1
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Raizenne B, Deyirmendjian C, Lafontaine ML, Balde M, Bechis S, Sur R, Nakada S, Antonelli J, Streeper N, Sivalingam S, Viprakasit D, Averch T, Landman J, Chi T, Pais Jr V, Chew B, Bird V, Andonian S, Canvasser N, Harper J, Penniston K, Bhojani N. The impact of bilateral stone disease on patients’ disease progression and quality of life. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00412-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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2
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Liu B, Jing Z, Zhang X, Chen Y, Mao S, Kaundal R, Zou Y, Wei G, Zang Y, Wang X, Lin W, Di M, Sun Y, Chen Q, Li Y, Xia J, Sun J, Lin CP, Huang X, Chi T. Large-scale multiplexed mosaic CRISPR perturbation in the whole organism. Cell 2022; 185:3008-3024.e16. [PMID: 35870449 DOI: 10.1016/j.cell.2022.06.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/23/2022] [Accepted: 06/20/2022] [Indexed: 12/13/2022]
Abstract
Here, we report inducible mosaic animal for perturbation (iMAP), a transgenic platform enabling in situ CRISPR targeting of at least 100 genes in parallel throughout the mouse body. iMAP combines Cre-loxP and CRISPR-Cas9 technologies and utilizes a germline-transmitted transgene carrying a large array of individually floxed, tandemly linked gRNA-coding units. Cre-mediated recombination triggers expression of all the gRNAs in the array but only one of them per cell, converting the mice to mosaic organisms suitable for phenotypic characterization and also for high-throughput derivation of conventional single-gene perturbation lines via breeding. Using gRNA representation as a readout, we mapped a miniature Perturb-Atlas cataloging the perturbations of 90 genes across 39 tissues, which yields rich insights into context-dependent gene functions and provides a glimpse of the potential of iMAP in genome decoding.
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Affiliation(s)
- Bo Liu
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhengyu Jing
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaoming Zhang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuxin Chen
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Shaoshuai Mao
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ravinder Kaundal
- Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
| | - Yan Zou
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ge Wei
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ying Zang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xinxin Wang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenyang Lin
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Minghui Di
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiwen Sun
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qin Chen
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yongqin Li
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jing Xia
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jianlong Sun
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chao-Po Lin
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xingxu Huang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tian Chi
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai 201210, China; Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA.
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3
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Zou Y, Liu B, Li L, Yin Q, Tang J, Jing Z, Huang X, Zhu X, Chi T. IKZF3 deficiency potentiates chimeric antigen receptor T cells targeting solid tumors. Cancer Lett 2022; 524:121-130. [PMID: 34687790 DOI: 10.1016/j.canlet.2021.10.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 09/28/2021] [Accepted: 10/13/2021] [Indexed: 12/11/2022]
Abstract
Chimeric antigen receptor (CAR) T cell therapy has been successful in treating hematological malignancy, but solid tumors remain refractory. Here, we demonstrated that knocking out transcription factor IKZF3 in HER2-specific CAR T cells targeting breast cancer cells did not affect CAR expression or CAR T cell differentiation, but markedly enhanced killing of the cancer cells in vitro and in a xenograft model, which was associated with increased T cell activation and proliferation. Furthermore, IKZF3 KO had similar effects on the CD133-specific CAR T cells targeting glioblastoma cells. AlphaLISA and RNA-seq analyses indicate that IKZF3 KO increased the expression of genes involved in cytokine signaling, chemotaxis and cytotoxicity. Our results suggest a general strategy for enhancing CAR T efficacy on solid tumors.
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Affiliation(s)
- Yan Zou
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Bo Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; 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
| | - Long Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Qinan Yin
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, Henan, 471000, China
| | - Jiaxing Tang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Zhengyu Jing
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; 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
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xuekai Zhu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
| | - Tian Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Department of Immunobiology, Yale University Medical School, New Haven, CT, USA.
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4
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Liu Y, Chen Y, Dang L, Liu Y, Huang S, Wu S, Ma P, Jiang H, Li Y, Pan Y, Wei Y, Ma X, Liu M, Ji Q, Chi T, Huang X, Wang X, Zhou F. EasyCatch, a convenient, sensitive and specific CRISPR detection system for cancer gene mutations. Mol Cancer 2021; 20:157. [PMID: 34856977 PMCID: PMC8638196 DOI: 10.1186/s12943-021-01456-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/05/2021] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yin Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, No.169 Donghu Road, Wuhan, 430072, China
| | - Yanling Chen
- Department of Hematology, Zhongnan Hospital of Wuhan University, No.169 Donghu Road, Wuhan, 430072, China
| | - Lu Dang
- Department of Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China
| | - Yixin Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No.169 Donghu Road, Wuhan, 430072, China
| | - Shisheng Huang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Sanyun Wu
- Department of Hematology, Zhongnan Hospital of Wuhan University, No.169 Donghu Road, Wuhan, 430072, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Hongqiang Jiang
- Department of Hematology, Zhongnan Hospital of Wuhan University, No.169 Donghu Road, Wuhan, 430072, China
| | - Yi Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No.169 Donghu Road, Wuhan, 430072, China
| | - Yunbao Pan
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, No.169 Donghu Road, Wuhan, 430072, China
| | - Yongchang Wei
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, No.169 Donghu Road, Wuhan, 430072, China
| | - Xiaodong Ma
- Institute for Brain Research and Rehabilitation, Guangdong Key Laboratory of Mental Health and Cognitive Science, Center for Studies of Psychological Application, South China Normal University, Guangzhou, 510631, China
| | - Ming Liu
- State Key Laboratory of Respiratory Disease/National Clinical Research Center for Respiratory Disease/National Center for Respiratory Medicine/Guangzhou Institute of Respiratory Health/The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Tian Chi
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China
| | - Xingxu Huang
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Pudong New Area, Shanghai, 201210, China.
| | - Xinjie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, No.169 Donghu Road, Wuhan, 430072, China.
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5
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Liu Y, Yang G, Huang S, Li X, Wang X, Li G, Chi T, Chen Y, Huang X, Wang X. Enhancing prime editing by Csy4-mediated processing of pegRNA. Cell Res 2021; 31:1134-1136. [PMID: 34103663 PMCID: PMC8486859 DOI: 10.1038/s41422-021-00520-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/13/2021] [Indexed: 02/07/2023] Open
Affiliation(s)
- Yao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Guang Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xin Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Tian Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
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6
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Meng Q, Wang X, Wang Y, Dang L, Liu X, Ma X, Chi T, Wang X, Zhao Q, Yang G, Liu M, Huang X, Ma P. Detection of the SARS-CoV-2 D614G mutation using engineered Cas12a guide RNA. Biotechnol J 2021; 16:e2100040. [PMID: 33595922 DOI: 10.1002/biot.202100040] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/19/2022]
Abstract
Detection of pathogens with single-nucleotide variations is indispensable for the disease tracing, but remains technically challenging. The D614G mutation in the SARS-CoV-2 spike protein is known to markedly enhance viral infectivity but is difficult to detect. Here, we report an effective approach called "synthetic mismatch integrated crRNA guided Cas12a detection" (symRNA-Cas12a) to detect the D614 and G614 variants effectively. Using this method, we systemically screened a pool of crRNAs that contain all the possible nucleotide substitutions covering the -2 to +2 positions around the mutation and identify one crRNA that can efficiently increase the detection specificity by 13-fold over the ancestral crRNA. With this selected crRNA, the symRNA-Cas12a assay can detect as low as 10 copies of synthetic mutant RNA and the results are confirmed to be accurate by Sanger sequencing. Overall, we have developed the symRNA-Cas12a method to specifically, sensitively and rapidly detect the SARS-CoV-2 D614G mutation.
