226 results on '"Du, Yushen"'
Search Results
2. CCL21-DC in situ vaccination in murine NSCLC overcomes resistance to immunotherapy and generates systemic tumor-specific immunity
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Salehi-Rad, Ramin, Lim, Raymond J, Du, Yushen, Tran, Linh M, Li, Rui, Ong, Stephanie L, Huang, Zi Ling, Dumitras, Camelia, Zhang, Tianhao, Park, Stacy J, Crosson, William, Kahangi, Bitta, Abascal, Jensen, Seet, Christopher, Oh, Michael, Shabihkhani, Maryam, Paul, Manash, Krysan, Kostyantyn, Lisberg, Aaron E, Garon, Edward B, Liu, Bin, and Dubinett, Steven M
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Lung ,Cancer ,Lung Cancer ,Immunization ,Vaccine Related ,Development of treatments and therapeutic interventions ,5.1 Pharmaceuticals ,Good Health and Well Being ,Humans ,Animals ,Mice ,Carcinoma ,Non-Small-Cell Lung ,Proto-Oncogene Proteins p21(ras) ,Tumor Suppressor Protein p53 ,Lung Neoplasms ,Immunotherapy ,Tumor Microenvironment ,Chemokine CCL21 ,Vaccination ,Non-Small Cell Lung Cancer ,Dendritic Cells ,Oncology and carcinogenesis - Abstract
BackgroundDespite recent advances in immunotherapy, many patients with non-small cell lung cancer (NSCLC) do not respond to immune checkpoint inhibitors (ICI). Resistance to ICI may be driven by suboptimal priming of antitumor T lymphocytes due to poor antigen presentation as well as their exclusion and impairment by the immunosuppressive tumor microenvironment (TME). In a recent phase I trial in patients with NSCLC, in situ vaccination (ISV) with dendritic cells engineered to secrete CCL21 (CCL21-DC), a chemokine that facilitates the recruitment of T cells and DC, promoted T lymphocyte tumor infiltration and PD-L1 upregulation.MethodsMurine models of NSCLC with distinct driver mutations (KrasG12D/P53+/-/Lkb1-/- (KPL); KrasG12D/P53+/- (KP); and KrasG12D (K)) and varying tumor mutational burden were used to evaluate the efficacy of combination therapy with CCL21-DC ISV plus ICI. Comprehensive analyses of longitudinal preclinical samples by flow cytometry, single cell RNA-sequencing (scRNA-seq) and whole-exome sequencing were performed to assess mechanisms of combination therapy.ResultsISV with CCL21-DC sensitized immune-resistant murine NSCLCs to ICI and led to the establishment of tumor-specific immune memory. Immunophenotyping revealed that CCL21-DC obliterated tumor-promoting neutrophils, promoted sustained infiltration of CD8 cytolytic and CD4 Th1 lymphocytes and enriched progenitor T cells in the TME. Addition of ICI to CCL21-DC further enhanced the expansion and effector function of T cells both locally and systemically. Longitudinal evaluation of tumor mutation profiles revealed that CCL21-DC plus ICI induced immunoediting of tumor subclones, consistent with the broadening of tumor-specific T cell responses.ConclusionsCCL21-DC ISV synergizes with anti-PD-1 to eradicate murine NSCLC. Our data support the clinical application of CCL21-DC ISV in combination with checkpoint inhibition for patients with NSCLC.
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- 2023
3. Design and synthesis of 7-membered lactam fused hydroxypyridinones as potent metal binding pharmacophores (MBPs) for inhibiting influenza virus PAN endonuclease
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Zhang, Lei, Ke, Di, Li, Yuting, Zhang, Hui, Zhang, Xi, Wang, Sihan, Ni, Shaokai, Peng, Bo, Zeng, Huixuan, Hou, Tingjun, Du, Yushen, Pan, Peichen, Yu, Yongping, and Chen, Wenteng
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- 2024
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4. Latency reversal plus natural killer cells diminish HIV reservoir in vivo
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Kim, Jocelyn T, Zhang, Tian-Hao, Carmona, Camille, Lee, Bryanna, Seet, Christopher S, Kostelny, Matthew, Shah, Nisarg, Chen, Hongying, Farrell, Kylie, Soliman, Mohamed SA, Dimapasoc, Melanie, Sinani, Michelle, Blanco, Kenia Yazmin Reyna, Bojorquez, David, Jiang, Hong, Shi, Yuan, Du, Yushen, Komarova, Natalia L, Wodarz, Dominik, Wender, Paul A, Marsden, Matthew D, Sun, Ren, and Zack, Jerome A
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Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,Infectious Diseases ,HIV/AIDS ,Aetiology ,5.1 Pharmaceuticals ,2.2 Factors relating to the physical environment ,Development of treatments and therapeutic interventions ,Infection ,Animals ,Anti-HIV Agents ,Bone Marrow ,CD4-Positive T-Lymphocytes ,Coculture Techniques ,Female ,HIV Infections ,HIV-1 ,Host-Pathogen Interactions ,Humans ,Killer Cells ,Natural ,Male ,Mice ,Mice ,Transgenic ,Protein Kinase C ,Protein Kinase Inhibitors ,Spleen ,Viral Load ,Viremia ,Virus Latency ,Virus Replication - Abstract
HIV is difficult to eradicate due to the persistence of a long-lived reservoir of latently infected cells. Previous studies have shown that natural killer cells are important to inhibiting HIV infection, but it is unclear whether the administration of natural killer cells can reduce rebound viremia when anti-retroviral therapy is discontinued. Here we show the administration of allogeneic human peripheral blood natural killer cells delays viral rebound following interruption of anti-retroviral therapy in humanized mice infected with HIV-1. Utilizing genetically barcoded virus technology, we show these natural killer cells efficiently reduced viral clones rebounding from latency. Moreover, a kick and kill strategy comprised of the protein kinase C modulator and latency reversing agent SUW133 and allogeneic human peripheral blood natural killer cells during anti-retroviral therapy eliminated the viral reservoir in a subset of mice. Therefore, combinations utilizing latency reversal agents with targeted cellular killing agents may be an effective approach to eradicating the viral reservoir.
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- 2022
5. Sustaining the advancement of new energy vehicles in the post-subsidy era: Carbon quota mechanisms and subsidy mechanisms for recycling of used batteries
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Guo, Zulong, Du, Yushen, and Zhao, Yuntong
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- 2024
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6. Smooth sailing ahead? Policy options for China's new energy vehicle industry in the post-subsidy era
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Du, Yushen, Guo, Zulong, and Bao, Hongli
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- 2024
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7. How can China's subsidy promote the transition to electric vehicles?
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Zhao, Yuntong, Jian, Zhaoquan, and Du, Yushen
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- 2024
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8. On-demand nanozyme signal enhancement at the push of a button for the improved detection of SARS-CoV-2 nucleocapsid protein in serum
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Bradbury, Daniel W, Trinh, Jasmine T, Ryan, Milo J, Cantu, Cassandra M, Lu, Jiakun, Nicklen, Frances D, Du, Yushen, Sun, Ren, Wu, Benjamin M, and Kamei, Daniel T
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Biodefense ,Infectious Diseases ,Prevention ,Emerging Infectious Diseases ,Vaccine Related ,Good Health and Well Being ,Antibodies ,Viral ,COVID-19 ,Humans ,Immunoassay ,SARS-CoV-2 ,Sensitivity and Specificity ,Analytical Chemistry ,Other Chemical Sciences - Abstract
We developed an innovative 3D printed casing that incorporates a lateral-flow immunoassay, dehydrated signal enhancement reagents, and a sealed buffer chamber. With only the push of a button for signal enhancement, our device detected the SARS-CoV-2 N-protein in 40 min at concentrations as low as 0.1 ng mL-1 in undiluted serum.
