1
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Yang Y, Zhang N, Jiang W. Functional DNA-Zn 2+ coordination nanospheres for sensitive imaging of 8-oxyguanine DNA glycosylase activity in living cells. Talanta 2024; 280:126779. [PMID: 39217713 DOI: 10.1016/j.talanta.2024.126779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/15/2024] [Accepted: 08/24/2024] [Indexed: 09/04/2024]
Abstract
Sensitive monitoring of human 8-oxyguanine DNA glycosylase (hOGG1) activity in living cells is helpful to understand its function in damage repair and evaluate its role in disease diagnosis. Herein, a functional DNA-Zn2+ coordination nanospheres was proposed for sensitive imaging of hOGG1 in living cells. The nanospheres were constructed through the coordination-driven self-assembly of the entropy driven reaction (EDR) -deoxyribozyme (DNAzyme) system with Zn2+, where DNAzyme was designed to split structure and assembled into the EDR system. When the nanospheres entered the cell, the competitive coordination between phosphate in the cell and Zn2+ leaded to the disintegration of the nanospheres, releasing DNA and some Zn2+. The released Zn2+ acted as a cofactor of DNAzyme. In the presence of hOGG1, the EDR was completed, accompanied by fluorescence recovery and the generation of a complete DNAzyme. With the assistance of Zn2+, DNAzyme continuously cleaved substrates to produce plenty of fluorescence signals, thus achieving sensitive imaging of hOGG1 activity. The nanospheres successfully achieved sensitive imaging of hOGG1 in human cervical cancer cells (HeLa), human non-small cell lung cancer cells and human normal colonic epithelial cells, and assayed changes in hOGG1 activity in HeLa cells. This nanospheres may provide a new tool for intracellular hOGG1 imaging and related biomedical studies.
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Affiliation(s)
- Yayun Yang
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China
| | - Nan Zhang
- Research Center of Basic Medicine, Breast Center, Central Hospital Affiliated to Shandong First Medical University, 250013, Jinan, PR China.
| | - Wei Jiang
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
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2
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Xue CY, Liu YH, Yu Y, Liu Y, Zhou YL, Zhang XX. Ultrasensitive mass spectrometric quantitation of apurinic/apyrimidinic sites in genomic DNA of mammalian cell lines exposed to genotoxic reagents. Anal Chim Acta 2024; 1329:343238. [PMID: 39396301 DOI: 10.1016/j.aca.2024.343238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 10/15/2024]
Abstract
The apurinic/apyrimidinic (AP) site is an important intermediate in the DNA base excision repair (BER) pathway, having the potential of being a biomarker for DNA damage. AP sites could lead to the stalling of polymerases, the misincorporation of bases and DNA strand breaks, which might affect physiological function of cells. However, the abundance of AP sites in genomic DNA is very low (less than 2 AP sites/106 nts), which requires a sensitive and accurate method to meet its detection requirements. Here, we described an ultrasensitive quantification method based on a hydrazine-s-triazine reagent (i-Pr2N) labeling for AP sites combining with high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The limit of detection reached an ultralow level (40 amol), realizing the most sensitive MS-based quantification for the AP site. To guarantee the accuracy of the quantitative results, the labeling reaction was carried out directly on DNA strands instead of labeling after DNA enzymatic digestion to reduce artifacts that might be produced during the enzymatic process of DNA strands. And selective detection was realized by MS to avoid introducing the false-positive signals from other aldehyde species, which could also react with i-Pr2N. Genomic DNA samples from different mammalian cell lines were successfully analyzed using this method. There were 0.4-0.8 AP sites per 106 nucleotides, and the values would increase 16.1 and 2.75 times when cells were treated with genotoxic substances methyl methanesulfonate and 5-fluorouracil, respectively. This method has good potential in the analysis of a small number of cell samples and clinical samples, is expected to be useful for evaluating the damage level of DNA bases, the genotoxicity of compounds and the drug resistance of cancer cells, and provides a new tool for cell function research and clinical precise treatment.
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Affiliation(s)
- Chen-Yu Xue
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China; Key Laboratory of Forensic Toxicology, Ministry of Public Security, Beijing, 100191, China
| | - Ya-Hong Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yue Yu
- Qilu Pharmaceutical Co., Ltd, Jinan, 250104, China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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3
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Tian H, Wang W, Liu W, Lv Z, Wang L. Exopolysaccharide from Leuconostoc mesenteroides XR1: Yield optimization, partial characterization and properties. Int J Biol Macromol 2024; 279:135225. [PMID: 39218184 DOI: 10.1016/j.ijbiomac.2024.135225] [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: 03/09/2024] [Revised: 08/08/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
The production conditions of exopolysaccharide (EPS) from Leuconostoc mesenteroides XR1 were optimized by response surface methodology (RSM). Maximum EPS yield was 56.59 ± 0.51 g/L under fermentation conditions with 2.6 g/L ammonium citrate, initial pH 6.5 and temperature 23 °C, which was 6.21-fold greater than the EPS yield before optimization. Characterization of the chain conformation using Congo red test and circular dichroism (CD) showed that EPS exhibited a random coil structure in aqueous solution. The CD results revealed that the EPS concentration altered its hydrogen-bond interactions and chirality, but did not change its chain conformation. The average polydispersity index (PDI) of the EPS solution was only 27.16 %, indicating that it was uniformly distributed in the aqueous solution with high stability. The degradation temperature of EPS was 253.11 °C, indicating high thermal stability. EPS possessed the ability to scavenge activities of free radicals and was protective against oxidative stress-induced plasmid DNA damage. In addition, stable hydrogels could be formed at EPS concentrations above 5 % (w/v). These results collectively showed that EPS can be used commercially as an antioxidant and drug delivery carrier.
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Affiliation(s)
- Huimin Tian
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, Jiangsu, PR China
| | - Wenhao Wang
- School of Materials Science and Engineering, Dalian Jiaotong University, Huanghe Road 794, Dalian 116028, Liaoning, PR China
| | - Wei Liu
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, Jiangsu, PR China
| | - Zili Lv
- School of Medical and Life Sciences, Reproductive & Women-Children Hospital, Chengdu University of Traditional Chinese Medicine, Chengdu 610041, PR China
| | - Liang Wang
- School of Food and Biological Engineering, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, Jiangsu, PR China.
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4
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Du J, Zhang J, Liu D, Gao L, Liao H, Chu L, Lin J, Li W, Meng X, Zou F, Cai S, Zou M, Dong H. 1G6-D7 Inhibits Homologous Recombination Repair by Targeting Extracellular HSP90α to Promote Apoptosis in Non-Small Cell Lung Cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:4884-4898. [PMID: 38899512 DOI: 10.1002/tox.24356] [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: 02/23/2024] [Revised: 05/07/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
Despite recent advances in treatment, non-small cell lung cancer (NSCLC) continues to have a high mortality rate. Currently, NSCLC pathogenesis requires further investigation, and therapeutic drugs are still under development. Homologous recombination repair (HRR) repairs severe DNA double-strand breaks. Homologous recombination repair deficiency (HRD) occurs when HRR is impaired and causes irreparable double-strand DNA damage, leading to genomic instability and increasing the risk of cancer development. Poly(ADP-ribose) polymerase (PARP) inhibitors can effectively treat HRD-positive tumors. Extracellular heat shock protein 90α (eHSP90α) is highly expressed in hypoxic environments and inhibits apoptosis, thereby increasing cellular tolerance. Here, we investigated the relationship between eHSP90α and HRR in NSCLC. DNA damage models were established in NSCLC cell lines (A549 and H1299). The activation of DNA damage and HRR markers, apoptosis, proliferation, and migration were investigated. In vivo tumor models were established using BALB/c nude mice and A549 cells. We found that human recombinant HSP90α stimulation further activated HRR and reduced DNA damage extent; however, eHSP90α monoclonal antibody, 1G6-D7, effectively inhibited HRR. HRR inhibition and increased apoptosis were observed after LRP1 knockdown; this effect could not be reversed with hrHSP90α addition. The combined use of 1G6-D7 and olaparib caused significant apoptosis and HRR inhibition in vitro and demonstrated promising anti-tumor effects in vivo. Extracellular HSP90α may be involved in HRR in NSCLC through LRP1. The combined use of 1G6-D7 and PARP inhibitors may exert anti-tumor effects by inhibiting DNA repair and further inducing apoptosis of NSCLC cells.
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Affiliation(s)
- Jiangzhou Du
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinming Zhang
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongyu Liu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lin Gao
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hua Liao
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Lanhe Chu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Lin
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Li
- Department of Dermatology, The USC-Norris Comprehensive Cancer Center, University of Southern California Keck Medical Center, California, Los Angeles, USA
| | - Xiaojing Meng
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Fei Zou
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Shaoxi Cai
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mengchen Zou
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hangming Dong
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
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5
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Du J, Chen F, Chen Z, Zhao W, Wang J, Zhou M. LncRNA LINC01664 promotes cancer resistance through facilitating homologous recombination-mediated DNA repair. DNA Repair (Amst) 2024; 143:103770. [PMID: 39357141 DOI: 10.1016/j.dnarep.2024.103770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 09/14/2024] [Accepted: 09/23/2024] [Indexed: 10/04/2024]
Abstract
The intracellular responses to DNA double-strand breaks (DSB) repair are crucial for genomic stability and play an essential role in cancer resistance. In addition to canonical DSB repair proteins, long non-coding RNAs (lncRNAs) have been found to be involved in this sophisticated network. In the present study, we performed a loss-of-function screen for a customized siRNA Premix Library to identify lncRNAs that participate in homologous recombination (HR) process. Among the candidates, we identified LINC01664 as a novel lncRNA required for HR repair. Furthermore, LINC01664 knockdown significantly increased the sensitivity of cancer cells to DNA damage agents such as ionizing radiation and genotoxic drugs. Mechanistically, LINC01664 interacted with Sirt1 promoter and then activated Sirt1 transcription, which contributed to HR-mediated DNA damage repair. In summary, our findings revealed a new mechanism of LINC01664 in DNA damage repair, providing evidence for a potential therapeutic strategy for eliminating the treatment bottlenecks caused by cancer resistance to chemotherapy and radiotherapy.
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Affiliation(s)
- Jie Du
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China; Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, China
| | - Fuqiang Chen
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Zihan Chen
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wenna Zhao
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jianyu Wang
- Key Laboratory of Occupational Environment and Health, Guangzhou Twelfth People's Hospital, Guangzhou, China
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.
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Naselli F, Cardinale PS, Volpes S, Martino C, Cruciata I, Valenti R, Luparello C, Caradonna F, Chiarelli R. An alternative approach of TUNEL assay to specifically characterize DNA fragmentation in cell model systems. Histochem Cell Biol 2024; 162:429-442. [PMID: 38940846 PMCID: PMC11393043 DOI: 10.1007/s00418-024-02306-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
DNA damage is one of the most important effects induced by chemical agents. We report a comparative analysis of DNA fragmentation on three different cell lines using terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, generally applied to detect apoptosis. Our approach combines cytogenetic techniques and investigation in detached cellular structures, recovered from the culture medium with the aim to compare the DNA fragmentation of three different cell line even beyond the cells adherent to substrate. Consequently, we detect any fragmentation points on single chromosomes, whole nuclei and other cellular structures. Cells were exposed to resveratrol (RSV) and doxorubicin (Doxo), in single and combined treatments. Control and treated astrocytes showed DNA damage in condensed nuclei and detached structures. Caco-2 cells showed fragmented DNA only after Doxo-treatment, while controls showed fragmented chromosomes, indicating DNA damage in replicating cells. MDA-MB-231 cells showed nuclear condensation and DNA fragmentation above all after RSV-treatment and related to detached structures. This model proved to perform a grading of genomic instability (GI). Astrocytes show a hybrid level of GI. Caco-2 cells showed fragmented metaphase chromosomes, proving that the DNA damage was transmitted to the daughter cells probably due to an absence of DNA repair mechanisms. Instead, MDA-MB-231 cells showed few or no fragmented metaphase, suggesting a probable activation of DNA repair mechanisms. By applying this alternative approach of TUNEL test, we obtained data that can more specifically characterize DNA fragmentation for a suitable application in various fields.
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Affiliation(s)
- Flores Naselli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy
| | - Paola Sofia Cardinale
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy
| | - Sara Volpes
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy
| | - Chiara Martino
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy
| | - Ilenia Cruciata
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy
| | - Rossella Valenti
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy
| | - Claudio Luparello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Fabio Caradonna
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy.