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Affiliation(s)
- Qingzhou Meng
- Guangzhou Laboratory, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Xinjie Wang
- Guangzhou Laboratory, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- Guangdong Key Laboratory of Mental Health and Cognitive Science, Institute for Brain Research and Rehabilitation, Centre for Studies of Psychological Application, South China Normal University, Guangzhou, China
| | - Yanqun Wang
- Guangzhou Laboratory, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lu Dang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
| | - Xinyi Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaodong Ma
- Guangdong Key Laboratory of Mental Health and Cognitive Science, Institute for Brain Research and Rehabilitation, Centre for Studies of Psychological Application, South China Normal University, Guangzhou, China
| | - Tian Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xian Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Ming Liu
- Guangzhou Laboratory, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xingxu Huang
- Guangzhou Laboratory, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Peixiang Ma
- Guangzhou Laboratory, State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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7
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Taguchi K, Unno R, Sugino T, Kawase K, Yang H, Hamamoto S, Okada A, Stoller M, Chi T, Yasui T. Fatty acid binding protein 4 attenuates macrophage and tubular cells crystal phagocytosis to drive renal calcium oxalate stone development. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)00612-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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Huang X, Lv J, Li Y, Mao S, Li Z, Jing Z, Sun Y, Zhang X, Shen S, Wang X, Di M, Ge J, Huang X, Zuo E, Chi T. Programmable C-to-U RNA editing using the human APOBEC3A deaminase. EMBO J 2021; 40:e108209. [PMID: 33938012 DOI: 10.15252/embj.2021108209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/16/2021] [Indexed: 11/09/2022] Open
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9
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Li Y, Chen Y, Mao S, Kaundal R, Jing Z, Chen Q, Wang X, Xia J, Liu D, Sun J, Wang H, Chi T. Author Correction: In situ conversion of defective Treg into SuperTreg cells to treat advanced IPEX-like disorders in mice. Nat Commun 2021; 12:2248. [PMID: 33833235 PMCID: PMC8032673 DOI: 10.1038/s41467-021-22629-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yongqin Li
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Yuxin Chen
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Shaoshuai Mao
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Ravinder Kaundal
- Deptartment Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhengyu Jing
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Qin Chen
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Xinxin Wang
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Jing Xia
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Dahai Liu
- Department of Basic Medicine and Biomedical Engineering, School of Stomatology and Medicine, Foshan University, Foshan, 528000, Guangdong, PR of China
| | - Jianlong Sun
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Haopeng Wang
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Tian Chi
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China. .,Deptartment Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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10
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Yu W, Li J, Huang S, Li X, Li P, Li G, Liang A, Chi T, Huang X. Harnessing A3G for efficient and selective C-to-T conversion at C-rich sequences. BMC Biol 2021; 19:34. [PMID: 33602235 PMCID: PMC7893952 DOI: 10.1186/s12915-020-00879-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Site-specific C>T DNA base editing has been achieved by recruiting cytidine deaminases to the target C using catalytically impaired Cas proteins; the target C is typically located within 5-nt editing window specified by the guide RNAs. The prototypical cytidine base editor BE3, comprising rat APOBEC1 (rA1) fused to nCas9, can indiscriminately deaminate multiple C's within the editing window and also create substantial off-target edits on the transcriptome. A powerful countermeasure for the DNA off-target editing is to replace rA1 with APOBEC proteins which selectively edit C's in the context of specific motifs, as illustrated in eA3A-BE3 which targets TC. However, analogous editors selective for other motifs have not been described. In particular, it has been challenging to target a particular C in C-rich sequences. Here, we sought to confront this challenge and also to overcome the RNA off-target effects seen in BE3. RESULTS By replacing rA1 with an optimized human A3G (oA3G), we developed oA3G-BE3, which selectively targets CC and CCC and is also free of global off-target effects on the transcriptome. Furthermore, we created oA3G-BE4max, an upgraded version of oA3G-BE3 with robust on-target editing. Finally, we showed that oA3G-BE4max has negligible Cas9-independent off-target effects at the genome. CONCLUSIONS oA3G-BE4max can edit C(C)C with high efficiency and selectivity, which complements eA3A-editors to broaden the collective editing scope of motif selective editors, thus filling a void in the base editing tool box.
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Affiliation(s)
- Wenxia Yu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianan Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Li
- Department of Hematology, Tongji Hospital of Tongji University, Shanghai, 200092, China
| | - Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Aibin Liang
- Department of Hematology, Tongji Hospital of Tongji University, Shanghai, 200092, China
| | - Tian Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Department Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.
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11
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Luo L, Li Z, Zhao T, Ju X, Ma P, Jin B, Zhou Y, He S, Huang J, Xu X, Zou Y, Li P, Liang A, Liu J, Chi T, Huang X, Ding Q, Jin Z, Huang C, Zhang Y. SARS-CoV-2 nucleocapsid protein phase separates with G3BPs to disassemble stress granules and facilitate viral production. Sci Bull (Beijing) 2021; 66:1194-1204. [PMID: 33495715 PMCID: PMC7816596 DOI: 10.1016/j.scib.2021.01.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/13/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022]
Abstract
A key to tackling the coronavirus disease 2019 (COVID-19) pandemic is to understand how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) manages to outsmart host antiviral defense mechanisms. Stress granules (SGs), which are assembled during viral infection and function to sequester host and viral mRNAs and proteins, are part of the antiviral responses. Here, we show that the SARS-CoV-2 nucleocapsid (N) protein, an RNA binding protein essential for viral production, interacted with Ras-GTPase-activating protein SH3-domain-binding protein (G3BP) and disrupted SG assembly, both of which require intrinsically disordered region1 (IDR1) in N protein. The N protein partitioned into SGs through liquid-liquid phase separation with G3BP, and blocked the interaction of G3BP1 with other SG-related proteins. Moreover, the N protein domains important for phase separation with G3BP and SG disassembly were required for SARS-CoV-2 viral production. We propose that N protein-mediated SG disassembly is crucial for SARS-CoV-2 production.
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Affiliation(s)
- Lingling Luo
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhean Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Tiejun Zhao
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xiaohui Ju
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Boxing Jin
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yulin Zhou
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Su He
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jinhua Huang
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xun Xu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yan Zou
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Ping Li
- Department of Hematology, Tongji Hospital of Tongji University, Shanghai 200065, China
| | - Aibin Liang
- Department of Hematology, Tongji Hospital of Tongji University, Shanghai 200065, China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Tian Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Qiang Ding
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Zhigang Jin
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Cheng Huang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yu Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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12
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Huang X, Lv J, Li Y, Mao S, Li Z, Jing Z, Sun Y, Zhang X, Shen S, Wang X, Di M, Ge J, Huang X, Zuo E, Chi T. Programmable C-to-U RNA editing using the human APOBEC3A deaminase. EMBO J 2020; 39:e104741. [PMID: 33058229 PMCID: PMC7667879 DOI: 10.15252/embj.2020104741] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/07/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Programmable RNA cytidine deamination has recently been achieved using a bifunctional editor (RESCUE-S) capable of deaminating both adenine and cysteine. Here, we report the development of "CURE", the first cytidine-specific C-to-U RNA Editor. CURE comprises the cytidine deaminase enzyme APOBEC3A fused to dCas13 and acts in conjunction with unconventional guide RNAs (gRNAs) designed to induce loops at the target sites. Importantly, CURE does not deaminate adenosine, enabling the high-specificity versions of CURE to create fewer missense mutations than RESCUE-S at the off-targets transcriptome-wide. The two editing approaches exhibit overlapping editing motif preferences, with CURE and RESCUE-S being uniquely able to edit UCC and AC motifs, respectively, while they outperform each other at different subsets of the UC targets. Finally, a nuclear-localized version of CURE, but not that of RESCUE-S, can efficiently edit nuclear RNAs. Thus, CURE and RESCUE are distinct in design and complementary in utility.