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- 2021
9. Riok3 inhibits the antiviral immune response by facilitating TRIM40-mediated RIG-I and MDA5 degradation
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Shen, Yong, Tang, Kejun, Chen, Dongdong, Hong, Mengying, Sun, Fangfang, Wang, SaiSai, Ke, Yuehai, Wu, Tingting, Sun, Ren, Qian, Jing, and Du, Yushen
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Prevention ,Biodefense ,Infectious Diseases ,Genetics ,Vaccine Related ,Emerging Infectious Diseases ,Aetiology ,2.1 Biological and endogenous factors ,Infection ,Inflammatory and immune system ,Animals ,Female ,Male ,Antiviral Agents ,Cells ,Cultured ,Cytokines ,DEAD Box Protein 58 ,Fibroblasts ,Immunity ,Interferon-Induced Helicase ,IFIH1 ,Macrophages ,Peritoneal ,Mice ,Inbred C57BL ,Protein Binding ,Protein Serine-Threonine Kinases ,Proteolysis ,RNA Viruses ,Ubiquitin-Protein Ligases ,Ubiquitination ,Up-Regulation ,Virus Replication ,Biochemistry and Cell Biology ,Medical Physiology - Abstract
The type I interferon (IFN) pathway is a key component of innate immune response upon invasion of foreign pathogens. It is also under precise control to prevent excessive upregulation and undesired inflammation cascade. In the present study, we report that Riok3, an atypical kinase, negatively regulates retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) sensing-induced type I IFN signaling. Riok3 deficiency selectively inhibits RNA viral replication in vitro, resulting from an upregulated type I IFN pathway. Mice with myeloid-specific Riok3 knockout also show a more robust induction of type I IFN upon RNA virus infection and are more resistant to RNA virus-induced pathogenesis. Mechanistically, Riok3 recruits and interacts with the E3 ubiquitin ligase TRIM40, leading to the degradation of RIG-I and melanoma differentiation-associated gene-5 (MDA5) via K48- and K27-linked ubiquitination. Collectively, our data reveal the mechanism that Riok3 employs to be a negative regulator of antiviral innate immunity.
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- 2021
10. Quantifying the Evolutionary Constraints and Potential of Hepatitis C Virus NS5A Protein.
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Dai, Lei, Du, Yushen, Qi, Hangfei, Huber, Christian, Chen, Dongdong, Zhang, Tian-Hao, Wu, Nicholas, Wang, Ergang, Lloyd-Smith, James, and Sun, Ren
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DFE ,HCV ,deep mutational scanning ,drug resistance ,fitness landscape ,viral evolution - Abstract
RNA viruses, such as hepatitis C virus (HCV), influenza virus, and SARS-CoV-2, are notorious for their ability to evolve rapidly under selection in novel environments. It is known that the high mutation rate of RNA viruses can generate huge genetic diversity to facilitate viral adaptation. However, less attention has been paid to the underlying fitness landscape that represents the selection forces on viral genomes, especially under different selection conditions. Here, we systematically quantified the distribution of fitness effects of about 1,600 single amino acid substitutions in the drug-targeted region of NS5A protein of HCV. We found that the majority of nonsynonymous substitutions incur large fitness costs, suggesting that NS5A protein is highly optimized. The replication fitness of viruses is correlated with the pattern of sequence conservation in nature, and viral evolution is constrained by the need to maintain protein stability. We characterized the adaptive potential of HCV by subjecting the mutant viruses to selection by the antiviral drug daclatasvir at multiple concentrations. Both the relative fitness values and the number of beneficial mutations were found to increase with the increasing concentrations of daclatasvir. The changes in the spectrum of beneficial mutations in NS5A protein can be explained by a pharmacodynamics model describing viral fitness as a function of drug concentration. Overall, our results show that the distribution of fitness effects of mutations is modulated by both the constraints on the biophysical properties of proteins (i.e., selection pressure for protein stability) and the level of environmental stress (i.e., selection pressure for drug resistance).IMPORTANCE Many viruses adapt rapidly to novel selection pressures, such as antiviral drugs. Understanding how pathogens evolve under drug selection is critical for the success of antiviral therapy against human pathogens. By combining deep sequencing with selection experiments in cell culture, we have quantified the distribution of fitness effects of mutations in hepatitis C virus (HCV) NS5A protein. Our results indicate that the majority of single amino acid substitutions in NS5A protein incur large fitness costs. Simulation of protein stability suggests viral evolution is constrained by the need to maintain protein stability. By subjecting the mutant viruses to selection under an antiviral drug, we find that the adaptive potential of viral proteins in a novel environment is modulated by the level of environmental stress, which can be explained by a pharmacodynamics model. Our comprehensive characterization of the fitness landscapes of NS5A can potentially guide the design of effective strategies to limit viral evolution.
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- 2021
11. Structural characterization of an isocytosine-specific deaminase VCZ reveals its application potential in the anti-cancer therapy
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Guo, Wenting, Li, Xiaojia, Fan, Jingyu, Li, Hongwei, Wen, Yan, Meng, Chunyan, Chen, Haitao, Zhao, Zhipeng, Zhang, Yuling, Du, Yushen, and Wu, Baixing
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- 2023
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12. Martynoside rescues 5-fluorouracil-impaired ribosome biogenesis by stabilizing RPL27A
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Hong, Mengying, Du, Yushen, Chen, Dongdong, Shi, Yuan, Hu, Menglong, Tang, Kejun, Hong, Zhuping, Meng, Xiangzhi, Xu, Wan, Wu, Gaoqi, Yao, Yuanyuan, Chen, Liubo, Chen, Wenteng, Lau, Chit Ying, Sheng, Li, Zhang, Tian-Hao, Huang, Haigen, Fang, Zheyu, Shen, Yong, Sun, Fangfang, Qian, Jing, Qu, Haibin, Zheng, Shu, Zhang, Suzhan, Ding, Kefeng, and Sun, Ren
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- 2023
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13. Subsidy policy and carbon quota mechanism of the Chinese vehicle industry
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Du, Yushen, Zhao, Yuntong, and Li, Hao
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- 2023
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14. Tracking HIV Rebound following Latency Reversal Using Barcoded HIV
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Marsden, Matthew D, Zhang, Tian-hao, Du, Yushen, Dimapasoc, Melanie, Soliman, Mohamed SA, Wu, Xiaomeng, Kim, Jocelyn T, Shimizu, Akira, Schrier, Adam, Wender, Paul A, Sun, Ren, and Zack, Jerome A
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Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,Infectious Diseases ,HIV/AIDS ,Genetics ,2.2 Factors relating to the physical environment ,Aetiology ,Infection ,Animals ,Anti-HIV Agents ,CD4-Positive T-Lymphocytes ,HIV Infections ,HIV-1 ,Humans ,Mice ,Protein Kinase C ,Virus Activation ,Virus Latency ,Virus Replication ,ART ,HIV ,LRA ,antiretroviral therapy ,cure ,humanized mice ,latency ,protein kinase C ,reservoir ,Biomedical and clinical sciences - Abstract
HIV latency prevents cure of infection with antiretroviral therapy (ART) alone. One strategy for eliminating latently infected cells involves the induction of viral protein expression via latency-reversing agents (LRAs), allowing killing of host cells by viral cytopathic effects or immune effector mechanisms. Here, we combine a barcoded HIV approach and a humanized mouse model to study the effects of a designed, synthetic protein kinase C modulating LRA on HIV rebound. We show that administration of this compound during ART results in a delay in rebound once ART is stopped. Furthermore, the rebounding virus appears composed of a smaller number of unique barcoded viruses than occurs in control-treated animals, suggesting that some reservoir cells that would have contributed virus to the rebound process are eliminated by LRA administration. These data support the use of barcoded virus to study rebound and suggest that LRAs may be useful in HIV cure efforts.
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- 2020
15. mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1.
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Du, Yushen, Hultquist, Judd F, Zhou, Quan, Olson, Anders, Tseng, Yenwen, Zhang, Tian-Hao, Hong, Mengying, Tang, Kejun, Chen, Liubo, Meng, Xiangzhi, McGregor, Michael J, Dai, Lei, Gong, Danyang, Martin-Sancho, Laura, Chanda, Sumit, Li, Xinming, Bensenger, Steve, Krogan, Nevan J, and Sun, Ren
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Humans ,Influenza A virus ,Interferons ,Viral Nonstructural Proteins ,RNA ,Messenger ,Virus Replication ,Protein Binding ,Mutation ,Gene Library ,Lipid Metabolism ,Fatty Acid Synthase ,Type I ,Gene Ontology ,A549 Cells ,Pneumonia & Influenza ,Influenza ,Genetics ,Prevention - Abstract
A comprehensive examination of protein-protein interactions (PPIs) is fundamental for the understanding of cellular machineries. However, limitations in current methodologies often prevent the detection of PPIs with low abundance proteins. To overcome this challenge, we develop a mRNA display with library of even-distribution (md-LED) method that facilitates the detection of low abundance binders with high specificity and sensitivity. As a proof-of-principle, we apply md-LED to IAV NS1 protein. Complementary to AP-MS, md-LED enables us to validate previously described PPIs as well as to identify novel NS1 interactors. We show that interacting with FASN allows NS1 to directly regulate the synthesis of cellular fatty acids. We also use md-LED to identify a mutant of NS1, D92Y, results in a loss of interaction with CPSF1. The use of high-throughput sequencing as the readout for md-LED enables sensitive quantification of interactions, ultimately enabling massively parallel experimentation for the investigation of PPIs.
