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Ng QY, Mahendran V, Lim ZQ, Tan JHY, Wong JJF, Chu JJH, Chow VTK, Sze NSK, Alonso S. Enterovirus-A71 exploits RAB11 to recruit chaperones for virus morphogenesis. J Biomed Sci 2024; 31:65. [PMID: 38943128 PMCID: PMC11212238 DOI: 10.1186/s12929-024-01053-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024] Open
Abstract
BACKGROUND Enterovirus 71 (EV-A71) causes Hand, Foot and Mouth Disease (HFMD) in children and has been associated with neurological complications. The molecular mechanisms involved in EV-A71 pathogenesis have remained elusive. METHODS A siRNA screen in EV-A71 infected-motor neurons was performed targeting 112 genes involved in intracellular membrane trafficking, followed by validation of the top four hits using deconvoluted siRNA. Downstream approaches including viral entry by-pass, intracellular viral genome quantification by qPCR, Western blot analyses, and Luciferase reporter assays allowed determine the stage of the infection cycle the top candidate, RAB11A was involved in. Proximity ligation assay, co-immunoprecipitation and multiplex confocal imaging were employed to study interactions between viral components and RAB11A. Dominant negative and constitutively active RAB11A constructs were used to determine the importance of the protein's GTPase activity during EV-A71 infection. Mass spectrometry and protein interaction analyses were employed for the identification of RAB11A's host interacting partners during infection. RESULTS Small GTPase RAB11A was identified as a novel pro-viral host factor during EV-A71 infection. RAB11A and RAB11B isoforms were interchangeably exploited by strains from major EV-A71 genogroups and by Coxsackievirus A16, another major causative agent of HFMD. We showed that RAB11A was not involved in viral entry, IRES-mediated protein translation, viral genome replication, and virus exit. RAB11A co-localized with replication organelles where it interacted with structural and non-structural viral components. Over-expression of dominant negative (S25N; GDP-bound) and constitutively active (Q70L; GTP-bound) RAB11A mutants had no effect on EV-A71 infection outcome, ruling out RAB11A's involvement in intracellular trafficking of viral or host components. Instead, decreased ratio of intracellular mature viral particles to viral RNA copies and increased VP0:VP2 ratio in siRAB11-treated cells supported a role in provirion maturation hallmarked by VP0 cleavage into VP2 and VP4. Finally, chaperones, not trafficking and transporter proteins, were found to be RAB11A's top interacting partners during EV-A71 infection. Among which, CCT8 subunit from the chaperone complex TRiC/CCT was further validated and shown to interact with viral structural proteins specifically, representing yet another novel pro-viral host factor during EV-A71 infection. CONCLUSIONS This study describes a novel, unconventional role for RAB11A during viral infection where it participates in the complex process of virus morphogenesis by recruiting essential chaperone proteins.
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Affiliation(s)
- Qing Yong Ng
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Vikneswari Mahendran
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Ze Qin Lim
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Jasmine Hwee Yee Tan
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Joel Jie Feng Wong
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Justin Jang Hann Chu
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Vincent T K Chow
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Newman Siu Kwan Sze
- Proteomics and Mass Spectrometry Services Core Facility, School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Health Sciences, Faculty of Applied Health Sciences, Brock University, St Catharines, ON, L2S 3A1, Canada
| | - Sylvie Alonso
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore, Singapore.