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Affiliation(s)
- Xinxin Huang
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Junjun Lv
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yongqin Li
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shaoshuai Mao
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Li
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Zhengyu Jing
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yidi Sun
- Institute of NeuroscienceState Key Laboratory of NeuroscienceKey Laboratory of Primate NeurobiologyCAS Center for Excellence in Brain Science and Intelligence TechnologyShanghai Research Center for Brain Science and Brain‐Inspired IntelligenceShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Xiaoming Zhang
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shengxi Shen
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xinxin Wang
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
| | - Minghui Di
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jianyang Ge
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xingxu Huang
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
| | - Erwei Zuo
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Tian Chi
- School of Life Sciences and TechnologyShanghaiTech UniversityShanghaiChina
- Department of ImmunobiologyYale University School of MedicineNew HavenCTUSA
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13
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Liu Y, Mao S, Huang S, Li Y, Chen Y, Di M, Huang X, Lv J, Wang X, Ge J, Shen S, Zhang X, Liu D, Huang X, Chi T. REPAIRx, a specific yet highly efficient programmable A > I RNA base editor. EMBO J 2020; 39:e104748. [PMID: 33058207 DOI: 10.15252/embj.2020104748] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/27/2020] [Accepted: 06/03/2020] [Indexed: 12/26/2022] Open
Abstract
Programmable A > I RNA editing is a valuable tool for basic research and medicine. A variety of editors have been created, but a genetically encoded editor that is both precise and efficient has not been described to date. The trade-off between precision and efficiency is exemplified in the state of the art editor REPAIR, which comprises the ADAR2 deaminase domain fused to dCas13b. REPAIR is highly efficient, but also causes significant off-target effects. Mutations that weaken the deaminase domain can minimize the undesirable effects, but this comes at the expense of on-target editing efficiency. We have now overcome this dilemma by using a multipronged approach: We have chosen an alternative Cas protein (CasRx), inserted the deaminase domain into the middle of CasRx, and redirected the editor to the nucleus. The new editor created, dubbed REPAIRx, is precise yet highly efficient, outperforming various previous versions on both mRNA and nuclear RNA targets. Thus, REPAIRx markedly expands the RNA editing toolkit and illustrates a novel strategy for base editor optimization.
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Affiliation(s)
- Yajing Liu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shaoshuai Mao
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Shisheng Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Li
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yuxin Chen
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Minghui Di
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinxin Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Junjun Lv
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xinxin Wang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Jianyang Ge
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Shengxi Shen
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoming Zhang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dahai Liu
- Department of Basic Medicine and Biomedical Engineering, School of Stomatology and Medicine, Foshan University, Foshan, China
| | - Xingxu Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Tian Chi
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China.,Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
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14
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Ma P, Meng Q, Sun B, Zhao B, Dang L, Zhong M, Liu S, Xu H, Mei H, Liu J, Chi T, Yang G, Liu M, Huang X, Wang X. MeCas12a, a Highly Sensitive and Specific System for COVID-19 Detection. Adv Sci (Weinh) 2020; 7:2001300. [PMID: 33042732 PMCID: PMC7536916 DOI: 10.1002/advs.202001300] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/30/2020] [Indexed: 05/04/2023]
Abstract
Cas12a-based systems, which detect specific nucleic acids via collateral cleavage of reporter DNA, display huge potentials for rapid diagnosis of infectious diseases. Here, the Manganese-enhanced Cas12a (MeCas12a) system is described, where manganese is used to increase the detection sensitivity up to 13-fold, enabling the detection of target RNAs as low as five copies. MeCas12a is also highly specific, and is able to distinguish between single nucleotide polymorphisms (SNPs) differing by a single nucleotide. MeCas12a can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in clinical samples and distinguish between SARS-CoV-2 and Middle East respiratory syndrome coronavirus (MERS-CoV) RNA in simulated samples, thus offering an attractive alternative to other methods for the diagnosis of infectious diseases including COVID-19 and MERS.
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Affiliation(s)
- Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Qingzhou Meng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University78 Hengzhigang RoadGuangzhou510095China
| | - Baoqing Sun
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated HospitalGuangzhou Medical UniversityGuangzhou510120China
| | - Bing Zhao
- Microbiological Testing LaboratoryShanghai Pudong New Area Center for Disease Control and PreventionShanghai200136China
| | - Lu Dang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University78 Hengzhigang RoadGuangzhou510095China
| | - Mingtian Zhong
- Institute for Brain Research and RehabilitationGuangdong Key Laboratory of Mental Health and Cognitive ScienceCenter for Studies of Psychological ApplicationSouth China Normal UniversityGuangzhou510631China
| | - Siyuan Liu
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Hongtao Xu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Hong Mei
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Tian Chi
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Ming Liu
- State Key Laboratory of Respiratory DiseaseNational Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated HospitalGuangzhou Medical UniversityGuangzhou510120China
| | - Xingxu Huang
- School of Life Science and TechnologyShanghaiTech UniversityShanghai201210China
| | - Xinjie Wang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
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15
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Nguyen DD, Luo J, Lim J, Scotland K, Bechis S, Sur R, Nakada S, Antonelli J, Streeper N, Sivalingam S, Viprakasit D, Averch T, Landman J, Chi T, Pais JV, Bird V, Andonian S, Canvasser N, Harper J, Chew B, Penniston K, Bhojani N. Wisconsin quality of life machine learning algorithm for predicting quality of life in kidney stone patients. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)33385-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Emiliani E, Kanashiro A, Chi T, Pérez-Fentes DA, Manzo BO, Angerri O, Somani BK. Fluoroless Endourological Surgery for Stone Disease: a Review of the Literature—Tips and Tricks. Curr Urol Rep 2020; 21:27. [DOI: 10.1007/s11934-020-00979-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Jia M, Yao L, Yang Q, Chi T. Association of MSH2 Expression With Tumor Mutational Burden and the Immune Microenvironment in Lung Adenocarcinoma. Front Oncol 2020; 10:168. [PMID: 32154170 PMCID: PMC7046689 DOI: 10.3389/fonc.2020.00168] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/30/2020] [Indexed: 12/20/2022] Open
Abstract
Immune checkpoint blockade (ICB) therapies that target programmed cell death 1 (PD1) and PD1 ligand 1 (PDL1) have demonstrated promising benefits in lung adenocarcinoma (LUAD), and tumor mutational burden (TMB) is the most robust biomarker associated with the efficacy of PD-1-PD-L1 axis blockade in LUAD, but the assessment of TMB by whole-exome sequencing (WES) is rather expensive and time-consuming. Although targeted panel sequencing has been developed and approved by the US Food and Drug Administration (FDA) to estimate TMB, we found that its predictive accuracy for ICB response was significantly lower than WES in LUAD. Given that previous studies were mainly focusing on genomic variations to explore surrogate biomarkers of TMB, we turned to examine the transcriptome-based correlation with TMB in this study. Combining three immunotherapeutic cohorts with two independent The Cancer Genome Atlas (TCGA) datasets, we revealed that the expression of mutS homolog 2 (MSH2), one of the most crucial genes involved in DNA mismatch repair (MMR) pathway, was the strongest feature associated with increased TMB in multivariate analysis. Furthermore, MSH2 expression also displayed a significantly positive correlation with smoking signature while an inverse association with MMR deficiency (MMRd) signature in LUAD. More importantly, high expression of MSH2 markedly correlated with increased PD-L1 expression and CD8+ T cell infiltration, both suggesting a prominent immunotherapy-responsive microenvironment in LUAD. Notably, detecting MSH2 expression is much easier, faster, and cheaper than TMB in clinical practice. Taken together, this study demonstrates the association of MSH2 expression with TMB and the immune microenvironment in LUAD. MSH2 expression may be developed as a potential surrogate biomarker of TMB to identify ICB responders in LUAD.
