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Sridalla K, Woodhouse MV, Hu J, Scheer J, Ferlez B, Crickard JB. The translocation activity of Rad54 reduces crossover outcomes during homologous recombination. Nucleic Acids Res 2024; 52:7031-7048. [PMID: 38828785 PMCID: PMC11229335 DOI: 10.1093/nar/gkae474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that requires the selection of an appropriate DNA sequence to facilitate repair. Selection occurs during a homology search that must be executed rapidly and with high fidelity. Failure to efficiently perform the homology search can result in complex intermediates that generate genomic rearrangements, a hallmark of human cancers. Rad54 is an ATP dependent DNA motor protein that functions during the homology search by regulating the recombinase Rad51. How this regulation reduces genomic exchanges is currently unknown. To better understand how Rad54 can reduce these outcomes, we evaluated several amino acid mutations in Rad54 that were identified in the COSMIC database. COSMIC is a collection of amino acid mutations identified in human cancers. These substitutions led to reduced Rad54 function and the discovery of a conserved motif in Rad54. Through genetic, biochemical and single-molecule approaches, we show that disruption of this motif leads to failure in stabilizing early strand invasion intermediates, causing increased crossovers between homologous chromosomes. Our study also suggests that the translocation rate of Rad54 is a determinant in balancing genetic exchange. The latch domain's conservation implies an interaction likely fundamental to eukaryotic biology.
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Affiliation(s)
- Krishay Sridalla
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Mitchell V Woodhouse
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jingyi Hu
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jessica Scheer
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Bryan Ferlez
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - J Brooks Crickard
- Deparment of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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2
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Hayman TJ. Rethinking the use of germline CHEK2 mutation as a marker for PARP inhibitor sensitivity. JNCI Cancer Spectr 2024; 8:pkae045. [PMID: 38950525 PMCID: PMC11216723 DOI: 10.1093/jncics/pkae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 06/02/2024] [Indexed: 07/03/2024] Open
Affiliation(s)
- Thomas J Hayman
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
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3
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Leu YL, Cheng SF, Wang TH, Feng CH, Chen YJ, Hsieh YC, Lan YH, Chen CC. Increasing DNA damage sensitivity through corylin-mediated inhibition of homologous recombination. Biomed Pharmacother 2024; 176:116864. [PMID: 38865847 DOI: 10.1016/j.biopha.2024.116864] [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: 03/24/2024] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND DNA repair allows the survival of cancer cells. Therefore, the development of DNA repair inhibitors is a critical need for sensitizing cancers to chemoradiation. Sae2CtIP has specific functions in initiating DNA end resection, as well as coordinating cell cycle checkpoints, and it also greatly interacts with the DDR at different levels. RESULTS In this study, we demonstrated that corylin, a potential sensitizer, causes deficiencies in DNA repair and DNA damage checkpoints in yeast cells. More specifically, corylin increases DNA damage sensitivity through the Sae2-dependent pathway and impairs the activation of Mec1-Ddc2, Rad53-p and γ-H2A. In breast cancer cells, corylin increases apoptosis and reduces proliferation following Dox treatment by inhibiting CtIP. Xenograft assays showed that treatment with corylin combined with Dox significantly reduced tumor growth in vivo. CONCLUSIONS Our findings herein delineate the mechanisms of action of corylin in regulating DNA repair and indicate that corylin has potential long-term clinical utility as a DDR inhibitor.
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Affiliation(s)
- Yann-Lii Leu
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC
| | - Shu-Fang Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City, Taiwan, ROC; Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Tong-Hong Wang
- Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC
| | - Chun-Hao Feng
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Yu-Ju Chen
- Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC
| | - Yi-Cheng Hsieh
- Office of the Texas State Chemist, Texas A&M AgriLife Research, Texas A&M University System, College Station, TX 77843, USA
| | - Yu-Hsuan Lan
- Department of Pharmacy, College of Pharmacy, China Medical University, No.100, Section 1, Jingmao Rd., Beitun Dist., Taichung City 406040, Taiwan, ROC.
| | - Chin-Chuan Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City, Taiwan, ROC; Graduate Institute of Natural products, College of Medicine, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Healthy Aging Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Taoyuan City 33302, Taiwan, ROC; Biobank, Chang Gung Memorial Hospital, No. 5, Fuxing St., Guishan Dist., Taoyuan City 33305, Taiwan, ROC.
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4
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Zhang Y, Sun Q, Liang Y, Yang X, Wang H, Song S, Wang Y, Feng Y. FAM20A: a potential diagnostic biomarker for lung squamous cell carcinoma. Front Immunol 2024; 15:1424197. [PMID: 38983866 PMCID: PMC11231076 DOI: 10.3389/fimmu.2024.1424197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 06/04/2024] [Indexed: 07/11/2024] Open
Abstract
Background Lung squamous cell carcinoma (LUSC) ranks among the carcinomas with the highest incidence and dismal survival rates, suffering from a lack of effective therapeutic strategies. Consequently, biomarkers facilitating early diagnosis of LUSC could significantly enhance patient survival. This study aims to identify novel biomarkers for LUSC. Methods Utilizing the TCGA, GTEx, and CGGA databases, we focused on the gene encoding Family with Sequence Similarity 20, Member A (FAM20A) across various cancers. We then corroborated these bioinformatic predictions with clinical samples. A range of analytical tools, including Kaplan-Meier, MethSurv database, Wilcoxon rank-sum, Kruskal-Wallis tests, Gene Set Enrichment Analysis, and TIMER database, were employed to assess the diagnostic and prognostic value of FAM20A in LUSC. These tools also helped evaluate immune cell infiltration, immune checkpoint genes, DNA repair-related genes, DNA methylation, and tumor-related pathways. Results FAM20A expression was found to be significantly reduced in LUSC, correlating with lower survival rates. It exhibited a negative correlation with key proteins in DNA repair signaling pathways, potentially contributing to LUSC's radiotherapy resistance. Additionally, FAM20A showed a positive correlation with immune checkpoints like CTLA-4, indicating potential heightened sensitivity to immunotherapies targeting these checkpoints. Conclusion FAM20A emerges as a promising diagnostic and prognostic biomarker for LUSC, offering potential clinical applications.
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Affiliation(s)
- Yalin Zhang
- Center for Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Qin Sun
- Center for Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yangbo Liang
- Center for Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Xian Yang
- Center for Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Hailian Wang
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Siyuan Song
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
| | - Yi Wang
- Center for Critical Care Medicine, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Yong Feng
- Department of Otorhinolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
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5
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Zhu H, Wang L, Wang Y, Jiang X, Qin Q, Song M, Huang Q. Directed-evolution mutations enhance DNA-binding affinity and protein stability of the adenine base editor ABE8e. Cell Mol Life Sci 2024; 81:257. [PMID: 38874784 DOI: 10.1007/s00018-024-05263-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 06/15/2024]
Abstract
Adenine base editors (ABEs), consisting of CRISPR Cas nickase and deaminase, can chemically convert the A:T base pair to G:C. ABE8e, an evolved variant of the base editor ABE7.10, contains eight directed evolution mutations in its deaminase TadA8e that significantly increase its base editing activity. However, the functional implications of these mutations remain unclear. Here, we combined molecular dynamics (MD) simulations and experimental measurements to investigate the role of the directed-evolution mutations in the base editing catalysis. MD simulations showed that the DNA-binding affinity of TadA8e is higher than that of the original deaminase TadA7.10 in ABE7.10 and is mainly driven by electrostatic interactions. The directed-evolution mutations increase the positive charge density in the DNA-binding region, thereby enhancing the electrostatic attraction of TadA8e to DNA. We identified R111, N119 and N167 as the key mutations for the enhanced DNA binding and confirmed them by microscale thermophoresis (MST) and in vivo reversion mutation experiments. Unexpectedly, we also found that the directed mutations improved the thermal stability of TadA8e by ~ 12 °C (Tm, melting temperature) and that of ABE8e by ~ 9 °C, respectively. Our results demonstrate that the directed-evolution mutations improve the substrate-binding ability and protein stability of ABE8e, thus providing a rational basis for further editing optimisation of the system.
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Affiliation(s)
- Haixia Zhu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinyi Jiang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qin Qin
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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6
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Chen R, Zhao MJ, Li YM, Liu AH, Wang RX, Mei YC, Chen X, Du HN. Di- and tri-methylation of histone H3K36 play distinct roles in DNA double-strand break repair. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1089-1105. [PMID: 38842635 DOI: 10.1007/s11427-024-2543-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 06/07/2024]
Abstract
Histone H3 Lys36 (H3K36) methylation and its associated modifiers are crucial for DNA double-strand break (DSB) repair, but the mechanism governing whether and how different H3K36 methylation forms impact repair pathways is unclear. Here, we unveil the distinct roles of H3K36 dimethylation (H3K36me2) and H3K36 trimethylation (H3K36me3) in DSB repair via non-homologous end joining (NHEJ) or homologous recombination (HR). Yeast cells lacking H3K36me2 or H3K36me3 exhibit reduced NHEJ or HR efficiency. yKu70 and Rfa1 bind H3K36me2- or H3K36me3-modified peptides and chromatin, respectively. Disrupting these interactions impairs yKu70 and Rfa1 recruitment to damaged H3K36me2- or H3K36me3-rich loci, increasing DNA damage sensitivity and decreasing repair efficiency. Conversely, H3K36me2-enriched intergenic regions and H3K36me3-enriched gene bodies independently recruit yKu70 or Rfa1 under DSB stress. Importantly, human KU70 and RPA1, the homologs of yKu70 and Rfa1, exclusively associate with H3K36me2 and H3K36me3 in a conserved manner. These findings provide valuable insights into how H3K36me2 and H3K36me3 regulate distinct DSB repair pathways, highlighting H3K36 methylation as a critical element in the choice of DSB repair pathway.
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Affiliation(s)
- Runfa Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Meng-Jie Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Yu-Min Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Ao-Hui Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Ru-Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Yu-Chao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China.
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7
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Shi Y, Tan Q, Yang C, Li S, Li Y, He B, Xie H, Duan X, Chen L. Establishment of a Cleavage-Based Single-Plasmid Dual-Luciferase Surrogate Reporter for the Cleavage Efficiency Evaluation of CRISPR-Cas12a Systems and Its Primary Application. CRISPR J 2024; 7:156-167. [PMID: 38922054 DOI: 10.1089/crispr.2024.0038] [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: 06/27/2024] Open
Abstract
CRISPR-Cas technology is a widely utilized gene-editing tool that involves gRNA-guided sequence recognition and Cas nuclease-mediated cleavage. The design and evaluation of gRNA are essential for enhancing CRISPR/Cas editing efficiency. Various assays such as single-strand annealing, in vitro cleavage, and T7 endonuclease I (T7EI) are commonly used to assess gRNA-mediated Cas protein cleavage activity. In this study, a firefly luciferase and Renilla luciferase co-expressed and a cleavage-based single-plasmid dual-luciferase surrogate reporter was built to evaluate the gRNA-mediated Cas12a cleavage efficiency. The cleavage activities of CRISPR-Cas12a can be quantitatively determined by the recovery degree of firefly luciferase activity. The cleavage efficiency of CRISPR-Cas12a can be quantitatively measured by the recovery of firefly luciferase activity. By using this system, the cleavage efficiency of CRISPR-Cas12a on hepatitis B virus (HBV)/D expression plasmid was evaluated, revealing a negative correlation between gRNA cleavage efficiency and HBV gene expression measured using an enzyme-linked immunosorbent assay. This simple, efficient, and quantifiable system only requires the dual-luciferase vector and CRISPR-Cas12a vector, making it a valuable tool for selecting effective gRNAs for gene editing.