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy.
| | - Roberto Chiarelli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale Delle Scienze Building 16, 90128, Palermo, Italy
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7
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Occhipinti M, Brambilla M, Di Liello R, Ambrosini P, Lobianco L, Leporati R, Salvarezza M, Vitiello F, Marchesi S, Manglaviti S, Beninato T, Mazzeo L, Proto C, Prelaj A, Ferrara R, Della Corte CM, Lo Russo G, de Braud F, Ganzinelli M, Viscardi G. Unleashing precision: A review of targeted approaches in pleural mesothelioma. Crit Rev Oncol Hematol 2024; 203:104481. [PMID: 39159705 DOI: 10.1016/j.critrevonc.2024.104481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 08/21/2024] Open
Abstract
This review delves into the intricate landscape of pleural mesothelioma (PM), emphasizing the need for nuanced therapeutic strategies. While platinum-based chemotherapy remains a cornerstone, the advent of immune checkpoint inhibitors (ICIs), notably through the Checkmate 743 trial, has reshaped treatment paradigms. Challenges persist due to patient heterogeneity and a lack of specific biomarkers. Targeting genotypic and phenotypic alterations emerges as a promising avenue, demanding precision oncology in this rare disease. CDKN2A loss, prevalent in PM, may respond to CDK4/6 inhibitors. Defects in MMR and HR suggest tailored approaches with ICI or PARP inhibitors, respectively. Ongoing trials explore novel inhibitors and promising targets like mesothelin. Implementing these strategies requires overcoming challenges in patient selection, combination therapies, biomarker identification, and cost considerations. Collaboration is crucial for transforming these insights into impactful clinical interventions, heralding the era of personalized and precision medicine for PM.
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Affiliation(s)
- Mario Occhipinti
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy; Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Marta Brambilla
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy.
| | | | - Paolo Ambrosini
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Lorenzo Lobianco
- Medical Oncology, Precision Medicine Department, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Rita Leporati
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Maria Salvarezza
- Medical Oncology, Precision Medicine Department, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Fabiana Vitiello
- Medical Oncology Unit, Ospedale Monaldi, AORN Ospedali dei Colli, Naples, Italy
| | - Silvia Marchesi
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Sara Manglaviti
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Teresa Beninato
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Laura Mazzeo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Claudia Proto
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Arsela Prelaj
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy; Department of Electronics, Information and Bioengineering, Polytechnic University of Milan, Milan, Italy
| | - Roberto Ferrara
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | | | - Giuseppe Lo Russo
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Filippo de Braud
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Monica Ganzinelli
- Medical Oncology Department, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Giuseppe Viscardi
- Medical Oncology Unit, Ospedale Monaldi, AORN Ospedali dei Colli, Naples, Italy
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8
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He M, Jiang H, Li S, Xue M, Wang H, Zheng C, Tong J. The crosstalk between DNA-damage responses and innate immunity. Int Immunopharmacol 2024; 140:112768. [PMID: 39088918 DOI: 10.1016/j.intimp.2024.112768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/14/2024] [Accepted: 07/22/2024] [Indexed: 08/03/2024]
Abstract
DNA damage is typically caused during cell growth by DNA replication stress or exposure to endogenous or external toxins. The accumulation of damaged DNA causes genomic instability, which is the root cause of many serious disorders. Multiple cellular organisms utilize sophisticated signaling pathways against DNA damage, collectively known as DNA damage response (DDR) networks. Innate immune responses are activated following cellular abnormalities, including DNA damage. Interestingly, recent studies have indicated that there is an intimate relationship between the DDR network and innate immune responses. Diverse kinds of cytosolic DNA sensors, such as cGAS and STING, recognize damaged DNA and induce signals related to innate immune responses, which link defective DDR to innate immunity. Moreover, DDR components operate in immune signaling pathways to induce IFNs and/or a cascade of inflammatory cytokines via direct interactions with innate immune modulators. Consistently, defective DDR factors exacerbate the innate immune imbalance, resulting in severe diseases, including autoimmune disorders and tumorigenesis. Here, the latest progress in understanding crosstalk between the DDR network and innate immune responses is reviewed. Notably, the dual function of innate immune modulators in the DDR network may provide novel insights into understanding and developing targeted immunotherapies for DNA damage-related diseases, even carcinomas.
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Affiliation(s)
- Mei He
- College of Life Sciences, Hebei University, Baoding 071002, China; Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hua Jiang
- Department of Hematology, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai 200000, China
| | - Shun Li
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu 610041, China
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450001, China.
| | - Huiqing Wang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
| | - Jie Tong
- College of Life Sciences, Hebei University, Baoding 071002, China.
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9
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Li T, Zeng F, Li Y, Li H, Wu J. The Integrator complex: an emerging complex structure involved in the regulation of gene expression by targeting RNA polymerase II. Funct Integr Genomics 2024; 24:192. [PMID: 39424688 DOI: 10.1007/s10142-024-01479-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 10/12/2024] [Accepted: 10/14/2024] [Indexed: 10/21/2024]
Abstract
The Integrator complex is a multisubunit complex that participates in the processing of small nuclear RNA molecules in eukaryotic cells by cleaving the 3' end. In protein-coding genes, Integrator is a key regulator of promoter-proximal pausing, release, and recruitment of RNA polymerase II. Research on Integrator has revealed its critical role in the regulation of gene expression and RNA processing. Dysregulation of the Integrator complex has been implicated in a variety of human diseases including cancer and developmental disorders. Therefore, understanding the structure and function of the Integrator complex is critical to uncovering the mechanisms of gene expression and developing potential therapeutic strategies for related diseases.
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Affiliation(s)
- Tingyue Li
- School of Stomatology, Affiliated Stomatological Hospital, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Fulei Zeng
- School of Stomatology, Affiliated Stomatological Hospital, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Yang Li
- School of Stomatology, Affiliated Stomatological Hospital, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Hu Li
- School of Stomatology, Affiliated Stomatological Hospital, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Jiayuan Wu
- School of Stomatology, Affiliated Stomatological Hospital, Zunyi Medical University, Zunyi, Guizhou, 563000, China.
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10
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Saini S, Gurung P. A comprehensive review of sensors of radiation-induced damage, radiation-induced proximal events, and cell death. Immunol Rev 2024. [PMID: 39425547 DOI: 10.1111/imr.13409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2024]
Abstract
Radiation, a universal component of Earth's environment, is categorized into non-ionizing and ionizing forms. While non-ionizing radiation is relatively harmless, ionizing radiation possesses sufficient energy to ionize atoms and disrupt DNA, leading to cell damage, mutation, cancer, and cell death. The extensive use of radionuclides and ionizing radiation in nuclear technology and medical applications has sparked global concern for their capacity to cause acute and chronic illnesses. Ionizing radiation induces DNA damage either directly through strand breaks and base change or indirectly by generating reactive oxygen species (ROS) and reactive nitrogen species (RNS) via radiolysis of water. This damage triggers a complex cellular response involving recognition of DNA damage, cell cycle arrest, DNA repair mechanisms, release of pro-inflammatory cytokines, and cell death. This review focuses on the mechanisms of radiation-induced cellular damage, recognition of DNA damage and subsequent activation of repair processes, and the critical role of the innate immune response in resolution of the injury. Emphasis is placed on pattern recognition receptors (PRRs) and related receptors that detect damage-associated molecular patterns (DAMPs) and initiate downstream signaling pathways. Radiation-induced cell death pathways are discussed in detail. Understanding these processes is crucial for developing strategies to mitigate the harmful effects of radiation and improve therapeutic outcomes.
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Affiliation(s)
- Saurabh Saini
- Inflammation Program, University of Iowa, Iowa City, Iowa, USA
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
- Iowa City Veterans Affairs (VA) Medical Center, Iowa City, Iowa, USA
| | - Prajwal Gurung
- Inflammation Program, University of Iowa, Iowa City, Iowa, USA
- Department of Internal Medicine, University of Iowa, Iowa City, Iowa, USA
- Iowa City Veterans Affairs (VA) Medical Center, Iowa City, Iowa, USA
- Interdisciplinary Graduate Program in Human Toxicology, University of Iowa, Iowa City, Iowa, USA
- Immunology Graduate Program, University of Iowa, Iowa City, Iowa, USA
- Center for Immunology and Immune Based Disease, University of Iowa, Iowa City, Iowa, USA
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11
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Mamontova V, Trifault B, Gribling-Burrer AS, Bohn P, Boten L, Preckwinkel P, Gallant P, Solvie D, Ade CP, Papadopoulos D, Eilers M, Gutschner T, Smyth RP, Burger K. NEAT1 promotes genome stability via m 6A methylation-dependent regulation of CHD4. Genes Dev 2024; 38:915-930. [PMID: 39362776 DOI: 10.1101/gad.351913.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 09/13/2024] [Indexed: 10/05/2024]
Abstract
Long noncoding (lnc)RNAs emerge as regulators of genome stability. The nuclear-enriched abundant transcript 1 (NEAT1) is overexpressed in many tumors and is responsive to genotoxic stress. However, the mechanism that links NEAT1 to DNA damage response (DDR) is unclear. Here, we investigate the expression, modification, localization, and structure of NEAT1 in response to DNA double-strand breaks (DSBs). DNA damage increases the levels and N6-methyladenosine (m6A) marks on NEAT1, which promotes alterations in NEAT1 structure, accumulation of hypermethylated NEAT1 at promoter-associated DSBs, and DSB signaling. The depletion of NEAT1 impairs DSB focus formation and elevates DNA damage. The genome-protective role of NEAT1 is mediated by the RNA methyltransferase 3 (METTL3) and involves the release of the chromodomain helicase DNA binding protein 4 (CHD4) from NEAT1 to fine-tune histone acetylation at DSBs. Our data suggest a direct role for NEAT1 in DDR.
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Affiliation(s)
- Victoria Mamontova
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum [MSNZ]) Würzburg, University Hospital Würzburg, 97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Barbara Trifault
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum [MSNZ]) Würzburg, University Hospital Würzburg, 97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Anne-Sophie Gribling-Burrer
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz-Center for Infection Research, 97808 Würzburg, Germany
| | - Patrick Bohn
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz-Center for Infection Research, 97808 Würzburg, Germany
| | - Lea Boten
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum [MSNZ]) Würzburg, University Hospital Würzburg, 97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Pit Preckwinkel
- Department of RNA Biology and Pathogenesis, Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Research Center, 06120 Halle, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Daniel Solvie
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Dimitrios Papadopoulos
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
| | - Tony Gutschner
- Department of RNA Biology and Pathogenesis, Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Research Center, 06120 Halle, Germany
| | - Redmond P Smyth
- Helmholtz Institute for RNA-Based Infection Research, Helmholtz-Center for Infection Research, 97808 Würzburg, Germany
| | - Kaspar Burger
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum [MSNZ]) Würzburg, University Hospital Würzburg, 97080 Würzburg, Germany;
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, 97074 Würzburg, Germany
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12
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Botêlho de Araújo CB, Alves de Mendonça S, de Lima Viana D, da Fontoura Martins M, Costa PG, Bianchini A, Vasconcelos de Oliveira PG, Torres RA, Vieira Hazin FH, Adam ML. Effects of blood metal(loid) concentrations on genomic damages in sharks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124569. [PMID: 39025294 DOI: 10.1016/j.envpol.2024.124569] [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: 05/06/2024] [Revised: 07/05/2024] [Accepted: 07/16/2024] [Indexed: 07/20/2024]
Abstract
The use of effect biomarkers has contributed to the understanding of the sublethal effects of contaminants on different organisms. However, the analysis of genotoxic markers as an indicator of organism and environmental health in sharks is underexplored. Thus, the present study investigated the relationship between the genomic damage frequency in erythrocytes and metal(loid) concentrations in whole blood of three shark species (Galeocerdo cuvier, Negaprion brevirostris and Ginglymostoma cirratum), taking into account climatic seasonality. The results showed that G. cuvier, an apex predator, presented the highest total erythrocyte genomic damage frequencies together with the highest mean whole blood concentrations of Al, Cd, Cr, Fe, Mn, Ni, Pb and Zn. The shark N. brevirostris also presented high levels of metal(loid), indicating a greater susceptibility to these contaminants in species that preferentially feed on fish. In contrast, G. cirratum, a mesopredator, presented the lowest erythrocyte damage frequencies and whole blood metal(loid) concentrations. The presence of micronuclei was the most responsive biomarker, and Al, As and Zn had an important effect on the genomic damage frequencies for all species evaluated. Zn concentration influenced the binucleated cells frequencies and Al concentration had an effect on the total damage and micronuclei frequencies in G. cuvier and N. brevirostris. Binucleated cells and blebbed nuclei frequencies were affected by As concentration, especially in G. cirratum, while showing a strong and positive correlation with most of the metals analyzed. Nonetheless, baseline levels of metal(loid) blood concentrations and erythrocyte genomic damage frequencies in sharks have not yet been established. Therefore, minimum risk levels of blood contaminants concentrations on the health of these animals have also not been determined. However, the high genomic instability observed in sharks is of concern considering the current health status of these animals, as well as the quality of the environment studied.