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Affiliation(s)
- Mingming Jia
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Linli Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qin Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tian Chi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,Department Immunobiology, Yale University School of Medicine, New Haven, CT, United States
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18
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Mao S, Liu Y, Huang S, Huang X, Chi T. Site-directed RNA editing (SDRE): Off-target effects and their countermeasures. J Genet Genomics 2019; 46:531-535. [PMID: 31889638 DOI: 10.1016/j.jgg.2019.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/08/2019] [Accepted: 11/04/2019] [Indexed: 12/20/2022]
Abstract
Site-directed RNA editing (SDRE) is invaluable to basic research and clinical applications and has emerged as a new frontier in genome editing. The past few years have witnessed a surge of interest in SDRE, with SDRE tools emerging at a breathtaking pace. However, off-target effects of SDRE remain a tough problem, which constitutes a major hurdle to their clinical applications. Here we discuss the diverse strategies for combating off-target editing, drawing lessons from the published studies as well as our ongoing research. Overall, SDRE is still at its infancy, with significant challenges and exciting opportunities ahead.
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Affiliation(s)
- Shaoshuai Mao
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yajing Liu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shisheng Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingxu Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Tian Chi
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, 201210, China; Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA.
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19
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Chi T, Hay-Kraus B. Evaluation of blood pressure effect of intravenous maropitant administration in healthy and anesthetized dogs. Vet Anaesth Analg 2019. [DOI: 10.1016/j.vaa.2019.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Mao S, Qi Y, Zhu H, Huang X, Zou Y, Chi T. A Tet/Q Hybrid System for Robust and Versatile Control of Transgene Expression in C. elegans. iScience 2018; 11:224-237. [PMID: 30634168 PMCID: PMC6327101 DOI: 10.1016/j.isci.2018.12.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/11/2018] [Accepted: 12/20/2018] [Indexed: 11/04/2022] Open
Abstract
Binary gene regulatory tools such as the Tetracycline (Tet)-controlled transcription system have revolutionized genetic research in multiple organisms, but their applications to the worm remain very limited. Here we report that the canonical Tet system is largely inactive in the worm but can be adapted for the worm by introducing multiple modifications, a crucial one being the use of the transcription activation domain from the fungal Q binary system. The resultant Tet/Q hybrid system proves more robust and flexible than either of its precursors, enabling elaborate modes of transgene manipulation previously hard to achieve in the worm, including inducible intersectional regulation and, in combination with the Q system, independent control of distinct transgenes within the same cells. Furthermore, we demonstrated, as an example of its applications, that the hybrid system can tightly and efficiently control Cre expression. This study establishes Tet/Q as a premier binary system for worm genetic research. The popular Tet-controlled gene regulatory system proves inapplicable to the worm The fungal Q binary gene regulatory system is moderately active in the worm A hybrid Tet/Q system is capable of robust, rapid and tunable transgene induction Further modifications enable sophisticated regulation previously hard to achieve
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Affiliation(s)
- Shaoshuai Mao
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yingchuan Qi
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Huanhu Zhu
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Xinxin Huang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China; CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zou
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Tian Chi
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China; Department Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
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21
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Moran SP, Chi T, Prucha MS, Engelhardt HR, Yuksel A, Chan AWS. 61 TRANSGENIC HUNTINGTON'S DISEASE MONKEY SPERM HAS A LOWER CRYOTOLERANCE. Reprod Fertil Dev 2014. [DOI: 10.1071/rdv26n1ab61] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Cryopreservation is an important tool routinely used for preserving sperm for artificial reproductive technologies (ART), as well as genetic preservation of unique animal models. The cryopreservation process is harsh and detrimental to the fragile gametes, and damage to the sperm is not only known, but inevitable. This study presents new data in which sperm from 3 transgenic Huntington's disease (HD) monkeys (rhesus macaques) are compared with 3 wild-type (WT) rhesus sperm donors. Currently, there are no data comparing HD versus WT sperm viability and cryotolerance in humans. The goal of this study was to investigate differences between fresh and frozen semen by quantitative analysis on sperm viability based on (1) motility, (2) membrane integrity, and (3) acrosome integrity. Sperm motility was determined by visual evaluation. Membrane and acrosome integrity were assessed simultaneously by Hoechst 33342, propidium iodide (PI), and fluorescein isothiocyanate-peanut agglutinin (FITC-PNA) triple staining. Sperm viability analysis was divided into 3 groups: (1) fresh HD versus fresh WT, (2) fresh versus cryopreserved-thawed WT, (3) and fresh HD versus cryopreserved-thawed HD sperm. Interestingly, fresh HD sperm had a lower percentage of membrane-damaged cells (38.57 ± 3.15) compared with WT (49.67 ± 3.56; P < 0.03). However, after cryopreservation and subsequent thawing, HD sperm had a significantly higher percentage increase in damaged membranes than WT sperm (27.91 ± 2.93 v. 8.27 ± 8.28; P < 0.001), respectively. No significant difference in acrosome damage between groups was identified in either fresh or cryopreserved sperm populations. Motility significantly declined in both cryopreserved populations [HD: 89.7 to 43.4% (P < 0.001) and WT: 90.0 to 45.6% (P < 0.001)]. There was no significant difference between either freeze-thawed group. These data illustrate that HD sperm have a lower cryotolerance than WT sperm. Our findings suggest that the optimization of the HD sperm cryopreservation method and investigation on biochemical differences (e.g. membrane lipid composition) are necessary to improve post-thaw survival. This in turn is important for the establishment of a sperm cryobank and future derivation of a unique animal model such as HD monkey. Our study also suggests that HD monkey could be a useful model for optimizing cryopreservation method for HD patients.
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22
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Wan M, Kaundal R, Huang H, Zhao J, Yang X, Chaiyachati BH, Li S, Chi T. A general approach for controlling transcription and probing epigenetic mechanisms: application to the CD4 locus. J Immunol 2013; 190:737-47. [PMID: 23293358 DOI: 10.4049/jimmunol.1201278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Synthetic regulatory proteins such as tetracycline (tet)-controlled transcription factors are potentially useful for repression as well as ectopic activation of endogenous genes and also for probing their regulatory mechanisms, which would offer a versatile genetic tool advantageous over conventional gene targeting methods. In this study, we provide evidence supporting this concept using Cd4 as a model. CD4 is expressed in double-positive and CD4 cells but irreversibly silenced in CD8 cells. The silencing is mediated by heterochromatin established during CD8 lineage development via transient action of the Cd4 silencer; once established, the heterochromatin becomes self-perpetuating independently of the Cd4 silencer. Using a tet-sensitive Cd4 allele harboring a removable Cd4 silencer, we found that a tet-controlled repressor recapitulated the phenotype of Cd4-deficient mice, inhibited Cd4 expression in a reversible and dose-dependent manner, and could surprisingly replace the Cd4 silencer to induce irreversible Cd4 silencing in CD8 cells, thus suggesting the Cd4 silencer is not the (only) determinant of heterochromatin formation. In contrast, a tet-controlled activator reversibly disrupted Cd4 silencing in CD8 cells. The Cd4 silencer impeded this disruption but was not essential for its reversal, which revealed a continuous role of the silencer in mature CD8 cells while exposing a remarkable intrinsic self-regenerative ability of heterochromatin after forced disruption. These data demonstrate an effective approach for gene manipulation and provide insights into the epigenetic Cd4 regulatory mechanisms that are otherwise difficult to obtain.
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Affiliation(s)
- Mimi Wan
- Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
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23
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Wan M, Gu H, Wang J, Huang H, Zhao J, Kaundal RK, Yu M, Kushwaha R, Chaiyachati BH, Deerhake E, Chi T. Inducible mouse models illuminate parameters influencing epigenetic inheritance. Development 2013; 140:843-52. [PMID: 23325759 DOI: 10.1242/dev.088229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Environmental factors can stably perturb the epigenome of exposed individuals and even that of their offspring, but the pleiotropic effects of these factors have posed a challenge for understanding the determinants of mitotic or transgenerational inheritance of the epigenetic perturbation. To tackle this problem, we manipulated the epigenetic states of various target genes using a tetracycline-dependent transcription factor. Remarkably, transient manipulation at appropriate times during embryogenesis led to aberrant epigenetic modifications in the ensuing adults regardless of the modification patterns, target gene sequences or locations, and despite lineage-specific epigenetic programming that could reverse the epigenetic perturbation, thus revealing extraordinary malleability of the fetal epigenome, which has implications for 'metastable epialleles'. However, strong transgenerational inheritance of these perturbations was observed only at transgenes integrated at the Col1a1 locus, where both activating and repressive chromatin modifications were heritable for multiple generations; such a locus is unprecedented. Thus, in our inducible animal models, mitotic inheritance of epigenetic perturbation seems critically dependent on the timing of the perturbation, whereas transgenerational inheritance additionally depends on the location of the perturbation. In contrast, other parameters examined, particularly the chromatin modification pattern and DNA sequence, appear irrelevant.
