aberrant phenotype sometimes referred to either as dystrophic or senescent. While aged microglia have been frequently identified in neurodegenerative diseases such as Alzheimer's disease, there is no conclusive evidence that proves a causal role. This has been hampered by a lack of models of aged microglia. We have recently generated a model of senescent microglia based on the observation that all dystrophic microglia show iron overload. Iron-overloading cultured microglia causes them to take on a senescent phenotype and can cause changes in models of neurodegeneration similar to those observed in patients. This review considers how this model could be used to determine the role of senescent microglia in neurodegenerative diseases.
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Affiliation(s)
- Dafina M Angelova
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - David R Brown
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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42
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Cell organelles and yeast longevity: an intertwined regulation. Curr Genet 2019; 66:15-41. [PMID: 31535186 DOI: 10.1007/s00294-019-01035-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022]
Abstract
Organelles are dynamic structures of a eukaryotic cell that compartmentalize various essential functions and regulate optimum functioning. On the other hand, ageing is an inevitable phenomenon that leads to irreversible cellular damage and affects optimum functioning of cells. Recent research shows compelling evidence that connects organelle dysfunction to ageing-related diseases/disorders. Studies in several model systems including yeast have led to seminal contributions to the field of ageing in uncovering novel pathways, proteins and their functions, identification of pro- and anti-ageing factors and so on. In this review, we present a comprehensive overview of findings that highlight the role of organelles in ageing and ageing-associated functions/pathways in yeast.
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43
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Sugaya K. Chromosome instability caused by mutations in the genes involved in transcription and splicing. RNA Biol 2019; 16:1521-1525. [PMID: 31385554 DOI: 10.1080/15476286.2019.1652523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Mutations in molecules involved in transcription and splicing can cause chromosome instability such as sister chromatid exchanges. We isolated and characterized responsible genes from mammalian temperature-sensitive mutant cells showing chromosome instability. A mutation in the largest subunit of RNA polymerase II affected DNA synthesis in S phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges. The yeast mutant harboring a homologous mutation showed very similar phenotype to that of the mammalian mutant. A mutation in Smu1, which is involved in splicing, also affected DNA synthesis in S and G2 phase-arrested cells, resulting in abnormal induction of sister chromatid exchanges and chromosomal aberrations. These cells showed a connection between defects of RNA metabolism and induction of chromosome instability. Genome instability appeared to be caused by links between RNA metabolism and replication resulting in genomic recombination. RNA metabolism can be regarded as one possible driver of genome modification triggering genome evolution.
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Affiliation(s)
- Kimihiko Sugaya
- Department of Molecular Imaging and Theranostics, National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST) , Chiba , Japan.,Group of Quantum-state Controlled MRI, QST , Chiba , Japan
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44
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Zhou Z, Wang L, Ge F, Gong P, Wang H, Wang F, Chen L, Liu L. Pold3 is required for genomic stability and telomere integrity in embryonic stem cells and meiosis. Nucleic Acids Res 2019; 46:3468-3486. [PMID: 29447390 PMCID: PMC6283425 DOI: 10.1093/nar/gky098] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/01/2018] [Indexed: 12/29/2022] Open
Abstract
Embryonic stem cells (ESCs) and meiosis are featured by relatively higher frequent homologous recombination associated with DNA double strand breaks (DSB) repair. Here, we show that Pold3 plays important roles in DSB repair, telomere maintenance and genomic stability of both ESCs and spermatocytes in mice. By attempting to generate Pold3 deficient mice using CRISPR/Cas9 or transcription activator-like effector nucleases, we show that complete loss of Pold3 (Pold3−/−) resulted in early embryonic lethality at E6.5. Rapid DNA damage response and massive apoptosis occurred in both outgrowths of Pold3-null (Pold3−/−) blastocysts and Pold3 inducible knockout (iKO) ESCs. While Pold3−/− ESCs were not achievable, Pold3 iKO led to increased DNA damage response, telomere loss and chromosome breaks accompanied by extended S phase. Meanwhile, loss of Pold3 resulted in replicative stress, micronucleation and aneuploidy. Also, DNA repair was impaired in Pold3+/− or Pold3 knockdown ESCs. Moreover, Pold3 mediates DNA replication and repair by regulating 53BP1, RIF1, ATR and ATM pathways. Furthermore, spermatocytes of Pold3 haploinsufficient (Pold3+/−) mice with increasing age displayed impaired DSB repair, telomere shortening and loss, and chromosome breaks, like Pold3 iKO ESCs. These data suggest that Pold3 maintains telomere integrity and genomic stability of both ESCs and meiosis by suppressing replicative stress.