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Affiliation(s)
- Yaoqiang Shi
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Qi Tan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Chunhui Yang
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Shilin Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Yujia Li
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Baoren He
- The Joint Laboratory on Transfusion-Transmitted Diseases (TTDs) Between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Nanning, China
| | - He Xie
- The Hospital of Xidian Group, Xi'an, China
| | - Xiaoqiong Duan
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Limin Chen
- Provincial Key Laboratory for Transfusion-Transmitted Infectious Diseases, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
- The Joint Laboratory on Transfusion-Transmitted Diseases (TTDs) Between Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Nanning Blood Center, Nanning Blood Center, Nanning, China
- The Hospital of Xidian Group, Xi'an, China
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8
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Zhong C, Wang H, Yuan X, He Y, Cong J, Yang R, Ma W, Gao L, Gao C, Cui Y, Wu J, Tan R, Pu D. The crucial role of HFM1 in regulating FUS ubiquitination and localization for oocyte meiosis prophase I progression in mice. Biol Res 2024; 57:36. [PMID: 38822414 PMCID: PMC11140966 DOI: 10.1186/s40659-024-00518-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/16/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Helicase for meiosis 1 (HFM1), a putative DNA helicase expressed in germ-line cells, has been reported to be closely associated with premature ovarian insufficiency (POI). However, the underlying molecular mechanism has not been clearly elucidated. The aim of this study was to investigate the function of HFM1 in the first meiotic prophase of mouse oocytes. RESULTS The results suggested that the deficiency of HFM1 resulting in increased apoptosis and depletion of oocytes in mice, while the oocytes were arrested in the pachytene stage of the first meiotic prophase. In addition, impaired DNA double-strand break repair and disrupted synapsis were observed in the absence of HFM1. Further investigation revealed that knockout of HFM1 promoted ubiquitination and degradation of FUS protein mediated by FBXW11. Additionally, the depletion of HFM1 altered the intranuclear localization of FUS and regulated meiotic- and oocyte development-related genes in oocytes by modulating the expression of BRCA1. CONCLUSIONS These findings elaborated that the critical role of HFM1 in orchestrating the regulation of DNA double-strand break repair and synapsis to ensure meiosis procession and primordial follicle formation. This study provided insights into the pathogenesis of POI and highlighted the importance of HFM1 in maintaining proper meiotic function in mouse oocytes.
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Affiliation(s)
- Chenyi Zhong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Center of Reproduction and Genetics, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215002, China
| | - Huiyuan Wang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Xiong Yuan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Yuheng He
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Jing Cong
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Rui Yang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Wenjie Ma
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Li Gao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Chao Gao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Yugui Cui
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China
| | - Jie Wu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China.
| | - Rongrong Tan
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China.
| | - Danhua Pu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University/Jiangsu Province Hospital/Jiangsu Women and Children Health Hospital, Nanjing, 210036, China.
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9
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Mikhova M, Goff NJ, Janovič T, Heyza JR, Meek K, Schmidt JC. Single-molecule imaging reveals the kinetics of non-homologous end-joining in living cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.22.546088. [PMID: 38826211 PMCID: PMC11142080 DOI: 10.1101/2023.06.22.546088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Non-homologous end joining (NHEJ) is the predominant pathway that repairs DNA double-stranded breaks (DSBs) in vertebrates. However, due to challenges in detecting DSBs in living cells, the repair capacity of the NHEJ pathway is unknown. The DNA termini of many DSBs must be processed to allow ligation while minimizing genetic changes that result from break repair. Emerging models propose that DNA termini are first synapsed ~115Å apart in one of several long-range synaptic complexes before transitioning into a short-range synaptic complex that juxtaposes DNA ends to facilitate ligation. The transition from long-range to short-range synaptic complexes involves both conformational and compositional changes of the NHEJ factors bound to the DNA break. Importantly, it is unclear how NHEJ proceeds in vivo because of the challenges involved in analyzing recruitment of NHEJ factors to DSBs over time in living cells. Here, we develop a new approach to study the temporal and compositional dynamics of NHEJ complexes using live cell single-molecule imaging. Our results provide direct evidence for stepwise maturation of the NHEJ complex, pinpoint key regulatory steps in NHEJ progression, and define the overall repair capacity NHEJ in living cells.
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Affiliation(s)
- Mariia Mikhova
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Noah J. Goff
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing
- Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing
| | - Tomáš Janovič
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Joshua R. Heyza
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Katheryn Meek
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing
- Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing
| | - Jens C. Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing
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Nicolle R, Boutaud L, Loeuillet L, Talhi N, Grotto S, Bourgon N, Feresin A, Coussement A, Barrois M, Beaujard MP, Rambaud T, Razavi F, Attié-Bitach T. Expanding the phenotypic spectrum of LIG4 pathogenic variations: neuro-histopathological description of 4 fetuses with stenosis of the aqueduct. Eur J Hum Genet 2024; 32:545-549. [PMID: 38351293 PMCID: PMC11061308 DOI: 10.1038/s41431-024-01558-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/16/2024] [Accepted: 01/30/2024] [Indexed: 05/02/2024] Open
Abstract
Severe ventriculomegaly is a rare congenital brain defect, usually detected in utero, of poor neurodevelopmental prognosis. This ventricular enlargement can be the consequence of different mechanisms: either by a disruption of the cerebrospinal fluid circulation or abnormalities of its production/absorption. The aqueduct stenosis is one of the most frequent causes of obstructive ventriculomegaly, however, fewer than 10 genes have been linked to this condition and molecular bases remain often unknown. We report here 4 fetuses from 2 unrelated families presenting with ventriculomegaly at prenatal ultra-sonography as well as an aqueduct stenosis and skeletal abnormalities as revealed by fetal autopsy. Genome sequencing identified biallelic pathogenic variations in LIG4, a DNA-repair gene responsible for the LIG4 syndrome which associates a wide range of clinical manifestations including developmental delay, microcephaly, short stature, radiation hypersensitivity and immunodeficiency. Thus, not only this report expands the phenotype spectrum of LIG4-related disorders, adding ventriculomegaly due to aqueduct stenosis, but we also provide the first neuropathological description of fetuses carrying LIG4 pathogenic biallelic variations.
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Affiliation(s)
- Romain Nicolle
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
| | - Lucile Boutaud
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Genetics and development of the cerebral cortex, F-75015, Paris, France
| | - Laurence Loeuillet
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
| | - Naima Talhi
- Centre Hospitalier Intercommunal de Créteil, Service d'anatomie pathologique, Université Paris-Est Créteil, 94000, Créteil, France
| | - Sarah Grotto
- AP-HP, Hôpital Trousseau, UF de génétique clinique, Centre de Référence anomalies du développement et syndromes malformatifs, Paris, France
| | - Nicolas Bourgon
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Genetics and development of the cerebral cortex, F-75015, Paris, France
- AP-HP, Hôpital Necker-Enfants Malades, Department of Obstetrics and Fetal Medicine, Paris, France
| | - Agnese Feresin
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
- University of Trieste, Department of medicine, Surgery and Health Sciences, Trieste, Italy
| | - Aurélie Coussement
- AP-HP, Hôpital Cochin, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies de Système et d'Organes, Paris, France
| | - Mathilde Barrois
- AP-HP, Hôpital Cochin, Service de Maternité Port-Royal, Paris, France
| | - Marie-Paule Beaujard
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
| | - Thomas Rambaud
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France
| | - Férechté Razavi
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Genetics and development of the cerebral cortex, F-75015, Paris, France
| | - Tania Attié-Bitach
- AP-HP, Hôpital Necker-Enfants Malades, Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Paris, France.
- Université Paris Cité, INSERM UMR 1163, Imagine Institute, Genetics and development of the cerebral cortex, F-75015, Paris, France.
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France.
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11
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Lu H, Toyoda JH, Wise SS, Browning CL, Speer RM, Croom-Pérez TJ, Bolt A, Meaza I, Wise JP. A whale of a tale: whale cells evade the driving mechanism for hexavalent chromium-induced chromosome instability. Toxicol Sci 2024; 199:49-62. [PMID: 38539048 PMCID: PMC11057468 DOI: 10.1093/toxsci/kfae030] [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: 04/26/2024] Open
Abstract
Chromosome instability, a hallmark of lung cancer, is a driving mechanism for hexavalent chromium [Cr(VI)] carcinogenesis in humans. Cr(VI) induces structural and numerical chromosome instability in human lung cells by inducing DNA double-strand breaks and inhibiting homologous recombination repair and causing spindle assembly checkpoint (SAC) bypass and centrosome amplification. Great whales are long-lived species with long-term exposures to Cr(VI) and accumulate Cr in their tissue, but exhibit a low incidence of cancer. Data show Cr(VI) induces fewer chromosome aberrations in whale cells after acute Cr(VI) exposure suggesting whale cells can evade Cr(VI)-induced chromosome instability. However, it is unknown if whales can evade Cr(VI)-induced chromosome instability. Thus, we tested the hypothesis that whale cells resist Cr(VI)-induced loss of homologous recombination repair activity and increased SAC bypass and centrosome amplification. We found Cr(VI) induces similar amounts of DNA double-strand breaks after acute (24 h) and prolonged (120 h) exposures in whale lung cells, but does not inhibit homologous recombination repair, SAC bypass, or centrosome amplification, and does not induce chromosome instability. These data indicate whale lung cells resist Cr(VI)-induced chromosome instability, the major driver for Cr(VI) carcinogenesis at a cellular level, consistent with observations that whales are resistant to cancer.
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Affiliation(s)
- Haiyan Lu
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, USA
| | - Jennifer H Toyoda
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, USA
| | - Sandra S Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, USA
| | - Cynthia L Browning
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, USA
| | - Rachel M Speer
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, USA
| | - Tayler J Croom-Pérez
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, USA
| | - Alicia Bolt
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - Idoia Meaza
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, USA
| | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky 40292, USA
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12
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Gu Y, Yang Y, Kou C, Peng Y, Yang W, Zhang J, Jin H, Han X, Wang Y, Shen X. Classical and novel properties of Holliday junction resolvase SynRuvC from Synechocystis sp. PCC6803. Front Microbiol 2024; 15:1362880. [PMID: 38699476 PMCID: PMC11063404 DOI: 10.3389/fmicb.2024.1362880] [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: 01/22/2024] [Accepted: 03/29/2024] [Indexed: 05/05/2024] Open
Abstract
Cyanobacteria, which have a photoautotrophic lifestyle, are threatened by ultraviolet solar rays and the reactive oxygen species generated during photosynthesis. They can adapt to environmental conditions primarily because of their DNA damage response and repair mechanisms, notably an efficient homologous recombination repair system. However, research on double-strand break (DSB) repair pathways, including the Holliday junction (HJ) resolution process, in Synechocystis sp. PCC6803 is limited. Here, we report that SynRuvC from cyanobacteria Synechocystis sp. PCC6803 has classical HJ resolution activity. We investigated the structural specificity, sequence preference, and biochemical properties of SynRuvC. SynRuvC strongly preferred Mn2+ as a cofactor, and its cleavage site predominantly resides within the 5'-TG↓(G/A)-3' sequence. Interestingly, novel flap endonuclease and replication fork intermediate cleavage activities of SynRuvC were also determined, which distinguish it from other reported RuvCs. To explore the effect of SynRuvC on cell viability, we constructed a knockdown mutant and an overexpression strain of Synechocystis sp. PCC6803 (synruvCKD and synruvCOE) and assessed their survival under a variety of conditions. Knockdown of synruvC increased the sensitivity of cells to MMS, HU, and H2O2. The findings suggest that a novel RuvC family HJ resolvase SynRuvC is important in a variety of DNA repair processes and stress resistance in Synechocystis sp. PCC6803.