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Affiliation(s)
- Camila Brasilino Botêlho de Araújo
- Laboratory of Fisheries Oceanography, Department of Fisheries and Aquaculture, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, Dois Irmãos, 52.171-030, Recife, Pernambuco, Brazil; Evolutionary and Environmental Genomics Laboratory, Federal Technological University of Paraná, Av. dos Pioneiros, 3131, Jardim Morumbi, 86036-370, Londrina, Paraná, Brazil.
| | - Sibele Alves de Mendonça
- Laboratory of Fisheries Oceanography, Department of Fisheries and Aquaculture, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, Dois Irmãos, 52.171-030, Recife, Pernambuco, Brazil.
| | - Danielle de Lima Viana
- Laboratory of Fisheries Oceanography, Department of Fisheries and Aquaculture, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, Dois Irmãos, 52.171-030, Recife, Pernambuco, Brazil.
| | - Mariana da Fontoura Martins
- Institute of Biological Sciences, Federal University of Rio Grande, Avenida Itália, km 8, 96203-900, Rio Grande, Rio Grande do Sul, Brazil.
| | - Patrícia Gomes Costa
- Institute of Biological Sciences, Federal University of Rio Grande, Avenida Itália, km 8, 96203-900, Rio Grande, Rio Grande do Sul, Brazil.
| | - Adalto Bianchini
- Institute of Biological Sciences, Federal University of Rio Grande, Avenida Itália, km 8, 96203-900, Rio Grande, Rio Grande do Sul, Brazil.
| | - Paulo Guilherme Vasconcelos de Oliveira
- Laboratory of Fisheries Oceanography, Department of Fisheries and Aquaculture, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, Dois Irmãos, 52.171-030, Recife, Pernambuco, Brazil.
| | - Rodrigo Augusto Torres
- Evolutionary and Environmental Genomics Laboratory, Federal Technological University of Paraná, Av. dos Pioneiros, 3131, Jardim Morumbi, 86036-370, Londrina, Paraná, Brazil.
| | - Fábio Hissa Vieira Hazin
- Laboratory of Fisheries Oceanography, Department of Fisheries and Aquaculture, Federal Rural University of Pernambuco, Rua Dom Manuel de Medeiros, Dois Irmãos, 52.171-030, Recife, Pernambuco, Brazil.
| | - Mônica Lúcia Adam
- Evolutionary and Environmental Genomics Laboratory, Federal Technological University of Paraná, Av. dos Pioneiros, 3131, Jardim Morumbi, 86036-370, Londrina, Paraná, Brazil.
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13
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Du J, Chen F, Du C, Zhao W, Chen Z, Ding Z, Zhou M. Amodiaquine ameliorates stress-induced premature cellular senescence via promoting SIRT1-mediated HR repair. Cell Death Discov 2024; 10:434. [PMID: 39394181 PMCID: PMC11470136 DOI: 10.1038/s41420-024-02201-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 09/21/2024] [Accepted: 09/30/2024] [Indexed: 10/13/2024] Open
Abstract
DNA damage is considered to be a potentially unifying driver of ageing, and the stalling of DNA damage repair accelerates the cellular senescence. However, augmenting DNA repair has remained a great challenge due to the intricate repair mechanisms specific for multiple types of lesions. Herein, we miniaturized our modified detecting system for homologous recombination (HR) into a 96-well-based platform and performed a high-throughput chemical screen for FDA-approved drugs. We uncovered that amodiaquine could significantly augment HR repair at the noncytotoxic concentration. Further experiments demonstrated that amodiaquine remarkably suppressed stress-induced premature cellular senescence (SIPS), as evidenced by senescence-associated beta-galactosidase (SA-β-gal) staining or senescence-related markers p21WAF1 and p16ink4a, and the expression of several cytokines. Mechanistic studies revealed that the stimulation of HR repair by amodiaquine might be mostly attributable to the promotion of SIRT1 at the transcriptional level. Additionally, SIRT1 depletion abolished the amodiaquine-mediated effects on DNA repair and cellular senescence, indicating that amodiaquine delayed the onset of SIPS via a SIRT1-dependent pathway. Taken together, this experimental approach paved the way for the identification of compounds that augment HR activity, which could help to underscore the therapeutic potential of targeting DNA repair for treating aging-related diseases.
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Affiliation(s)
- Jie Du
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Fuqiang Chen
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Chenghong Du
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Wenna Zhao
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Zihan Chen
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhenhua Ding
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
| | - Meijuan Zhou
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-sen University, Jiangmen, Guangdong, China.
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China.
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14
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Chen Z, Wang X, Gao X, Arslanovic N, Chen K, Tyler JK. Transcriptional inhibition after irradiation occurs preferentially at highly expressed genes in a manner dependent on cell cycle progression. eLife 2024; 13:RP94001. [PMID: 39392398 PMCID: PMC11469672 DOI: 10.7554/elife.94001] [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: 10/12/2024] Open
Abstract
In response to DNA double-strand damage, ongoing transcription is inhibited to facilitate accurate DNA repair while transcriptional recovery occurs after DNA repair is complete. However, the mechanisms at play and the identity of the transcripts being regulated in this manner are unclear. In contrast to the situation following UV damage, we found that transcriptional recovery after ionizing radiation (IR) occurs in a manner independent of the HIRA histone chaperone. Sequencing of the nascent transcripts identified a programmed transcriptional response, where certain transcripts and pathways are rapidly downregulated after IR, while other transcripts and pathways are upregulated. Specifically, most of the loss of nascent transcripts occurring after IR is due to inhibition of transcriptional initiation of the highly transcribed histone genes and the rDNA. To identify factors responsible for transcriptional inhibition after IR in an unbiased manner, we performed a whole genome gRNA library CRISPR/Cas9 screen. Many of the top hits on our screen were factors required for protein neddylation. However, at short times after inhibition of neddylation, transcriptional inhibition still occurred after IR, even though neddylation was effectively inhibited. Persistent inhibition of neddylation blocked transcriptional inhibition after IR, and it also leads to cell cycle arrest. Indeed, we uncovered that many inhibitors and conditions that lead to cell cycle arrest in G1 or G2 phase also prevent transcriptional inhibition after IR. As such, it appears that transcriptional inhibition after IR occurs preferentially at highly expressed genes in cycling cells.
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Affiliation(s)
- Zulong Chen
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - Xin Wang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's HospitalBostonUnited States
- Department of Pediatrics, Harvard Medical SchoolBostonUnited States
| | - Xinlei Gao
- Basic and Translational Research Division, Department of Cardiology, Boston Children's HospitalBostonUnited States
- Department of Pediatrics, Harvard Medical SchoolBostonUnited States
| | - Nina Arslanovic
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's HospitalBostonUnited States
- Department of Pediatrics, Harvard Medical SchoolBostonUnited States
| | - Jessica K Tyler
- Weill Cornell Medicine, Department of Pathology and Laboratory MedicineNew YorkUnited States
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15
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Canchi Sistla H, Talluri S, Rajagopal T, Venkatabalasubramanian S, Rao Dunna N. Genomic instability in ovarian cancer: Through the lens of single nucleotide polymorphisms. Clin Chim Acta 2024; 565:119992. [PMID: 39395774 DOI: 10.1016/j.cca.2024.119992] [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: 08/06/2024] [Revised: 10/04/2024] [Accepted: 10/04/2024] [Indexed: 10/14/2024]
Abstract
Ovarian cancer (OC) is the deadliest gynecological malignancy among all female reproductive cancers. It is characterized by high mortality rate and poor prognosis. Genomic instability caused by mutations, single nucleotide polymorphisms (SNPs), copy number variations (CNVs), microsatellite instability (MSI), and chromosomal instability (CIN) are associated with OC predisposition. SNPs, which are highly prevalent in the general population, show a greater relative risk contribution, particularly in sporadic cancers. Understanding OC etiology in terms of genetic basis can increase the use of molecular diagnostics and provide promising approaches for designing novel treatment modalities. This will help deliver personalized medicine to OC patients, which may soon be within reach. Given the pivotal impact of SNPs in cancers, the primary emphasis of this review is to shed light on their prevalence in key caretaker genes that closely monitor genomic integrity, viz., DNA damage response, repair, cell cycle checkpoints, telomerase maintenance, and apoptosis and their clinical implications in OC. We highlight the current challenges faced in different SNP-based studies. Various computational methods and bioinformatic tools employed to predict the functional impact of SNPs have also been comprehensively reviewed concerning OC research. Overall, this review identifies that variants in the DDR and HRR pathways are the most studied, implying their critical role in the disease. Conversely, variants in other pathways, such as NHEJ, MMR, cell cycle, apoptosis, telomere maintenance, and PARP genes, have been explored the least.
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Affiliation(s)
- Harshavardhani Canchi Sistla
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA- Deemed University, Thanjavur 613 401, India
| | - Srikanth Talluri
- Dana Farber Cancer Institute, Boston, MA 02215, USA; Veterans Administration Boston Healthcare System, West Roxbury, MA 02132, USA
| | | | - Sivaramakrishna Venkatabalasubramanian
- Department of Genetic Engineering, Faculty of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur Campus, Chennai 603 203, India
| | - Nageswara Rao Dunna
- Cancer Genomics Laboratory, Department of Biotechnology, School of Chemical and Biotechnology, SASTRA- Deemed University, Thanjavur 613 401, India.
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16
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Tromans J, Zhang B, Golding BT. Unlocking nature's antioxidants: a novel method for synthesising plasmalogens. Org Biomol Chem 2024; 22:7989-7995. [PMID: 39233652 DOI: 10.1039/d4ob01233j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
Abstract
Plasmalogens are glycerophospholipids distinguished by their O-(Z)-vinyl ether at the sn-1 position. These lipids are implicated in several disease states requiring analytical, diagnostic and therapeutic interventions, which demand synthetic availability for a variety of structural types. By deploying the new O-protecting group 1,4-dimethoxynaphthyl-2-methyl ('DIMON') and a new stereospecific method for accessing Z-vinyl ethers, a reproducible, versatile synthetic route to plasmalogens [plasmenyl phosphocholines] has been developed. A key intermediate is (S,Z)-1-((1,4-dimethoxynaphthalen-2-yl)methoxy)-3-(hexadec-1-en-1-yloxy)propan-2-ol, which in principle, permits plasmalogen synthesis 'à la carte' at scale. The methodology compares favourably with all previous synthetic routes by virtue of the very high configurational (>99% Z) and optical purity (>99% ee), including the ability to incorporate polyunsaturated fatty acyl chains (e.g. all Z docosahexaenoic acid) reliably at the sn-2 position.
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Affiliation(s)
- Jay Tromans
- School of Natural and Environmental Science - Chemistry, Newcastle University, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
| | - Bian Zhang
- BiBerChem Research Ltd, The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne, NE4 5BX, UK
| | - Bernard T Golding
- School of Natural and Environmental Science - Chemistry, Newcastle University, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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17
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Chen L, Liu H, Zhan W, Long C, Xu F, Li X, Tian XL, Chen S. Alteration of N-glycosylation of CDON promotes H 2O 2-induced DNA damage in H9c2 cardiomyocytes. Int J Biochem Cell Biol 2024; 176:106671. [PMID: 39389454 DOI: 10.1016/j.biocel.2024.106671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 09/20/2024] [Accepted: 10/01/2024] [Indexed: 10/12/2024]
Abstract
Protein glycosylation is involved in DNA damage. Recently, DNA damage has been connected with the pathogenesis of heart failure. Cell adhesion associated, oncogene regulated (CDON), considered as an N-linked glycoprotein, is a transmembrane receptor for modulating cardiac function. But the role of CDON and its glycosylation in DNA damage remains unknown. In this study, we found that the knockdown of CDON caused DNA double-strand breaks as indicated by an increase in phosphorylated histone H2AX (γH2AX) protein level, immunofluorescent intensity of γH2AX and tail DNA moment in H9c2 cardiomyocytes. Conversely, overexpression of CDON led to decreasing DNA damage induced by hydrogen peroxide (H2O2) and upregulating the expression of genes related to DNA repair pathways-homologous recombination (HR) and non-homologous end joining (NHEJ). Moreover, we expressed nine predicted N-glycosylation site mutants in H9c2 cells prior to treatment with H2O2. The results showed that mutation of N-glycosylation sites (N99Q, N179Q, and N870Q) increased the accumulation of DNA damage and downregulated the expression of HR-related genes, demonstrating that CDON N-glycosylation on DNA damage is site-specific and these specific N-glycan sites may regulate HR repair-related transcript abundance of genes. Our data highlight that N-glycosylation of CDON is critical to cardiomyocyte DNA lesion. It may uncover the potential strategies targeting DNA damage pathway in heart disease.
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Affiliation(s)
- Liping Chen
- Vascular Function Laboratory, Human Aging Research Institute, School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China.
| | - Hongfei Liu
- Vascular Function Laboratory, Human Aging Research Institute, School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China.
| | - Wenxing Zhan
- Vascular Function Laboratory, Human Aging Research Institute, School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China.
| | - Changkun Long
- Vascular Function Laboratory, Human Aging Research Institute, School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China.
| | - Fang Xu
- Epigenetic regulation and Aging, Human Aging Research Institute, School of Life Science, Jiangxi Key Laboratory of Human Aging, Nanchang University, Nanchang 330031, China.
| | - Xueer Li
- Aging and Vascular Diseases, Human Aging Research Institute, School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China.
| | - Xiao-Li Tian
- Aging and Vascular Diseases, Human Aging Research Institute, School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China.
| | - Shenghan Chen
- Vascular Function Laboratory, Human Aging Research Institute, School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Human Aging, Nanchang 330031, China.