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- 2020
16. Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease
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Zhang, Tian-hao, Dai, Lei, Barton, John P, Du, Yushen, Tan, Yuxiang, Pang, Wenwen, Chakraborty, Arup K, Lloyd-Smith, James O, and Sun, Ren
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Biological Sciences ,Genetics ,HIV/AIDS ,Antimicrobial Resistance ,Infectious Diseases ,5.1 Pharmaceuticals ,6.1 Pharmaceuticals ,Evaluation of treatments and therapeutic interventions ,Development of treatments and therapeutic interventions ,Infection ,Good Health and Well Being ,Drug Resistance ,Viral ,Epistasis ,Genetic ,Genetic Fitness ,HIV Infections ,HIV Protease ,HIV-1 ,Humans ,Mutation ,Protease Inhibitors ,Virus Replication ,Developmental Biology - Abstract
Drug-resistant mutations often have deleterious impacts on replication fitness, posing a fitness cost that can only be overcome by compensatory mutations. However, the role of fitness cost in the evolution of drug resistance has often been overlooked in clinical studies or in vitro selection experiments, as these observations only capture the outcome of drug selection. In this study, we systematically profile the fitness landscape of resistance-associated sites in HIV-1 protease using deep mutational scanning. We construct a mutant library covering combinations of mutations at 11 sites in HIV-1 protease, all of which are associated with resistance to protease inhibitors in clinic. Using deep sequencing, we quantify the fitness of thousands of HIV-1 protease mutants after multiple cycles of replication in human T cells. Although the majority of resistance-associated mutations have deleterious effects on viral replication, we find that epistasis among resistance-associated mutations is predominantly positive. Furthermore, our fitness data are consistent with genetic interactions inferred directly from HIV sequence data of patients. Fitness valleys formed by strong positive epistasis reduce the likelihood of reversal of drug resistance mutations. Overall, our results support the view that strong compensatory effects are involved in the emergence of clinically observed resistance mutations and provide insights to understanding fitness barriers in the evolution and reversion of drug resistance.
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- 2020
17. Synthesis and structure-activity optimization of 7-azaindoles containing aza-β-amino acids targeting the influenza PB2 subunit
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Wang, Sihan, Ying, Zhimin, Huang, Youchun, Li, Yuting, Hu, Menglong, Kang, Ke, Wang, Haiyang, Shao, Jiaan, Wu, Gaoqi, Yu, Yongping, Du, Yushen, and Chen, Wenteng
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- 2023
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18. Open knowledge disclosure and technical standard competition in transition economies: A legitimacy perspective
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Liu, Ziyu and Du, Yushen
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- 2022
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19. Emergence of Integrase Resistance Mutations During Initial Therapy Containing Dolutegravir
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Fulcher, Jennifer A, Du, Yushen, Zhang, Tian-hao, Sun, Ren, and Landovitz, Raphael J
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Medical Microbiology ,Biomedical and Clinical Sciences ,Infection ,Good Health and Well Being ,Antiretroviral Therapy ,Highly Active ,Drug Resistance ,Viral ,Genotype ,HIV Infections ,HIV Integrase Inhibitors ,HIV-1 ,Heterocyclic Compounds ,3-Ring ,Humans ,Integrases ,Male ,Middle Aged ,Mutation ,Oxazines ,Piperazines ,Pyridones ,Sequence Analysis ,DNA ,Treatment Failure ,antiretroviral therapy ,drug resistance ,integrase strand transfer inhibitors ,Biological Sciences ,Medical and Health Sciences ,Microbiology ,Clinical sciences - Abstract
Dolutegravir (DTG) is a preferred drug for initial treatment of human immunodeficiency virus type 1 infection. We present next-generation sequencing analysis of integrase genotypes during a period of virologic failure in a treatment-naive man who initiated tenofovir disoproxil fumarate/emtricitabine plus DTG.
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- 2018
20. High-Throughput Fitness Profiling of Zika Virus E Protein Reveals Different Roles for Glycosylation during Infection of Mammalian and Mosquito Cells.
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Gong, Danyang, Zhang, Tian-Hao, Zhao, Dawei, Du, Yushen, Chapa, Travis J, Shi, Yuan, Wang, Laurie, Contreras, Deisy, Zeng, Gang, Shi, Pei-Yong, Wu, Ting-Ting, Arumugaswami, Vaithilingaraja, and Sun, Ren
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Entomology ,Genomics ,Protein Structure Aspects ,Virology ,Vector-Borne Diseases ,Infectious Diseases ,Prevention ,Vaccine Related ,Emerging Infectious Diseases ,Genetics ,Biodefense ,Rare Diseases ,2.2 Factors relating to the physical environment ,2.1 Biological and endogenous factors ,Infection - Abstract
Zika virus (ZIKV) infection causes Guillain-Barré syndrome and severe birth defects. ZIKV envelope (E) protein is the major viral protein involved in cell receptor binding and entry and is therefore considered one of the major determinants in ZIKV pathogenesis. Here we report a gene-wide mapping of functional residues of ZIKV E protein using a mutant library, with changes covering every nucleotide position. By comparing the replication fitness of every viral mutant between mosquito and human cells, we identified that mutations affecting glycosylation display the most divergence. By characterizing individual mutants, we show that ablation of glycosylation selectively benefits ZIKV infection of mosquito cells by enhancing cell entry, whereas it either has little impact on ZIKV infection on certain human cells or leads to decreased infection through the entry factor DC-SIGN. In conclusion, we define the roles of individual residues of ZIKV envelope protein, which contribute to ZIKV replication fitness in human and mosquito cells.
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- 2018
21. Effects of Mutations on Replicative Fitness and Major Histocompatibility Complex Class I Binding Affinity Are Among the Determinants Underlying Cytotoxic-T-Lymphocyte Escape of HIV-1 Gag Epitopes
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Du, Yushen, Zhang, Tian-Hao, Dai, Lei, Zheng, Xiaojuan, Gorin, Aleksandr M, Oishi, John, Wu, Ting-Ting, Yoshizawa, Janice M, Li, Xinmin, Yang, Otto O, Martinez-Maza, Otoniel, Detels, Roger, and Sun, Ren
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Medical Microbiology ,Biomedical and Clinical Sciences ,Immunology ,Vaccine Related ,HIV/AIDS ,Sexually Transmitted Infections ,Genetics ,Immunization ,Infectious Diseases ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Epitopes ,HIV-1 ,Histocompatibility Antigens Class I ,Humans ,Immune Evasion ,Mutation ,Missense ,Protein Binding ,T-Lymphocytes ,Cytotoxic ,Virus Replication ,gag Gene Products ,Human Immunodeficiency Virus ,CTL escape ,Gag epitopes ,HIV-I ,high-throughput fitness profiling ,MHC binding prediction ,intrapatient viral evolution ,Microbiology ,Biochemistry and cell biology ,Medical microbiology - Abstract
Certain "protective" major histocompatibility complex class I (MHC-I) alleles, such as B*57 and B*27, are associated with long-term control of HIV-1 in vivo mediated by the CD8+ cytotoxic-T-lymphocyte (CTL) response. However, the mechanism of such superior protection is not fully understood. Here we combined high-throughput fitness profiling of mutations in HIV-1 Gag, in silico prediction of MHC-peptide binding affinity, and analysis of intraperson virus evolution to systematically compare differences with respect to CTL escape mutations between epitopes targeted by protective MHC-I alleles and those targeted by nonprotective MHC-I alleles. We observed that the effects of mutations on both viral replication and MHC-I binding affinity are among the determinants of CTL escape. Mutations in Gag epitopes presented by protective MHC-I alleles are associated with significantly higher fitness cost and lower reductions in binding affinity with respect to MHC-I. A linear regression model accounting for the effect of mutations on both viral replicative capacity and MHC-I binding can explain the protective efficacy of MHC-I alleles. Finally, we found a consistent pattern in the evolution of Gag epitopes in long-term nonprogressors versus progressors. Overall, our results suggest that certain protective MHC-I alleles allow superior control of HIV-1 by targeting epitopes where mutations typically incur high fitness costs and small reductions in MHC-I binding affinity.IMPORTANCE Understanding the mechanism of viral control achieved in long-term nonprogressors with protective HLA alleles provides insights for developing functional cure of HIV infection. Through the characterization of CTL escape mutations in infected persons, previous researchers hypothesized that protective alleles target epitopes where escape mutations significantly reduce viral replicative capacity. However, these studies were usually limited to a few mutations observed in vivo Here we utilized our recently developed high-throughput fitness profiling method to quantitatively measure the fitness of mutations across the entirety of HIV-1 Gag. The data enabled us to integrate the results with in silico prediction of MHC-peptide binding affinity and analysis of intraperson virus evolution to systematically determine the differences in CTL escape mutations between epitopes targeted by protective HLA alleles and those targeted by nonprotective HLA alleles. We observed that the effects of Gag epitope mutations on HIV replicative fitness and MHC-I binding affinity are among the major determinants of CTL escape.