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Affiliation(s)
- Yanchao Gu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yantao Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Chunhua Kou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ying Peng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenguang Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayu Zhang
- Suzhou XinBio Co., Ltd., Suzhou, Jiangsu, China
| | - Han Jin
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoru Han
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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13
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Shen MZ, Zhang Y, Wu F, Shen MZ, Liang JL, Zhang XL, Liu XJ, Li XS, Wang RS. MicroRNA-298 determines the radio-resistance of colorectal cancer cells by directly targeting human dual-specificity tyrosine(Y)-regulated kinase 1A. World J Gastrointest Oncol 2024; 16:1453-1464. [PMID: 38660649 PMCID: PMC11037043 DOI: 10.4251/wjgo.v16.i4.1453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/31/2023] [Accepted: 02/02/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Radiotherapy stands as a promising therapeutic modality for colorectal cancer (CRC); yet, the formidable challenge posed by radio-resistance significantly undermines its efficacy in achieving CRC remission. AIM To elucidate the role played by microRNA-298 (miR-298) in CRC radio-resistance. METHODS To establish a radio-resistant CRC cell line, HT-29 cells underwent exposure to 5 gray ionizing radiation that was followed by a 7-d recovery period. The quantification of miR-298 levels within CRC cells was conducted through quantitative RT-PCR, and protein expression determination was realized through Western blotting. Cell viability was assessed by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and proliferation by clonogenic assay. Radio-induced apoptosis was discerned through flow cytometry analysis. RESULTS We observed a marked upregulation of miR-298 in radio-resistant CRC cells. MiR-298 emerged as a key determinant of cell survival following radiation exposure, as its overexpression led to a notable reduction in radiation-induced apoptosis. Intriguingly, miR-298 expression exhibited a strong correlation with CRC cell viability. Further investigation unveiled human dual-specificity tyrosine(Y)-regulated kinase 1A (DYRK1A) as miR-298's direct target. CONCLUSION Taken together, our findings underline the role played by miR-298 in bolstering radio-resistance in CRC cells by means of DYRK1A downregulation, thereby positioning miR-298 as a promising candidate for mitigating radio-resistance in CRC.
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Affiliation(s)
- Mei-Zhu Shen
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Yong Zhang
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Fang Wu
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Mei-Zhen Shen
- Department of Radiotherapy, People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Jun-Lin Liang
- Department of Colorectal Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Long Zhang
- Department of Colorectal Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Jian Liu
- Department of Colorectal Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Xin-Shu Li
- Department of Clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Ren-Sheng Wang
- Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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14
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Chen Z, Hu J, Dai J, Zhou C, Hua Y, Hua X, Zhao Y. Precise CRISPR/Cpf1 genome editing system in the Deinococcus radiodurans with superior DNA repair mechanisms. Microbiol Res 2024; 284:127713. [PMID: 38608339 DOI: 10.1016/j.micres.2024.127713] [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: 12/04/2023] [Revised: 02/20/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Deinococcus radiodurans, with its high homologous recombination (HR) efficiency of double-stranded DNA breaks (DSBs), is a model organism for studying genome stability maintenance and an attractive microbe for industrial applications. Here, we developed an efficient CRISPR/Cpf1 genome editing system in D. radiodurans by evaluating and optimizing double-plasmid strategies and four Cas effector proteins from various organisms, which can precisely introduce different types of template-dependent mutagenesis without off-target toxicity. Furthermore, the role of DNA repair genes in determining editing efficiency in D. radiodurans was evaluated by introducing the CRISPR/Cpf1 system into 13 mutant strains lacking various DNA damage response and repair factors. In addition to the crucial role of RecA-dependent HR required for CRISPR/Cpf1 editing, D. radiodurans showed higher editing efficiency when lacking DdrB, the single-stranded DNA annealing (SSA) protein involved in the RecA-independent DSB repair pathway. This suggests a possible competition between HR and SSA pathways in the CRISPR editing of D. radiodurans. Moreover, off-target effects were observed during the genome editing of the pprI knockout strain, a master DNA damage response gene in Deinococcus species, which suggested that precise regulation of DNA damage response is critical for a high-fidelity genome editing system.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Hu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingli Dai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Congli Zhou
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China.
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15
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Zhou Y, Zhang Q, Zhao Z, Hu X, You Q, Jiang Z. Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives. Eur J Med Chem 2024; 269:116270. [PMID: 38490062 DOI: 10.1016/j.ejmech.2024.116270] [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: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
Kelch-like proteins (KLHLs) are a large family of BTB-containing proteins. KLHLs function as the substrate adaptor of Cullin 3-RING ligases (CRL3) to recognize substrates. KLHLs play pivotal roles in regulating various physiological and pathological processes by modulating the ubiquitination of their respective substrates. Mounting evidence indicates that mutations or abnormal expression of KLHLs are associated with various human diseases. Targeting KLHLs is a viable strategy for deciphering the KLHLs-related pathways and devising therapies for associated diseases. Here, we comprehensively review the known KLHLs inhibitors to date and the brilliant ideas underlying their development.
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Affiliation(s)
- Yangguo Zhou
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiong Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ziquan Zhao
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiuqi Hu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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16
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Wang YJ, Cao JB, Yang J, Liu T, Yu HL, He ZX, Bao SL, He XX, Zhu XJ. PRMT5-mediated homologous recombination repair is essential to maintain genomic integrity of neural progenitor cells. Cell Mol Life Sci 2024; 81:123. [PMID: 38459149 PMCID: PMC10923982 DOI: 10.1007/s00018-024-05154-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 03/10/2024]
Abstract
Maintaining genomic stability is a prerequisite for proliferating NPCs to ensure genetic fidelity. Though histone arginine methylation has been shown to play important roles in safeguarding genomic stability, the underlying mechanism during brain development is not fully understood. Protein arginine N-methyltransferase 5 (PRMT5) is a type II protein arginine methyltransferase that plays a role in transcriptional regulation. Here, we identify PRMT5 as a key regulator of DNA repair in response to double-strand breaks (DSBs) during NPC proliferation. Prmt5F/F; Emx1-Cre (cKO-Emx1) mice show a distinctive microcephaly phenotype, with partial loss of the dorsal medial cerebral cortex and complete loss of the corpus callosum and hippocampus. This phenotype is resulted from DSBs accumulation in the medial dorsal cortex followed by cell apoptosis. Both RNA sequencing and in vitro DNA repair analyses reveal that PRMT5 is required for DNA homologous recombination (HR) repair. PRMT5 specifically catalyzes H3R2me2s in proliferating NPCs in the developing mouse brain to enhance HR-related gene expression during DNA repair. Finally, overexpression of BRCA1 significantly rescues DSBs accumulation and cell apoptosis in PRMT5-deficient NSCs. Taken together, our results show that PRMT5 maintains genomic stability by regulating histone arginine methylation in proliferating NPCs.
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Affiliation(s)
- Ya-Jun Wang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jian-Bo Cao
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Jing Yang
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Tong Liu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Hua-Li Yu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Zi-Xuan He
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China
| | - Shi-Lai Bao
- State Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao-Xiao He
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China.
| | - Xiao-Juan Zhu
- Key Laboratory of Molecular Epigenetics, Ministry of Education, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China.
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17
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Bakhshalizadeh S, Bird AD, Sreenivasan R, Bell KM, Robevska G, van den Bergen J, Asghari-Jafarabadi M, Kueh AJ, Touraine P, Lokchine A, Jaillard S, Ayers KL, Wilhelm D, Sinclair AH, Tucker EJ. A Human Homozygous HELQ Missense Variant Does Not Cause Premature Ovarian Insufficiency in a Mouse Model. Genes (Basel) 2024; 15:333. [PMID: 38540391 PMCID: PMC10970702 DOI: 10.3390/genes15030333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 04/02/2024] Open
Abstract
Disruption of meiosis and DNA repair genes is associated with female fertility disorders like premature ovarian insufficiency (POI). In this study, we identified a homozygous missense variant in the HELQ gene (c.596 A>C; p.Gln199Pro) through whole exome sequencing in a POI patient, a condition associated with disrupted ovarian function and female infertility. HELQ, an enzyme involved in DNA repair, plays a crucial role in repairing DNA cross-links and has been linked to germ cell maintenance, fertility, and tumour suppression in mice. To explore the potential association of the HELQ variant with POI, we used CRISPR/Cas9 to create a knock-in mouse model harbouring the equivalent of the human HELQ variant identified in the POI patient. Surprisingly, Helq knock-in mice showed no discernible phenotype, with fertility levels, histological features, and follicle development similar to wild-type mice. Despite the lack of observable effects in mice, the potential role of HELQ in human fertility, especially in the context of POI, should not be dismissed. Larger studies encompassing diverse ethnic populations and alternative functional approaches will be necessary to further examine the role of HELQ in POI. Our results underscore the potential uncertainties associated with genomic variants and the limitations of in vivo animal modelling.
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Affiliation(s)
- Shabnam Bakhshalizadeh
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Anthony D. Bird
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC 3010, Australia; (A.D.B.); (D.W.)
- Hudson Institute of Medical Research, Monash Medical Centre, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Rajini Sreenivasan
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
| | - Katrina M. Bell
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
| | - Gorjana Robevska
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
| | - Jocelyn van den Bergen
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
| | - Mohammad Asghari-Jafarabadi
- Biostatistics Unit, School of Public Health and Preventative Medicine, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3004, Australia;
- Department of Psychiatry, School of Clinical Sciences, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Andrew J. Kueh
- The Walter and Eliza Hall Institute, Parkville, VIC 3052, Australia;
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Philippe Touraine
- Department of Endocrinology and Reproductive Medicine, Pitie Salpetriere Hospital, AP-HP, Sorbonne University Medicine, 75013 Paris, France;
| | - Anna Lokchine
- IRSET (Institut de Recherche en Santé, Environnement et Travail), INSERM/EHESP/Univ Rennes/CHU Rennes–UMR_S 1085, 35000 Rennes, France; (A.L.); (S.J.)
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, 35033 Rennes, France
| | - Sylvie Jaillard
- IRSET (Institut de Recherche en Santé, Environnement et Travail), INSERM/EHESP/Univ Rennes/CHU Rennes–UMR_S 1085, 35000 Rennes, France; (A.L.); (S.J.)
- CHU Rennes, Service de Cytogénétique et Biologie Cellulaire, 35033 Rennes, France
| | - Katie L. Ayers
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Dagmar Wilhelm
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC 3010, Australia; (A.D.B.); (D.W.)
| | - Andrew H. Sinclair
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Elena J. Tucker
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC 3052, Australia; (S.B.); (R.S.); (K.M.B.); (G.R.); (J.v.d.B.); (K.L.A.); (A.H.S.)
