1
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Li Y, Li L, Wang X, Zhao F, Yang Y, Zhou Y, Zhang J, Wang L, Jiang Z, Zhang Y, Chen Y, Wu C, Li K, Zhang T, Wang P, Mao Z, Zhu W, Xu X, Liang S, Lou Z, Yuan J. USP25 Elevates SHLD2-Mediated DNA Double-Strand Break Repair and Regulates Chemoresponse in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2403485. [PMID: 38803048 DOI: 10.1002/advs.202403485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Indexed: 05/29/2024]
Abstract
DNA damage plays a significant role in the tumorigenesis and progression of the disease. Abnormal DNA repair affects the therapy and prognosis of cancer. In this study, it is demonstrated that the deubiquitinase USP25 promotes non-homologous end joining (NHEJ), which in turn contributes to chemoresistance in cancer. It is shown that USP25 deubiquitinates SHLD2 at the K64 site, which enhances its binding with REV7 and promotes NHEJ. Furthermore, USP25 deficiency impairs NHEJ-mediated DNA repair and reduces class switch recombination (CSR) in USP25-deficient mice. USP25 is overexpressed in a subset of colon cancers. Depletion of USP25 sensitizes colon cancer cells to IR, 5-Fu, and cisplatin. TRIM25 is also identified, an E3 ligase, as the enzyme responsible for degrading USP25. Downregulation of TRIM25 leads to an increase in USP25 levels, which in turn induces chemoresistance in colon cancer cells. Finally, a peptide that disrupts the USP25-SHLD2 interaction is successfully identified, impairing NHEJ and increasing sensitivity to chemotherapy in PDX model. Overall, these findings reveal USP25 as a critical effector of SHLD2 in regulating the NHEJ repair pathway and suggest its potential as a therapeutic target for cancer therapy.
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Affiliation(s)
- Yunhui Li
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Lei Li
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
| | - Xinshu Wang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Fei Zhao
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yuntong Yang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Yujuan Zhou
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Jiyuan Zhang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Li Wang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Zeshan Jiang
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
| | - Yuanyuan Zhang
- Department of General Surgery and Colorectal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Yuping Chen
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200080, China
| | - Chenming Wu
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
| | - Ke Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Tingting Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, China
| | - Ping Wang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Shanghai, 200072, China
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal-Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, Tongji University School of Medicine, Shanghai, 200040, China
| | - Weiguo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, 518037, China
| | - Xingzhi Xu
- The Sixth Affiliated Hospital of Shenzhen University, Guangdong Key Laboratory for Genome Stability and Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Shikang Liang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, 999077, Hong Kong
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jian Yuan
- Medical Innovation Center, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, 200120, China
- Cancer Center, Tongji University School of Medicine, Shanghai, 200331, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, 200331, China
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2
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Huang ME, Qin Y, Shang Y, Hao Q, Zhan C, Lian C, Luo S, Liu LD, Zhang S, Zhang Y, Wo Y, Li N, Wu S, Gui T, Wang B, Luo Y, Cai Y, Liu X, Xu Z, Dai P, Li S, Zhang L, Dong J, Wang J, Zheng X, Xu Y, Sun Y, Wu W, Yeap LS, Meng FL. C-to-G editing generates double-strand breaks causing deletion, transversion and translocation. Nat Cell Biol 2024; 26:294-304. [PMID: 38263276 DOI: 10.1038/s41556-023-01342-2] [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: 03/05/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024]
Abstract
Base editors (BEs) introduce base substitutions without double-strand DNA cleavage. Besides precise substitutions, BEs generate low-frequency 'stochastic' byproducts through unclear mechanisms. Here, we performed in-depth outcome profiling and genetic dissection, revealing that C-to-G BEs (CGBEs) generate substantial amounts of intermediate double-strand breaks (DSBs), which are at the centre of several byproducts. Imperfect DSB end-joining leads to small deletions via end-resection, templated insertions or aberrant transversions during end fill-in. Chromosomal translocations were detected between the editing target and off-targets of Cas9/deaminase origin. Genetic screenings of DNA repair factors disclosed a central role of abasic site processing in DSB formation. Shielding of abasic sites by the suicide enzyme HMCES reduced CGBE-initiated DSBs, providing an effective way to minimize DSB-triggered events without affecting substitutions. This work demonstrates that CGBEs can initiate deleterious intermediate DSBs and therefore require careful consideration for therapeutic applications, and that HMCES-aided CGBEs hold promise as safer tools.