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- 2017
22. Technical standard competition: An ecosystem-view analysis based on stochastic evolutionary game theory
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Zhao, Yuntong and Du, Yushen
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- 2021
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23. Ex vivo and in vivo chemoprotective activity and potential mechanism of Martynoside against 5-fluorouracil-induced bone marrow cytotoxicity
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Hong, Mengying, Chen, Dongdong, Hong, Zhuping, Tang, Kejun, Yao, Yuanyuan, Chen, Liubo, Ye, Tingting, Qian, Jing, Du, Yushen, and Sun, Ren
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- 2021
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24. HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes.
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Gorin, Aleksandr M, Du, Yushen, Liu, Franklin Y, Zhang, Tian-Hao, Ng, Hwee L, Hofmann, Christian, Cumberland, William G, Sun, Ren, and Yang, Otto O
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T-Lymphocytes ,Cytotoxic ,Humans ,HIV-1 ,Viremia ,HIV Infections ,Histocompatibility Antigens Class I ,Epitopes ,T-Lymphocyte ,Immunodominant Epitopes ,Mutagenesis ,Site-Directed ,Antigen Presentation ,Immune Evasion ,High-Throughput Nucleotide Sequencing ,Prevention ,Genetics ,HIV/AIDS ,Vaccine Related ,Virology ,Microbiology ,Immunology ,Medical Microbiology - Abstract
Certain Major Histocompatibility-I (MHC-I) types are associated with superior immune containment of HIV-1 infection by CD8+ cytotoxic T lymphocytes (CTLs), but the mechanisms mediating this containment are difficult to elucidate in vivo. Here we provide controlled assessments of fitness landscapes and CTL-imposed constraints for immunodominant epitopes presented by two protective (B*57 and B*27) and one non-protective (A*02) MHC-I types. Libraries of HIV-1 with saturation mutagenesis of CTL epitopes are propagated with and without CTL selective pressure to define the fitness landscapes for epitope mutation and escape from CTLs via deep sequencing. Immunodominant B*57- and B*27- present epitopes are highly limited in options for fit mutations, with most viable variants recognizable by CTLs, whereas an immunodominant A*02 epitope-presented is highly permissive for mutation, with many options for CTL evasion without loss of viability. Generally, options for evasion overlap considerably between CTL clones despite highly distinct T cell receptors. Finally, patterns of variant recognition suggest population-wide CTL selection for the A*02-presented epitope. Overall, these findings indicate that these protective MHC-I types yield CTL targeting of highly constrained epitopes, and underscore the importance of blocking public escape pathways for CTL-based interventions against HIV-1.
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- 2017
25. Virus-Like Vesicles of Kaposi's Sarcoma-Associated Herpesvirus Activate Lytic Replication by Triggering Differentiation Signaling
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Gong, Danyang, Dai, Xinghong, Xiao, Yuchen, Du, Yushen, Chapa, Travis J, Johnson, Jeffrey R, Li, Xinmin, Krogan, Nevan J, Deng, Hongyu, Wu, Ting-Ting, and Sun, Ren
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Biochemistry and Cell Biology ,Biological Sciences ,Rare Diseases ,Sexually Transmitted Infections ,Infectious Diseases ,HIV/AIDS ,Emerging Infectious Diseases ,Cancer ,Genetics ,2.1 Biological and endogenous factors ,2.2 Factors relating to the physical environment ,Infection ,Cell Differentiation ,Cell Line ,Gene Expression Regulation ,Viral ,Herpesvirus 8 ,Human ,Host-Pathogen Interactions ,Humans ,Immediate-Early Proteins ,Positive Regulatory Domain I-Binding Factor 1 ,Repressor Proteins ,Signal Transduction ,Trans-Activators ,Up-Regulation ,Virosomes ,Virus Replication ,EBV ,herpesvirus ,KSHV ,PRDM1 ,RTA ,tegument protein ,envelope protein ,extracellular vesicle ,microRNA ,virus-like vesicle ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Virology ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
Virus-like vesicles (VLVs) are membrane-enclosed vesicles that resemble native enveloped viruses in organization but lack the viral capsid and genome. During the productive infection of tumor-associated gammaherpesviruses, both virions and VLVs are produced and are released into the extracellular space. However, studies of gammaherpesvirus-associated VLVs have been largely restricted by the technical difficulty of separating VLVs from mature virions. Here we report a strategy of selectively isolating VLVs by using a Kaposi's sarcoma-associated herpesvirus (KSHV) mutant that is defective in small capsid protein and is unable to produce mature virions. Using mass spectrometry analysis, we found that VLVs contained viral glycoproteins required for cellular entry, as well as tegument proteins involved in regulating lytic replication, but lacked capsid proteins. Functional analysis showed that VLVs induced the expression of the viral lytic activator RTA, initiating KSHV lytic gene expression. Furthermore, employing RNA sequencing, we performed a genomewide analysis of cellular responses triggered by VLVs and found that PRDM1, a master regulator in cell differentiation, was significantly upregulated. In the context of KSHV replication, we demonstrated that VLV-induced upregulation of PRDM1 was necessary and sufficient to reactivate KSHV by activating its RTA promoter. In sum, our study systematically examined the composition of VLVs and demonstrated their biological roles in manipulating host cell responses and facilitating KSHV lytic replication.IMPORTANCE Cells lytically infected with tumor-associated herpesviruses produce a high proportion of virus-like vesicles (VLVs). The composition and function of VLVs have not been well defined, largely due to the inability to efficiently isolate VLVs that are free of virions. Using a cell system capable of establishing latent KSHV infection and robust reactivation, we successfully isolated VLVs from a KSHV mutant defective in the small capsid protein. We quantitatively analyzed proteins and microRNAs in VLVs and characterized the roles of VLVs in manipulating host cells and facilitating viral infection. More importantly, we demonstrated that by upregulating PRDM1 expression, VLVs triggered differentiation signaling in targeted cells and facilitated viral lytic infection via activation of the RTA promoter. Our study not only demonstrates a new strategy for isolating VLVs but also shows the important roles of KSHV-associated VLVs in intercellular communication and the viral life cycle.
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- 2017
26. Correction: Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality.
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Wu, Nicholas C, Olson, C Anders, Du, Yushen, Le, Shuai, Tran, Kevin, Remenyi, Roland, Gong, Danyang, Al-Mawsawi, Laith Q, Qi, Hangfei, Wu, Ting-Ting, and Sun, Ren
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Developmental Biology ,Genetics - Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1005310.].
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- 2017
27. Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein
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Qi, Hangfei, Chu, Virginia, Wu, Nicholas C, Chen, Zugen, Truong, Shawna, Brar, Gurpreet, Su, Sheng-Yao, Du, Yushen, Arumugaswami, Vaithilingaraja, Olson, C Anders, Chen, Shu-Hua, Lin, Chung-Yen, Wu, Ting-Ting, and Sun, Ren
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Biological Sciences ,Immunology ,Digestive Diseases ,Hepatitis ,Chronic Liver Disease and Cirrhosis ,Liver Disease ,Genetics ,Infectious Diseases ,Emerging Infectious Diseases ,Hepatitis - C ,Biotechnology ,Aetiology ,2.1 Biological and endogenous factors ,Infection ,Inflammatory and immune system ,Good Health and Well Being ,CRISPR-Cas Systems ,Cell Line ,Gene Expression Profiling ,Gene Knockout Techniques ,Gene Library ,Genome ,Viral ,Hepacivirus ,Hepatitis C ,Host-Pathogen Interactions ,Humans ,Immune Evasion ,Immunity ,Innate ,Interferons ,Liver ,Membrane Potential ,Mitochondrial ,Mitochondrial Proteins ,Mutagenesis ,Insertional ,Signal Transduction ,Viral Proteins ,Virus Replication ,HCV ,innate immune evasion mechanism ,IF6-16 antiviral function ,high-throughput mutagenesis ,p7 ion channel protein - Abstract
Hepatitis C virus (HCV) encodes mechanisms to evade the multilayered antiviral actions of the host immune system. Great progress has been made in elucidating the strategies HCV employs to down-regulate interferon (IFN) production, impede IFN signaling transduction, and impair IFN-stimulated gene (ISG) expression. However, there is a limited understanding of the mechanisms governing how viral proteins counteract the antiviral functions of downstream IFN effectors due to the lack of an efficient approach to identify such interactions systematically. To study the mechanisms by which HCV antagonizes the IFN responses, we have developed a high-throughput profiling platform that enables mapping of HCV sequences critical for anti-IFN function at high resolution. Genome-wide profiling performed with a 15-nt insertion mutant library of HCV showed that mutations in the p7 region conferred high levels of IFN sensitivity, which could be alleviated by the expression of WT p7 protein. This finding suggests that p7 protein of HCV has an immune evasion function. By screening a liver-specific ISG library, we identified that IFI6-16 significantly inhibits the replication of p7 mutant viruses without affecting WT virus replication. In contrast, knockout of IFI6-16 reversed the IFN hypersensitivity of p7 mutant virus. In addition, p7 was found to be coimmunoprecipitated with IFI6-16 and to counteract the function of IFI6-16 by depolarizing the mitochondria potential. Our data suggest that p7 is a critical immune evasion protein that suppresses the antiviral IFN function by counteracting the function of IFI6-16.