- Department of Paediatrics, The University of Melbourne, Melbourne, VIC 3052, Australia
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18
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Allen AG, Khan SQ, Margulies CM, Viswanathan R, Lele S, Blaha L, Scott SN, Izzo KM, Gerew A, Pattali R, Cochran NR, Holland CS, Zhao AH, Sherman SE, Jaskolka MC, Wu M, Wilson AC, Sun X, Ciulla DM, Zhang D, Nelson JD, Zhang P, Mazzucato P, Huang Y, Giannoukos G, Marco E, Nehil M, Follit JA, Chang KH, Shearman MS, Wilson CJ, Zuris JA. A highly efficient transgene knock-in technology in clinically relevant cell types. Nat Biotechnol 2024; 42:458-469. [PMID: 37127662 DOI: 10.1038/s41587-023-01779-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/04/2023] [Indexed: 05/03/2023]
Abstract
Inefficient knock-in of transgene cargos limits the potential of cell-based medicines. In this study, we used a CRISPR nuclease that targets a site within an exon of an essential gene and designed a cargo template so that correct knock-in would retain essential gene function while also integrating the transgene(s) of interest. Cells with non-productive insertions and deletions would undergo negative selection. This technology, called SLEEK (SeLection by Essential-gene Exon Knock-in), achieved knock-in efficiencies of more than 90% in clinically relevant cell types without impacting long-term viability or expansion. SLEEK knock-in rates in T cells are more efficient than state-of-the-art TRAC knock-in with AAV6 and surpass more than 90% efficiency even with non-viral DNA cargos. As a clinical application, natural killer cells generated from induced pluripotent stem cells containing SLEEK knock-in of CD16 and mbIL-15 show substantially improved tumor killing and persistence in vivo.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meng Wu
- Editas Medicine, Cambridge, MA, USA
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19
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Hu J, Crickard JB. All who wander are not lost: the search for homology during homologous recombination. Biochem Soc Trans 2024; 52:367-377. [PMID: 38323621 PMCID: PMC10903458 DOI: 10.1042/bst20230705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
Homologous recombination (HR) is a template-based DNA double-strand break repair pathway that functions to maintain genomic integrity. A vital component of the HR reaction is the identification of template DNA to be used during repair. This occurs through a mechanism known as the homology search. The homology search occurs in two steps: a collision step in which two pieces of DNA are forced to collide and a selection step that results in homologous pairing between matching DNA sequences. Selection of a homologous template is facilitated by recombinases of the RecA/Rad51 family of proteins in cooperation with helicases, translocases, and topoisomerases that determine the overall fidelity of the match. This menagerie of molecular machines acts to regulate critical intermediates during the homology search. These intermediates include recombinase filaments that probe for short stretches of homology and early strand invasion intermediates in the form of displacement loops (D-loops) that stabilize paired DNA. Here, we will discuss recent advances in understanding how these specific intermediates are regulated on the molecular level during the HR reaction. We will also discuss how the stability of these intermediates influences the ultimate outcomes of the HR reaction. Finally, we will discuss recent physiological models developed to explain how the homology search protects the genome.
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Affiliation(s)
- Jingyi Hu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, U.S.A
| | - J Brooks Crickard
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, U.S.A
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20
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Li S, Liu B, Tan M, Juillard F, Szymula A, Álvarez Á, Van Sciver N, George A, Ramachandran A, Raina K, Tumuluri VS, Costa C, Simas J, Kaye K. Kaposi's sarcoma herpesvirus exploits the DNA damage response to circularize its genome. Nucleic Acids Res 2024; 52:1814-1829. [PMID: 38180827 PMCID: PMC10899755 DOI: 10.1093/nar/gkad1224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/07/2024] Open
Abstract
To establish lifelong, latent infection, herpesviruses circularize their linear, double-stranded, DNA genomes through an unknown mechanism. Kaposi's sarcoma (KS) herpesvirus (KSHV), a gamma herpesvirus, is tightly linked with KS, primary effusion lymphoma, and multicentric Castleman's disease. KSHV persists in latently infected cells as a multi-copy, extrachromosomal episome. Here, we show the KSHV genome rapidly circularizes following infection, and viral protein expression is unnecessary for this process. The DNA damage response (DDR) kinases, ATM and DNA-PKcs, each exert roles, and absence of both severely compromises circularization and latency. These deficiencies were rescued by expression of ATM and DNA-PKcs, but not catalytically inactive mutants. In contrast, γH2AX did not function in KSHV circularization. The linear viral genomic ends resemble a DNA double strand break, and non-homologous DNA end joining (NHEJ) and homologous recombination (HR) reporters indicate both NHEJ and HR contribute to KSHV circularization. Last, we show, similar to KSHV, ATM and DNA-PKcs have roles in circularization of the alpha herpesvirus, herpes simplex virus-1 (HSV-1), while γH2AX does not. Therefore, the DDR mediates KSHV and HSV-1 circularization. This strategy may serve as a general herpesvirus mechanism to initiate latency, and its disruption may provide new opportunities for prevention of herpesvirus disease.
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Affiliation(s)
- Shijun Li
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Bing Liu
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Min Tan
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Franceline Juillard
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Agnieszka Szymula
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Ángel L Álvarez
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas Van Sciver
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Athira George
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Akshaya Ramachandran
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Komal Raina
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Vinayak Sadasivam Tumuluri
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Catarina N Costa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Universidade Católica Portuguesa, Católica Medical School, Católica Biomedical Research, Palma de Cima, 1649-023 Lisboa, Portugal
| | - J Pedro Simas
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Universidade Católica Portuguesa, Católica Medical School, Católica Biomedical Research, Palma de Cima, 1649-023 Lisboa, Portugal
| | - Kenneth M Kaye
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Program in Virology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard University and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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21
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Chang CR, Vykunta VS, Goodman DB, Muldoon JJ, Nyberg WA, Liu C, Allain V, Rothrock A, Wang CH, Marson A, Shy BR, Eyquem J. Ultra-high efficiency T cell reprogramming at multiple loci with SEED-Selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.576175. [PMID: 38370809 PMCID: PMC10871224 DOI: 10.1101/2024.02.06.576175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Multiplexed reprogramming of T cell specificity and function can generate powerful next-generation cellular therapies. However, current manufacturing methods produce heterogenous mixtures of partially engineered cells. Here, we develop a one-step process to enrich for unlabeled cells with knock-ins at multiple target loci using a family of repair templates named Synthetic Exon/Expression Disruptors (SEEDs). SEED engineering associates transgene integration with the disruption of a paired endogenous surface protein, allowing non-modified and partially edited cells to be immunomagnetically depleted (SEED-Selection). We design SEEDs to fully reprogram three critical loci encoding T cell specificity, co-receptor expression, and MHC expression, with up to 98% purity after selection for individual modifications and up to 90% purity for six simultaneous edits (three knock-ins and three knockouts). These methods are simple, compatible with existing clinical manufacturing workflows, and can be readily adapted to other loci to facilitate production of complex gene-edited cell therapies.
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Affiliation(s)
- Christopher R Chang
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Vivasvan S Vykunta
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel B Goodman
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Joseph J Muldoon
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - William A Nyberg
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chang Liu
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Vincent Allain
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Université Paris Cité, INSERM UMR976, Hôpital Saint-Louis, Paris, France
| | - Allison Rothrock
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charlotte H Wang
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Alexander Marson
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Justin Eyquem
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
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22
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Leem J, Lee C, Choi DY, Oh JS. Distinct characteristics of the DNA damage response in mammalian oocytes. Exp Mol Med 2024; 56:319-328. [PMID: 38355825 PMCID: PMC10907590 DOI: 10.1038/s12276-024-01178-2] [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: 08/20/2023] [Revised: 11/15/2023] [Accepted: 12/07/2023] [Indexed: 02/16/2024] Open
Abstract
DNA damage is a critical threat that poses significant challenges to all cells. To address this issue, cells have evolved a sophisticated molecular and cellular process known as the DNA damage response (DDR). Among the various cell types, mammalian oocytes, which remain dormant in the ovary for extended periods, are particularly susceptible to DNA damage. The occurrence of DNA damage in oocytes can result in genetic abnormalities, potentially leading to infertility, birth defects, and even abortion. Therefore, understanding how oocytes detect and repair DNA damage is of paramount importance in maintaining oocyte quality and preserving fertility. Although the fundamental concept of the DDR is conserved across various cell types, an emerging body of evidence reveals striking distinctions in the DDR between mammalian oocytes and somatic cells. In this review, we highlight the distinctive characteristics of the DDR in oocytes and discuss the clinical implications of DNA damage in oocytes.
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Affiliation(s)
- Jiyeon Leem
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Crystal Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Da Yi Choi
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Jeong Su Oh
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea.
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23
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Tischler JD, Tsuchida H, Bosire R, Oda TT, Park A, Adeyemi RO. FLIP(C1orf112)-FIGNL1 complex regulates RAD51 chromatin association to promote viability after replication stress. Nat Commun 2024; 15:866. [PMID: 38286805 PMCID: PMC10825145 DOI: 10.1038/s41467-024-45139-9] [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: 05/24/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Homologous recombination (HR) plays critical roles in repairing lesions that arise during DNA replication and is thus essential for viability. RAD51 plays important roles during replication and HR, however, how RAD51 is regulated downstream of nucleofilament formation and how the varied RAD51 functions are regulated is not clear. We have investigated the protein c1orf112/FLIP that previously scored in genome-wide screens for mediators of DNA inter-strand crosslink (ICL) repair. Upon ICL agent exposure, FLIP loss leads to marked cell death, elevated chromosomal instability, increased micronuclei formation, altered cell cycle progression and increased DNA damage signaling. FLIP is recruited to damage foci and forms a complex with FIGNL1. Both proteins have epistatic roles in ICL repair, forming a stable complex. Mechanistically, FLIP loss leads to increased RAD51 amounts and foci on chromatin both with or without exogenous DNA damage, defective replication fork progression and reduced HR competency. We posit that FLIP is essential for limiting RAD51 levels on chromatin in the absence of damage and for RAD51 dissociation from nucleofilaments to properly complete HR. Failure to do so leads to replication slowing and inability to complete repair.
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Affiliation(s)
- Jessica D Tischler
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | - Hiroshi Tsuchida
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
| | | | - Tommy T Oda
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- University of Washington, Seattle, 98195, USA
| | - Ana Park
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA
- University of Washington, Seattle, 98195, USA
| | - Richard O Adeyemi
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, 98109, USA.
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24
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Kawaguchi K, Kazama M, Hata T, Matsuo M, Obokata J, Satoh S. Inducible Expression of the Restriction Enzyme Uncovered Genome-Wide Distribution and Dynamic Behavior of Histones H4K16ac and H2A.Z at DNA Double-Strand Breaks in Arabidopsis. PLANT & CELL PHYSIOLOGY 2024; 65:142-155. [PMID: 37930797 DOI: 10.1093/pcp/pcad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/07/2023]
Abstract
DNA double-strand breaks (DSBs) are among the most serious types of DNA damage, causing mutations and chromosomal rearrangements. In eukaryotes, DSBs are immediately repaired in coordination with chromatin remodeling for the deposition of DSB-related histone modifications and variants. To elucidate the details of DSB-dependent chromatin remodeling throughout the genome, artificial DSBs need to be reproducibly induced at various genomic loci. Recently, a comprehensive method for elucidating chromatin remodeling at multiple DSB loci via chemically induced expression of a restriction enzyme was developed in mammals. However, this DSB induction system is unsuitable for investigating chromatin remodeling during and after DSB repair, and such an approach has not been performed in plants. Here, we established a transgenic Arabidopsis plant harboring a restriction enzyme gene Sbf I driven by a heat-inducible promoter. Using this transgenic line, we performed chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) of histones H4K16ac and H2A.Z and investigated the dynamics of these histone marks around the endogenous 623 Sbf I recognition sites. We also precisely quantified DSB efficiency at all cleavage sites using the DNA resequencing data obtained by the ChIP-seq procedure. From the results, Sbf I-induced DSBs were detected at 360 loci, which induced the transient deposition of H4K16ac and H2A.Z around these regions. Interestingly, we also observed the co-localization of H4K16ac and H2A.Z at some DSB loci. Overall, DSB-dependent chromatin remodeling was found to be highly conserved between plants and animals. These findings provide new insights into chromatin remodeling that occurs in response to DSBs in Arabidopsis.