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Affiliation(s)
- Min Emma Huang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yining Qin
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yafang Shang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Qian Hao
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chuanzong Zhan
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaoyang Lian
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Simin Luo
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liu Daisy Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Senxin Zhang
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Wo
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Institute of Thoracic Oncology, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuheng Wu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Tuantuan Gui
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Binbin Wang
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yifeng Luo
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Yanni Cai
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Liu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Ziye Xu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Pengfei Dai
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Simiao Li
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Liang Zhang
- Hefei National Research Center for Cross Disciplinary Science, Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Junchao Dong
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jian Wang
- International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingjie Xu
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihua Sun
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Institute of Thoracic Oncology, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Wu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China
| | - Leng-Siew Yeap
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Endocrinology and Metabolic Diseases, Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Fei-Long Meng
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of Sciences, Shanghai, China.
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China.
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3
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Denis-Lagache N, Oblet C, Marchiol T, Baylet A, Têteau O, Dalloul I, Dalloul Z, Zawil L, Dézé O, Cook-Moreau J, Saintamand A, Boutouil H, Khamlichi AA, Carrion C, Péron S, Le Noir S, Laffleur B, Cogné M. Attempts to evaluate locus suicide recombination and its potential role in B cell negative selection in the mouse. Front Immunol 2023; 14:1155906. [PMID: 37359540 PMCID: PMC10288998 DOI: 10.3389/fimmu.2023.1155906] [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: 01/31/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction In mature B cells, activation-induced deaminase reshapes Ig genes through somatic hypermutation and class switch recombination of the Ig heavy chain (IgH) locus under control of its 3' cis-regulatory region (3'RR). The 3'RR is itself transcribed and can undergo "locus suicide recombination" (LSR), then deleting the constant gene cluster and terminating IgH expression. The relative contribution of LSR to B cell negative selection remains to be determined. Methods Here, we set up a knock-in mouse reporter model for LSR events with the aim to get clearer insights into the circumstances triggering LSR. In order to explore the consequences of LSR defects, we reciprocally explored the presence of autoantibodies in various mutant mouse lines in which LSR was perturbed by the lack of Sµ or of the 3'RR. Results Evaluation of LSR events in a dedicated reporter mouse model showed their occurrence in various conditions of B cell activation, notably in antigen-experienced B cells Studies of mice with LSR defects evidenced increased amounts of self-reactive antibodies. Discussion While the activation pathways associated with LSR are diverse, in vivo as well as in vitro, this study suggests that LSR may contribute to the elimination of self-reactive B cells.
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Affiliation(s)
- Nicolas Denis-Lagache
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Christelle Oblet
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Tiffany Marchiol
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Audrey Baylet
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Ophélie Têteau
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Iman Dalloul
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Zeinab Dalloul
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Lina Zawil
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | | | - Jeanne Cook-Moreau
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Alexis Saintamand
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Hend Boutouil
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Ahmed Amine Khamlichi
- Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS), Toulouse University, Toulouse, France
| | - Claire Carrion
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Sophie Péron
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | - Sandrine Le Noir
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
| | | | - Michel Cogné
- Limoges University, Centre National de la Recherche Scientifique (CNRS), Limoges, France
- Rennes University, Inserm, Rennes, France
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4
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Wang Y, Zhang S, Yang X, Hwang JK, Zhan C, Lian C, Wang C, Gui T, Wang B, Xie X, Dai P, Zhang L, Tian Y, Zhang H, Han C, Cai Y, Hao Q, Ye X, Liu X, Liu J, Cao Z, Huang S, Song J, Pan-Hammarström Q, Zhao Y, Alt FW, Zheng X, Da LT, Yeap LS, Meng FL. Mesoscale DNA feature in antibody-coding sequence facilitates somatic hypermutation. Cell 2023; 186:2193-2207.e19. [PMID: 37098343 DOI: 10.1016/j.cell.2023.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/06/2023] [Accepted: 03/24/2023] [Indexed: 04/27/2023]
Abstract
Somatic hypermutation (SHM), initiated by activation-induced cytidine deaminase (AID), generates mutations in the antibody-coding sequence to allow affinity maturation. Why these mutations intrinsically focus on the three nonconsecutive complementarity-determining regions (CDRs) remains enigmatic. Here, we found that predisposition mutagenesis depends on the single-strand (ss) DNA substrate flexibility determined by the mesoscale sequence surrounding AID deaminase motifs. Mesoscale DNA sequences containing flexible pyrimidine-pyrimidine bases bind effectively to the positively charged surface patches of AID, resulting in preferential deamination activities. The CDR hypermutability is mimicable in in vitro deaminase assays and is evolutionarily conserved among species using SHM as a major diversification strategy. We demonstrated that mesoscale sequence alterations tune the in vivo mutability and promote mutations in an otherwise cold region in mice. Our results show a non-coding role of antibody-coding sequence in directing hypermutation, paving the way for the synthetic design of humanized animal models for optimal antibody discovery and explaining the AID mutagenesis pattern in lymphoma.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Senxin Zhang
- Department of Mathematics, Shanghai Normal University, Shanghai 200234, China
| | - Xinrui Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Joyce K Hwang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Chuanzong Zhan
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chaoyang Lian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chong Wang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tuantuan Gui
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Binbin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xia Xie
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Lu Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ying Tian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huizhi Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chong Han
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanni Cai
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Qian Hao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141-83 Stockholm, Sweden; Kindstar Global Precision Medicine Institute, Wuhan 430000, China
| | - Xiaojing Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaquan Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shaohui Huang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Biosciences, University of Chinese Academy of Sciences, Beijing 101499, China
| | - Jie Song
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141-83 Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yaofeng Zhao
- State Key Laboratory of Farm Animal Biotech Breeding, China Agricultural University, Beijing 100193, China
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Leng-Siew Yeap
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; Shanghai Huashen Institute of Microbes and Infections, Shanghai 200052, China.