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Li H, Ma Q, Ren J, Guo W, Feng K, Li Z, Huang T, Cai YD. Immune responses of different COVID-19 vaccination strategies by analyzing single-cell RNA sequencing data from multiple tissues using machine learning methods. Front Genet 2023; 14:1157305. [PMID: 37007947 PMCID: PMC10065150 DOI: 10.3389/fgene.2023.1157305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
Multiple types of COVID-19 vaccines have been shown to be highly effective in preventing SARS-CoV-2 infection and in reducing post-infection symptoms. Almost all of these vaccines induce systemic immune responses, but differences in immune responses induced by different vaccination regimens are evident. This study aimed to reveal the differences in immune gene expression levels of different target cells under different vaccine strategies after SARS-CoV-2 infection in hamsters. A machine learning based process was designed to analyze single-cell transcriptomic data of different cell types from the blood, lung, and nasal mucosa of hamsters infected with SARS-CoV-2, including B and T cells from the blood and nasal cavity, macrophages from the lung and nasal cavity, alveolar epithelial and lung endothelial cells. The cohort was divided into five groups: non-vaccinated (control), 2*adenovirus (two doses of adenovirus vaccine), 2*attenuated (two doses of attenuated virus vaccine), 2*mRNA (two doses of mRNA vaccine), and mRNA/attenuated (primed by mRNA vaccine, boosted by attenuated vaccine). All genes were ranked using five signature ranking methods (LASSO, LightGBM, Monte Carlo feature selection, mRMR, and permutation feature importance). Some key genes that contributed to the analysis of immune changes, such as RPS23, DDX5, PFN1 in immune cells, and IRF9 and MX1 in tissue cells, were screened. Afterward, the five feature sorting lists were fed into the feature incremental selection framework, which contained two classification algorithms (decision tree [DT] and random forest [RF]), to construct optimal classifiers and generate quantitative rules. Results showed that random forest classifiers could provide relative higher performance than decision tree classifiers, whereas the DT classifiers provided quantitative rules that indicated special gene expression levels under different vaccine strategies. These findings may help us to develop better protective vaccination programs and new vaccines.
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Affiliation(s)
- Hao Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Qinglan Ma
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Wei Guo
- Key Laboratory of Stem Cell Biology, Shanghai Institutes for Biological Sciences (SIBS), Shanghai Jiao Tong University School of Medicine (SJTUSM), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic College, Guangzhou, China
| | - Zhandong Li
- College of Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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3
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Shi H, Liu S, Tan Z, Yin L, Zeng L, Liu T, Zhang S, Zhang L. Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway. Proteomics 2023; 23:e2200362. [PMID: 36254857 DOI: 10.1002/pmic.202200362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/04/2022] [Indexed: 01/19/2023]
Abstract
Enterovirus A71 (EV71) infection can cause hand, foot, and mouth disease (HFMD) and severe neurological complications in children. However, the biological processes regulated by EV71 remain poorly understood. Herein, proteomics and metabonomics studies were conducted to uncover the mechanism of EV71 infection in rhabdomyosarcoma (RD) cells and identify potential drug targets. Differential expressed proteins from enriched membrane were analyzed by isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics technology. Twenty-six differential proteins with 1.5-fold (p < 0.05) change were detected, including 14 upregulated proteins and 12 downregulated proteins. The upregulated proteins are mainly involved in metabolic process, especially in the glycolysis pathway. Alpha-enolase (ENO1) protein was found to increase with temporal dependence following EV71 infection. The targeted metabolomics analysis revealed that glucose absorption and glycolysis metabolites were increased after EV71 infection. The glycolysis pathway was inhibited by knocking down ENO1 or the use of a glycolysis inhibitor (dichloroacetic acid [DCA]); and we found that EV71 infection was inhibited by depleting ENO1 or using DCA. Our study indicates that EV71 may reprogram glucose metabolism by activating glycolysis, and EV71 infection can be inhibited by interrupting the glycolysis pathway. ENO1 may be a potential target against EV71, and DCA could act as an inhibitor of EV71.