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Affiliation(s)
- Mimi Wan
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
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24
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Chaiyachati BH, Jani A, Wan Y, Huang H, Flavell R, Chi T. BRG1-mediated immune tolerance: facilitation of Treg activation and partial independence of chromatin remodelling. EMBO J 2013; 32:395-408. [PMID: 23321680 DOI: 10.1038/emboj.2012.350] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/05/2012] [Indexed: 02/02/2023] Open
Abstract
Treg activation in response to environmental cues is necessary for regulatory T cells (Tregs) to suppress inflammation, but little is known about the transcription mechanisms controlling Treg activation. We report that despite the known proinflammatory role of the chromatin-remodelling factor BRG1 in CD4 cells, deleting Brg1 in all αβ T cell lineages led to fatal inflammation, which reflected essential roles of BRG1 in Tregs. Brg1 deletion impaired Treg activation, concomitant with the onset of the inflammation. Remarkably, as the inflammation progressed, Tregs became increasingly activated, but the activation levels could not catch up with the severity of inflammation. In vitro assays indicate that BRG1 regulates a subset of TCR target genes including multiple chemokine receptor genes. Finally, using a method that can create littermates bearing either a tissue-specific point mutation or deletion, we found the BRG1 ATPase activity partially dispensable for BRG1 function. Collectively, these data suggest that BRG1 acts in part via remodelling-independent functions to sensitize Tregs to inflammatory cues, thus allowing Tregs to promptly and effectively suppress autoimmunity.
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Affiliation(s)
- Barbara H Chaiyachati
- Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
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25
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Abstract
Background Conditional gene knockout (cKO) mediated by the Cre/LoxP system is indispensable for exploring gene functions in mice. However, a major limitation of this method is that gene KO is not reversible. A number of methods have been developed to overcome this, but each method has its own limitations. Results We describe a simple method we have named LOFT [LoxP-flippase (FLP) recognition target (FRT) Trap], which is capable of reversible cKO and free of the limitations associated with existing techniques. This method involves two alleles of a target gene: a standard floxed allele, and a multi-functional allele bearing an FRT-flanked gene-trap cassette, which inactivates the target gene while reporting its expression with green fluorescent protein (GFP); the trapped allele is thus a null and GFP reporter by default, but is convertible into a wild-type allele. The floxed and trapped alleles can typically be generated using a single construct bearing a gene-trap cassette doubly flanked by LoxP and FRT sites, and can be used independently to achieve conditional and constitutive gene KO, respectively. More importantly, in mice bearing both alleles and also expressing the Cre and FLP recombinases, sequential function of the two enzymes should lead to deletion of the target gene, followed by restoration of its expression, thus achieving reversible cKO. LOFT should be generally applicable to mouse genes, including the growing numbers of genes already floxed; in the latter case, only the trapped alleles need to be generated to confer reversibility to the pre-existing cKO models. LOFT has other applications, including the creation and reversal of hypomorphic mutations. In this study we proved the principle of LOFT in the context of T-cell development, at a hypomorphic allele of Baf57/Smarce1 encoding a subunit of the chromatin-remodeling Brg/Brahma-associated factor (BAF) complex. Interestingly, the FLP used in the current work caused efficient reversal in peripheral T cells but not thymocytes, which is advantageous for studying developmental epigenetic programming of T-cell functions, a fundamental issue in immunology. Conclusions LOFT combines well-established basic genetic methods into a simple and reliable method for reversible gene targeting, with the flexibility of achieving traditional constitutive and conditional KO.
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Affiliation(s)
- Barbara H Chaiyachati
- Department of Immunobiology, Yale University Medical School, 300 Cedar Street, New Haven, CT 06520, USA
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Abstract
Mammalian spermatogenesis is a complex process that involves spatiotemporal regulation of gene expression and meiotic recombination, both of which require the modulation of chromatin structure. Proteins important for chromatin regulation during spermatogenesis remain poorly understood. Here we addressed the role of BRG1, the catalytic subunit of the mammalian Swi/Snf-like BAF chromatin-remodeling complex, during spermatogenesis in mice. BRG1 expression is dynamically regulated in the male germline, being weakly detectable in spermatogonia, highly expressed in pachytene spermatocytes, and turned off in maturing round spermatids. This expression pattern overlaps that of Brm, the Brg1 homolog. While Brm knockout males are known to be fertile, germline-specific Brg1 deletion completely arrests spermatogenesis at the midpachytene stage, which is associated with spermatocyte apoptosis and apparently also with impaired homologous recombination and meiotic sex chromosome inactivation. However, Brg1 is dispensable for gammaH2AX formation during meiotic recombination, contrary to its reported role in DNA repair in somatic cells. Our study reveals the essential role of Brg1 in meiosis and underscores the differences in the mechanisms of DNA repair between germ cells and somatic cells.
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Affiliation(s)
- Jianguan Wang
- Department of Cell Biology, Yale University, New Haven, Connecticut, USA
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Yang X, Wang L, Ge C, Hu B, Chi T. Factors associated with occupational strain among Chinese teachers: a cross-sectional study. Public Health 2011; 125:106-13. [PMID: 21288545 DOI: 10.1016/j.puhe.2010.10.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 09/17/2010] [Accepted: 10/28/2010] [Indexed: 11/15/2022]
Abstract
OBJECTIVES With the reform of the education system in China, teachers are suffering from more occupational strain, which is believed to impair their working state indirectly and affect their health. This study assessed occupational strain and explored the related factors among Chinese teachers. STUDY DESIGN Cross-sectional with cluster sampling. METHODS The study population was composed of 3570 school teachers working in 64 primary and middle schools in Heping District in Shenyang, China. Data were collected using a self-administered questionnaire (the Chinese version of the Occupational Stress Inventory scale). Multivariate linear regression analyses were performed to study the factors related to occupational strain. RESULTS The average score on the Personal Strain Questionnaire (PSQ) for the whole study population was 106.5 (107.5 in men and 106.3 in women). Teachers with chronic disease, a greater number of days of sick leave, recent experience of a stressful life event and divorced/separated/widowed status tended to suffer greater strain than their peers. Regression analyses showed that the PSQ score was significantly associated with role overload, role boundary, responsibility and physical environment, and inversely associated with recreation and rational coping. The most crucial predictors of occupational strain were chronic disease, days of sick leave, recent experience of a stressful life event and marital status. Being a class teacher was the strongest indicator of interpersonal strain. Self-care was associated with vocational strain and psychological strain, and inversely associated with physical strain. CONCLUSIONS Most teachers in this study experienced a high degree of occupational strain. Chronic disease, days of sick leave, recent experience of a stressful life event and divorced/separated/widowed status played prominent roles in occupational strain. In addition, role overload, role boundary, responsibility and physical environment induce occupational strain, while recreation and rational coping have a positive effect on occupational strain. Interventions such as proper management of chronic diseases and establishment of a balanced work-family life are crucial to reduce occupational strain. Recreation and training in coping abilities are needed to enhance positive working environments and attenuate the occupational strain imposed on teachers.