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Affiliation(s)
- Kohei Kawaguchi
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Mei Kazama
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
| | - Takayuki Hata
- Graduate School of Medicine, Hirosaki University, Hirosaki, Aomori 036-8560, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata, Osaka 573-0101, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, Kyoto 606-8522, Japan
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25
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Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [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: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
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Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
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26
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Lonez C, Breman E. Allogeneic CAR-T Therapy Technologies: Has the Promise Been Met? Cells 2024; 13:146. [PMID: 38247837 PMCID: PMC10814647 DOI: 10.3390/cells13020146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
This last decade, chimeric antigen receptor (CAR) T-cell therapy has become a real treatment option for patients with B-cell malignancies, while multiple efforts are being made to extend this therapy to other malignancies and broader patient populations. However, several limitations remain, including those associated with the time-consuming and highly personalized manufacturing of autologous CAR-Ts. Technologies to establish "off-the-shelf" allogeneic CAR-Ts with low alloreactivity are currently being developed, with a strong focus on gene-editing technologies. Although these technologies have many advantages, they have also strong limitations, including double-strand breaks in the DNA with multiple associated safety risks as well as the lack of modulation. As an alternative, non-gene-editing technologies provide an interesting approach to support the development of allogeneic CAR-Ts in the future, with possibilities of fine-tuning gene expression and easy development. Here, we will review the different ways allogeneic CAR-Ts can be manufactured and discuss which technologies are currently used. The biggest hurdles for successful therapy of allogeneic CAR-Ts will be summarized, and finally, an overview of the current clinical evidence for allogeneic CAR-Ts in comparison to its autologous counterpart will be given.
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27
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Liu Z, Feng C, Li C, He T, Wu G, Fu C, Li H, Shen M, Liu H. IGF-I protects porcine granulosa cells from hypoxia-induced apoptosis by promoting homologous recombination repair through the PI3K/AKT/E2F8/RAD51 pathway. FASEB J 2024; 38:e23332. [PMID: 38095232 DOI: 10.1096/fj.202301464r] [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: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
Severe hypoxia induced by vascular compromise (ovarian torsion, surgery), obliteration of vessels (aging, chemotherapy, particularly platinum drugs) can cause massive follicle atresia. On the other hand, hypoxia increases the occurrence of DNA double-strand breaks (DSBs) and triggers cellular damage repair mechanisms; however, if the damage is not promptly repaired, it can also induce the apoptosis program. Insulin-like growth factor-I (IGF-I) is a polypeptide hormone that plays essential roles in stimulating mammalian follicular development. Here, we report a novel role for IGF-I in protecting hypoxic GCs from apoptosis by promoting DNA repair through the homologous recombination (HR) process. Indeed, the hypoxic environment within follicles significantly inhibited the efficiency of HR-directed DNA repair. The presence of IGF-I-induced HR pathway to alleviate hypoxia-induced DNA damage and apoptosis primarily through upregulating the expression of the RAD51 recombinase. Importantly, we identified a new transcriptional regulator of RAD51, namely E2F8, which mediates the protective effects of IGF-I on hypoxic GCs by facilitating the transcriptional activation of RAD51. Furthermore, we demonstrated that the PI3K/AKT pathway is crucial for IGF-I-induced E2F8 expression, resulting in increased RAD51 expression and enhanced HR activity, which mitigates hypoxia-induced DNA damage and thereby protects against GCs apoptosis. Together, these findings define a novel mechanism of IGF-I-mediated GCs protection by activating the HR repair through the PI3K/AKT/E2F8/RAD51 pathway under hypoxia.
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Affiliation(s)
- Zhaojun Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chengyu Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Tong He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Gang Wu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chen Fu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Hongmin Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Ming Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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Kim S, Kim Y, Lee JY. Real-time single-molecule visualization using DNA curtains reveals the molecular mechanisms underlying DNA repair pathways. DNA Repair (Amst) 2024; 133:103612. [PMID: 38128155 DOI: 10.1016/j.dnarep.2023.103612] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 12/10/2023] [Indexed: 12/23/2023]
Abstract
The demand for direct observation of biomolecular interactions provides new insights into the molecular mechanisms underlying many biological processes. Single-molecule imaging techniques enable real-time visualization of individual biomolecules, providing direct observations of protein machines. Various single-molecule imaging techniques have been developed and have contributed to breakthroughs in biological research. One such technique is the DNA curtain, a novel, high-throughput, single-molecule platform that integrates lipid fluidity, nano-fabrication, microfluidics, and fluorescence imaging. Many DNA metabolic reactions, such as replication, transcription, and chromatin dynamics, have been studied using DNA curtains. In particular, the DNA curtain platform has been intensively applied in investigating the molecular details of DNA repair processes. This article reviews DNA curtain techniques and their applications for imaging DNA repair proteins.
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Affiliation(s)
- Subin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Youngseo Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Ja Yil Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan, South Korea.
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29
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Wei L, Bai Y, Na L, Sun Y, Zhao C, Wang W. E2F3 induces DNA damage repair, stem-like properties and therapy resistance in breast cancer. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166816. [PMID: 37499929 DOI: 10.1016/j.bbadis.2023.166816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 07/29/2023]
Abstract
Therapy resistance is a major hurdle to the treatment of human malignant tumors. Both DNA damage repair and stem-like properties contribute to chemoresistance and radioresistance. E2F transcription factor 3 (E2F3) is overexpressed in breast cancer tissues, and promotes proliferation of breast cancer cells. Higher E2F3 level is associated with shorter survival of breast cancer patients. Functional studies further showed that E2F3 promotes S-phage entry, DNA replication, DNA damage repair and stem-like properties. Accordingly, E2F3 knockdown sensitizes breast cancer cells to DNA-damaging agents Adriamycin, Cisplatin, Olaparib and X-ray. Forkhead box M1 (FOXM1) is a downstream molecule of E2F3 signaling, mediating the effects of E2F3 on breast cancer cells. In an m6A methyltransferase METTL14-dependent manner, YTH RNA binding protein F2 (YTHDF2) increase E2F3 mRNA stability and expression, promotes DNA damage repair and induces therapy resistance. These data demonstrate that YTHDF2-E2F3 pathway is a novel target to overcome chemoresistance and radioresistance in breast cancer.
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Affiliation(s)
- Linlin Wei
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China; Cancer Hospital of China Medical University, Shenyang, China
| | - Yu Bai
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China; Department of Nephrology, Shengjing Hospital, China Medical University, Shenyang, China
| | - Lei Na
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Yu Sun
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China
| | - Chenghai Zhao
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China.
| | - Wei Wang
- Department of Pathophysiology, College of Basic Medical Science, China Medical University, Shenyang, China.
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30
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Han J, Mu Y, Huang J. Preserving genome integrity: The vital role of SUMO-targeted ubiquitin ligases. CELL INSIGHT 2023; 2:100128. [PMID: 38047137 PMCID: PMC10692494 DOI: 10.1016/j.cellin.2023.100128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 12/05/2023]
Abstract
Various post-translational modifications (PTMs) collaboratively fine-tune protein activities. SUMO-targeted ubiquitin E3 ligases (STUbLs) emerge as specialized enzymes that recognize SUMO-modified substrates through SUMO-interaction motifs and subsequently ubiquitinate them via the RING domain, thereby bridging the SUMO and ubiquitin signaling pathways. STUbLs participate in a wide array of molecular processes, including cell cycle regulation, DNA repair, replication, and mitosis, operating under both normal conditions and in response to challenges such as genotoxic stress. Their ability to catalyze various types of ubiquitin chains results in diverse proteolytic and non-proteolytic outcomes for target substrates. Importantly, STUbLs are strategically positioned in close proximity to SUMO proteases and deubiquitinases (DUBs), ensuring precise and dynamic control over their target proteins. In this review, we provide insights into the unique properties and indispensable roles of STUbLs, with a particular emphasis on their significance in preserving genome integrity in humans.
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Affiliation(s)
- Jinhua Han
- Institute of Geriatrics, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Yanhua Mu
- National-Local Joint Engineering Research Center of Biodiagnosis & Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Jun Huang
- Institute of Geriatrics, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, Zhejiang, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, Zhejiang, China
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31
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Classen S, Petersen C, Borgmann K. Crosstalk between immune checkpoint and DNA damage response inhibitors for radiosensitization of tumors. Strahlenther Onkol 2023; 199:1152-1163. [PMID: 37420037 PMCID: PMC10674014 DOI: 10.1007/s00066-023-02103-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/16/2023] [Indexed: 07/09/2023]
Abstract
PURPOSE This review article is intended to provide a perspective overview of potential strategies to overcome radiation resistance of tumors through the combined use of immune checkpoint and DNA repair inhibitors. METHODS A literature search was conducted in PubMed using the terms ("DNA repair* and DNA damage response* and intracellular immune response* and immune checkpoint inhibition* and radio*") until January 31, 2023. Articles were manually selected based on their relevance to the topics analyzed. RESULTS Modern radiotherapy offers a wide range of options for tumor treatment. Radiation-resistant subpopulations of the tumor pose a particular challenge for complete cure. This is due to the enhanced activation of molecular defense mechanisms that prevent cell death because of DNA damage. Novel approaches to enhance tumor cure are provided by immune checkpoint inhibitors, but their effectiveness, especially in tumors without increased mutational burden, also remains limited. Combining inhibitors of both immune checkpoints and DNA damage response with radiation may be an attractive option to augment existing therapies and is the subject of the data summarized here. CONCLUSION The combination of tested inhibitors of DNA damage and immune responses in preclinical models opens additional attractive options for the radiosensitization of tumors and represents a promising application for future therapeutic approaches.
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Affiliation(s)
- Sandra Classen
- Laboratory of Radiobiology and Radiation Oncology, Department of Radiotherapy and Radiation Oncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Cordula Petersen
- Department of Radiotherapy and Radiation Oncology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Kerstin Borgmann
- Laboratory of Radiobiology and Radiation Oncology, Department of Radiotherapy and Radiation Oncology, Center of Oncology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany.