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18
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Amirnorouzi M, Karimi A, Daryani NE, Rajaei A, Hashemi M, Alebouyeh M. Negative feedback loop in the activation of non-homologous end joining DNA repair pathway in Helicobacter pylori infected patients with gastritis. Sci Rep 2024; 14:23363. [PMID: 39375425 PMCID: PMC11458588 DOI: 10.1038/s41598-024-74138-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 09/24/2024] [Indexed: 10/09/2024] Open
Abstract
This study aimed to investigate the activation of error-prone DNA repair pathway in response to Helicobacter pylori infection. Relative changes in the expression levels of genes involved in the non-homologous end-joining pathway (NHEJ) in H. pylori-infected (Cases) and non-infected patients (Controls) with chronic gastritis were measured. A significant increase in the relative expression level of TP53, and significant decrease in the relative transcription of lncRNA LINP1 and XRCC5 were detected in the case group. The transcription of Lig4 and XRCC6 was increased in the case group, which was not statistically significant. The Spearman's Correlation Coefficient analysis showed a significant positive-correlation between the transcriptional levels of LINP1 and XRCC4/XRCC5/Lig4, and between XRCC5 and TP53/Lig4 both in the case and control groups. Moreover, a significant positive correlation between LinP1 and XRCC6 in the case, and a significant positive correlation between XRCC4 and Lig4, and a negative correlation between TP53 and LinP1/XRCC4/XRCC5 in the control group was detected. Although a relative difference was detected in transcriptional levels of the NHEJ gene mediators, downregulation of LinP1 in H. pylori-infected patients proposed the activation of a negative feedback loop, which may interfere with the NHEJ activity at the early stages of gastritis.
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Affiliation(s)
- Mohsen Amirnorouzi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ahmadmoeen Karimi
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Naser Ebrahimi Daryani
- Department of Gastroenterology and Hepatology, Imam Khomeini Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Amiratabak Rajaei
- Department of Molecular Biosciences, University of South Florida, Tampa, FL, USA
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Masoud Alebouyeh
- Pediatric Infections Research Center, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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19
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Zalenski N, He Y, Suo Z. Mechanistic Basis for a Single Amino Acid Residue Mutation Causing Human DNA Ligase 1 Deficiency, A Rare Pediatric Disease. J Mol Biol 2024; 436:168813. [PMID: 39374888 DOI: 10.1016/j.jmb.2024.168813] [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: 08/09/2024] [Revised: 09/26/2024] [Accepted: 10/01/2024] [Indexed: 10/09/2024]
Abstract
In mammalian cells, DNA ligase 1 (LIG1) functions as the primary DNA ligase in both genomic replication and single-strand break repair. Several reported mutations in human LIG1, including R305Q, R641L, and R771W, cause LIG1 syndrome, a primary immunodeficiency. While the R641L and R771W mutations, respectively located in the nucleotidyl transferase and oligonucleotide binding domains, have been biochemically characterized and shown to reduce catalytic efficiency, the recently reported R305Q mutation within the DNA binding domain (DBD) remains mechanistically unexplored. The R641L and R771W mutations are known to decrease the catalytic activity of LIG1 by affecting both interdomain interactions and DNA binding during catalysis, without significantly impacting overall DNA affinity. To elucidate the molecular basis of the LIG1 syndrome-causing R305Q mutation, we purified this single-residue mutant protein and investigated its secondary structure, protein stability, DNA binding affinity, and catalytic efficiency. Our findings reveal that the R305Q mutation significantly impairs the function of LIG1 by disrupting the DBD-DNA interactions, leading to a 7-21-fold lower DNA binding affinity and a 33-300-fold reduced catalytic efficiency of LIG1. Additionally, the R305Q mutation slightly decreases LIG1's protein stability by 2 to 3.6 °C, on par with the effect observed previously with either the R641L or R771W mutant. Collectively, our results uncover a new mechanism whereby the R305Q mutation impairs LIG1-catalyzed nicked DNA ligation, resulting in LIG1 syndrome, and highlight the crucial roles of the DBD-DNA interactions in tight DNA binding and efficient LIG1 catalysis.
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Affiliation(s)
- Nikita Zalenski
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA
| | - Yufan He
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA
| | - Zucai Suo
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA.
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20
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Varghese SS, Hernandez-De La Peña AG, Dhawan S. Safeguarding genomic integrity in beta-cells: implications for beta-cell differentiation, growth, and dysfunction. Biochem Soc Trans 2024:BST20231519. [PMID: 39364746 DOI: 10.1042/bst20231519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
The maintenance of optimal glucose levels in the body requires a healthy reserve of the insulin producing pancreatic beta-cells. Depletion of this reserve due to beta-cell dysfunction and death results in development of diabetes. Recent findings highlight unresolved DNA damage as a key contributor to beta-cell defects in diabetes. Beta-cells face various stressors and metabolic challenges throughout life, rendering them susceptible to DNA breaks. The post-mitotic, long-lived phenotype of mature beta-cells further warrants robust maintenance of genomic integrity. Failure to resolve DNA damage during beta-cell development, therefore, can result in an unhealthy reserve of beta-cells and predispose to diabetes. Yet, the molecular mechanisms safeguarding beta-cell genomic integrity remain poorly understood. Here, we focus on the significance of DNA damage in beta-cell homeostasis and postulate how cellular expansion, epigenetic programming, and metabolic shifts during development may impact beta-cell genomic integrity and health. We discuss recent findings demonstrating a physiological role for DNA breaks in modulating transcriptional control in neurons, which share many developmental programs with beta-cells. Finally, we highlight key gaps in our understanding of beta-cell genomic integrity and discuss emerging areas of interest.
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Affiliation(s)
- Sneha S Varghese
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, U.S.A
| | | | - Sangeeta Dhawan
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, U.S.A
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21
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Xhemalçe B, Miller KM, Gromak N. Epitranscriptome in action: RNA modifications in the DNA damage response. Mol Cell 2024; 84:3610-3626. [PMID: 39366350 DOI: 10.1016/j.molcel.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 08/20/2024] [Accepted: 09/05/2024] [Indexed: 10/06/2024]
Abstract
Complex pathways involving the DNA damage response (DDR) contend with cell-intrinsic and -extrinsic sources of DNA damage. DDR mis-regulation results in genome instability that can contribute to aging and diseases including cancer and neurodegeneration. Recent studies have highlighted key roles for several RNA species in the DDR, including short RNAs and RNA/DNA hybrids (R-loops) at DNA break sites, all contributing to efficient DNA repair. RNAs can undergo more than 170 distinct chemical modifications. These RNA modifications have emerged as key orchestrators of the DDR. Here, we highlight the function of enzyme- and non-enzyme-induced RNA modifications in the DDR, with particular emphasis on m6A, m5C, and RNA editing. We also discuss stress-induced RNA damage, including RNA alkylation/oxidation, RNA-protein crosslinks, and UV-induced RNA damage. Uncovering molecular mechanisms that underpin the contribution of RNA modifications to DDR and genome stability will have direct application to disease and approaches for therapeutic intervention.
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Affiliation(s)
- Blerta Xhemalçe
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road OX1 3RE, UK.
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22
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Ryder EL, Nasir N, Durgan AEO, Jenkyn-Bedford M, Tye S, Zhang X, Wu Q. Structural mechanisms of SLF1 interactions with Histone H4 and RAD18 at the stalled replication fork. Nucleic Acids Res 2024:gkae831. [PMID: 39360622 DOI: 10.1093/nar/gkae831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 08/26/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024] Open
Abstract
DNA damage that obstructs the replication machinery poses a significant threat to genome stability. Replication-coupled repair mechanisms safeguard stalled replication forks by coordinating proteins involved in the DNA damage response (DDR) and replication. SLF1 (SMC5-SMC6 complex localization factor 1) is crucial for facilitating the recruitment of the SMC5/6 complex to damage sites through interactions with SLF2, RAD18, and nucleosomes. However, the structural mechanisms of SLF1's interactions are unclear. In this study, we determined the crystal structure of SLF1's ankyrin repeat domain bound to an unmethylated histone H4 tail, illustrating how SLF1 reads nascent nucleosomes. Using structure-based mutagenesis, we confirmed a phosphorylation-dependent interaction necessary for a stable complex between SLF1's tandem BRCA1 C-Terminal domain (tBRCT) and the phosphorylated C-terminal region (S442 and S444) of RAD18. We validated a functional role of conserved phosphate-binding residues in SLF1, and hydrophobic residues in RAD18 that are adjacent to phosphorylation sites, both of which contribute to the strong interaction. Interestingly, we discovered a DNA-binding property of this RAD18-binding interface, providing an additional domain of SLF1 to enhance binding to nucleosomes. Our results provide critical structural insights into SLF1's interactions with post-replicative chromatin and phosphorylation-dependent DDR signalling, enhancing our understanding of SMC5/6 recruitment and/or activity during replication-coupled DNA repair.
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Affiliation(s)
- Emma L Ryder
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nazia Nasir
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Amy E O Durgan
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Michael Jenkyn-Bedford
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CambridgeCB2 1GA, UK
| | - Stephanie Tye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Xiaodong Zhang
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Qian Wu
- Astbury Centre for Structural Molecular Biology, School of Molecular & Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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23
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Siachisumo C, Luzzi S, Aldalaqan S, Hysenaj G, Dalgliesh C, Cheung K, Gazzara MR, Yonchev ID, James K, Kheirollahi Chadegani M, Ehrmann IE, Smith GR, Cockell SJ, Munkley J, Wilson SA, Barash Y, Elliott DJ. An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression. eLife 2024; 12:RP89705. [PMID: 39356106 PMCID: PMC11446547 DOI: 10.7554/elife.89705] [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: 10/03/2024] Open
Abstract
Previously, we showed that the germ cell-specific nuclear protein RBMXL2 represses cryptic splicing patterns during meiosis and is required for male fertility (Ehrmann et al., 2019). Here, we show that in somatic cells the similar yet ubiquitously expressed RBMX protein has similar functions. RBMX regulates a distinct class of exons that exceed the median human exon size. RBMX protein-RNA interactions are enriched within ultra-long exons, particularly within genes involved in genome stability, and repress the selection of cryptic splice sites that would compromise gene function. The RBMX gene is silenced during male meiosis due to sex chromosome inactivation. To test whether RBMXL2 might replace the function of RBMX during meiosis we induced expression of RBMXL2 and the more distantly related RBMY protein in somatic cells, finding each could rescue aberrant patterns of RNA processing caused by RBMX depletion. The C-terminal disordered domain of RBMXL2 is sufficient to rescue proper splicing control after RBMX depletion. Our data indicate that RBMX and RBMXL2 have parallel roles in somatic tissues and the germline that must have been conserved for at least 200 million years of mammalian evolution. We propose RBMX family proteins are particularly important for the splicing inclusion of some ultra-long exons with increased intrinsic susceptibility to cryptic splice site selection.
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Affiliation(s)
- Chileleko Siachisumo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Sara Luzzi
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Saad Aldalaqan
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Gerald Hysenaj
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Caroline Dalgliesh
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Kathleen Cheung
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Matthew R Gazzara
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhildelphiaUnited States
| | - Ivaylo D Yonchev
- School of Biosciences, University of SheffieldSheffieldUnited Kingdom
| | - Katherine James
- School of Computing, Newcastle UniversityNewcastleUnited Kingdom
| | | | - Ingrid E Ehrmann
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Graham R Smith
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Simon J Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Jennifer Munkley
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
| | - Stuart A Wilson
- School of Biosciences, University of SheffieldSheffieldUnited Kingdom
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine, University of PennsylvaniaPhildelphiaUnited States
| | - David J Elliott
- Biosciences Institute, Faculty of Medical Sciences, Newcastle UniversityNewcastleUnited Kingdom
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24
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Niu Q, Zhou C, Li R, Guo J, Qiao S, Chen XX, Zhang G. Proteomic analysis reveals the antiviral effects of baicalin on pseudorabies virus. Int J Biol Macromol 2024; 277:134149. [PMID: 39059539 DOI: 10.1016/j.ijbiomac.2024.134149] [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: 04/15/2024] [Revised: 06/28/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Pseudorabies virus (PRV) poses a significant threat to livestock and even humans. Baicalin, a bioactive flavonoid glycoside with medicinal potential, has been reported to have various biological activities. However, its inhibitory effect on PRV remains poorly understood. In this study, we proved that baicalin effectively inhibits PRV infection. Proteomic analysis revealed that baicalin reduces the expression of 14 viral proteins, which are associated with virus replication, release and immune evasion. Furthermore, the abundance of 116 host proteins was altered by PRV infection, but restored to normal levels after treatment with baicalin. Pathway analysis indicated that baicalin mitigates reactive oxygen species (ROS) and suppresses abnormal mitochondrion by reducing the expression of NFU1 iron‑sulfur cluster scaffold homolog (NFU1) protein induced by PRV. Notably, baicalin also activates the complete coagulation cascade by increasing the expression of coagulation factor III (F3) protein and enhances nucleoplasm by upregulating the expression of solute carrier family 3 member 2 (SLC3A2) and CCAAT enhancer binding protein beta (CEBPB) proteins, contributing to its inhibitory effects on PRV. Our findings implied that baicalin has the potential to be developed as an anti-PRV drug and provide insights into the underlying molecular basis.
