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Zhang N, Tan Z, Wei J, Zhang S, Liu Y, Miao Y, Ding Q, Yi W, Gan M, Li C, Liu B, Wang H, Zheng Z. Identification of novel anti-ZIKV drugs from viral-infection temporal gene expression profiles. Emerg Microbes Infect 2023; 12:2174777. [PMID: 36715162 PMCID: PMC9946313 DOI: 10.1080/22221751.2023.2174777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Indexed: 01/31/2023]
Abstract
Zika virus (ZIKV) infections are typically asymptomatic but cause severe neurological complications (e.g. Guillain-Barré syndrome in adults, and microcephaly in newborns). There are currently no specific therapy or vaccine options available to prevent ZIKV infections. Temporal gene expression profiles of ZIKV-infected human brain microvascular endothelial cells (HBMECs) were used in this study to identify genes essential for viral replication. These genes were then used to identify novel anti-ZIKV agents and validated in publicly available data and functional wet-lab experiments. Here, we found that ZIKV effectively evaded activation of immune response-related genes and completely reprogrammed cellular transcriptional architectures. Knockdown of genes, which gradually upregulated during viral infection but showed distinct expression patterns between ZIKV- and mock infection, discovered novel proviral and antiviral factors. One-third of the 74 drugs found through signature-based drug repositioning and cross-reference with the Drug Gene Interaction Database (DGIdb) were known anti-ZIKV agents. In cellular assays, two promising antiviral candidates (Luminespib/NVP-AUY922, L-161982) were found to reduce viral replication without causing cell toxicity. Overall, our time-series transcriptome-based methods offer a novel and feasible strategy for antiviral drug discovery. Our strategies, which combine conventional and data-driven analysis, can be extended for other pathogens causing pandemics in the future.
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Affiliation(s)
- Nailou Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhongyuan Tan
- The Joint Laboratory for Translational Precision Medicine, a. Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China and b. Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Jinbo Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Sai Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Yan Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Yuanjiu Miao
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Qingwen Ding
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Wenfu Yi
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Min Gan
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Chunjie Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Bin Liu
- Characteristic Medical Center of Chinese People’s Armed Police Forces, Tianjin, People’s Republic of China
| | - Hanzhong Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhenhua Zheng
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China, Zhenhua Zheng CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
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Li C, Hong Y, Sun J, Wang G, Zhou H, Xu L, Wang L, Xu G. Temporal transcriptome analysis reveals several key pathways involve in cadmium stress response in Nicotiana tabacum L. Front Plant Sci 2023; 14:1143349. [PMID: 36959946 PMCID: PMC10027936 DOI: 10.3389/fpls.2023.1143349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Tobacco has a strong cadmium (Cd) enrichment capacity, meaning that it can absorb large quantities from the environment, but too much Cd will cause damage to the plant. It is not yet clear how the plant can dynamically respond to Cd stress. Here, we performed a temporal transcriptome analysis of tobacco roots under Cd treatment from 0 to 48 h. The number of differentially expressed genes (DEGs) was found to change significantly at 3 h of Cd treatment, which we used to define the early and middle stages of the Cd stress response. The gene ontology (GO) term analysis indicates that genes related to photosynthesis and fatty acid synthesis were enriched during the early phases of the stress response, and in the middle phase biological process related to metal ion transport, DNA damage repair, and metabolism were enriched. It was also found that plants use precursor mRNA (pre-mRNA) processes to first resist Cd stress, and with the increasing of Cd treatment time, the overlapped genes number of DEGs and DAS increased, suggesting the transcriptional levels and post-transcriptional level might influence each other. This study allowed us to better understand how plants dynamically respond to cadmium stress at the transcriptional and post-transcriptional levels and provided a reference for the screening of Cd-tolerant genes in the future.
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Affiliation(s)
- Chenyang Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, China
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Yi Hong
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, China
| | - Jinhao Sun
- Technology Center, China Tobacco Jiangsu Industrial Co. Ltd., Nanjing, China
| | - Guoping Wang
- Yuxi Zhongyan Tobacco Seed Co., Ltd., Yuxi, Yunnan, China
| | - Huina Zhou
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, China
| | - Liangtao Xu
- Technology Center, China Tobacco Jiangsu Industrial Co. Ltd., Nanjing, China
| | - Long Wang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, and Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Guoyun Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou, China
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