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5
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Zhao Y, Zhao S, Qin XY, He TT, Hu MM, Gong Z, Wang HM, Gong FY, Gao XM, Wang J. Altered Phenotype and Enhanced Antibody-Producing Ability of Peripheral B Cells in Mice with Cd19-Driven Cre Expression. Cells 2022; 11:cells11040700. [PMID: 35203346 PMCID: PMC8870415 DOI: 10.3390/cells11040700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
Given the importance of B lymphocytes in inflammation and immune defense against pathogens, mice transgenic for Cre under the control of Cd19 promoter (Cd19Cre/+ mice) have been widely used to specifically investigate the role of loxP-flanked genes in B cell development/function. However, impacts of expression/insertion of the Cre transgene on the phenotype and function of B cells have not been carefully studied. Here, we show that the number of marginal zone B and B1a cells was selectively reduced in Cd19Cre/+ mice, while B cell development in the bone marrow and total numbers of peripheral B cells were comparable between Cd19Cre/+ and wild type C57BL/6 mice. Notably, humoral responses to both T cell-dependent and independent antigens were significantly increased in Cd19Cre/+ mice. We speculate that these differences are mainly attributable to reduced surface CD19 levels caused by integration of the Cre-expressing cassette that inactivates one Cd19 allele. Moreover, our literature survey showed that expression of Cd19Cre/+ alone may affect the development/progression of inflammatory and anti-infectious responses. Thus, our results have important implications for the design and interpretation of results on gene functions specifically targeted in B cells in the Cd19Cre/+ mouse strain, for instance, in the context of (auto) inflammatory/infectious diseases.
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Affiliation(s)
- Ying Zhao
- Department of Pathophysiology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China;
| | - Sai Zhao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
| | - Xiao-Yuan Qin
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
| | - Ting-Ting He
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
| | - Miao-Miao Hu
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
| | - Zheng Gong
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
| | - Hong-Min Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
| | - Fang-Yuan Gong
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
- Correspondence: (X.-M.G.); (J.W.); Tel./Fax: +86-512-65882135 (J.W.)
| | - Jun Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; (S.Z.); (X.-Y.Q.); (T.-T.H.); (M.-M.H.); (Z.G.); (H.-M.W.); (F.-Y.G.)
- Correspondence: (X.-M.G.); (J.W.); Tel./Fax: +86-512-65882135 (J.W.)
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6
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Molecular mechanisms of assembly and TRIP13-mediated remodeling of the human Shieldin complex. Proc Natl Acad Sci U S A 2021; 118:2024512118. [PMID: 33597306 PMCID: PMC7923543 DOI: 10.1073/pnas.2024512118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The Shieldin complex, composed of REV7, SHLD1, SHLD2, and SHLD3, protects DNA double-strand breaks (DSBs) to promote nonhomologous end joining. The AAA+ ATPase TRIP13 remodels Shieldin to regulate DNA repair pathway choice. Here we report crystal structures of human SHLD3-REV7 binary and fused SHLD2-SHLD3-REV7 ternary complexes, revealing that assembly of Shieldin requires fused SHLD2-SHLD3 induced conformational heterodimerization of open (O-REV7) and closed (C-REV7) forms of REV7. We also report the cryogenic electron microscopy (cryo-EM) structures of the ATPγS-bound fused SHLD2-SHLD3-REV7-TRIP13 complexes, uncovering the principles underlying the TRIP13-mediated disassembly mechanism of the Shieldin complex. We demonstrate that the N terminus of REV7 inserts into the central channel of TRIP13, setting the stage for pulling the unfolded N-terminal peptide of C-REV7 through the central TRIP13 hexameric channel. The primary interface involves contacts between the safety-belt segment of C-REV7 and a conserved and negatively charged loop of TRIP13. This process is mediated by ATP hydrolysis-triggered rotatory motions of the TRIP13 ATPase, thereby resulting in the disassembly of the Shieldin complex.