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Affiliation(s)
- X Yang
- Department of Social Medicine, School of Public Health, China Medical University, No. 92th Second Road, Heping District, Shenyang 110001, China
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Yang X, Ge C, Hu B, Chi T, Wang L. Relationship between quality of life and occupational stress among teachers. Public Health 2009; 123:750-5. [PMID: 19883926 DOI: 10.1016/j.puhe.2009.09.018] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 09/18/2009] [Accepted: 09/27/2009] [Indexed: 11/15/2022]
Abstract
OBJECTIVES With major changes in the education system and limited resources supplied by the Government, Chinese teachers have been suffering from greater occupational stress in recent years, which is believed to affect their physical and mental health. The aim of this study was to explore the relationship between quality of life and occupational stress in primary and middle school teachers. STUDY DESIGN Originals. METHODS A cross-sectional study was conducted using cluster sampling. The study population was composed of 3570 school teachers working in 64 primary and middle schools in Heping District in Shenyang, China. A demographic questionnaire, the 36-item Short-Form Health Survey (SF-36) and the Occupational Stress Inventory Revised Edition were employed to collect demographic variables and assess quality of life and occupational stress. Multivariate stepwise linear regression analyses were performed to study the relationship between quality of life and occupational stress. RESULTS The mean scores for both male and female teachers in this study were significantly lower than those for the Chinese general population for all dimensions of quality of life, except mental health and vitality (P<0.05). Male teachers scored significantly higher than female teachers for physical functioning, bodily pain, vitality and physical health (P<0.05). Age, role overload, role insufficiency, vocational strain, psychological strain, physical strain, recreation and rational coping were significantly associated with both the physical and mental component summaries of the SF-36 (P<0.05). Gender, physical environment and self-care appeared to be robust indicators of physical health (P<0.05), while role insufficiency, interpersonal strain and social support were strong indicators of mental health (P<0.05). CONCLUSIONS In China, teachers have a lower health status than the general population. The quality of life of female teachers is worse than that of male teachers, and deteriorates with age. Occupational stress and strain induce worsening physical and mental conditions for teachers, while coping resources could promote their health. This study suggests that having adequate coping resources, especially social support, in workplaces may be an important factor for improving teachers' quality of life. Moreover, psychological interventions should be set up for teachers, and psychological counselling should be provided to relieve stress and enhance quality of life.
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Affiliation(s)
- X Yang
- Department of Social Medicine, School of Public Health, China Medical University, No.92 North Second Road, Heping District, Shenyang 110001, China
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Wan M, Zhang J, Lai D, Jani A, Prestone-Hurlburt P, Zhao L, Ramachandran A, Schnitzler GR, Chi T. Molecular basis of CD4 repression by the Swi/Snf-like BAF chromatin remodeling complex. Eur J Immunol 2009; 39:580-8. [PMID: 19180471 DOI: 10.1002/eji.200838909] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The Brg1/Brm-associated factor (BAF) chromatin remodeling complex directly binds the CD4 silencer and is essential for CD4 repression during T-cell development, because deletion of the ATPase subunit Brg1 or a dominant negative mutant of BAF57 each impairs CD4 repression in early thymocytes. Paradoxically, BAF57 is dispensable for remodeling nucleosomes in vitro or for binding of the BAF complex to the CD4 silencer in vivo. Thus, it is unclear whether BAF57-dependent CD4 repression involves chromatin remodeling and, if so, how the remodeling translates into CD4 repression. Here we show that nucleosomes at the CD4 silencer occupy multiple translational frames. BAF57 dominant negative mutant does not alter these frames, but reduces the accessibility of the entire silencer without affecting the flanking regions, concomitant with localized accumulation of linker histone H1 and eviction of Runx1, a key repressor of CD4 transcription that directly binds the CD4 silencer. Our data indicate that precise nucleosome positioning is not critical for the CD4 silencer function and that BAF57 participates in remodeling H1-containing chromatin at the CD4 silencer, which enables Runx1 to access the silencer and repress CD4. In addition to BAF57, multiple other subunits in the BAF complex are also dispensable for chromatin remodelling in vitro. Our data suggest that these subunits could also help remodel chromatin at a step after the recruitment of the BAF complex to target genes.
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Affiliation(s)
- Mimi Wan
- Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
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Abstract
Regulatory T cells (Treg), formerly known as suppressor T cells, are essential for maintaining self-tolerance as well as immune homeostasis. Lack of Treg or normal function of Treg often leads to lymphoproliferative syndrome and autoimmunity in human and mouse. The chromatin remodeling BAF complex regulates gene expression through the activity of Brg. Genetic ablation of Brg gene in mouse resulted in early embryonic lethality. T cell failed to develop in the thymus when Brg is deleted at DN stage. Using a Brg conditional KO mouse model, we deleted Brg at the DP stage in the thymus. Unexpectedly, T cells developed and matured normally. However, these mice displayed lympho-proliferative syndrome 2-4 months of age with enlarged peripheral lymphoid organs and leukocyte infiltration in non-lymphoid organs. T cells from these mice turned into effector cells producing increased amounts of effector cytokines as early as 4 weeks after birth. Further analysis revealed that the Treg population was specifically affected by Brg deletion. In this mini-review, we will discuss in detail the properties of Tregs controlled by Brg and the potential underlying mechanisms for an unanticipated, specific role of the Brg-containing BAF complex in controlling Treg functions.
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Affiliation(s)
- Anant Jani
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
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Jani A, Wan M, Zhang J, Cui K, Wu J, Preston-Hurlburt P, Khatri R, Zhao K, Chi T. A novel genetic strategy reveals unexpected roles of the Swi–Snf–like chromatin-remodeling BAF complex in thymocyte development. J Biophys Biochem Cytol 2008. [DOI: 10.1083/jcb1833oia7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Jani A, Wan M, Zhang J, Cui K, Wu J, Preston-Hurlburt P, Khatri R, Zhao K, Chi T. A novel genetic strategy reveals unexpected roles of the Swi-Snf-like chromatin-remodeling BAF complex in thymocyte development. ACTA ACUST UNITED AC 2008; 205:2813-25. [PMID: 18955569 PMCID: PMC2585832 DOI: 10.1084/jem.20080938] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have developed a general strategy for creating littermates bearing either a tissue-specific point mutation or deletion in any target gene, and used the method to dissect the roles of Brg, the ATPase subunit of the chromatin-remodeling Brg-associated factor (BAF) complex, in early thymocyte development. We found that a point mutation that inactivates the Brg ATPase recapitulates multiple defects previously described for Brg deletion (Chi, T.H., M. Wan, P.P. Lee, K. Akashi, D. Metzger, P. Chambon, C.B. Wilson, and G.R. Crabtree. 2003. Immunity. 19:169-182). However, the point mutant helps reveal unexpected roles of Brg in CD25 repression and CD4 activation. Surprisingly, CD4 activation occurs independently of the Brg ATPase and is perhaps mediated by physical interactions between Brg and the CD4 locus. Our study thus suggests that the BAF complex harbors novel activities that can be necessary and even sufficient for stimulating transcription from an endogenous chromatin template in the absence of Brg-dependent remodeling of that template. We conclude that conditional point mutants, rarely used in mammalian genetics, can help uncover important gene functions undetectable or overlooked in deletion mutants.