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32
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Li B. Telomere maintenance in African trypanosomes. Front Mol Biosci 2023; 10:1302557. [PMID: 38074093 PMCID: PMC10704157 DOI: 10.3389/fmolb.2023.1302557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024] Open
Abstract
Telomere maintenance is essential for genome integrity and chromosome stability in eukaryotic cells harboring linear chromosomes, as telomere forms a specialized structure to mask the natural chromosome ends from DNA damage repair machineries and to prevent nucleolytic degradation of the telomeric DNA. In Trypanosoma brucei and several other microbial pathogens, virulence genes involved in antigenic variation, a key pathogenesis mechanism essential for host immune evasion and long-term infections, are located at subtelomeres, and expression and switching of these major surface antigens are regulated by telomere proteins and the telomere structure. Therefore, understanding telomere maintenance mechanisms and how these pathogens achieve a balance between stability and plasticity at telomere/subtelomere will help develop better means to eradicate human diseases caused by these pathogens. Telomere replication faces several challenges, and the "end replication problem" is a key obstacle that can cause progressive telomere shortening in proliferating cells. To overcome this challenge, most eukaryotes use telomerase to extend the G-rich telomere strand. In addition, a number of telomere proteins use sophisticated mechanisms to coordinate the telomerase-mediated de novo telomere G-strand synthesis and the telomere C-strand fill-in, which has been extensively studied in mammalian cells. However, we recently discovered that trypanosomes lack many telomere proteins identified in its mammalian host that are critical for telomere end processing. Rather, T. brucei uses a unique DNA polymerase, PolIE that belongs to the DNA polymerase A family (E. coli DNA PolI family), to coordinate the telomere G- and C-strand syntheses. In this review, I will first briefly summarize current understanding of telomere end processing in mammals. Subsequently, I will describe PolIE-mediated coordination of telomere G- and C-strand synthesis in T. brucei and implication of this recent discovery.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Arts and Sciences, Cleveland State University, Cleveland, OH, United States
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, United States
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33
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Thomas C, Avalos-Irving L, Victorino J, Green S, Andrews M, Rodrigues N, Ebirim S, Mudd A, Towle-Weicksel JB. Melanoma-derived DNA polymerase theta variants exhibit altered DNA polymerase activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566933. [PMID: 38014040 PMCID: PMC10680777 DOI: 10.1101/2023.11.14.566933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
DNA Polymerase θ (Pol θ or POLQ) is primarily involved in repairing double-stranded breaks in DNA through the alternative pathway known as microhomology-mediated end joining (MMEJ) or theta-mediated end joining (TMEJ). Unlike other DNA repair polymerases, Pol θ is thought to be highly error prone, yet critical for cell survival. We have identified several mutations in the POLQ gene from human melanoma tumors. Through biochemical analysis, we have demonstrated that all three cancer-associated variants experienced altered DNA polymerase activity including a propensity for incorrect nucleotide selection and reduced polymerization rates compared to WT Pol θ. Moreover, the variants are 30 fold less efficient at incorporating a nucleotide during repair and up to 70 fold less accurate at selecting the correct nucleotide opposite a templating base. Taken together, this suggests that aberrant Pol θ has reduced DNA repair capabilities and may also contribute to increased mutagenesis. While this may be beneficial to normal cell survival, the variants were identified in established tumors suggesting that cancer cells may use this promiscuous polymerase to its advantage to promote metastasis and drug resistance.
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34
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Allison RM, Johnson DJ, Neale MJ, Gray S. Recombinase-independent chromosomal rearrangements between dispersed inverted repeats in Saccharomyces cerevisiae meiosis. Nucleic Acids Res 2023; 51:9703-9715. [PMID: 37548404 PMCID: PMC10570019 DOI: 10.1093/nar/gkad650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 07/16/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) uses a DNA template with similar sequence to restore genetic identity. Allelic DNA repair templates can be found on the sister chromatid or homologous chromosome. During meiotic recombination, DSBs preferentially repair from the homologous chromosome, with a proportion of HR events generating crossovers. Nevertheless, regions of similar DNA sequence exist throughout the genome, providing potential DNA repair templates. When DSB repair occurs at these non-allelic loci (termed ectopic recombination), chromosomal duplications, deletions and rearrangements can arise. Here, we characterize in detail ectopic recombination arising between a dispersed pair of inverted repeats in wild-type Saccharomyces cerevisiae at both a local and a chromosomal scale-the latter identified via gross chromosomal acentric and dicentric chromosome rearrangements. Mutation of the DNA damage checkpoint clamp loader Rad24 and the RecQ helicase Sgs1 causes an increase in ectopic recombination. Unexpectedly, additional mutation of the RecA orthologues Rad51 and Dmc1 alters-but does not abolish-the type of ectopic recombinants generated, revealing a novel class of inverted chromosomal rearrangement driven by the single-strand annealing pathway. These data provide important insights into the role of key DNA repair proteins in regulating DNA repair pathway and template choice during meiosis.
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Affiliation(s)
- Rachal M Allison
- Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, UK
| | - Dominic J Johnson
- Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, UK
| | - Matthew J Neale
- Genome Damage and Stability Centre, University of Sussex, Falmer BN1 9RQ, UK
| | - Stephen Gray
- School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
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35
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Rodríguez‐Real G, Domínguez‐Calvo A, Prados‐Carvajal R, Bayona‐Feliú A, Gomes‐Pereira S, Balestra FR, Huertas P. Centriolar subdistal appendages promote double-strand break repair through homologous recombination. EMBO Rep 2023; 24:e56724. [PMID: 37664992 PMCID: PMC10561181 DOI: 10.15252/embr.202256724] [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: 12/23/2022] [Revised: 07/18/2023] [Accepted: 08/19/2023] [Indexed: 09/05/2023] Open
Abstract
The centrosome is a cytoplasmic organelle with roles in microtubule organization that has also been proposed to act as a hub for cellular signaling. Some centrosomal components are required for full activation of the DNA damage response. However, whether the centrosome regulates specific DNA repair pathways is not known. Here, we show that centrosome presence is required to fully activate recombination, specifically to completely license its initial step, the so-called DNA end resection. Furthermore, we identify a centriolar structure, the subdistal appendages, and a specific factor, CEP170, as the critical centrosomal component involved in the regulation of recombination and resection. Cells lacking centrosomes or depleted for CEP170 are, consequently, hypersensitive to DNA damaging agents. Moreover, low levels of CEP170 in multiple cancer types correlate with an increase of the mutation burden associated with specific mutational signatures and a better prognosis, suggesting that changes in CEP170 can act as a mutation driver but could also be targeted to improve current oncological treatments.
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Affiliation(s)
- Guillermo Rodríguez‐Real
- Departamento de Genética, Facultad de BiologíaUniversidad de SevillaSevillaSpain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevillaSpain
| | - Andrés Domínguez‐Calvo
- Departamento de Genética, Facultad de BiologíaUniversidad de SevillaSevillaSpain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevillaSpain
| | - Rosario Prados‐Carvajal
- Departamento de Genética, Facultad de BiologíaUniversidad de SevillaSevillaSpain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevillaSpain
| | - Aleix Bayona‐Feliú
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Sonia Gomes‐Pereira
- Department of Cell Biology, Sciences IIIUniversity of GenevaGenevaSwitzerland
| | - Fernando R Balestra
- Departamento de Genética, Facultad de BiologíaUniversidad de SevillaSevillaSpain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevillaSpain
| | - Pablo Huertas
- Departamento de Genética, Facultad de BiologíaUniversidad de SevillaSevillaSpain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa‐CABIMERUniversidad de Sevilla‐CSIC‐Universidad Pablo de OlavideSevillaSpain
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Pugh K, Davies M, Powathil G. A Mathematical Model to Investigate the Effects of Ceralasertib and Olaparib in Targeting the Cellular DNA Damage Response Pathway. J Pharmacol Exp Ther 2023; 387:55-65. [PMID: 37391224 DOI: 10.1124/jpet.122.001558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/11/2023] [Accepted: 05/25/2023] [Indexed: 07/02/2023] Open
Abstract
The ataxia-telangiectasia and Rad3-related (ATR) inhibitor ceralasertib and the poly (ADP-ribose) polymerase (PARP) inhibitor olaparib have shown synergistic activity, in vitro, in the FaDu ATM-knockout cell line. It was found that combining these drugs with lower doses and for shorter treatment periods induced greater or equal toxicity in cancer cells than using either as a single agent. Here, we developed a biologically motivated mathematical model governed by a set of ordinary differential equations, considering the cell cycle-specific interactions of olaparib and ceralasertib. By exploring a range of different possible drug mechanisms, we have studied the effects of their combination as well as which drug interactions are the most prominent. After careful model selection, the model was calibrated and compared with relevant experimental data. We have used this developed model further to investigate other doses of olaparib and ceralasertib in combination, which can be potentially helpful in exploring optimized dosage and delivery. SIGNIFICANCE STATEMENT: Drugs that target cellular DNA damage repair pathways are now being used as a new way to maximize the effect of multimodality treatments such as radiotherapy. Here, we develop a mathematical model to investigate the effects of ceralasertib and olaparib, two drugs that target DNA damage response pathways.
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Affiliation(s)
- Kira Pugh
- Department of Mathematics, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom (K.P., G.P.) and Oncology R&D, AstraZeneca, Cambridge, United Kingdom (M.D.)
| | - Michael Davies
- Department of Mathematics, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom (K.P., G.P.) and Oncology R&D, AstraZeneca, Cambridge, United Kingdom (M.D.)
| | - Gibin Powathil
- Department of Mathematics, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom (K.P., G.P.) and Oncology R&D, AstraZeneca, Cambridge, United Kingdom (M.D.)
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37
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Petit C, Bonnet C, Safieddine S. Deafness: from genetic architecture to gene therapy. Nat Rev Genet 2023; 24:665-686. [PMID: 37173518 DOI: 10.1038/s41576-023-00597-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/15/2023]
Abstract
Progress in deciphering the genetic architecture of human sensorineural hearing impairment (SNHI) or loss, and multidisciplinary studies of mouse models, have led to the elucidation of the molecular mechanisms underlying auditory system function, primarily in the cochlea, the mammalian hearing organ. These studies have provided unparalleled insights into the pathophysiological processes involved in SNHI, paving the way for the development of inner-ear gene therapy based on gene replacement, gene augmentation or gene editing. The application of these approaches in preclinical studies over the past decade has highlighted key translational opportunities and challenges for achieving effective, safe and sustained inner-ear gene therapy to prevent or cure monogenic forms of SNHI and associated balance disorders.
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Affiliation(s)
- Christine Petit
- Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, F-75012, Paris, France.
- Collège de France, F-75005, Paris, France.
| | - Crystel Bonnet
- Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, F-75012, Paris, France
| | - Saaïd Safieddine
- Institut Pasteur, Université Paris Cité, Inserm, Institut de l'Audition, F-75012, Paris, France
- Centre National de la Recherche Scientifique, F-75016, Paris, France
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38
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Tischler JD, Tsuchida H, Oda TT, Park A, Adeyemi RO. RADIF(C1orf112)-FIGNL1 Complex Regulates RAD51 Chromatin Association to Promote Viability After Replication Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.556595. [PMID: 37808755 PMCID: PMC10557588 DOI: 10.1101/2023.09.25.556595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Homologous recombination (HR) plays critical roles in repairing lesions that arise during DNA replication and is thus essential for viability. RAD51 plays important roles during replication and HR, however, how RAD51 is regulated downstream of nucleofilament formation and how the varied RAD51 functions are regulated is not clear. We have investigated the poorly characterized protein c1orf112/RADIF that previously scored in genome-wide screens for mediators of DNA inter-strand crosslink (ICL) repair. Upon ICL agent exposure, RADIF loss leads to marked cell death, elevated chromosomal instability, increased micronuclei formation, altered cell cycle progression and increased DNA damage signaling. RADIF is recruited to damage foci and forms a complex with FIGNL1. Both proteins have epistatic roles in ICL repair, forming a co-stable complex. Mechanistically, RADIF loss leads to increased RAD51 amounts and foci on chromatin both with or without exogenous DNA damage, defective replication fork progression and reduced HR competency. We posit that RADIF is essential for limiting RAD51 levels on chromatin in the absence of damage and for RAD51 dissociation from nucleofilaments to properly complete HR. Failure to do so leads to replication slowing and inability to complete repair.