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- 2017
28. In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus
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Dai, Xinghong, Li, Zhihai, Lai, Mason, Shu, Sara, Du, Yushen, Zhou, Z Hong, and Sun, Ren
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Biological Sciences ,Genetics ,Infection ,Capsid ,Capsid Proteins ,Cryoelectron Microscopy ,Fimbriae ,Bacterial ,Genome ,Viral ,Levivirus ,Models ,Molecular ,Molecular Conformation ,Protein Multimerization ,RNA ,Viral ,Virus Assembly ,General Science & Technology - Abstract
Packaging of the genome into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike double-stranded DNA viruses, which pump their genome into a preformed capsid, single-stranded RNA (ssRNA) viruses, such as bacteriophage MS2, co-assemble their capsid with the genome; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via the host 'sex pilus' (F-pilus); it was the first fully sequenced organism and is a model system for studies of translational gene regulation, RNA-protein interactions, and RNA virus assembly. Its positive-sense ssRNA genome of 3,569 bases is enclosed in a capsid with one maturation protein monomer and 89 coat protein dimers arranged in a T = 3 icosahedral lattice. The maturation protein is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection, but how the genome is organized and delivered is not known. Here we describe the MS2 structure at 3.6 Å resolution, determined by electron-counting cryo-electron microscopy (cryoEM) and asymmetric reconstruction. We traced approximately 80% of the backbone of the viral genome, built atomic models for 16 RNA stem-loops, and identified three conserved motifs of RNA-coat protein interactions among 15 of these stem-loops with diverse sequences. The stem-loop at the 3' end of the genome interacts extensively with the maturation protein, which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus and joins 89 coat protein dimers to form a capsid. This atomic description of genome-capsid interactions in a spherical ssRNA virus provides insight into genome delivery via the host sex pilus and mechanisms underlying ssRNA-capsid co-assembly, and inspires speculation about the links between nucleoprotein complexes and the origins of viruses.
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- 2017
29. Quantifying perinatal transmission of Hepatitis B viral quasispecies by tag linkage deep sequencing
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Du, Yushen, Chi, Xiumei, Wang, Chong, Jiang, Jing, Kong, Fei, Yan, Hongqing, Wang, Xiaomei, Li, Jie, Wu, Nicholas C, Dai, Lei, Zhang, Tian-Hao, Shu, Sara, Zhou, Jian, Yoshizawa, Janice M, Li, Xinmin, Bhattacharya, Debika, Wu, Ting-ting, Niu, Junqi, and Sun, Ren
- Subjects
Biomedical and Clinical Sciences ,Immunology ,HIV/AIDS ,Digestive Diseases ,Genetics ,Liver Disease ,Infectious Diseases ,Pediatric ,Perinatal Period - Conditions Originating in Perinatal Period ,Hepatitis ,Hepatitis - B ,Chronic Liver Disease and Cirrhosis ,Infection ,Good Health and Well Being ,Child ,DNA ,Viral ,Evolution ,Molecular ,Female ,Haplotypes ,Hepatitis B ,Hepatitis B virus ,High-Throughput Nucleotide Sequencing ,Humans ,Infectious Disease Transmission ,Vertical ,Phylogeny ,Pregnancy ,Pregnancy Complications ,Infectious ,Quasispecies ,Sequence Analysis ,DNA - Abstract
Despite full immunoprophylaxis, mother-to-child transmission (MTCT) of Hepatitis B Virus still occurs in approximately 2-5% of HBsAg positive mothers. Little is known about the bottleneck of HBV transmission and the evolution of viral quasispecies in the context of MTCT. Here we adopted a newly developed tag linkage deep sequencing method and analyzed the quasispecies of four MTCT pairs that broke through immunoprophylaxis. By assigning unique tags to individual viral sequences, we accurately reconstructed HBV haplotypes in a region of 836 bp, which contains the major immune epitopes and drug resistance mutations. The detection limit of minor viral haplotypes reached 0.1% for individual patient sample. Dominance of "a determinant" polymorphisms were observed in two children, which pre-existed as minor quasispecies in maternal samples. In all four pairs of MTCT samples, we consistently observed a significant overlap of viral haplotypes shared between mother and child. We also demonstrate that the data can be potentially useful to estimate the bottleneck effect during HBV MTCT, which provides information to optimize treatment for reducing the frequency of MTCT.
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- 2017
30. Clofazimine broadly inhibits coronaviruses including SARS-CoV-2
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Yuan, Shuofeng, Yin, Xin, Meng, Xiangzhi, Chan, Jasper Fuk-Woo, Ye, Zi-Wei, Riva, Laura, Pache, Lars, Chan, Chris Chun-Yiu, Lai, Pok-Man, Chan, Chris Chung-Sing, Poon, Vincent Kwok-Man, Lee, Andrew Chak-Yiu, Matsunaga, Naoko, Pu, Yuan, Yuen, Chun-Kit, Cao, Jianli, Liang, Ronghui, Tang, Kaiming, Sheng, Li, Du, Yushen, Xu, Wan, Lau, Chit-Ying, Sit, Ko-Yung, Au, Wing-Kuk, Wang, Runming, Zhang, Yu-Yuan, Tang, Yan-Dong, Clausen, Thomas Mandel, Pihl, Jessica, Oh, Juntaek, Sze, Kong-Hung, Zhang, Anna Jinxia, Chu, Hin, Kok, Kin-Hang, Wang, Dong, Cai, Xue-Hui, Esko, Jeffrey D., Hung, Ivan Fan-Ngai, Li, Ronald Adolphus, Chen, Honglin, Sun, Hongzhe, Jin, Dong-Yan, Sun, Ren, Chanda, Sumit K., and Yuen, Kwok-Yung
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- 2021
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31. Annotating Protein Functional Residues by Coupling High-Throughput Fitness Profile and Homologous-Structure Analysis
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Du, Yushen, Wu, Nicholas C, Jiang, Lin, Zhang, Tianhao, Gong, Danyang, Shu, Sara, Wu, Ting-Ting, and Sun, Ren
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Biochemistry and Cell Biology ,Bioinformatics and Computational Biology ,Biological Sciences ,Biotechnology ,Biodefense ,Influenza ,Pneumonia & Influenza ,Emerging Infectious Diseases ,Genetics ,Infectious Diseases ,1.1 Normal biological development and functioning ,Generic health relevance ,Amino Acids ,DNA Mutational Analysis ,Data Curation ,High-Throughput Nucleotide Sequencing ,Influenza A virus ,Models ,Molecular ,Protein Conformation ,Protein Sorting Signals ,Protein Transport ,Viral Proteins ,Virus Replication ,Microbiology ,Biochemistry and cell biology ,Medical microbiology - Abstract
Identification and annotation of functional residues are fundamental questions in protein sequence analysis. Sequence and structure conservation provides valuable information to tackle these questions. It is, however, limited by the incomplete sampling of sequence space in natural evolution. Moreover, proteins often have multiple functions, with overlapping sequences that present challenges to accurate annotation of the exact functions of individual residues by conservation-based methods. Using the influenza A virus PB1 protein as an example, we developed a method to systematically identify and annotate functional residues. We used saturation mutagenesis and high-throughput sequencing to measure the replication capacity of single nucleotide mutations across the entire PB1 protein. After predicting protein stability upon mutations, we identified functional PB1 residues that are essential for viral replication. To further annotate the functional residues important to the canonical or noncanonical functions of viral RNA-dependent RNA polymerase (vRdRp), we performed a homologous-structure analysis with 16 different vRdRp structures. We achieved high sensitivity in annotating the known canonical polymerase functional residues. Moreover, we identified a cluster of noncanonical functional residues located in the loop region of the PB1 β-ribbon. We further demonstrated that these residues were important for PB1 protein nuclear import through the interaction with Ran-binding protein 5. In summary, we developed a systematic and sensitive method to identify and annotate functional residues that are not restrained by sequence conservation. Importantly, this method is generally applicable to other proteins about which homologous-structure information is available.ImportanceTo fully comprehend the diverse functions of a protein, it is essential to understand the functionality of individual residues. Current methods are highly dependent on evolutionary sequence conservation, which is usually limited by sampling size. Sequence conservation-based methods are further confounded by structural constraints and multifunctionality of proteins. Here we present a method that can systematically identify and annotate functional residues of a given protein. We used a high-throughput functional profiling platform to identify essential residues. Coupling it with homologous-structure comparison, we were able to annotate multiple functions of proteins. We demonstrated the method with the PB1 protein of influenza A virus and identified novel functional residues in addition to its canonical function as an RNA-dependent RNA polymerase. Not limited to virology, this method is generally applicable to other proteins that can be functionally selected and about which homologous-structure information is available.