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Affiliation(s)
- Qiaoge Niu
- College of Veterinary Medicine, Jilin University, Changchun, China; Institute for Animal Health, Henan Academy of Agricultural Sciences, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Zhengzhou, China
| | - Chuanjie Zhou
- Institute for Animal Health, Henan Academy of Agricultural Sciences, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Zhengzhou, China
| | - Rui Li
- Institute for Animal Health, Henan Academy of Agricultural Sciences, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Zhengzhou, China
| | - Junqing Guo
- Institute for Animal Health, Henan Academy of Agricultural Sciences, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Zhengzhou, China
| | - Songlin Qiao
- Institute for Animal Health, Henan Academy of Agricultural Sciences, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Zhengzhou, China
| | - Xin-Xin Chen
- Institute for Animal Health, Henan Academy of Agricultural Sciences, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Zhengzhou, China.
| | - Gaiping Zhang
- College of Veterinary Medicine, Jilin University, Changchun, China; Institute for Animal Health, Henan Academy of Agricultural Sciences, Key Laboratory of Animal Immunology of the Ministry of Agriculture, Zhengzhou, China; Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Nanjing, China.
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25
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Guo X, Huang T, Xu Y, Zhao J, Huang Y, Zhou Z, Xing B, Li Y, Meng S, Chen X, Yu L, Wang H. Early inhibition of the ATM/p53 pathway reduces the susceptibility to atrial fibrillation and atrial remodeling following acute myocardial infarction. Cell Signal 2024; 122:111322. [PMID: 39067835 DOI: 10.1016/j.cellsig.2024.111322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Atrial fibrillation (AF) emerges as a critical complication following acute myocardial infarction (AMI) and is associated with a significant increased risk of heart failure, stroke and mortality. Ataxia telangiectasia mutated (ATM), a key player in DNA damage repair (DDR), has been implicated in multiple cardiovascular conditions, however, its involvement in the development of AF following AMI remains unexplored. This study seeks to clarify the contribution of the ATM/p53 pathway in the onset of AF post-AMI and to investigate the underlying mechanisms. The rat model of AMI was established by ligating left anterior descending coronary artery in the presence or absence of Ku55933 (an ATM kinase inhibitor, 5 mg/kg/d) treatment. Rats receiving Ku55933 were further divided into the early administration group (administered on days 1, 2, 4, and 7 post-AMI) and the late administration group (administered on days 8, 9, 11 and 14 post-AMI). RNA-sequencing was performed 14 days post-operation. In vitro, H2O2-challenged HL-1 atrial muscle cells were utilized to evaluate the potential effects of different ATM inhibition schemes, including earlier, middle, and late periods of intervention. Fourteen days post-AMI injury, the animals exhibited significantly increased AF inducibility, exacerbated atrial electrical/structural remodeling, reduced ventricular function and exacerbated atrial DNA damage, as evidenced by enhanced ATM/p53 signaling as well as γH2AX level. These effects were partially consistent with the enrichment results of bioinformatics analysis. Notably, the deleterious effects were ameliorated by early, but not late, administration of Ku55933. Mechanistically, inhibition of ATM signaling successfully suppressed atrial NLRP3 inflammasome-mediated pyroptotic pathway. Additionally, the results were validated in the in vitro experiments demonstrating that early inhibition of Ku55933 not only attenuated cellular ATM/p53 signaling, but also mitigated inflammatory response by reducing NLRP3 activation. Collectively, hyperactivation of ATM/p53 contributed to the pathogenesis of AF following AMI. Early intervention with ATM inhibitors substantially mitigated AF susceptibility and atrial electrical/structural remodeling, highlighting a novel therapeutic avenue against cardiac arrhythmia following AMI.
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Affiliation(s)
- Xiaodong Guo
- Graduate School of Dalian Medical University, Dalian 116000, Liaoning Province, China; State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Tao Huang
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Yinli Xu
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Jikai Zhao
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Yuting Huang
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Zijun Zhou
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Bo Xing
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Yao Li
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Shan Meng
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Xin Chen
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China
| | - Liming Yu
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China.
| | - Huishan Wang
- Graduate School of Dalian Medical University, Dalian 116000, Liaoning Province, China; State Key Laboratory of Frigid Zone Cardiovascular Disease, Department of Cardiovascular Surgery, General Hospital of Northern Theater Command, Shenyang 110016, Liaoning Province, China.
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26
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Splichal RC, Chen K, Walton SP, Chan C. The Role of Endoplasmic Reticulum Stress on Reducing Recombinant Protein Production in Mammalian Cells. Biochem Eng J 2024; 210:109434. [PMID: 39220803 PMCID: PMC11360842 DOI: 10.1016/j.bej.2024.109434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Therapeutic recombinant protein production relies on industrial scale culture of mammalian cells to produce active proteins in quantities sufficient for clinical use. The combination of stresses from industrial cell culture environment and recombinant protein production can overwhelm the protein synthesis machinery in the endoplasmic reticulum (ER). This leads to a buildup of improperly folded proteins which induces ER stress. Cells respond to ER stress by activating the Unfolded Protein Response (UPR). To restore proteostasis, ER sensor proteins reduce global protein synthesis and increase chaperone protein synthesis, and if that is insufficient the proteins are degraded. If proteostasis is still not restored, apoptosis is initiated. Increasing evidence suggests crosstalk between ER proteostasis and DNA damage repair (DDR) pathways. External factors (e.g., metabolites) from the cellular environment as well as internal factors (e.g., transgene copy number) can impact genome stability. Failure to maintain genome integrity reduces cell viability and in turn protein production. This review focuses on the association between ER stress and processes that affect protein production and secretion. The processes mediated by ER stress, including inhibition of global protein translation, chaperone protein production, degradation of misfolded proteins, DNA repair, and protein secretion, impact recombinant protein production. Recombinant protein production can be reduced by ER stress through increased autophagy and protein degradation, reduced protein secretion, and reduced DDR response.
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Affiliation(s)
- R. Chauncey Splichal
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
| | - Kevin Chen
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
| | - S. Patrick Walton
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
| | - Christina Chan
- Department of Chemical Engineering and Materials Science, Michigan State University, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, MI, USA
- Department of Computer Science and Engineering, Michigan State University, MI, USA
- Institute for Quantitative Health Science and Engineering, Division of Medical Devices, Michigan State University, MI, USA
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27
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Ajit K, Gullerova M. From silence to symphony: transcriptional repression and recovery in response to DNA damage. Transcription 2024:1-15. [PMID: 39353089 DOI: 10.1080/21541264.2024.2406717] [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: 08/15/2024] [Revised: 09/10/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
Genotoxic stress resulting from DNA damage is resolved through a signaling cascade known as the DNA Damage Response (DDR). The repair of damaged DNA is essential for cell survival, often requiring the DDR to attenuate other cellular processes such as the cell cycle, DNA replication, and transcription of genes not involved in DDR. The complex relationship between DDR and transcription has only recently been investigated. Transcription can facilitate the DDR in response to double-strand breaks (DSBs) and stimulate nucleotide excision repair (NER). However, transcription may need to be reduced to prevent potential interference with the repair machinery. In this review, we discuss various mechanisms that regulate transcription repression in response to different types of DNA damage, categorizing them by their range and duration of effect. Finally, we explore various models of transcription recovery following DNA damage-induced repression.
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Affiliation(s)
- Kamal Ajit
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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28
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Lee YJ, Lee SY, Kim S, Kim SH, Lee SH, Park S, Kim JJ, Kim DW, Kim H. REXO5 promotes genomic integrity through regulating R-loop using its exonuclease activity. Leukemia 2024; 38:2150-2161. [PMID: 39080354 PMCID: PMC11436357 DOI: 10.1038/s41375-024-02362-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 09/29/2024]
Abstract
Chronic myeloid leukemia (CML), caused by BCR::ABL1 fusion gene, is known to regulate disease progression by altering the expression of genes. However, the molecular mechanisms underlying these changes are largely unknown. In this study, we identified RNA Exonuclease 5 (REXO5/LOC81691) as a novel gene with elevated mRNA expression levels in chronic myeloid leukemia (CML) patients. Additionally, using the REXO5 knockout (KO) K562 cell lines, we revealed a novel role for REXO5 in the DNA damage response (DDR). Compared to wild-type (WT) cells, REXO5 KO cells showed an accumulation of R-loops and increased DNA damage. We demonstrated that REXO5 translocates to sites of DNA damage through its RNA recognition motif (RRM) and selectively binds to R loops. Interestingly, we identified that REXO5 regulates R-loop levels by degrading mRNA within R-loop using its exonuclease domain. REXO5 KO showed ATR-CHK1 activation. Collectively, we demonstrated that REXO5 plays a key role in the physiological control of R-loops using its exonuclease domain. These findings may provide novel insights into how REXO5 expression changes contribute to CML pathogenesis.
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Affiliation(s)
- Ye Jin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Seo Yun Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea
| | - Soomi Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Soo-Hyun Kim
- Department of Hematology, Hematology Center, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu, South Korea
- Leukemia Omics Research Institute, Eulji University Uijeongbu Campus, Uijeongbu, South Korea
| | - Soo Hyeon Lee
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea
| | - Sungho Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jae Jin Kim
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Republic of Korea.
| | - Dong-Wook Kim
- Department of Hematology, Hematology Center, Uijeongbu Eulji Medical Center, Eulji University, Uijeongbu, South Korea.
- Leukemia Omics Research Institute, Eulji University Uijeongbu Campus, Uijeongbu, South Korea.
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
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29
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Stoyanov M, Martinikova AS, Matejkova K, Horackova K, Zemankova P, Burdova K, Zemanova Z, Kleiblova P, Kleibl Z, Macurek L. PPM1D activity promotes cellular transformation by preventing senescence and cell death. Oncogene 2024; 43:3081-3093. [PMID: 39237765 PMCID: PMC11473410 DOI: 10.1038/s41388-024-03149-3] [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: 05/02/2024] [Revised: 08/23/2024] [Accepted: 08/29/2024] [Indexed: 09/07/2024]
Abstract
Cell cycle checkpoints, oncogene-induced senescence and programmed cell death represent intrinsic barriers to tumorigenesis. Protein phosphatase magnesium-dependent 1 (PPM1D) is a negative regulator of the tumour suppressor p53 and has been implicated in termination of the DNA damage response. Here, we addressed the consequences of increased PPM1D activity resulting from the gain-of-function truncating mutations in exon 6 of the PPM1D. We show that while control cells permanently exit the cell cycle and reside in senescence in the presence of DNA damage caused by ionising radiation or replication stress induced by the active RAS oncogene, RPE1-hTERT and BJ-hTERT cells carrying the truncated PPM1D continue proliferation in the presence of DNA damage, form micronuclei and accumulate genomic rearrangements revealed by karyotyping. Further, we show that increased PPM1D activity promotes cell growth in the soft agar and formation of tumours in xenograft models. Finally, expression profiling of the transformed clones revealed dysregulation of several oncogenic and tumour suppressor pathways. Our data support the oncogenic potential of PPM1D in the context of exposure to ionising radiation and oncogene-induced replication stress.
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Affiliation(s)
- Miroslav Stoyanov
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Andra S Martinikova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katerina Matejkova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Klara Horackova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Zemankova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Kamila Burdova
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Zemanova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Petra Kleiblova
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Zdenek Kleibl
- Institute of Medical Biochemistry and Laboratory Diagnostics, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Libor Macurek
- Cancer Cell Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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30
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Ejaz U, Dou Z, Yao PY, Wang Z, Liu X, Yao X. Chromothripsis: an emerging crossroad from aberrant mitosis to therapeutic opportunities. J Mol Cell Biol 2024; 16:mjae016. [PMID: 38710586 PMCID: PMC11487160 DOI: 10.1093/jmcb/mjae016] [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: 09/19/2023] [Revised: 02/23/2024] [Accepted: 05/04/2024] [Indexed: 05/08/2024] Open
Abstract
Chromothripsis, a type of complex chromosomal rearrangement originally known as chromoanagenesis, has been a subject of extensive investigation due to its potential role in various diseases, particularly cancer. Chromothripsis involves the rapid acquisition of tens to hundreds of structural rearrangements within a short period, leading to complex alterations in one or a few chromosomes. This phenomenon is triggered by chromosome mis-segregation during mitosis. Errors in accurate chromosome segregation lead to formation of aberrant structural entities such as micronuclei or chromatin bridges. The association between chromothripsis and cancer has attracted significant interest, with potential implications for tumorigenesis and disease prognosis. This review aims to explore the intricate mechanisms and consequences of chromothripsis, with a specific focus on its association with mitotic perturbations. Herein, we discuss a comprehensive analysis of crucial molecular entities and pathways, exploring the intricate roles of the CIP2A-TOPBP1 complex, micronuclei formation, chromatin bridge processing, DNA damage repair, and mitotic checkpoints. Moreover, the review will highlight recent advancements in identifying potential therapeutic targets and the underlying molecular mechanisms associated with chromothripsis, paving the way for future therapeutic interventions in various diseases.