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Affiliation(s)
- Huichun Shi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Siyuan Liu
- The College of Information, Mechanical and Electrical Engineering, Shanghai Normal University, Shanghai, China
| | - Zhimi Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lin Yin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Liyan Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Tiefu Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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Zhao Y, Li L, Wang X, He S, Shi W, Chen S. Temporal Proteomic and Phosphoproteomic Analysis of EV-A71-Infected Human Cells. J Proteome Res 2022; 21:2367-2384. [DOI: 10.1021/acs.jproteome.2c00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Zhao
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Xinhui Wang
- CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, Jiangsu, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
| | - Sudan He
- CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, Jiangsu, China
- Suzhou Institute of Systems Medicine, Suzhou 215123, Jiangsu, China
| | - Weifeng Shi
- Department of Laboratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou 213003, Jiangsu, China
| | - She Chen
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
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Budhraja A, Basu A, Gheware A, Abhilash D, Rajagopala S, Pakala S, Sumit M, Ray A, Subramaniam A, Mathur P, Nambirajan A, Kumar S, Gupta R, Wig N, Trikha A, Guleria R, Sarkar C, Gupta I, Jain D. Molecular signature of postmortem lung tissue from COVID-19 patients suggests distinct trajectories driving mortality. Dis Model Mech 2022; 15:dmm049572. [PMID: 35438176 PMCID: PMC9194484 DOI: 10.1242/dmm.049572] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 04/07/2022] [Indexed: 12/19/2022] Open
Abstract
To elucidate the molecular mechanisms that manifest lung abnormalities during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, we performed whole-transcriptome sequencing of lung autopsies from 31 patients with severe COVID-19 and ten uninfected controls. Using metatranscriptomics, we identified the existence of two distinct molecular signatures of lethal COVID-19. The dominant 'classical' signature (n=23) showed upregulation of the unfolded protein response, steroid biosynthesis and complement activation, supported by massive metabolic reprogramming leading to characteristic lung damage. The rarer signature (n=8) that potentially represents 'cytokine release syndrome' (CRS) showed upregulation of cytokines such as IL1 and CCL19, but absence of complement activation. We found that a majority of patients cleared SARS-CoV-2 infection, but they suffered from acute dysbiosis with characteristic enrichment of opportunistic pathogens such as Staphylococcus cohnii in 'classical' patients and Pasteurella multocida in CRS patients. Our results suggest two distinct models of lung pathology in severe COVID-19 patients, which can be identified through complement activation, presence of specific cytokines and characteristic microbiome. These findings can be used to design personalized therapy using in silico identified drug molecules or in mitigating specific secondary infections.
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Affiliation(s)
- Anshul Budhraja
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Anubhav Basu
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Atish Gheware
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Dasari Abhilash
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Seesandra Rajagopala
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Suman Pakala
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Madhuresh Sumit
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Animesh Ray
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Arulselvi Subramaniam
- Department of Laboratory Medicine, JPNATC, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Purva Mathur
- Department of Laboratory Medicine, JPNATC, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Aruna Nambirajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sachin Kumar
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ritu Gupta
- Laboratory Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital (IRCH), All India Institute of Medical Sciences, New Delhi 110029, India
| | - Naveet Wig
- Department of Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Anjan Trikha
- Department of Anaesthesiology, Critical Care and Pain Medicine, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Randeep Guleria
- Department of Pulmonary Medicine and Sleep Disorders, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ishaan Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi 110016, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
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Abstract
Enterovirus 71 (EV71) is the major pathogen of hand, foot, and mouth disease. In severe cases, it can cause life-threatening neurological complications, such as aseptic meningitis and polio-like paralysis. There are no specific antiviral treatments for EV71 infections. In a previous study, the host protein growth arrest and DNA damage-inducible protein 34 (GADD34) expression was upregulated during EV71 infection determined by ribosome profiling and RNA-sequencing. Here, we investigated the interactions of host protein GADD34 and EV71 during infections. Rhabdomyosarcoma (RD) cells were infected with EV71 resulting in a significant increase in expression of GADD34 mRNA and protein. Through screening of EV71 protein we determined that the non-structural precursor protein 3CD is responsible for upregulating GADD34. EV71 3CD increased the RNA and protein levels of GADD34, while the 3CD mutant Y441S could not. 3CD upregulated GADD34 translation via the upstream open reading frame (uORF) of GADD34 5'untranslated regions (UTR). EV71 replication was attenuated by the knockdown of GADD34. The function of GADD34 to dephosphorylate eIF2α was unrelated to the upregulation of EV71 replication, but the PEST 1, 2, and 3 regions of GADD34 were required. GADD34 promoted the EV71 internal ribosome entry site (IRES) activity through the PEST repeats and affected several other viruses. Finally, GADD34 amino acids 563 to 565 interacted with 3CD, assisting GADD34 to target the EV71 IRES. Our research reveals a new mechanism by which GADD34 promotes viral IRES and how the EV71 non-structural precursor protein 3CD regulates host protein expression to support viral replication. IMPORTANCE Identification of host factors involved in viral replication is an important approach in discovering viral pathogenic mechanisms and identifying potential therapeutic targets. Previously, we screened host proteins that were upregulated by EV71 infection. Here, we report the interaction between the upregulated host protein GADD34 and EV71. EV71 non-structural precursor protein 3CD activates the RNA and protein expression of GADD34. Our study reveals that 3CD regulates the uORF of the 5′-UTR to increase GADD34 translation, providing a new explanation for how viral proteins regulate host protein expression. GADD34 is important for EV71 replication, and the key functional domains of GADD34 that promote EV71 are PEST 1, 2, and 3 regions. We report that GADD34 promotes viral IRES for the first time and this process is independent of its eIF2α phosphatase activity.