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- 2016
32. Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment
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Wu, Nicholas C, Du, Yushen, Le, Shuai, Young, Arthur P, Zhang, Tian-Hao, Wang, Yuanyuan, Zhou, Jian, Yoshizawa, Janice M, Dong, Ling, Li, Xinmin, Wu, Ting-Ting, and Sun, Ren
- Subjects
Medical Microbiology ,Biomedical and Clinical Sciences ,Biological Sciences ,Pneumonia & Influenza ,Genetics ,Influenza ,Infectious Diseases ,Emerging Infectious Diseases ,Infection ,Amino Acid Substitution ,Epistasis ,Genetic ,High-Throughput Screening Assays ,Humans ,Influenza A virus ,Phylogeny ,Sequence Deletion ,Viral Matrix Proteins ,Mutagenesis ,Fitness profiling ,Natural sequence variation ,Coevolution analysis ,Compensatory mutation ,Information and Computing Sciences ,Medical and Health Sciences ,Bioinformatics ,Biological sciences ,Biomedical and clinical sciences - Abstract
BackgroundEpistasis is one of the central themes in viral evolution due to its importance in drug resistance, immune escape, and interspecies transmission. However, there is a lack of experimental approach to systematically probe for epistatic residues.ResultsBy utilizing the information from natural occurring sequences and high-throughput genetics, this study established a novel strategy to identify epistatic residues. The rationale is that a substitution that is deleterious in one strain may be prevalent in nature due to the presence of a naturally occurring compensatory substitution. Here, high-throughput genetics was applied to influenza A virus M segment to systematically identify deleterious substitutions. Comparison with natural sequence variation showed that a deleterious substitution M1 Q214H was prevalent in circulating strains. A coevolution analysis was then performed and indicated that M1 residues 121, 207, 209, and 214 naturally coevolved as a group. Subsequently, we experimentally validated that M1 A209T was a compensatory substitution for M1 Q214H.ConclusionsThis work provided a proof-of-concept to identify epistatic residues by coupling high-throughput genetics with phylogenetic information. In particular, we were able to identify an epistatic interaction between M1 substitutions A209T and Q214H. This analytic strategy can potentially be adapted to study any protein of interest, provided that the information on natural sequence variants is available.
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- 2016
33. A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export
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Gong, Danyang, Kim, Yong Hoon, Xiao, Yuchen, Du, Yushen, Xie, Yafang, Lee, Kevin K, Feng, Jun, Farhat, Nisar, Zhao, Dawei, Shu, Sara, Dai, Xinghong, Chanda, Sumit K, Rana, Tariq M, Krogan, Nevan J, Sun, Ren, and Wu, Ting-Ting
- Subjects
Emerging Infectious Diseases ,Rare Diseases ,Infectious Diseases ,Biotechnology ,Genetics ,HIV/AIDS ,2.2 Factors relating to the physical environment ,2.1 Biological and endogenous factors ,Aetiology ,Infection ,Active Transport ,Cell Nucleus ,Animals ,Cell Line ,Gene Expression Regulation ,Herpesvirus 8 ,Human ,Host-Pathogen Interactions ,Humans ,Models ,Biological ,Nuclear Matrix-Associated Proteins ,Nucleocytoplasmic Transport Proteins ,Protein Binding ,RNA ,Messenger ,Viral Proteins ,Virus Replication ,3′ UTR ,KSHV ,Nup98 ,ORF10 ,Rae1 ,herpesvirus ,late gene ,mRNA nuclear export ,Microbiology ,Medical Microbiology ,Immunology - Abstract
Nuclear mRNA export is highly regulated to ensure accurate cellular gene expression. Viral inhibition of cellular mRNA export can enhance viral access to the cellular translation machinery and prevent anti-viral protein production but is generally thought to be nonselective. We report that ORF10 of Kaposi's sarcoma-associated herpesvirus (KSHV), a nuclear DNA virus, inhibits mRNA export in a transcript-selective manner to control cellular gene expression. Nuclear export inhibition by ORF10 requires an interaction with an RNA export factor, Rae1. Genome-wide analysis reveals a subset of cellular mRNAs whose nuclear export is blocked by ORF10 with the 3' UTRs of ORF10-targeted transcripts conferring sensitivity to export inhibition. The ORF10-Rae1 interaction is important for the virus to express viral genes and produce infectious virions. These results suggest that a nuclear DNA virus can selectively interfere with RNA export to restrict host gene expression for optimal replication.
- Published
- 2016
34. Open knowledge disclosure and firm value: a signalling theory perspective.
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Liu, Ziyu, Du, Yushen, and Pennings, Enrico
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ENTERPRISE value ,DISCLOSURE ,SMALL business ,NON-monogamous relationships ,OPEN scholarship ,ELECTRONIC journals - Abstract
A growing number of firms are openly disclosing knowledge through academic journals and conferences; however, the impact of this practice on their market value needs further research. From a signalling theory perspective, we investigate the relationship between open knowledge disclosure and firm value and identify potential contingency factors. We propose that open knowledge disclosure conveys a firm's technical capability and commitment to open science, consequently contributing to its market value. Drawing upon data from listed companies within China's information and communication technology sector, we confirm that open knowledge disclosure enhances firm value. Furthermore, this enhancement is more pronounced for small firms, young firms, private firms, firms with few patents, firms drafting few technical standards, or firms operating in an immature technology market. Our findings suggest that firms, especially those facing high information asymmetry or lacking alternative signals, can increase their market value by sending positive signals through open knowledge disclosure. [ABSTRACT FROM AUTHOR]
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- 2024
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35. Platforms Competition: An Ecosystem-View Analysis Based on Evolutionary Game Theory
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Ma, Lina, primary, Zhao, Wanying, additional, Dong, Longzhu, additional, and Du, Yushen, additional
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- 2023
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36. MYC-induced reprogramming of glutamine catabolism supports optimal virus replication.
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Thai, Minh, Thaker, Shivani K, Feng, Jun, Du, Yushen, Hu, Hailiang, Ting Wu, Ting, Graeber, Thomas G, Braas, Daniel, and Christofk, Heather R
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Cell Line ,Humans ,Adenoviridae ,Glutamine ,Proto-Oncogene Proteins c-myc ,Virus Replication ,Mutation ,Infectious Diseases ,2.1 Biological and endogenous factors ,Infection - Abstract
Viruses rewire host cell glucose and glutamine metabolism to meet the bioenergetic and biosynthetic demands of viral propagation. However, the mechanism by which viruses reprogram glutamine metabolism and the metabolic fate of glutamine during adenovirus infection have remained elusive. Here, we show MYC activation is necessary for adenovirus-induced upregulation of host cell glutamine utilization and increased expression of glutamine transporters and glutamine catabolism enzymes. Adenovirus-induced MYC activation promotes increased glutamine uptake, increased use of glutamine in reductive carboxylation and increased use of glutamine in generating hexosamine pathway intermediates and specific amino acids. We identify glutaminase (GLS) as a critical enzyme for optimal adenovirus replication and demonstrate that GLS inhibition decreases replication of adenovirus, herpes simplex virus 1 and influenza A in cultured primary cells. Our findings show that adenovirus-induced reprogramming of glutamine metabolism through MYC activation promotes optimal progeny virion generation, and suggest that GLS inhibitors may be useful therapeutically to reduce replication of diverse viruses.
- Published
- 2015
37. Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality.