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Affiliation(s)
- Umer Ejaz
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
- Anhui Key Laboratory for Chemical Biology, Hefei National Science Center for Inter-disciplinary Sciences, Hefei 230027, China
| | - Zhen Dou
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
- Anhui Key Laboratory for Chemical Biology, Hefei National Science Center for Inter-disciplinary Sciences, Hefei 230027, China
| | - Phil Y Yao
- University of California San Diego School of Medicine, San Diego, CA 92103, USA
| | - Zhikai Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
- Anhui Key Laboratory for Chemical Biology, Hefei National Science Center for Inter-disciplinary Sciences, Hefei 230027, China
| | - Xing Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
- Anhui Key Laboratory for Chemical Biology, Hefei National Science Center for Inter-disciplinary Sciences, Hefei 230027, China
| | - Xuebiao Yao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, University of Science and Technology of China School of Life Sciences, Hefei 230027, China
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Tassone G, Maramai S, Paolino M, Lamponi S, Poggialini F, Dreassi E, Petricci E, Alcaro S, Pozzi C, Romeo I. Exploiting the bile acid binding protein as transporter of a Cholic Acid/Mirin bioconjugate for potential applications in liver cancer therapy. Sci Rep 2024; 14:22514. [PMID: 39341955 PMCID: PMC11439058 DOI: 10.1038/s41598-024-73636-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 09/19/2024] [Indexed: 10/01/2024] Open
Abstract
Bioconjugation is one of the most promising strategies to improve drug delivery, especially in cancer therapy. Biomolecules such as bile acids (BAs) have been intensively explored as carriers, due to their peculiar physicochemical properties and biocompatibility. BAs trafficking is regulated by intracellular lipid-binding proteins and their transport in the liver can be studied using chicken liver Bile Acid-Binding Proteins (cL-BABPs) as a reference model. Therefore, we conceived the idea of developing a BA-conjugate with Mirin, an exonuclease inhibitor of Mre11 endowed with different anticancer activities, to direct its transport to the liver. Following computational analysis of various BAs in complex with cL-BABP, we identified cholic acid (CA) as the most promising candidate as carrier, leading to the synthesis of a novel bioconjugate named CA-M11. As predicted by computational data and confirmed by X-ray crystallographic studies, CA-M11 was able to accommodate into the binding pocket of BABP. Hence, it can enter BAs trafficking in the hepatic compartment and here release Mirin. The effect of CA-M11, evaluated in combination with varying concentrations of Doxorubicin on HepG2 cell line, demonstrated a significant increase in cell mortality compared to the use of the cytotoxic drug or Mirin alone, thus highlighting chemo-sensitizing properties. The promising results regarding plasma stability for CA-M11 validate its potential as a valuable agent or adjuvant for hepatic cancer therapy.
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Affiliation(s)
- Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Samuele Maramai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy.
| | - Marco Paolino
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Stefania Lamponi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Federica Poggialini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Elena Dreassi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Elena Petricci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Stefano Alcaro
- Department of Health Science, Università "Magna Graecia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100, Catanzaro, Italy
- Net4Science Academic Spin-Off, Università "Magna Graecia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, 53100, Siena, Italy.
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Via Sacconi 6, 50019, Sesto Fiorentino (FI), Italy.
| | - Isabella Romeo
- Department of Health Science, Università "Magna Graecia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100, Catanzaro, Italy
- Net4Science Academic Spin-Off, Università "Magna Graecia" di Catanzaro, Campus "S. Venuta", Viale Europa, 88100, Catanzaro, Italy
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Hernández-Carralero E, Quinet G, Freire R. ATXN3: a multifunctional protein involved in the polyglutamine disease spinocerebellar ataxia type 3. Expert Rev Mol Med 2024; 26:e19. [PMID: 39320846 PMCID: PMC11440613 DOI: 10.1017/erm.2024.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/24/2024] [Accepted: 03/15/2024] [Indexed: 09/26/2024]
Abstract
ATXN3 is a ubiquitin hydrolase (or deubiquitinase, DUB), product of the ATXN3 gene, ubiquitously expressed in various cell types including peripheral and neuronal tissues and involved in several cellular pathways. Importantly, the expansion of the CAG trinucleotides within the ATXN3 gene leads to an expanded polyglutamine domain in the encoded protein, which has been associated with the onset of the spinocerebellar ataxia type 3, also known as Machado-Joseph disease, the most common dominantly inherited ataxia worldwide. ATXN3 has therefore been under intensive investigation for decades. In this review, we summarize the main functions of ATXN3 in proteostasis, DNA repair and transcriptional regulation, as well as the emerging role in regulating chromatin structure. The mentioned molecular functions of ATXN3 are also reviewed in the context of the pathological expanded form of ATXN3.
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Affiliation(s)
- Esperanza Hernández-Carralero
- Fundación Canaria Instituto de Investigación Sanitaria de Canarias (FIISC), Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Grégoire Quinet
- Fundación Canaria Instituto de Investigación Sanitaria de Canarias (FIISC), Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
| | - Raimundo Freire
- Fundación Canaria Instituto de Investigación Sanitaria de Canarias (FIISC), Unidad de Investigación, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Centro de Investigaciones Biomédicas de Canarias, Facultad de Medicina, Campus Ciencias de la Salud, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
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33
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Huang Y, Chen S, Yao N, Lin S, Zhang J, Xu C, Wu C, Chen G, Zhou D. Molecular mechanism of PARP inhibitor resistance. Oncoscience 2024; 11:69-91. [PMID: 39318358 PMCID: PMC11420906 DOI: 10.18632/oncoscience.610] [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: 07/18/2024] [Accepted: 09/10/2024] [Indexed: 09/26/2024] Open
Abstract
Poly (ADP-ribose) polymerases (PARP) inhibitors (PARPi) are the first-approved anticancer drug designed to exploit synthetic lethality. PARPi selectively kill cancer cells with homologous recombination repair deficiency (HRD), as a result, PARPi are widely employed to treated BRCA1/2-mutant ovarian, breast, pancreatic and prostate cancers. Currently, four PARPi including Olaparib, Rucaparib, Niraparib, and Talazoparib have been developed and greatly improved clinical outcomes in cancer patients. However, accumulating evidences suggest that required or de novo resistance emerged. In this review, we discuss the molecular mechanisms leading to PARPi resistances and review the potential strategies to overcome PARPi resistance.
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Affiliation(s)
- Yi Huang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P.R. China
- Equal contribution
| | - Simin Chen
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P.R. China
- Equal contribution
| | - Nan Yao
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P.R. China
- Equal contribution
| | - Shikai Lin
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P.R. China
| | - Junyi Zhang
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P.R. China
| | - Chengrui Xu
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P.R. China
| | - Chenxuan Wu
- School of Public Health, Nanjing Medical University, Nanjing 210029, P.R. China
| | - Guo Chen
- School of Biopharmacy, China Pharmaceutical University, Nanjing 211198, P.R. China
| | - Danyang Zhou
- Department of Respiratory, Nanjing First Hospital, China Pharmaceutical University, Nanjing 210012, Jiangsu, P.R. China
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34
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Jun CS, Lee W. Development of Lasing Silica Microsphere for High-Speed DNA Molecular Detection. SENSORS (BASEL, SWITZERLAND) 2024; 24:6088. [PMID: 39338832 PMCID: PMC11435820 DOI: 10.3390/s24186088] [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: 08/08/2024] [Revised: 09/06/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024]
Abstract
Laser and molecular detection techniques that have been used to overcome the limitations of fluorescent DNA labeling have presented new challenges. To address some of these challenges, we developed a DNA laser that uses a solid-state silica microsphere as a ring resonator and a site for DNA-binding reactions, as well as a platform to detect and sequence target DNA molecules. We detected target DNA using laser emission from a DNA-labeling dye and a developed solid-state silica microsphere ring resonator. The microsphere was sensitive; a single base mismatch in the DNA resulted in the absence of an optical signal. As each individual microsphere can be utilized as a parallel DNA analysis chamber, this optical digital detection scheme allows for high-throughput and rapid analysis. More importantly, the solid-state DNA laser is free from deformation, which guarantees stable lasing characteristics, and can be manipulated freely outside the solution. Thus, this promising advanced DNA laser scheme can be implemented on platforms other than optofluidic chips.
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Affiliation(s)
- Chan Seok Jun
- Department of Material Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Wonsuk Lee
- Nanophotonics Research Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
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35
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Li Y, Jiang Y, Yan H, Qin Z, Peng Y, Lv D, Zhang H. Global isonicotinylome analysis identified SMAD3 isonicotinylation promotes liver cancer cell epithelial-mesenchymal transition and invasion. iScience 2024; 27:110775. [PMID: 39286495 PMCID: PMC11403401 DOI: 10.1016/j.isci.2024.110775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/02/2024] [Accepted: 08/16/2024] [Indexed: 09/19/2024] Open
Abstract
Histone lysine isonicotinylation (Kinic) induced by isoniazid (INH) was recently identified as a post-translational modification in cells. However, global cellular non-histone proteins Kinic remains unclear. Using proteomic technology, we identified 11,442 Kinic sites across 2,792 proteins and demonstrated that Kinic of non-histone proteins is involved in multiple function pathways. Non-histone proteins Kinic can be regulated by isonicotinyl-transferases, including CBP and Tip60, and deisonicotinylases, including HDAC8 and HDAC6. In particular, the Kinic of poly (ADP-ribose) (PAR) polymerase 1 (PARP1) can be catalyzed by CBP and deisonicotinylation can be catalyzed by HDAC8. Tip60 and HDAC6 are isonicotinyl-transferase and the deisonicotinylase of SMAD3, respectively. Importantly, we found the K378inic of SMAD3 increases its phosphorylation, activates TGFβ pathway, and promotes liver cancer cells migration and invasion. In conclusion, our study demonstrated non-histone proteins Kinic occur extensively in cells and plays an important role in regulation of various cellular functions, including cancer progression.
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Affiliation(s)
- Yixiao Li
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Yuhan Jiang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Haoyi Yan
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Ziheng Qin
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Yidi Peng
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Danyu Lv
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
| | - Hongquan Zhang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing 100191, China
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36
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Chen L, Liu M, Li Y, Guan Y, Ruan J, Mao Z, Wang W, Yang HQ, Guo T. Arabidopsis cryptochromes interact with SOG1 to promote the repair of DNA double-strand breaks. Biochem Biophys Res Commun 2024; 724:150233. [PMID: 38865814 DOI: 10.1016/j.bbrc.2024.150233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
Cryptochromes (CRYs) are blue light (BL) photoreceptors to regulate a variety of physiological processes including DNA double-strand break (DSB) repair. SUPPRESSOR OF GAMMA RADIATION 1 (SOG1) acts as the central transcription factor of DNA damage response (DDR) to induce the transcription of downstream genes, including DSB repair-related genes BRCA1 and RAD51. Whether CRYs regulate DSB repair by directly modulating SOG1 is unknown. Here, we demonstrate that CRYs physically interact with SOG1. Disruption of CRYs and SOG1 leads to increased sensitivity to DSBs and reduced DSB repair-related genes' expression under BL. Moreover, we found that CRY1 enhances SOG1's transcription activation of DSB repair-related gene BRCA1. These results suggest that the mechanism by which CRYs promote DSB repair involves positive regulation of SOG1's transcription of its target genes, which is likely mediated by CRYs-SOG1 interaction.
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Affiliation(s)
- Li Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Minqing Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yupeng Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yan Guan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jiaqi Ruan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhilei Mao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wenxiu Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Hong-Quan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Tongtong Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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37
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Rossetti GG, Dommann N, Karamichali A, Dionellis VS, Asensio Aldave A, Yarahmadov T, Rodriguez-Carballo E, Keogh A, Candinas D, Stroka D, Halazonetis TD. In vivo DNA replication dynamics unveil aging-dependent replication stress. Cell 2024:S0092-8674(24)00963-2. [PMID: 39293447 DOI: 10.1016/j.cell.2024.08.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 03/16/2024] [Accepted: 08/19/2024] [Indexed: 09/20/2024]
Abstract
The genome duplication program is affected by multiple factors in vivo, including developmental cues, genotoxic stress, and aging. Here, we monitored DNA replication initiation dynamics in regenerating livers of young and old mice after partial hepatectomy to investigate the impact of aging. In young mice, the origin firing sites were well defined; the majority were located 10-50 kb upstream or downstream of expressed genes, and their position on the genome was conserved in human cells. Old mice displayed the same replication initiation sites, but origin firing was inefficient and accompanied by a replication stress response. Inhibitors of the ATR checkpoint kinase fully restored origin firing efficiency in the old mice but at the expense of an inflammatory response and without significantly enhancing the fraction of hepatocytes entering the cell cycle. These findings unveil aging-dependent replication stress and a crucial role of ATR in mitigating the stress-associated inflammation, a hallmark of aging.
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Affiliation(s)
- Giacomo G Rossetti
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 1205, Switzerland
| | - Noëlle Dommann
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Angeliki Karamichali
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 1205, Switzerland
| | - Vasilis S Dionellis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 1205, Switzerland
| | - Ainhoa Asensio Aldave
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Tural Yarahmadov
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Adrian Keogh
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Daniel Candinas
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Deborah Stroka
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland; Department for BioMedical Research, University of Bern, Bern, Switzerland.
| | - Thanos D Halazonetis
- Department of Molecular and Cellular Biology, University of Geneva, Geneva 1205, Switzerland.