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39
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Davó-Martínez C, Helfricht A, Ribeiro-Silva C, Raams A, Tresini M, Uruci S, van Cappellen W, Taneja N, Demmers JA, Pines A, Theil A, Vermeulen W, Lans H. Different SWI/SNF complexes coordinately promote R-loop- and RAD52-dependent transcription-coupled homologous recombination. Nucleic Acids Res 2023; 51:9055-9074. [PMID: 37470997 PMCID: PMC10516656 DOI: 10.1093/nar/gkad609] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 07/05/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023] Open
Abstract
The SWI/SNF family of ATP-dependent chromatin remodeling complexes is implicated in multiple DNA damage response mechanisms and frequently mutated in cancer. The BAF, PBAF and ncBAF complexes are three major types of SWI/SNF complexes that are functionally distinguished by their exclusive subunits. Accumulating evidence suggests that double-strand breaks (DSBs) in transcriptionally active DNA are preferentially repaired by a dedicated homologous recombination pathway. We show that different BAF, PBAF and ncBAF subunits promote homologous recombination and are rapidly recruited to DSBs in a transcription-dependent manner. The PBAF and ncBAF complexes promote RNA polymerase II eviction near DNA damage to rapidly initiate transcriptional silencing, while the BAF complex helps to maintain this transcriptional silencing. Furthermore, ARID1A-containing BAF complexes promote RNaseH1 and RAD52 recruitment to facilitate R-loop resolution and DNA repair. Our results highlight how multiple SWI/SNF complexes perform different functions to enable DNA repair in the context of actively transcribed genes.
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Affiliation(s)
- Carlota Davó-Martínez
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Angela Helfricht
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Anja Raams
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Maria Tresini
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Sidrit Uruci
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Wiggert A van Cappellen
- Erasmus Optical Imaging Center, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam 3015 GD, The Netherlands
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van de Kooij B, van der Wal FJ, Rother MB, Creixell P, Stout M, Wiegant W, Joughin BA, Vornberger J, van Vugt MA, Altmeyer M, Yaffe MB, van Attikum H. The Fanconi anemia core complex promotes CtIP-dependent end-resection to drive homologous recombination at DNA double-strand breaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556391. [PMID: 37732274 PMCID: PMC10508776 DOI: 10.1101/2023.09.05.556391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Homologous Recombination (HR) is a high-fidelity repair mechanism of DNA Double-Strand Breaks (DSBs), which are induced by irradiation, genotoxic chemicals or physiological DNA damaging processes. DSBs are also generated as intermediates during the repair of interstrand crosslinks (ICLs). In this context, the Fanconi anemia (FA) core complex, which is effectively recruited to ICLs, promotes HR-mediated DSB-repair. However, whether the FA core complex also promotes HR at ICL-independent DSBs remains controversial. Here, we identified the FA core complex members FANCL and Ube2T as HR-promoting factors in a CRISPR/Cas9-based screen with cells carrying the DSB-repair reporter DSB-Spectrum. Using isogenic cell-line models, we validated the HR-function of FANCL and Ube2T, and demonstrated a similar function for their ubiquitination-substrate FANCD2. We further show that FANCL and Ube2T are directly recruited to DSBs and are required for the accumulation of FANCD2 at these break sites. Mechanistically, we demonstrate that FANCL ubiquitin ligase activity is required for the accumulation of the nuclease CtIP at DSBs, and consequently for optimal end-resection and Rad51 loading. CtIP overexpression rescues HR in FANCL-deficient cells, validating that FANCL primarily regulates HR by promoting CtIP recruitment. Together, these data demonstrate that the FA core complex and FANCD2 have a dual genome maintenance function by promoting repair of DSBs as well as the repair of ICLs.
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Affiliation(s)
- Bert van de Kooij
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Current address: Department of Medical Oncology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Fenna J. van der Wal
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Magdalena B. Rother
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Pau Creixell
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Current address: CRUK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Merula Stout
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Wouter Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Brian A. Joughin
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Julia Vornberger
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Marcel A.T.M. van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, the Netherlands
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich (UZH), Zurich, Switzerland
| | - Michael B. Yaffe
- Koch Institute for Integrative Cancer Research, MIT Center for Precision Cancer Medicine, Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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Gong R, Ma Z, He L, Jiang S, Cao D, Cheng Y. Identification and evaluation of a novel PARP1 inhibitor for the treatment of triple-negative breast cancer. Chem Biol Interact 2023; 382:110567. [PMID: 37271214 DOI: 10.1016/j.cbi.2023.110567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/20/2023] [Accepted: 05/24/2023] [Indexed: 06/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is a particularly invasive subtype of breast cancer and usually has a poor prognosis due to the lack of effective therapeutic targets. Approximately 25% of TNBC patients carry a breast cancer susceptibility gene1/2 (BRCA1/2) mutation. Clinically, PARP1 inhibitors have been approved for the treatment of patients with BRCA1/2-mutated breast cancer through the mechanism of synthetic lethality. In this study, we identified compound 6 {systematic name: 2-[2-(4-Hydroxy-phenyl)-vinyl]-3H-quinazolin-4-one} as a novel PARP1 inhibitor from established virtual screening methods. Compound 6 exerted stronger PARP1 inhibitory activity and anti-cancer activity as compared to olaparib in BRCA1-mutated TNBC cells and TNBC patient-derived organoids. Unexpectedly, we found that compound 6 also significantly inhibited cell viability, proliferation, and induced cell apoptosis in BRCA wild-type TNBC cells. To further elucidate the underlying molecular mechanism, we found that tankyrase (TNKS), a vital promoter of homologous-recombination repair, was a potential target of compound 6 by cheminformatics analysis. Compound 6 not only decreased the expression of PAR, but also down-regulated the expression of TNKS, thus resulting in significant DNA single-strand and double-strand breaks in BRCA wild-type TNBC cells. In addition, we demonstrated that compound 6 enhanced the sensitivity of BRCA1-mutated and wild-type TNBC cells to chemotherapy including paclitaxel and cisplatin. Collectively, our study identified a novel PARP1 inhibitor, providing a therapeutic candidate for the treatment of TNBC.
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Affiliation(s)
- Rong Gong
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China; Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
| | - ZhongYe Ma
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China; Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
| | - LinHao He
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China; Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China
| | - ShiLong Jiang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - DongSheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China.
| | - Yan Cheng
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China; Hunan Provincial Engineering Research Centre of Translational Medicine and Innovative Drug, Changsha, China.
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42
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El Gazzar WB, Albakri KA, Hasan H, Badr AM, Farag AA, Saleh OM. Poly(ADP-ribose) polymerase inhibitors in the treatment landscape of triple-negative breast cancer (TNBC). J Oncol Pharm Pract 2023; 29:1467-1479. [PMID: 37559370 DOI: 10.1177/10781552231188903] [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: 08/11/2023]
Abstract
OBJECTIVE Chemotherapy is the mainstay for triple-negative breast cancer (TNBC) patients. Over the years, the use of chemotherapy for these patients has demonstrated many adversities, including toxicity and resistance, which suggested the need to develop novel alternative therapeutic options, such as poly(ADP-ribose) polymerase inhibitors (PARPi). Herein, we provide an overview on PARPi, mechanisms of action and the role of biomarkers in PARPi sensitivity trials, clinical advances in PARPi therapy for TNBC patients based on the most recent studies and findings of clinical trials, and challenges that prevent PARP inhibitors from achieving high efficacy such as resistance and overlapping toxicities with other chemotherapies. DATA SOURCES Searching for relevant articles was done using PubMed and Cochrane Library databases by using the keywords including TNBC; chemotherapy; PARPi; BRCA; homologous recombination repair (HRR). Studies had to be published in full-text in English in order to be considered. DATA SUMMARY Although PARPi have been used in the treatment of local/metastatic breast malignancies that are HER2 negative and has a germline BRCA mutation, several questions are still to be answered in order to maximize the clinical benefit of PARP inhibitors in TNBC treatment, such as questions related to the optimal use in the neoadjuvant and metastatic settings as well as the best combinations with various chemotherapies. CONCLUSIONS PARPi are emerging treatment options for patients with gBRCA1/2 mutations. Determining patients that are most likely to benefit from PARPi and identifying the optimal treatment combinations with high efficacy and fewer side effects are currently ongoing.
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Affiliation(s)
- Walaa Bayoumie El Gazzar
- Department of Anatomy, Physiology and Biochemistry, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Benha University, Benha City, Egypt
| | | | - Hanan Hasan
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman, Jordan
| | - Amira M Badr
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Pharmacology and Toxicology, College of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Amina A Farag
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Benha University, Benha City, Egypt
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Canoy RJ, Shmakova A, Karpukhina A, Lomov N, Tiukacheva E, Kozhevnikova Y, André F, Germini D, Vassetzky Y. Specificity of cancer-related chromosomal translocations is linked to proximity after the DNA double-strand break and subsequent selection. NAR Cancer 2023; 5:zcad049. [PMID: 37750169 PMCID: PMC10518054 DOI: 10.1093/narcan/zcad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/01/2023] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Most cancer-related chromosomal translocations appear to be cell type specific. It is currently unknown why different chromosomal translocations occur in different cells. This can be due to either the occurrence of particular translocations in specific cell types or adaptive survival advantage conferred by translocations only in specific cells. We experimentally addressed this question by double-strand break (DSB) induction at MYC, IGH, AML and ETO loci in the same cell to generate chromosomal translocations in different cell lineages. Our results show that any translocation can potentially arise in any cell type. We have analyzed different factors that could affect the frequency of the translocations, and only the spatial proximity between gene loci after the DSB induction correlated with the resulting translocation frequency, supporting the 'breakage-first' model. Furthermore, upon long-term culture of cells with the generated chromosomal translocations, only oncogenic MYC-IGH and AML-ETO translocations persisted over a 60-day period. Overall, the results suggest that chromosomal translocation can be generated after DSB induction in any type of cell, but whether the cell with the translocation would persist in a cell population depends on the cell type-specific selective survival advantage that the chromosomal translocation confers to the cell.