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Wu, Nicholas C, Olson, C Anders, Du, Yushen, Le, Shuai, Tran, Kevin, Remenyi, Roland, Gong, Danyang, Al-Mawsawi, Laith Q, Qi, Hangfei, Wu, Ting-Ting, and Sun, Ren
- Subjects
Cell Line ,Humans ,Influenza A virus ,Influenza B virus ,Viral Proteins ,Sequence Analysis ,DNA ,Computational Biology ,Base Sequence ,Conserved Sequence ,Gene Library ,Biological Evolution ,HEK293 Cells ,RNA-Dependent RNA Polymerase ,Vaccine Related ,Biodefense ,Infectious Diseases ,Biotechnology ,Influenza ,Pneumonia & Influenza ,Emerging Infectious Diseases ,Genetics ,Prevention ,2.2 Factors relating to the physical environment ,Infection ,Developmental Biology - Abstract
Viruses often encode proteins with multiple functions due to their compact genomes. Existing approaches to identify functional residues largely rely on sequence conservation analysis. Inferring functional residues from sequence conservation can produce false positives, in which the conserved residues are functionally silent, or false negatives, where functional residues are not identified since they are species-specific and therefore non-conserved. Furthermore, the tedious process of constructing and analyzing individual mutations limits the number of residues that can be examined in a single study. Here, we developed a systematic approach to identify the functional residues of a viral protein by coupling experimental fitness profiling with protein stability prediction using the influenza virus polymerase PA subunit as the target protein. We identified a significant number of functional residues that were influenza type-specific and were evolutionarily non-conserved among different influenza types. Our results indicate that type-specific functional residues are prevalent and may not otherwise be identified by sequence conservation analysis alone. More importantly, this technique can be adapted to any viral (and potentially non-viral) protein where structural information is available.
- Published
- 2015
38. Kaposi's Sarcoma-Associated Herpesvirus ORF18 and ORF30 Are Essential for Late Gene Expression during Lytic Replication
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Gong, Danyang, Wu, Nicholas C, Xie, Yafang, Feng, Jun, Tong, Leming, Brulois, Kevin F, Luan, Harding, Du, Yushen, Jung, Jae U, Wang, Cun-yu, Kang, Mo Kwan, Park, No-Hee, Sun, Ren, and Wu, Ting-Ting
- Subjects
Microbiology ,Medical Microbiology ,Biomedical and Clinical Sciences ,Biological Sciences ,Dental/Oral and Craniofacial Disease ,Genetics ,Cancer ,Biotechnology ,Infectious Diseases ,Emerging Infectious Diseases ,2.2 Factors relating to the physical environment ,Aetiology ,Infection ,Base Sequence ,Cell Line ,Chromosomes ,Artificial ,Bacterial ,Gene Expression Regulation ,Viral ,Herpesvirus 8 ,Human ,High-Throughput Nucleotide Sequencing ,Humans ,Keratinocytes ,Molecular Sequence Data ,Mouth Mucosa ,Open Reading Frames ,Sequence Deletion ,Signal Transduction ,Viral Proteins ,Virus Activation ,Virus Replication ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Virology ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
UnlabelledKaposi's sarcoma-associated herpesvirus (KSHV) is associated with several human malignances. As saliva is likely the major vehicle for KSHV transmission, we studied in vitro KSHV infection of oral epithelial cells. Through infection of two types of oral epithelial cells, normal human oral keratinocytes (NHOKs) and papilloma-immortalized human oral keratinocyte (HOK16B) cells, we found that KSHV can undergo robust lytic replication in oral epithelial cells. By employing de novo lytic infection of HOK16B cells, we studied the functions of two previously uncharacterized genes, ORF18 and ORF30, during the KSHV lytic cycle. For this purpose, an ORF18-deficient virus and an ORF30-deficient virus were generated using a mutagenesis strategy based on bacterial artificial chromosome (BAC) technology. We found that neither ORF18 nor ORF30 is required for immediately early or early gene expression or viral DNA replication, but each is essential for late gene expression during both de novo lytic replication and reactivation. This critical role of ORF18 and ORF30 in late gene expression was also observed during KSHV reactivation. In addition, global analysis of viral transcripts by RNA sequencing indicated that ORF18 and ORF30 control the same set of viral genes. Therefore, we suggest that these two viral ORFs are involved in the same mechanism or pathway that coregulates the viral late genes as a group.ImportanceWhile KSHV can infect multiple cell types in vitro, only a few can support a full lytic replication cycle with progeny virions produced. Consequently, KSHV lytic replication is mostly studied through reactivation, which requires chemicals to induce the lytic cycle or overexpression of the viral transcriptional activator, RTA. In this study, we present a robust de novo lytic infection system based on oral epithelial cells. Using this system, we demonstrate the role of two viral ORFs, ORF18 and ORF30, in regulating viral gene expression during KSHV lytic replication. As the major route of KSHV transmission is thought to be via saliva, this new KSHV lytic replication system will have important utility in the field.
- Published
- 2014
39. A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.
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Qi, Hangfei, Olson, C Anders, Wu, Nicholas C, Ke, Ruian, Loverdo, Claude, Chu, Virginia, Truong, Shawna, Remenyi, Roland, Chen, Zugen, Du, Yushen, Su, Sheng-Yao, Al-Mawsawi, Laith Q, Wu, Ting-Ting, Chen, Shu-Hua, Lin, Chung-Yen, Zhong, Weidong, Lloyd-Smith, James O, and Sun, Ren
- Subjects
Cell Line ,Humans ,Hepacivirus ,Hepatitis C ,Imidazoles ,Viral Nonstructural Proteins ,Gene Expression Profiling ,Drug Resistance ,Viral ,Virus Replication ,Genetic Fitness ,Liver Disease ,Drug Abuse (NIDA Only) ,Digestive Diseases ,Infectious Diseases ,Chronic Liver Disease and Cirrhosis ,Genetics ,Biotechnology ,Prevention ,Emerging Infectious Diseases ,Hepatitis - C ,Antimicrobial Resistance ,Human Genome ,Substance Abuse ,Hepatitis ,5.1 Pharmaceuticals ,Infection ,Virology ,Microbiology ,Immunology ,Medical Microbiology - Abstract
Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients.
- Published
- 2014
40. HIV-1 Quasispecies Delineation by Tag Linkage Deep Sequencing
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Wu, Nicholas C, De La Cruz, Justin, Al-Mawsawi, Laith Q, Olson, C Anders, Qi, Hangfei, Luan, Harding H, Nguyen, Nguyen, Du, Yushen, Le, Shuai, Wu, Ting-Ting, Li, Xinmin, Lewis, Martha J, Yang, Otto O, and Sun, Ren
- Subjects
Biological Sciences ,Bioinformatics and Computational Biology ,HIV/AIDS ,Genetics ,Infectious Diseases ,Clinical Research ,Biotechnology ,Genome ,Viral ,HIV-1 ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,General Science & Technology - Abstract
Trade-offs between throughput, read length, and error rates in high-throughput sequencing limit certain applications such as monitoring viral quasispecies. Here, we describe a molecular-based tag linkage method that allows assemblage of short sequence reads into long DNA fragments. It enables haplotype phasing with high accuracy and sensitivity to interrogate individual viral sequences in a quasispecies. This approach is demonstrated to deduce ∼ 2000 unique 1.3 kb viral sequences from HIV-1 quasispecies in vivo and after passaging ex vivo with a detection limit of ∼ 0.005% to ∼ 0.001%. Reproducibility of the method is validated quantitatively and qualitatively by a technical replicate. This approach can improve monitoring of the genetic architecture and evolution dynamics in any quasispecies population.