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Affiliation(s)
- Anant Jani
- Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
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Godwin AK, Rink L, Chi T, Flieder D, Testa J, Corless CL, Heinrich MC, Eisenberg BL, von Mehren M. Insulin-like growth factor 1 receptor (IGF-1R): A potential therapeutic target for gastrointestinal stromal tumors (GIST). J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.10507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Elliott S, McAninch J, Chi T, Doyle S, Master V. MP-17.07. Urology 2006. [DOI: 10.1016/j.urology.2006.08.520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Joel A, Rubenstein J, Hsieh M, Chi T, Meng M, Stoller M. Failed Percutaneous Balloon Dilation for Renal Access: Incidence and Risk Factors. J Urol 2006. [DOI: 10.1016/s0022-5347(05)00427-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- A.B. Joel
- Department of Urology, University of California, San Francisco, School of Medicine, San Francisco, California
| | - J.N. Rubenstein
- Department of Urology, University of California, San Francisco, School of Medicine, San Francisco, California
| | - M.H. Hsieh
- Department of Urology, University of California, San Francisco, School of Medicine, San Francisco, California
| | - T. Chi
- Department of Urology, University of California, San Francisco, School of Medicine, San Francisco, California
| | - M.V. Meng
- Department of Urology, University of California, San Francisco, School of Medicine, San Francisco, California
| | - M.L. Stoller
- Department of Urology, University of California, San Francisco, School of Medicine, San Francisco, California
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Abstract
Chromatin structure dictates whether DNA templates are accessible to nuclear proteins; therefore, it is tightly regulated. To reconfigure chromatin, cells often mobilize 'chromatin-remodelling complexes' that use energy to disrupt histone-DNA contacts. BAF complexes, which are related to the yeast SWI-SNF complex, are the prototypical mammalian chromatin-remodelling complexes. In the past few years, studies have revealed the crucial and diverse roles of BAF complexes in the regulation of the immune system - from lymphocyte development to immune responses. This review surveys these advances, highlighting the general insights these studies provide into the modes of action of BAF complexes, and it concludes with a discussion of some of the key opportunities and challenges in this field.
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Affiliation(s)
- Tian Chi
- Section of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
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Abstract
Detection thresholds for spectral and temporal modulations are measured using broadband spectra with sinusoidally rippled profiles that drift up or down the log-frequency axis at constant velocities. Spectro-temporal modulation transfer functions (MTFs) are derived as a function of ripple peak density (omega cycles/octave) and drifting velocity (omega Hz). The MTFs exhibit a low-pass function with respect to both dimensions, with 50% bandwidths of about 16 Hz and 2 cycles/octave. The data replicate (as special cases) previously measured purely temporal MTFs (omega = 0) [Viemeister, J. Acoust. Soc. Am. 66, 1364-1380 (1979)] and purely spectral MTFs (omega = 0) [Green, in Auditory Frequency Selectivity (Plenum, Cambridge, 1986), pp. 351-359]. A computational auditory model is presented that exhibits spectro-temporal MTFs consistent with the salient trends in the data. The model is used to demonstrate the potential relevance of these MTFs to the assessment of speech intelligibility in noise and reverberant conditions.
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Affiliation(s)
- T Chi
- Electrical Engineering Department, University of Maryland, College Park 20742, USA
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Ellwood K, Chi T, Huang W, Mitsouras K, Carey M. Cooperative assembly of RNA polymerase II transcription complexes. Cold Spring Harb Symp Quant Biol 1999; 63:253-61. [PMID: 10384289 DOI: 10.1101/sqb.1998.63.253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- K Ellwood
- Department of Biological Chemistry, University of California School of Medicine, Los Angeles 90095-1737, USA
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Chi T, Yang CC. Iatrogenic abdominal scar endometriosis: a case report. Zhonghua Yi Xue Za Zhi (Taipei) 1999; 62:236-8. [PMID: 10367485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
We report the case of a patient with abdominal scar endometriosis following a cesarean section. The rarity of this localization and its appearance on computerized tomography is shown. We emphasize the combination of history and image study of this pathology in the differential diagnosis of other diseases.
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Affiliation(s)
- T Chi
- Department of Radiology, Minshen General Hospital, Taoyuan, Taiwan, ROC
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40
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Chi T, Shin SL. Delayed intestinal stenosis after blunt abdominal trauma: report of a case. Kaohsiung J Med Sci 1998; 14:734-7. [PMID: 9838770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Major intestinal injury may be present with very subtle clinical and/or imaging findings. Sometimes, delayed intestinal stenosis may occur even several months after the blunt abdominal trauma. We present a 12-year-old boy with delayed jejunal stenosis following blunt abdominal injury in a car collision. Computed tomography (CT) scan showed streaky infiltrates in the mesentery and fluid densities in the bilateral anterior pararenal spaces as well as enhancement of bowel wall on the 2nd day after trauma. A "bird-beak" sign at the proximal jejunum with diffuse mucosal swelling of jejunal loops were seen on barium follow-up study on the 7th day. Complete obstruction at the duodenojejunal junction was identified by the follow-up barium examination on the 29th day.
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Affiliation(s)
- T Chi
- Department of Radiology, Minshen General Hospital, Taoyuan, Republic of China
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Holsinger LJ, Graef IA, Swat W, Chi T, Bautista DM, Davidson L, Lewis RS, Alt FW, Crabtree GR. Defects in actin-cap formation in Vav-deficient mice implicate an actin requirement for lymphocyte signal transduction. Curr Biol 1998; 8:563-72. [PMID: 9601640 DOI: 10.1016/s0960-9822(98)70225-8] [Citation(s) in RCA: 344] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Antigen-receptor interactions on lymphocytes result in local clustering of actin, receptors and signaling molecules into an asymmetric membrane structure termed a cap. Although actin polymerization is known to be required, the mechanisms underlying cap formation are unclear. We have studied the events underlying cap formation using mice bearing a null mutation in vav (vav-/-), a gene that encodes a guanine-nucleotide exchange factor for the GTPase Rac. RESULTS Lymphocytes from vav-/- mice failed to form T-cell receptor caps following activation and had a defective actin cytoskeleton. The vav-/- T cells were deficient in interleukin-2 (IL-2) production and proliferation, and the peak of Ca2+ mobilization was reduced although of normal duration. Activation of Jun N-terminal kinase or stress-activated kinase (JNK or SAPK) and mitogen-activated protein kinase (MAPK) and the induction of the transcription factor NF-ATc1 and egr-1 genes was normal. Despite the reduced Ca2+ mobilization, translocation of cytoplasmic NF-ATc to the nucleus was normal, reflecting that the lower levels of Ca2+ in vav-/- cells were still sufficient to activate calcineurin. Treatment of lymphocytes with cytochalasin D, which blocks actin polymerization, inhibited cap formation and produced defects in signaling and IL-2 transcriptional induction in response to antigen-receptor signaling that were nearly identical to those seen in vav-/- cells. In transfection studies, either constitutively active Vav or Rac could complement constitutively active calcineurin to activate NF-AT-dependent transcription. CONCLUSIONS These results indicate that Vav is required for cap formation in lymphocytes. Furthermore, the correlation between cap formation, IL-2 production and proliferation supports the hypothesis that an actin-dependent pathway is a source of specialized growth regulatory signals.
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Affiliation(s)
- L J Holsinger
- Department of Pathology, Howard Hughes Medical Institute, Beckman Center for Molecular and Genetic Medicine, Stanford University School of Medicine, California 94305, USA
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Wang W, Chi T, Xue Y, Zhou S, Kuo A, Crabtree GR. Architectural DNA binding by a high-mobility-group/kinesin-like subunit in mammalian SWI/SNF-related complexes. Proc Natl Acad Sci U S A 1998; 95:492-8. [PMID: 9435219 PMCID: PMC18447 DOI: 10.1073/pnas.95.2.492] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The SWI/SNF complex in yeast and Drosophila is thought to facilitate transcriptional activation of specific genes by antagonizing chromatin-mediated transcriptional repression. The mechanism by which it is targeted to specific genes is poorly understood and may involve direct DNA binding and/or interactions with specific or general transcription factors. We have previously purified a mammalian complex by using antibodies against BRG1, a human homologue of SWI2/SNF2. This complex is likely functionally related to the yeast SWI/SNF complex because all five subunit identified so far (referred to as BAFs, for BRG1-associated factors) are homologues of the yeast SWI/SNF subunits. However, we now describe the cloning of the 57-kDa subunit (BAF57), which is present only in higher eukaryotes but not in yeast. BAF57 is shared by all mammalian complexes and contains a high-mobility-group (HMG) domain adjacent to a kinesin-like region. Both recombinant BAF57 and the whole complex bind four-way junction (4WJ) DNA, which is thought to mimic the topology of DNA as it enters or exits the nucleosome. Surprisingly, complexes with mutations in the HMG domain of BAF57 can still bind 4WJ DNA and mediate ATP-dependent nucleosome disruption. Our work describes the first DNA binding subunit for SWI/SNF-like complexes and suggest that the mechanism by which mammalian and Drosophila SWI/SNF-like complexes interact with chromatin may involve recognition of higher-order chromatin structure by two or more DNA binding domains.