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7
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de Krijger I, Boersma V, Jacobs JJL. REV7: Jack of many trades. Trends Cell Biol 2021; 31:686-701. [PMID: 33962851 DOI: 10.1016/j.tcb.2021.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 01/01/2023]
Abstract
The HORMA domain protein REV7, also known as MAD2L2, interacts with a variety of proteins and thereby contributes to the establishment of different complexes. With doing so, REV7 impacts a diverse range of cellular processes and gained increasing interest as more of its activities became uncovered. REV7 has important roles in translesion synthesis and mitotic progression, and acts as a central component in the recently discovered shieldin complex that operates in DNA double-strand break repair. Here we discuss the roles of REV7 in its various complexes, focusing on its activity in genome integrity maintenance. Moreover, we will describe current insights on REV7 structural features that allow it to be such a versatile protein.
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Affiliation(s)
- Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Vera Boersma
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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8
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Repair of programmed DNA lesions in antibody class switch recombination: common and unique features. ACTA ACUST UNITED AC 2021; 2:115-125. [PMID: 33817557 PMCID: PMC7996122 DOI: 10.1007/s42764-021-00035-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 02/22/2021] [Accepted: 03/04/2021] [Indexed: 01/31/2023]
Abstract
The adaptive immune system can diversify the antigen receptors to eliminate various pathogens through programmed DNA lesions at antigen receptor genes. In immune diversification, general DNA repair machineries are applied to transform the programmed DNA lesions into gene mutation or recombination events with common and unique features. Here we focus on antibody class switch recombination (CSR), and review the initiation of base damages, the conversion of damaged base to DNA double-strand break, and the ligation of broken ends. With an emphasis on the unique features in CSR, we discuss recent advances in the understanding of DNA repair/replication coordination, and ERCC6L2-mediated deletional recombination. We further elaborate the application of CSR in end-joining, resection and translesion synthesis assays. In the time of the COVID-19 pandemic, we hope it help to understand the generation of therapeutic antibodies.
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9
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Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Di Noia JM. The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID. NAR Cancer 2021; 2:zcaa019. [PMID: 33554121 PMCID: PMC7848951 DOI: 10.1093/narcan/zcaa019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
In B lymphocytes, the uracil N-glycosylase (UNG) excises genomic uracils made by activation-induced deaminase (AID), thus underpinning antibody gene diversification and oncogenic chromosomal translocations, but also initiating faithful DNA repair. Ung−/− mice develop B-cell lymphoma (BCL). However, since UNG has anti- and pro-oncogenic activities, its tumor suppressor relevance is unclear. Moreover, how the constant DNA damage and repair caused by the AID and UNG interplay affects B-cell fitness and thereby the dynamics of cell populations in vivo is unknown. Here, we show that UNG specifically protects the fitness of germinal center B cells, which express AID, and not of any other B-cell subset, coincident with AID-induced telomere damage activating p53-dependent checkpoints. Consistent with AID expression being detrimental in UNG-deficient B cells, Ung−/− mice develop BCL originating from activated B cells but lose AID expression in the established tumor. Accordingly, we find that UNG is rarely lost in human BCL. The fitness preservation activity of UNG contingent to AID expression was confirmed in a B-cell leukemia model. Hence, UNG, typically considered a tumor suppressor, acquires tumor-enabling activity in cancer cell populations that express AID by protecting cell fitness.
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Affiliation(s)
- Shiva Safavi
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Ariane Larouche
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Anne-Marie Patenaude
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Diana Domanska
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Kiersten Dionne
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Felix Dingler
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Seong-Kwi Kang
- ITR Laboratories Canada, Inc., 19601 Clark Graham Ave, Baie-D'Urfe, QC H9X 3T1, Canada
| | - Yan Liu
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Nathalie Johnson
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Josée Hébert
- Department of Medicine, Université de Montréal, C.P. 6128, Montreal, QC H3C 3J7, Canada
| | - Ramiro E Verdun
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | | | - Francisco Vega
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | - Hilde Nilsen
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
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