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Affiliation(s)
- Zhongcheng Zhou
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.,Department of Cell Biology and Genetics, The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lingling Wang
- Department of Cell Biology and Genetics, The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Feixiang Ge
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.,Department of Cell Biology and Genetics, The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Peng Gong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.,Department of Cell Biology and Genetics, The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Hua Wang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.,Department of Cell Biology and Genetics, The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Feng Wang
- Department of Genetics, School of basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Lingyi Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.,Department of Cell Biology and Genetics, The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.,Department of Cell Biology and Genetics, The Key Laboratory of Bioactive Materials Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
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45
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Dukić M, Berner D, Haag CR, Ebert D. How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna. J Evol Biol 2019; 32:619-628. [PMID: 30888725 PMCID: PMC6850383 DOI: 10.1111/jeb.13443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 03/04/2019] [Indexed: 12/25/2022]
Abstract
Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within‐individual allelic divergence (heterozygosity); however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high‐throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by restriction site‐associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re‐sequenced the top 17 candidate RAD‐loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.
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Affiliation(s)
- Marinela Dukić
- Zoological Institute, University of Basel, Basel, Switzerland.,Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Daniel Berner
- Zoological Institute, University of Basel, Basel, Switzerland
| | - Christoph R Haag
- Centre d'Ecologie Fonctionnelle et Evolutive-CEFE UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, campus CNRS, Montpellier, France.,Department of Biology, Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
| | - Dieter Ebert
- Zoological Institute, University of Basel, Basel, Switzerland
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46
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Deprez MA, Eskes E, Winderickx J, Wilms T. The TORC1-Sch9 pathway as a crucial mediator of chronological lifespan in the yeast Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:4980911. [PMID: 29788208 DOI: 10.1093/femsyr/foy048] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 04/19/2018] [Indexed: 12/18/2022] Open
Abstract
The concept of ageing is one that has intrigued mankind since the beginning of time and is now more important than ever as the incidence of age-related disorders is increasing in our ageing population. Over the past decades, extensive research has been performed using various model organisms. As such, it has become apparent that many fundamental aspects of biological ageing are highly conserved across large evolutionary distances. In this review, we illustrate that the unicellular eukaryotic organism Saccharomyces cerevisiae has proven to be a valuable tool to gain fundamental insights into the molecular mechanisms of cellular ageing in multicellular eukaryotes. In addition, we outline the current knowledge on how downregulation of nutrient signaling through the target of rapamycin (TOR)-Sch9 pathway or reducing calorie intake attenuates many detrimental effects associated with ageing and leads to the extension of yeast chronological lifespan. Given that both TOR Complex 1 (TORC1) and Sch9 have mammalian orthologues that have been implicated in various age-related disorders, unraveling the connections of TORC1 and Sch9 with yeast ageing may provide additional clues on how their mammalian orthologues contribute to the mechanisms underpinning human ageing and health.