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Affiliation(s)
- W Wang
- Howard Hughes Medical Institute, Department of Developmental Biology, Stanford University, CA 94305-5323, USA
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Abstract
The prevailing view of eukaryotic gene activation poses that activators stimulate transcription by recruiting limiting components of the general transcription machinery to a core promoter. In one such model case, activation by the Epstein-Barr virus ZEBRA protein correlated closely with recruitment of the general transcription factors TFIIA and TFIID (the DA complex) as measured by DNase I footprinting and gel mobility shift assays. We now report that simple recruitment is not sufficient for full-level activation. An additional concentration-independent, rate-limiting step is activator-mediated isomerization of the DA complex characterized by an extended TFIID footprint. The isomerized complex supports both binding of TFIIB in gel mobility shift assays and activated transcription in heat-treated nuclear extracts, even after removal of ZEBRA. Surprisingly, the regulatory phenomenon of synergy was manifested only when the concentration of TFIID was limiting. When the DA complex was saturating, transcription was not synergistic, as indicated by the ability of a single activator to induce isomerization effectively and turn on a gene. On the basis of these observations, we propose a new biochemical model for eukaryotic gene activation and synergy.
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Affiliation(s)
- T Chi
- Department of Biological Chemistry, University of California, Los Angeles, School of Medicine, 90095-1737, USA
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Affiliation(s)
- D Tantin
- Molecular Biology Institute, University of California, Los Angeles 90095, USA
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Shortkroff S, Barone L, Hsu HP, Wrenn C, Gagne T, Chi T, Breinan H, Minas T, Sledge CB, Tubo R, Spector M. Healing of chondral and osteochondral defects in a canine model: the role of cultured chondrocytes in regeneration of articular cartilage. Biomaterials 1996; 17:147-54. [PMID: 8624391 DOI: 10.1016/0142-9612(96)85759-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this study a canine model was developed to investigate the nature of early healing responses to both chondral and osteochondral defects and to evaluate the tissue regenerative capacity of cultured autologous chondrocytes in chondral defects. The healing response to surgically created chondral defects was minor, with little cellular infiltration. In contrast, osteochondral defects exhibited a rapid cellular response, resulting ultimately in the formation of fibrous tissue. The lack of significant cellular activity in chondral defects suggests that an evaluation of the capacity of cultured autologous chondrocytes to regenerate articular cartilage is best studied in chondral defects using the canine model. When dedifferentiated cultured articular chondrocytes were implanted into chondral defects, islands of type II collagen staining were demonstrated in the regenerative tissue within 6 weeks. The relatively early expression of cartilage specific markers by the implanted chondrocytes, coupled with the inability of untreated chondral defects to repair or regenerate, demonstrates the utility of the canine model in evaluating novel materials for cartilage repair and regeneration.
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Affiliation(s)
- S Shortkroff
- Brigham & Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Abstract
One of the important regulatory concepts to emerge from studies of eukaryotic gene expression is that RNA polymerase II promoters and their upstream activators are composed of functional modules whose synergistic action regulates the transcriptional activity of a nearby gene. Biochemical analysis of synergy by ZEBRA, a non-acidic activator of the Epstein-Barr virus (EBV) lytic cycle, showed that the synergistic transcriptional effect of promoter sites and activation modules correlates with assembly of the TFIID:TFIIA (DA) complex in DNase I footprinting and gel shift assays. The activator-dependent DA complex differs from a basal DA complex by its ability to bind TFIIB stably in an interaction regulated by TATA-binding protein-associated factors (TAFs). TFIIB enhances the degree of synergism by increasing complex stability. Similar findings were made with the acidic activator GAL4-VP16. Our data suggest a unifying mechanism for gene activation and synergy by acidic and non-acidic activators, and indicate that synergy is manifested at the earliest stage of preinitiation complex assembly.
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Affiliation(s)
- T Chi
- Department of Biological Chemistry, University of California, Los Angeles, School of Medicine 90095-1737, USA
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Ma Q, Wadleigh D, Chi T, Herschman H. The Drosophila TIS11 homologue encodes a developmentally controlled gene. Oncogene 1994; 9:3329-34. [PMID: 7936658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We previously identified a murine primary response gene family containing three members; TIS11, TIS11B and TIS11D. Using degenerate oligonucleotides derived from conserved regions of the mouse TIS11 family cDNAs as primers and Drosophila genomic DNA as template for polymerase chain reaction amplification, we have identified a fly TIS11 homologue called DTIS11. The DTIS11 protein shares 90% sequence identity with the murine TIS11B and TIS11D proteins, over a 74 amino acid region that contains two CX8CX5CX3H repeated motifs separated by 18 amino acids. DTIS11 maps to region 11B(14-16) on the X-chromosome. Northern blot and in situ hybridization show that a maternal 3 kb message is present in embryos of early developmental stages. A 6 kb DTIS11 mRNA subsequently appears. In KC embryonal cells, both a strong 3 kb message and a less intense 6 kb message are present. The larger (6 kb) message is modestly induced in KC cells by both forskolin and tetradecanoyl phorbol acetate, and is stabilized by cycloheximide.
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Affiliation(s)
- Q Ma
- Department of Biological Chemistry, UCLA-DOE Laboratory of Structural Biology and Molecular Medicine
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Grayson D, Chi T, Liebmann J, Ritch R. Initial argon laser trabeculoplasty to the inferior vs superior half of trabecular meshwork. Arch Ophthalmol 1994; 112:446-7. [PMID: 8155044 DOI: 10.1001/archopht.1994.01090160020004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Miller G, Himmelfarb H, Heston L, Countryman J, Gradoville L, Baumann R, Chi T, Carey M. Comparing regions of the Epstein-Barr virus ZEBRA protein which function as transcriptional activating sequences in Saccharomyces cerevisiae and in B cells. J Virol 1993; 67:7472-81. [PMID: 8230468 PMCID: PMC238213 DOI: 10.1128/jvi.67.12.7472-7481.1993] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The ZEBRA protein activates expression of Epstein-Barr virus early-lytic-cycle genes in human B lymphocytes. Here it is shown that ZEBRA also behaves as a sequence-specific transcriptional activator in Saccharomyces cerevisiae. Deletional mutagenesis defined three regions of ZEBRA that participate in activation in S. cerevisiae. These regions are designated YI (amino acids [aa] 1 to 25), YII (aa 51 to 102), and YIII (aa 228 to 245). Two of the three regions of the native ZEBRA protein act together to mediate activation when assayed on ZEBRA binding sites. However, when fused to the DNA binding domain of GAL4 and assayed on GAL4 binding sites, regions YII and YIII were each sufficient to confer activation in S. cerevisiae. Regions of ZEBRA which affected activation in S. cerevisiae were also required in human B lymphocytes. The amino-terminal region of ZEBRA (aa 1 to 98) was required for activation both in S. cerevisiae and in human B cells; deletion of the carboxy-terminal 18 aa also significantly reduced activation in both cell types. Thus, the behavior of ZEBRA in human B cells and S. cerevisiae suggests that the protein contains universal activation motifs that interact with conserved components of the transcription machinery. However, certain deletion mutants of ZEBRA containing mutations in the N-terminal region exhibited discordant behaviors in S. cerevisiae and in B cells. For example, deletion of ZEBRA aa 26 to 51 impaired activation to a great extent in B cells but had little or no effect in S. cerevisiae. The discordant mutants may reflect interactions with a variable domain of a conserved component or unique interactions with specialized components of the basal transcription apparatus in different cells.
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Affiliation(s)
- G Miller
- Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut 06510-8064
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