- Published
- 2014
41. Deep mutational scanning of influenza A virus neuraminidase facilitates the identification of drug resistance mutations in vivo
- Author
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Wang, Sihan, primary, Zhang, Tian-hao, additional, Hu, Menglong, additional, Tang, Kejun, additional, Sheng, Li, additional, Hong, Mengying, additional, Chen, Dongdong, additional, Chen, Liubo, additional, Shi, Yuan, additional, Feng, Jun, additional, Qian, Jing, additional, Sun, Lifeng, additional, Ding, Kefeng, additional, Sun, Ren, additional, and Du, Yushen, additional
- Published
- 2023
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42. Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design
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Du, Yushen, Xin, Li, Shi, Yuan, Zhang, Tian-Hao, Wu, Nicholas C., Dai, Lei, Gong, Danyang, Brar, Gurpreet, Shu, Sara, Luo, Jiadi, Reiley, William, Tseng, Yen-Wen, Bai, Hongyan, Wu, Ting-Ting, Wang, Jieru, Shu, Yuelong, and Sun, Ren
- Published
- 2018
43. Emerging roles of N6-methyladenosine (m6A) modification in breast cancer
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Wang, Yanyan, Zhang, Yujie, Du, Yushen, Zhou, Meiqi, Hu, Yue, and Zhang, Suzhan
- Published
- 2020
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44. Abstract 4206: In situ vaccination with CCL21-DC sensitizes non-responsive murine NSCLCs to anti-PD-1 therapy and generates systemic tumor-specific immune memory
- Author
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Salehi-Rad, Ramin, primary, Lim, Raymond J., additional, Tran, Linh M., additional, Du, Yushen, additional, Dumitras, Camelia, additional, Zhang, Tianhao, additional, Crosson, William, additional, Abascal, Jensen, additional, Krysan, Kostyantyn, additional, Liu, Bin, additional, and Dubinett, Steven M., additional
- Published
- 2022
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45. Approaches for discovery of small-molecular antivirals targeting to influenza A virus PB2 subunit
- Author
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Chen, Wenteng, primary, Shao, Jiaan, additional, Ying, Zhimin, additional, Du, Yushen, additional, and Yu, Yongping, additional
- Published
- 2022
- Full Text
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46. Quantitative high-throughput genomics in RNA viruses
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Du, Yushen
- Subjects
Virology ,Genetics - Abstract
The high mutation rate and rapid genome replication of RNA viruses drive their adaptation to diverse selection pressures. The emergence of drug resistant or immune escape viral strains is always a major concern to public health. A comprehensive understanding of the mutation tolerability of viral genome is thus crucial to understand the evolution potential of viruses and guild the accurate risk assessments.Traditional genetics has proven to be a powerful tool for virology studies. Including forward genetics – determine the genetic basis responsible for a phenotype, and reverse genetics – determine the phenotype of a genetic change, it reveals the functional role of many important mutations. However, traditional genetics is usually restricted by limited and biased sampling, and is time and money consuming. To overcome these limitations, we have developed a qantatative high-throughput genomic system that enables us to quantify the phenotype of thousands to millions of mutations as a massive parallel process. Using random mutagenesis or satuated mutagenesis, we can generate a diverse pool of viral library containing desired mutations. The library can be used to assess the function of every amino acid/nucleotide in a variety of protein functional assays as well as viral growth assay, with the frequency of each mutant changed according to their competitive strength. We were able to quantify the relative frequency change of each variant pre and post selection by high-throughput sequencing, which represented their “relative fitness” under the particular selection condition. Since the first inception of the system, we have optimized and successfully applied it to human immunodeficiency virus (HIV), Hepatitis C Virus (HCV) and influenza A virus. We also explored the applications of the system to a variety of biological questions, with a specicial focus in the following 4 areas:Firstly, a direct application of the system is to better understand the distribution of fitness effect (DFE), which is fundamental to a variety of evolution theories. We systematically quantified the DFE of single amino acid substitutions (86 amino acids total) in the drug-targeted region of NS5A protein of Hepatitis C Virus (HCV). We found that the majority of non-synonymous substitutions incur large fitness costs, suggesting that NS5A protein is highly optimized in natural conditions. Furthermore, we characterized the evolutionary potential of HCV by subjecting the mutant viruses to varying concentrations of an NS5A inhibitor Daclatasvir. As the selection pressure increases, the DFE of beneficial mutations shifts from an exponential distribution to a heavy-tailed distribution with a disproportionate number of exceptionally fit mutants. The number of available beneficial mutations and the selection coefficient both increase at higher levels of antiviral drug concentration, as predicted by a pharmacodynamics model describing viral fitness as a function of drug concentration. Our large-scale fitness data of mutant viruses also provide insights into the biophysical basis of evolutionary constraints and the role of the genetic code in protein evolution.Secondly, we explored the usage of fitness profiling to identify and annotate protein functional residues. Using influenza A virus PB1 protein as an example, we developed an approach to achieve this task: Firstly, the effect of PB1 point mutations on viral replication was examined by saturation mutagenesis and high-throughput sequencing. Secondly, functional PB1 residues that are essential for viral growth but do not affect protein stability were identified by protein stability prediction. Lastly, homologous structural alignment was utilized to further annotate specific biological functions (canonical versus non-canonical functions) for each functional residue. We achieved high sensitivity in identifying and annotating the canonical polymerase functional residues. Moreover, we identified non-canonical functional residues, which are exemplified by a cluster of residues located in the loop region of PB1 β ribbon. These previously uncharacterized residues were shown to be important for PB1 protein nuclear import by interacting with Ran-binding protein 5 (RanBP5).Thirdly, the system was shown to be valuable for the identification of drug resistant mutations and the design of personalized therapy. Using influenza NA protein as an example, we characterized the fitness effects of single nucleotide mutations of neuraminidase (NA) and systematically identified resistant mutations for three neuraminidase inhibitors (NAIs): zanamivir, oseltamivir and AV5080. We observed that both the numbers and the effects of resistant mutations of AV5080 are smaller than those of zanamivir and oseltamivir, but so are their fitness costs. We used population genetic models to estimate the rate of increase in fitness under drug selection as a function of drug dosage. AV5080 showed a higher rate of increase in fitness at low drug concentrations due to the low fitness cost of resistant mutations, but also exhibited a steep drop with high drug concentrations because of lower strength of resistance. Our approach also enabled the systematic analyses of cross-resistance against different drugs, which showed to be uncommon between AV5080 and zanamivir. Lastly and importantly, the system can be utilized to explore new functions of viral proteins. To this end, we systematically identified type I interferon sensitive mutations across the entire influenza A viral genome. We have identified novel IFN-sensitive mutations on PB2, PA, PB1 and M1, in addition to NS1, which provides a foundation to determine multiple anti-IFN mechanisms encoded in different viral segments. Moreover, this quantitative functional information of every amino acid in the genome enabled us to rationally design vaccine to increase the safety and immunogenicity. By selecting and combining 8 mutations into one viral genome, we successfully generated a deficient in anti-interferon (DAI) influenza strain as a live attenuated vaccine candidate. DAI is replication-competent in IFN-deficient host, but able to induce transient IFN response and highly attenuated in IFN competent host. Impressively, DAI is capable of inducing a robust humoral response and a strong T cell response, which collectively leads to broad protection. The superior property of DAI strain demonstrated the capacity of our approach to construct a safe, effective and broadly protecting live attenuated influenza vaccine. Thus we proposed a novel and generally applicable approach for vaccine design: systematically identifying and eliminating immune evasion functions on the virus genome, while maintaining the replication fitness in vitro for vaccine production. In summary, we have developed the quantitative high-throughput genomic system, and applied it to a variety of biological questions. It is proven to be a powerful system to investigate fundamental evolution problems, identify functional residues and new functions of target proteins, and facilitate drug development. With the maturation of DNA systhesis technology and ever increasing sequencing power, we foresee the further improvement and more broad applications of this system to address foundamental mechanistic questions and practical applications.
- Published
- 2017
47. Influence Mechanism on Supplier Emission Reduction Based on a Two-Level Supply Chain
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Ma, Lina, primary, Zhang, Xinran, additional, and Du, Yushen, additional
- Published
- 2021
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48. The Effect Mechanism of Tie Strength of Supply Networks on Risk Sharing: Based on the Empirical Data of China’s Automobile Manufacturing Industry
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Ma, Lina, primary, Wan, Min, additional, and Du, Yushen, additional
- Published
- 2021
- Full Text
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49. Clofazimine is a broad-spectrum coronavirus inhibitor that antagonizes SARS-CoV-2 replication in primary human cell culture and hamsters
- Author
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Yuan, Shuofeng, primary, Yin, Xin, additional, Meng, XiangZhi, additional, Chan, Jasper, additional, Ye, Zi-Wei, additional, Riva, Laura, additional, Pache, Lars, additional, Chan, Chris Chun-Yiu, additional, Lai, Pok-Man, additional, Chan, Chris, additional, Poon, Vincent, additional, Matsunaga, Naoko, additional, Pu, Yuan, additional, Yuen, Chun-Kit, additional, Cao, Jianli, additional, Liang, Ronghui, additional, Tang, Kaiming, additional, Sheng, Li, additional, Du, Yushen, additional, Xu, Wan, additional, Sze, Kong-Hung, additional, Zhang, Jinxia, additional, Chu, Hin, additional, Kok, Kin-Hang, additional, To, Kelvin, additional, Jin, Dong-Yan, additional, Sun, Ren, additional, Chanda, Sumit, additional, and Yuen, Kwok-Yung, additional
- Published
- 2020
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50. Culture, social class, and independence–interdependence: The case of Chinese adolescents
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Hamamura, Takeshi, Xu, Qinmei, and Du, Yushen
- Published
- 2013
- Full Text
- View/download PDF
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