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Affiliation(s)
- Marie-Anne Deprez
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Elja Eskes
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Joris Winderickx
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
| | - Tobias Wilms
- Department of Biology, Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium
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Coluzzi E, Leone S, Sgura A. Oxidative Stress Induces Telomere Dysfunction and Senescence by Replication Fork Arrest. Cells 2019; 8:cells8010019. [PMID: 30609792 PMCID: PMC6356380 DOI: 10.3390/cells8010019] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/29/2018] [Indexed: 12/12/2022] Open
Abstract
Oxidative DNA damage, particularly 8-oxoguanine, represents the most frequent DNA damage in human cells, especially at the telomeric level. The presence of oxidative lesions in the DNA can hinder the replication fork and is able to activate the DNA damage response. In this study, we wanted to understand the mechanisms by which oxidative damage causes telomere dysfunction and senescence in human primary fibroblasts. After acute oxidative stress at telomeres, our data demonstrated a reduction in TRF1 and TRF2, which are involved in proper telomere replication and T-loop formation, respectively. Furthermore, we observed a higher level of γH2AX with respect to 53BP1 at telomeres, suggesting a telomeric replication fork stall rather than double-strand breaks. To confirm this finding, we studied the replication of telomeres by Chromosome Orientation-FISH (CO-FISH). The data obtained show an increase in unreplicated telomeres after hydrogen peroxide treatment, corroborating the idea that the presence of 8-oxoG can induce replication fork arrest at telomeres. Lastly, we analyzed the H3K9me3 histone mark after oxidative stress at telomeres, and our results showed an increase of this marker, most likely inducing the heterochromatinization of telomeres. These results suggest that 8-oxoG is fundamental in oxidative stress-induced telomeric damage, principally causing replication fork arrest.
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Affiliation(s)
- Elisa Coluzzi
- Department of Science, University of Rome "Roma TRE", Viale Guglielmo Marconi, 446, 00146 Rome, Italy.
| | - Stefano Leone
- Department of Science, University of Rome "Roma TRE", Viale Guglielmo Marconi, 446, 00146 Rome, Italy.
| | - Antonella Sgura
- Department of Science, University of Rome "Roma TRE", Viale Guglielmo Marconi, 446, 00146 Rome, Italy.
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Thakre PK, SV A, Golla U, Chauhan S, Tomar RS. Previously uncharacterized amino acid residues in histone H3 and H4 mutants with roles in
DNA
damage repair response and cellular aging. FEBS J 2018; 286:1154-1173. [DOI: 10.1111/febs.14723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/01/2018] [Accepted: 12/04/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Pilendra K. Thakre
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Athira SV
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Upendarrao Golla
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Sakshi Chauhan
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Bethesda MD USA
| | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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49
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Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition. Mol Cell 2018; 72:222-238.e11. [PMID: 30293786 DOI: 10.1016/j.molcel.2018.08.047] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 07/11/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023]
Abstract
DNA polymerase stalling activates the ATR checkpoint kinase, which in turn suppresses fork collapse and breakage. Herein, we describe use of ATR inhibition (ATRi) as a means to identify genomic sites of problematic DNA replication in murine and human cells. Over 500 high-resolution ATR-dependent sites were ascertained using two distinct methods: replication protein A (RPA)-chromatin immunoprecipitation (ChIP) and breaks identified by TdT labeling (BrITL). The genomic feature most strongly associated with ATR dependence was repetitive DNA that exhibited high structure-forming potential. Repeats most reliant on ATR for stability included structure-forming microsatellites, inverted retroelement repeats, and quasi-palindromic AT-rich repeats. Notably, these distinct categories of repeats differed in the structures they formed and their ability to stimulate RPA accumulation and breakage, implying that the causes and character of replication fork collapse under ATR inhibition can vary in a DNA-structure-specific manner. Collectively, these studies identify key sources of endogenous replication stress that rely on ATR for stability.
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50
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Label-free fluorescent and electrochemical biosensors based on defective G-quadruplexes. Biosens Bioelectron 2018; 118:1-8. [DOI: 10.1016/j.bios.2018.07.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022]
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