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Affiliation(s)
- Reynand Jay Canoy
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Institute of Human Genetics, National Institutes of Health, University of the Philippines Manila, 1000 Manila, The Philippines
| | - Anna Shmakova
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Laboratory of Molecular Endocrinology, Institute of Experimental Cardiology, Federal State Budgetary Organization ‘National Cardiology Research Center’ of the Ministry of Health of the Russian Federation, 127994 Moscow, Russia
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Anna Karpukhina
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Nikolai Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugenia Tiukacheva
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
| | - Yana Kozhevnikova
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Franck André
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Diego Germini
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
| | - Yegor Vassetzky
- UMR 9018, CNRS, Univ. Paris-Sud, Université Paris Saclay, Institut Gustave Roussy, F-94805 Villejuif, France
- Koltzov Institute of Developmental Biology, 117334 Moscow, Russia
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Niu H, An X, Wang X, Yang M, Cheng F, Lei A, Luo J. Dynamic role of Scd1 gene during mouse oocyte growth and maturation. Int J Biol Macromol 2023; 247:125307. [PMID: 37315672 DOI: 10.1016/j.ijbiomac.2023.125307] [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: 01/01/2023] [Revised: 05/07/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
Mammalian reproductive ability is regulated by many factors, among which the fatty acid metabolism network provides energy for oocyte growth and primordial follicle formation during early mouse oogenesis. But the mechanism behind that is still unknown. Stearoyl-CoA desaturase 1 (Scd1) gene expression is increased during the oogenesis process, supporting the oocyte's healthy growth. Taking advantage of gene-edited mice lacking stearoyl-Coenzyme A desaturase 1 gene (Scd1-/-), we analyzed relative gene expression in perinatal ovaries from wildtype, and Scd1-/- mice. Scd1 deficiency dysregulates expression of meiosis-related genes (e.g., Sycp1, Sycp2, Sycp3, Rad51, Ddx4) and a variety of genes (e.g., Nobox, Lhx8, Bmp15, Ybx2, Dppa3, Oct4, Sohlh1, Zp3) associated with oocyte growth and differentiation, leading to a lower oocyte maturation rate. The absence of Scd1 significantly impedes meiotic progression, causes DNA damage, and inhibits damage repair in Scd1-/- ovaries. Moreover, we find that Scd1 absense dramatically disrupts the abundance of fatty acid metabolism genes (e.g., Fasn, Srebp1, Acaca) and the lipid droplet content. Thus, our findings substantiate a major role for Scd1 as a multifunctional regulator of fatty acid networks necessary for oocyte maintenance and differentiation during early follicular genesis.
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Affiliation(s)
- Huimin Niu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xuetong An
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xinpei Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Min Yang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Fei Cheng
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Anmin Lei
- Institute of Shaanxi Stem Cell Engineering and Technology Center, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Jun Luo
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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45
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Bian X, Sun C, Cheng J, Hong B. Targeting DNA Damage Repair and Immune Checkpoint Proteins for Optimizing the Treatment of Endometrial Cancer. Pharmaceutics 2023; 15:2241. [PMID: 37765210 PMCID: PMC10536053 DOI: 10.3390/pharmaceutics15092241] [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: 06/05/2023] [Revised: 08/04/2023] [Accepted: 08/12/2023] [Indexed: 09/29/2023] Open
Abstract
The dependence of cancer cells on the DNA damage response (DDR) pathway for the repair of endogenous- or exogenous-factor-induced DNA damage has been extensively studied in various cancer types, including endometrial cancer (EC). Targeting one or more DNA damage repair protein with small molecules has shown encouraging treatment efficacy in preclinical and clinical models. However, the genes coding for DDR factors are rarely mutated in EC, limiting the utility of DDR inhibitors in this disease. In the current review, we recapitulate the functional role of the DNA repair system in the development and progression of cancer. Importantly, we discuss strategies that target DDR proteins, including PARP, CHK1 and WEE1, as monotherapies or in combination with cytotoxic agents in the treatment of EC and highlight the compounds currently being evaluated for their efficacy in EC in clinic. Recent studies indicate that the application of DNA damage agents in cancer cells leads to the activation of innate and adaptive immune responses; targeting immune checkpoint proteins could overcome the immune suppressive environment in tumors. We further summarize recently revolutionized immunotherapies that have been completed or are now being evaluated for their efficacy in advanced EC and propose future directions for the development of DDR-based cancer therapeutics in the treatment of EC.
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Affiliation(s)
- Xing Bian
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China; (X.B.); (C.S.); (J.C.)
| | - Chuanbo Sun
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China; (X.B.); (C.S.); (J.C.)
| | - Jin Cheng
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China; (X.B.); (C.S.); (J.C.)
| | - Bo Hong
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
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46
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Palovcak A, Yuan F, Verdun R, Luo L, Zhang Y. Fanconi anemia associated protein 20 (FAAP20) plays an essential role in homology-directed repair of DNA double-strand breaks. Commun Biol 2023; 6:873. [PMID: 37620397 PMCID: PMC10449828 DOI: 10.1038/s42003-023-05252-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
FAAP20 is a Fanconi anemia (FA) protein that associates with the FA core complex to promote FANCD2/FANCI monoubiquitination and activate the damage response to interstrand crosslink damage. Here, we report that FAAP20 has a marked role in homologous recombination at a DNA double-strand break not associated with an ICL and separable from its binding partner FANCA. While FAAP20's role in homologous recombination is not dependent on FANCA, we found that FAAP20 stimulates FANCA's biochemical activity in vitro and participates in the single-strand annealing pathway of double-strand break repair in a FANCA-dependent manner. This indicates that FAAP20 has roles in several homology-directed repair pathways. Like other homology-directed repair factors, FAAP20 loss causes a reduction in nuclear RAD51 Irradiation-induced foci; and sensitizes cancer cells to ionizing radiation and PARP inhibition. In summary, FAAP20 participates in DNA double strand break repair by supporting homologous recombination in a non-redundant manner to FANCA, and single-strand annealing repair via FANCA-mediated strand annealing activity.
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Affiliation(s)
- Anna Palovcak
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Ramiro Verdun
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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47
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Sakasai R, Matsui T, Sunatani Y, Iwabuchi K. UbcH5c-dependent activation of DNA-dependent protein kinase in response to replication-mediated DNA double-strand breaks. Biochem Biophys Res Commun 2023; 668:42-48. [PMID: 37244033 DOI: 10.1016/j.bbrc.2023.05.068] [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: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/29/2023]
Abstract
Camptothecin (CPT) exhibits strong cytotoxicity by inducing DNA double-strand breaks (DSBs) through DNA replication. Unlike radiation-induced DSBs, which have two DNA ends, CPT-induced DSBs are considered to have only one DNA end. However, the differences in cellular responses to one-ended and two-ended DSBs are not well understood. Our previous study showed that proteasome inhibitor treatment suppressed CPT-induced activation of DNA-PK, a factor required for non-homologous end-joining in DSB repair, suggesting that the ubiquitin-proteasome pathway is involved in DNA-PK activation in response to one-ended DSBs. To identify the ubiquitination factors required for DNA-PK activation, we screened an siRNA library against E2 ubiquitin-conjugating enzymes and identified UbcH5c. Knockdown of UbcH5c suppressed DNA-PK activation caused by CPT, but not by the radio-mimetic drug neocarzinostatin. UbcH5c-dependent DNA-PK activation occurred independent of DNA end resection. Furthermore, loss of UbcH5c reduced DNA-PK-dependent chromosomal aberrations and suppressed the activation of cell cycle checkpoint in response to CPT. These results suggest that UbcH5c regulates DNA-PK activation in response to one-ended DSBs caused by replication fork collapse. To our knowledge, this is the first report of a DSB repair-related factor that is differentially involved in the response to one- and two-ended DSBs.
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Affiliation(s)
- Ryo Sakasai
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Tadashi Matsui
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Yumi Sunatani
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan
| | - Kuniyoshi Iwabuchi
- Department of Biochemistry I, Kanazawa Medical University, Kahoku, Ishikawa, 920-0293, Japan.
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48
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Xu X, An H, Wu C, Sang R, Wu L, Lou Y, Yang X, Xi Y. HR repair pathway plays a crucial role in maintaining neural stem cell fate under irradiation stress. Life Sci Alliance 2023; 6:e202201802. [PMID: 37197982 PMCID: PMC10192720 DOI: 10.26508/lsa.202201802] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023] Open
Abstract
Environmental stress can cause mutation or genomic instability in stem cells which, in some cases, leads to tumorigenesis. Mechanisms to monitor and eliminate these mutant stem cells remain elusive. Here, using the Drosophila larval brain as a model, we show that X-ray irradiation (IR) at the early larval stage leads to accumulation of nuclear Prospero (Pros), resulting in premature differentiation of neural stem cells (neuroblasts, NBs). Through NB-specific RNAi screenings, we determined that it is the Mre11-Rad50-Nbs1 complex and the homologous recombination (HR) repair pathway, rather than non-homologous end-joining pathway that plays, a dominant role in the maintenance of NBs under IR stress. The DNA damage sensor ATR/mei-41 is shown to act to prevent IR-induced nuclear Pros in a WRNexo-dependent manner. The accumulation of nuclear Pros in NBs under IR stress, leads to NB cell fate termination, rather than resulting in mutant cell proliferation. Our study reveals an emerging mechanism for the HR repair pathway in maintaining neural stem cell fate under irradiation stress.
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Affiliation(s)
- Xiao Xu
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Huanping An
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Clinical Molecular Biology of Hanzhong City, Hanzhong Vocational and Technique College, Hanzhong, China
| | - Cheng Wu
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Rong Sang
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Litao Wu
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuhan Lou
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaohang Yang
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
- Joint Institute of Genetics and Genomic Medicine, Between Zhejiang University and University of Toronto, Zhejiang University, Hangzhou, China
| | - Yongmei Xi
- The Women's Hospital, Institute of Genetics, Zhejiang Provincial Key Laboratory of Genetic & Development Disorders, School of Medicine, Zhejiang University, Hangzhou, China
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49
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Mikkelsen NS, Bak RO. Enrichment strategies to enhance genome editing. J Biomed Sci 2023; 30:51. [PMID: 37393268 PMCID: PMC10315055 DOI: 10.1186/s12929-023-00943-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Genome editing technologies hold great promise for numerous applications including the understanding of cellular and disease mechanisms and the development of gene and cellular therapies. Achieving high editing frequencies is critical to these research areas and to achieve the overall goal of being able to manipulate any target with any desired genetic outcome. However, gene editing technologies sometimes suffer from low editing efficiencies due to several challenges. This is often the case for emerging gene editing technologies, which require assistance for translation into broader applications. Enrichment strategies can support this goal by selecting gene edited cells from non-edited cells. In this review, we elucidate the different enrichment strategies, their many applications in non-clinical and clinical settings, and the remaining need for novel strategies to further improve genome research and gene and cellular therapy studies.
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Affiliation(s)
- Nanna S Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark.
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50
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Chen H, Liu X, Li L, Tan Q, Li S, Li L, Li C, Fu J, Lu Y, Wang Y, Sun Y, Luo ZG, Lu Z, Sun Q, Liu Z. CATI: an efficient gene integration method for rodent and primate embryos by MMEJ suppression. Genome Biol 2023; 24:146. [PMID: 37353834 PMCID: PMC10288798 DOI: 10.1186/s13059-023-02987-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/13/2023] [Indexed: 06/25/2023] Open
Abstract
The efficiency of homology-directed repair (HDR) plays a crucial role in the development of animal models and gene therapy. We demonstrate that microhomology-mediated end-joining (MMEJ) constitutes a substantial proportion of DNA repair during CRISPR-mediated gene editing. Using CasRx to downregulate a key MMEJ factor, Polymerase Q (Polq), we improve the targeted integration efficiency of linearized DNA fragments and single-strand oligonucleotides (ssODN) in mouse embryos and offspring. CasRX-assisted targeted integration (CATI) also leads to substantial improvements in HDR efficiency during the CRISPR/Cas9 editing of monkey embryos. We present a promising tool for generating monkey models and developing gene therapies for clinical trials.
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Affiliation(s)
- Hongyu Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Xingchen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Lanxin Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qingtong Tan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Shiyan Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- University of Chinese Academy of Sciences, 19A Yu-Quan Road, Beijing, 100049, China
| | - Li Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Chunyang Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Jiqiang Fu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yong Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
| | - Yidi Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China
| | - Zhen-Ge Luo
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zongyang Lu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Qiang Sun
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| | - Zhen Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science & Intelligence Technology, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
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