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38
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Gál Z, Boukoura S, Oxe KC, Badawi S, Nieto B, Korsholm LM, Geisler SB, Dulina E, Rasmussen AV, Dahl C, Lv W, Xu H, Pan X, Arampatzis S, Stratou DE, Galanos P, Lin L, Guldberg P, Bartek J, Luo Y, Larsen DH. Hyper-recombination in ribosomal DNA is driven by long-range resection-independent RAD51 accumulation. Nat Commun 2024; 15:7797. [PMID: 39242676 PMCID: PMC11379943 DOI: 10.1038/s41467-024-52189-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 08/28/2024] [Indexed: 09/09/2024] Open
Abstract
Ribosomal DNA (rDNA) encodes the ribosomal RNA genes and represents an intrinsically unstable genomic region. However, the underlying mechanisms and implications for genome integrity remain elusive. Here, we use Bloom syndrome (BS), a rare genetic disease characterized by DNA repair defects and hyper-unstable rDNA, as a model to investigate the mechanisms leading to rDNA instability. We find that in Bloom helicase (BLM) proficient cells, the homologous recombination (HR) pathway in rDNA resembles that in nuclear chromatin; it is initiated by resection, replication protein A (RPA) loading and BRCA2-dependent RAD51 filament formation. However, BLM deficiency compromises RPA-loading and BRCA1/2 recruitment to rDNA, but not RAD51 accumulation. RAD51 accumulates at rDNA despite depletion of long-range resection nucleases and rDNA damage results in micronuclei when BLM is absent. In summary, our findings indicate that rDNA is permissive to RAD51 accumulation in the absence of BLM, leading to micronucleation and potentially global genomic instability.
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Affiliation(s)
- Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200, Copenhagen, Denmark
| | - Stavroula Boukoura
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Kezia Catharina Oxe
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Sara Badawi
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Lea Milling Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | | | - Christina Dahl
- Molecular Diagnostics, Danish Cancer Institute, 2100, Copenhagen, Denmark
| | - Wei Lv
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
| | - Huixin Xu
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
| | - Xiaoguang Pan
- Department of Biology, University of Copenhagen, Copenhagen N, DK-2200, Denmark
| | | | | | - Panagiotis Galanos
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark
| | - Per Guldberg
- Molecular Diagnostics, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, 5000, Denmark
| | - Jiri Bartek
- Genome Integrity Group, Danish Cancer Institute, 2100, Copenhagen, Denmark
- Karolinska Institutet, Department of Medical Biochemistry and Biophysics, Division of Genome Biology, Science for Life Laboratory, Stockholm, Sweden
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, 8000, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, 8200, Denmark
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, 2100, Copenhagen, Denmark.
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Schou KB, Mandacaru S, Tahir M, Tom N, Nilsson AS, Andersen JS, Tiberti M, Papaleo E, Bartek J. Exploring the structural landscape of DNA maintenance proteins. Nat Commun 2024; 15:7748. [PMID: 39237506 PMCID: PMC11377751 DOI: 10.1038/s41467-024-49983-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 06/25/2024] [Indexed: 09/07/2024] Open
Abstract
Evolutionary annotation of genome maintenance (GM) proteins has conventionally been established by remote relationships within protein sequence databases. However, often no significant relationship can be established. Highly sensitive approaches to attain remote homologies based on iterative profile-to-profile methods have been developed. Still, these methods have not been systematically applied in the evolutionary annotation of GM proteins. Here, by applying profile-to-profile models, we systematically survey the repertoire of GM proteins from bacteria to man. We identify multiple GM protein candidates and annotate domains in numerous established GM proteins, among other PARP, OB-fold, Macro, TUDOR, SAP, BRCT, KU, MYB (SANT), and nuclease domains. We experimentally validate OB-fold and MIS18 (Yippee) domains in SPIDR and FAM72 protein families, respectively. Our results indicate that, surprisingly, despite the immense interest and long-term research efforts, the repertoire of genome stability caretakers is still not fully appreciated.
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Affiliation(s)
- Kenneth Bødkter Schou
- Genome Integrity, Danish Cancer Institute, Danish Cancer Society, Strandboulevarden 49, 2100, Copenhagen, Denmark.
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Laboratory, Karolinska Institute, Solna, 171 77, Sweden.
| | - Samuel Mandacaru
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Muhammad Tahir
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Nikola Tom
- Lipidomics Core Facility, Danish Cancer Institute (DCI), DK-2100, Copenhagen, Denmark
| | - Ann-Sofie Nilsson
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Laboratory, Karolinska Institute, Solna, 171 77, Sweden
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Jiri Bartek
- Genome Integrity, Danish Cancer Institute, Danish Cancer Society, Strandboulevarden 49, 2100, Copenhagen, Denmark.
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Science for Laboratory, Karolinska Institute, Solna, 171 77, Sweden.
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40
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Wu Y, Sun C. Salidroside prevents cadmium chloride-induced DNA damage in human fetal lung fibroblasts. J Trace Elem Med Biol 2024; 86:127521. [PMID: 39243731 DOI: 10.1016/j.jtemb.2024.127521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/28/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Cadmium (Cd) is an environmental pollutant and a heavy metal known for its genotoxic effects, which can lead to cancer and other related diseases. Preventing Cd-induced genotoxicity is crucial; however, there is limited research on this topic. Salidroside (SAL), a phenylpropanoid glycoside isolated from Rhodiola rosea L., is a popular medicinal compound with several health benefits. Nevertheless, its therapeutic effect on Cd-induced genotoxicity remains unexplored. METHODS Human fetal lung fibroblasts were treated with 20 μM Cd2+ (CdCl2) for 12 h and 5-20 μM SAL was used to test the anti-DNA damage effect. DNA damage was evaluated using γH2AX expression and the alkaline comet assay. Intracellular reactive oxygen species (ROS) levels were measured using flow cytometry. RESULTS Exposure to 20 μM Cd2+ for 12 h induced significant DNA damage in human fetal lung fibroblasts, and this effect was notably attenuated by SAL treatment. SAL treatment did not decrease ROS levels in cells treated with Cd2+. CONCLUSION SAL effectively prevented Cd2+-induced DNA damage in human fetal lung fibroblasts. However, the underlying mechanism requires further investigation.
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Affiliation(s)
- Yufei Wu
- Anglo-Chinese School (International), Singapore
| | - Chuan Sun
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Zhejiang Hospital, Hangzhou 310030, China.
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41
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Lewin TD, Liao IJY, Luo YJ. Annelid Comparative Genomics and the Evolution of Massive Lineage-Specific Genome Rearrangement in Bilaterians. Mol Biol Evol 2024; 41:msae172. [PMID: 39141777 PMCID: PMC11371463 DOI: 10.1093/molbev/msae172] [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: 05/15/2024] [Revised: 08/05/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024] Open
Abstract
The organization of genomes into chromosomes is critical for processes such as genetic recombination, environmental adaptation, and speciation. All animals with bilateral symmetry inherited a genome structure from their last common ancestor that has been highly conserved in some taxa but seemingly unconstrained in others. However, the evolutionary forces driving these differences and the processes by which they emerge have remained largely uncharacterized. Here, we analyze genome organization across the phylum Annelida using 23 chromosome-level annelid genomes. We find that while many annelid lineages have maintained the conserved bilaterian genome structure, the Clitellata, a group containing leeches and earthworms, possesses completely scrambled genomes. We develop a rearrangement index to quantify the extent of genome structure evolution and show that, compared to the last common ancestor of bilaterians, leeches and earthworms have among the most highly rearranged genomes of any currently sampled species. We further show that bilaterian genomes can be classified into two distinct categories-high and low rearrangement-largely influenced by the presence or absence, respectively, of chromosome fission events. Our findings demonstrate that animal genome structure can be highly variable within a phylum and reveal that genome rearrangement can occur both in a gradual, stepwise fashion, or rapid, all-encompassing changes over short evolutionary timescales.
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Affiliation(s)
- Thomas D Lewin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Yi-Jyun Luo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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42
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King A, Reichl PI, Metson JS, Parker R, Munro D, Oliveira C, Sommerova L, Becker JR, Biggs D, Preece C, Davies B, Chapman JR. Shieldin and CST co-orchestrate DNA polymerase-dependent tailed-end joining reactions independently of 53BP1-governed repair pathway choice. Nat Struct Mol Biol 2024:10.1038/s41594-024-01381-9. [PMID: 39227718 DOI: 10.1038/s41594-024-01381-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 08/01/2024] [Indexed: 09/05/2024]
Abstract
Tumor suppressor p53-binding protein 1 (53BP1) regulates DNA end joining in lymphocytes, diversifying immune antigen receptors. This involves nucleosome-bound 53BP1 at DNA double-stranded breaks (DSBs) recruiting Rap1-interacting factor 1 homolog (RIF1) and shieldin, a poorly understood DNA-binding complex. The 53BP1-RIF1-shieldin axis is pathological in BRCA1-mutated cancers, blocking homologous recombination (HR) and driving illegitimate nonhomologous end joining (NHEJ). However, how this axis regulates DNA end joining and HR suppression remains unresolved. We investigated shieldin and its interplay with the Ctc1-Stn1-Ten1 (CST) complex, which was recently implicated downstream of 53BP1. Immunophenotypically, mice lacking shieldin or CST are equivalent, with class-switch recombination coreliant on both complexes. Ataxia-telangiectasia mutated kinase-dependent DNA damage signaling underpins this cooperation, inducing physical interactions between these complexes that reveal shieldin as a DSB-responsive CST adaptor. Furthermore, DNA polymerase ζ functions downstream of shieldin, establishing DNA fill-in synthesis as the physiological function of shieldin-CST. Lastly, we demonstrate that 53BP1 suppresses HR and promotes NHEJ in BRCA1-deficient mice and cells independently of shieldin. These findings showcase the versatility of the 53BP1 pathway, achieved through the collaboration of chromatin-bound 53BP1 complexes and DNA end-processing effector proteins.
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Affiliation(s)
- Ashleigh King
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Pia I Reichl
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jean S Metson
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Robert Parker
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniella Munro
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Catarina Oliveira
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Lucia Sommerova
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Jordan R Becker
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Biggs
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Chris Preece
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Francis Crick Institute, London, UK
| | - J Ross Chapman
- Genome Integrity laboratory, Medical Research Council Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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43
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Gardner LL, Thompson SJ, O'Connor JD, McMahon SJ. Modelling radiobiology. Phys Med Biol 2024; 69:18TR01. [PMID: 39159658 DOI: 10.1088/1361-6560/ad70f0] [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: 04/25/2024] [Accepted: 08/19/2024] [Indexed: 08/21/2024]
Abstract
Radiotherapy has played an essential role in cancer treatment for over a century, and remains one of the best-studied methods of cancer treatment. Because of its close links with the physical sciences, it has been the subject of extensive quantitative mathematical modelling, but a complete understanding of the mechanisms of radiotherapy has remained elusive. In part this is because of the complexity and range of scales involved in radiotherapy-from physical radiation interactions occurring over nanometres to evolution of patient responses over months and years. This review presents the current status and ongoing research in modelling radiotherapy responses across these scales, including basic physical mechanisms of DNA damage, the immediate biological responses this triggers, and genetic- and patient-level determinants of response. Finally, some of the major challenges in this field and potential avenues for future improvements are also discussed.
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Affiliation(s)
- Lydia L Gardner
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - Shannon J Thompson
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
| | - John D O'Connor
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
- Ulster University School of Engineering, York Street, Belfast BT15 1AP, United Kingdom
| | - Stephen J McMahon
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast BT9 7AE, United Kingdom
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44
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Al-Rahahleh RQ, Sobol RW. Poly-ADP-ribosylation dynamics, signaling, and analysis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024. [PMID: 39221603 DOI: 10.1002/em.22623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 08/15/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
ADP-ribosylation is a reversible post-translational modification that plays a role as a signaling mechanism in various cellular processes. This modification is characterized by its structural diversity, highly dynamic nature, and short half-life. Hence, it is tightly regulated at many levels by cellular factors that fine-tune its formation, downstream signaling, and degradation that together impacts cellular outcomes. Poly-ADP-ribosylation is an essential signaling mechanism in the DNA damage response that mediates the recruitment of DNA repair factors to sites of DNA damage via their poly-ADP-ribose (PAR)-binding domains (PBDs). PAR readers, encoding PBDs, convey the PAR signal to mediate cellular outcomes that in some cases can be dictated by PAR structural diversity. Several PBD families have been identified, each with variable PAR-binding affinity and specificity, that also recognize and bind to distinct parts of the PAR chain. PARylation signaling has emerged as an attractive target for the treatment of specific cancer types, as the inhibition of PAR formation or degradation can selectively eliminate cancer cells with specific DNA repair defects and can enhance radiation or chemotherapy response. In this review, we summarize the key players of poly-ADP-ribosylation and its regulation and highlight PBDs as tools for studying PARylation dynamics and the expanding potential to target PARylation signaling in cancer treatment.
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Affiliation(s)
- Rasha Q Al-Rahahleh
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Legorreta Cancer Center, Brown University, Providence, Rhode Island, USA
| | - Robert W Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Legorreta Cancer Center, Brown University, Providence, Rhode Island, USA
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Barnieh FM, Morais GR, Loadman PM, Falconer RA, El‐Khamisy SF. Hypoxia-Responsive Prodrug of ATR Inhibitor, AZD6738, Selectively Eradicates Treatment-Resistant Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2403831. [PMID: 38976561 PMCID: PMC11425890 DOI: 10.1002/advs.202403831] [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: 04/11/2024] [Revised: 05/31/2024] [Indexed: 07/10/2024]
Abstract
Targeted therapy remains the future of anti-cancer drug development, owing to the lack of specificity of current treatments which lead to damage in healthy normal tissues. ATR inhibitors have in recent times demonstrated promising clinical potential, and are currently being evaluated in the clinic. However, despite the considerable optimism for clinical success of these inhibitors, reports of associated normal tissues toxicities remain a concern and can compromise their utility. Here, ICT10336 is reported, a newly developed hypoxia-responsive prodrug of ATR inhibitor, AZD6738, which is hypoxia-activated and specifically releases AZD6738 only in hypoxic conditions, in vitro. This hypoxia-selective release of AZD6738 inhibited ATR activation (T1989 and S428 phosphorylation) and subsequently abrogated HIF1a-mediated adaptation of hypoxic cancers cells, thus selectively inducing cell death in 2D and 3D cancer models. Importantly, in normal tissues, ICT10336 is demonstrated to be metabolically stable and less toxic to normal cells than its active parent agent, AZD6738. In addition, ICT10336 exhibited a superior and efficient multicellular penetration ability in 3D tumor models, and selectively eradicated cells at the hypoxic core compared to AZD6738. In summary, the preclinical data demonstrate a new strategy of tumor-targeted delivery of ATR inhibitors with significant potential of enhancing the therapeutic index.
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Affiliation(s)
- Francis M. Barnieh
- Institute of Cancer TherapeuticsFaculty of Life SciencesUniversity of BradfordRichmond RoadBradfordBD7 1DPUnited Kingdom
| | - Goreti Ribeiro Morais
- Institute of Cancer TherapeuticsFaculty of Life SciencesUniversity of BradfordRichmond RoadBradfordBD7 1DPUnited Kingdom
| | - Paul M. Loadman
- Institute of Cancer TherapeuticsFaculty of Life SciencesUniversity of BradfordRichmond RoadBradfordBD7 1DPUnited Kingdom
| | - Robert A. Falconer
- Institute of Cancer TherapeuticsFaculty of Life SciencesUniversity of BradfordRichmond RoadBradfordBD7 1DPUnited Kingdom
| | - Sherif F. El‐Khamisy
- Institute of Cancer TherapeuticsFaculty of Life SciencesUniversity of BradfordRichmond RoadBradfordBD7 1DPUnited Kingdom
- School of Biosciences, the Healthy Lifespan Institute and the Institute of NeuroscienceUniversity of SheffieldSheffieldS10 2TNUnited Kingdom
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Chen W, Ma C, Wang M, Huang X, Chen X, Xu Z, Huang W, Wang R, Zheng Z, Fang J, Shen Y, Zhao D, Zhang H. BaP/BPDE suppresses homologous recombination repair in human trophoblast cells to induce miscarriage: The roles of lnc-HZ08. ENVIRONMENT INTERNATIONAL 2024; 191:108975. [PMID: 39190976 DOI: 10.1016/j.envint.2024.108975] [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: 02/05/2024] [Revised: 07/17/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
Benzo(a)pyrene (BaP) or benzo (a) pyrene 7,8-dihydrodiol-9,10-epoxide (BPDE) exposure causes trophoblast cell dysfunctions and induces miscarriage, which is generally epigenetically regulated. Homologous recombination (HR) repair of DNA double strand break (DSB) plays a crucial role in maintenance of genetic stability and cell normal functions. However, whether BaP/BPDE might suppress HR repair in human trophoblast cells to induce miscarriage, as well as its epigenetic regulatory mechanism, is largely unclear. In this study, we find that BaP/BPDE suppresses HR repair of DSB in trophoblast cells and eventually induces miscarriage by up-regulating lnc-HZ08. In mechanism, lnc-HZ08 (1) down-regulates the expression levels of FOXA1 (forkhead box A1) and thus suppresses FOXA1-mediated mRNA transcription of BRCA1 (Breast cancer susceptibility gene 1) and CtIP (CtBP-interacting protein), (2) impairs BRCA1 and CtIP protein interactions by competitive binding with CtIP through lnc-HZ08-1 fragment, and also (3) suppresses BRCA1-mediated CtIP ubiquitination without affecting CtIP stability, three of which eventually suppress HR repair in human trophoblast cells. Supplement with murine Ctip could efficiently restore (i.e. increase) HR repair and alleviate miscarriage in BaP-exposed mouse model. Collectively, this study not only reveals the association and causality among BaP/BPDE exposure, the defective HR repair, and miscarriage, but also discovers novel mechanism in lnc-HZ08-regulated BRCA1/CtIP-mediated HR repair, bridging epigenetic regulation and genetic instability and also providing an efficient approach for treatment against BaP/BPDE-induced unexplained miscarriage.
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Affiliation(s)
- Weina Chen
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; Department of Endocrinology, Translational Research of Diabetes Key Laboratory of Chongqing Education Commission of China, the Second Affiliated Hospital of Army Medical University, Chongqing 400037, China
| | - Chenglong Ma
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Manli Wang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Xinying Huang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China; Jimei District Center for Disease Control and Prevention, Xiamen, Fujian, 361022, China
| | - Xueyu Chen
- Department of Reproductive Medicine, Affiliated Shenzhen maternity and child healthcare hospital, Southern Medical University, Shenzhen 518033, China
| | - Zhongyan Xu
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Wenxin Huang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Rong Wang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Zhaodian Zheng
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Jing Fang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Yanqiu Shen
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
| | - Depeng Zhao
- Department of Reproductive Medicine, Affiliated Shenzhen maternity and child healthcare hospital, Southern Medical University, Shenzhen 518033, China.
| | - Huidong Zhang
- Research Center for Environment and Female Reproductive Health, the Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China.
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Vitantonio AT, Dimovasili C, Mortazavi F, Vaughan KL, Mattison JA, Rosene DL. Long-term calorie restriction reduces oxidative DNA damage to oligodendroglia and promotes homeostatic microglia in the aging monkey brain. Neurobiol Aging 2024; 141:1-13. [PMID: 38788462 DOI: 10.1016/j.neurobiolaging.2024.05.005] [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: 04/11/2024] [Revised: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]
Abstract
Calorie restriction (CR) is a robust intervention that can slow biological aging and extend lifespan. In the brain, terminally differentiated neurons and glia accumulate oxidative damage with age, reducing their optimal function. We investigated if CR could reduce oxidative DNA damage to white matter oligodendrocytes and microglia. This study utilized post-mortem brain tissue from rhesus monkeys that died after decades on a 30 % reduced calorie diet. We found that CR subjects had significantly fewer cells with oxidative damage within the corpus callosum and the cingulum bundle. Oligodendrocytes specifically showed the greatest response to CR with a robust reduction in DNA damage. Additionally, we observed alterations in microglia morphology with CR subjects having a higher proportion of ramified, homeostatic microglia and fewer pro-inflammatory, hypertrophic microglia relative to controls. Furthermore, we determined that the observed attenuation in damaged DNA occurs primarily within mitochondria. Overall, these data suggest that long-term CR can reduce oxidative DNA damage and offer a neuroprotective effect in a cell-type-specific manner in the aging monkey brain.
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Affiliation(s)
- Ana T Vitantonio
- Boston University Chobanian and Avedisian School of Medicine, Department of Pharmacology, Physiology, and Biophysics, 700 Albany St., Room 308, Boston, MA 02118, USA; Boston University Chobanian and Avedisian School of Medicine, Department of Anatomy & Neurobiology, 72 East Concord St, Room L1004, Boston, MA 02118, USA.
| | - Christina Dimovasili
- Boston University Chobanian and Avedisian School of Medicine, Department of Anatomy & Neurobiology, 72 East Concord St, Room L1004, Boston, MA 02118, USA
| | - Farzad Mortazavi
- Boston University Chobanian and Avedisian School of Medicine, Department of Anatomy & Neurobiology, 72 East Concord St, Room L1004, Boston, MA 02118, USA
| | - Kelli L Vaughan
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA
| | - Douglas L Rosene
- Boston University Chobanian and Avedisian School of Medicine, Department of Anatomy & Neurobiology, 72 East Concord St, Room L1004, Boston, MA 02118, USA; Boston University, Center for Systems Neuroscience, 610 Commonwealth Ave., 7th Floor, Boston, MA 02215, USA
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48
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Liu C, Han X, Zhang S, Huang M, Guo B, Zhao Z, Yang S, Jin J, Pu W, Yu H. The role of NCAPH in cancer treatment. Cell Signal 2024; 121:111262. [PMID: 38901722 DOI: 10.1016/j.cellsig.2024.111262] [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: 04/11/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Many solid tumors frequently overexpress Non-SMC Condensin I Complex Subunit H (NCAPH), and new studies suggest that NCAPH may be a target gene for clinical cancer therapy. Numerous investigations have shown that a variety of transcription factors, including as MYBL2, FOXP3, GATA3, and OTC1, can stimulate the transcription of NCAPH. Additionally, NCAPH stimulates many oncogenic signaling pathways, such as β-Catenin/PD-L1, PI3K/AKT/SGK3, MEK/ERK, AURKB/AKT/mTOR, PI3K/PDK1/AKT, and Chk1/Chk2. Tumor immune microenvironment modification and tumor growth, apoptosis, metastasis, stemness, and treatment resistance all depend on these signals. NCAPH has the ability to form complexes with other proteins that are involved in glycolysis, DNA damage repair, and chromatin remodeling. This review indicates that NCAPH expression in most malignant tumors is associated with poor prognosis and low recurrence-free survival.
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Affiliation(s)
- Caiyan Liu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xiao Han
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Siqi Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Manru Huang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Bin Guo
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Zixuan Zhao
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shenshen Yang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Jun Jin
- International Education College, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Weiling Pu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
| | - Haiyang Yu
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China.
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49
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Lee JH. Oxidative stress and the multifaceted roles of ATM in maintaining cellular redox homeostasis. Redox Biol 2024; 75:103269. [PMID: 39018798 PMCID: PMC11301354 DOI: 10.1016/j.redox.2024.103269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/12/2024] [Accepted: 07/13/2024] [Indexed: 07/19/2024] Open
Abstract
The ataxia telangiectasia mutated (ATM) protein kinase is best known as a master regulator of the DNA damage response. However, accumulating evidence has unveiled an equally vital function for ATM in sensing oxidative stress and orchestrating cellular antioxidant defenses to maintain redox homeostasis. ATM can be activated through a non-canonical pathway involving intermolecular disulfide crosslinking of the kinase dimers, distinct from its canonical activation by DNA double-strand breaks. Structural studies have elucidated the conformational changes that allow ATM to switch into an active redox-sensing state upon oxidation. Notably, loss of ATM function results in elevated reactive oxygen species (ROS) levels, altered antioxidant profiles, and mitochondrial dysfunction across multiple cell types and tissues. This oxidative stress arising from ATM deficiency has been implicated as a central driver of the neurodegenerative phenotypes in ataxia-telangiectasia (A-T) patients, potentially through mechanisms involving oxidative DNA damage, PARP hyperactivation, and widespread protein aggregation. Moreover, defective ATM oxidation sensing disrupts transcriptional programs and RNA metabolism, with detrimental impacts on neuronal homeostasis. Significantly, antioxidant therapy can ameliorate cellular and organismal abnormalities in various ATM-deficient models. This review synthesizes recent advances illuminating the multifaceted roles of ATM in preserving redox balance and mitigating oxidative insults, providing a unifying paradigm for understanding the complex pathogenesis of A-T disease.
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Affiliation(s)
- Ji-Hoon Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Lee JH. Targeting the ATM pathway in cancer: Opportunities, challenges and personalized therapeutic strategies. Cancer Treat Rev 2024; 129:102808. [PMID: 39106770 DOI: 10.1016/j.ctrv.2024.102808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/09/2024]
Abstract
Ataxia telangiectasia mutated (ATM) kinase plays a pivotal role in orchestrating the DNA damage response, maintaining genomic stability, and regulating various cellular processes. This review provides a comprehensive analysis of ATM's structure, activation mechanisms, and various functions in cancer development, progression, and treatment. I discuss ATM's dual nature as both a tumor suppressor and potential promoter of cancer cell survival in certain contexts. The article explores the complex signaling pathways mediated by ATM, its interactions with other DNA repair mechanisms, and its influence on cell cycle checkpoints, apoptosis, and metabolism. I examine the clinical implications of ATM alterations, including their impact on cancer predisposition, prognosis, and treatment response. The review highlights recent advances in ATM-targeted therapies, discussing ongoing clinical trials of ATM inhibitors and their potential in combination with other treatment modalities. I also address the challenges in developing effective biomarkers for ATM activity and patient selection strategies for personalized cancer therapy. Finally, I outline future research directions, emphasizing the need for refined biomarker development, optimized combination therapies, and strategies to overcome potential resistance mechanisms. This comprehensive overview underscores the critical importance of ATM in cancer biology and its emerging potential as a therapeutic target in precision oncology.
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Affiliation(s)
- Ji-Hoon Lee
- Department of Biological Sciences, Research Center of Ecomimetics, Chonnam National University, Gwangju 61186, Republic of Korea.
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