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7
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Cheng YW, Chuang YC, Huang SW, Liu CC, Wang JR. An auto-antibody identified from phenotypic directed screening platform shows host immunity against EV-A71 infection. J Biomed Sci 2022; 29:10. [PMID: 35130884 PMCID: PMC8822709 DOI: 10.1186/s12929-022-00794-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/01/2022] [Indexed: 02/08/2023] Open
Abstract
Background Enterovirus A71 (EV-A71) is a neurotropic virus which may cause severe neural complications, especially in infants and children. The clinical manifestations include hand-foot-and-mouth disease, herpangina, brainstem encephalitis, pulmonary edema, and other severe neurological diseases. Although there are some vaccines approved, the post-marketing surveillance is still unavailable. In addition, there is no antiviral drugs against EV-A71 available. Methods In this study, we identified a novel antibody that could inhibit viral growth through a human single chain variable fragment (scFv) library expressed in mammalian cells and panned by infection with lethal dose of EV-A71. Results We identified that the host protein α-enolase (ENO1) is the target of this scFv, and anti-ENO1 antibody was found to be more in mild cases than severe EV-A71 cases. Furthermore, we examined the antiviral activity in a mouse model. We found that the treatment of the identified 07-human IgG1 antibody increased the survival rate after virus challenge, and significantly decreased the viral RNA and the level of neural pathology in brain tissue. Conclusions Collectively, through a promising intracellular scFv library expression and screening system, we found a potential scFv/antibody which targets host protein ENO1 and can interfere with the infection of EV-A71. The results indicate that the usage and application of this antibody may offer a potential treatment against EV-A71 infection.
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Affiliation(s)
- Yu-Wei Cheng
- The Institute of Basic Medical Sciences, National Cheng Kung University, Tainan, Taiwan.,Leadgene Biomedical, Inc., Tainan, Taiwan
| | - Yung-Chun Chuang
- Leadgene Biomedical, Inc., Tainan, Taiwan.,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Ching-Chuan Liu
- Department of Pediatrics, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- The Institute of Basic Medical Sciences, National Cheng Kung University, Tainan, Taiwan. .,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan. .,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan. .,National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan.
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Meng Y, Yang L, Wei X, Luo H, Hu Y, Tao X, He J, Zheng X, Xu Q, Luo K, Yu G, Luo Q. CCT5 interacts with cyclin D1 promoting lung adenocarcinoma cell migration and invasion. Biochem Biophys Res Commun 2021; 567:222-229. [PMID: 34217974 DOI: 10.1016/j.bbrc.2021.04.105] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
Cyclin D1 (CCND1) has been identified as a metastatic promoter in various tumors including lung adenocarcinoma (LUAD), a subtype of non small cell lung cancer (NSCLC). The previous observation revealed that CCND1 was upregulated in NSCLC and predicted poor prognosis of LUAD patients. In this study, we examined a chaperonin containing TCP1 subunit 5 (CCT5) protein interacts with CCND1 in LUAD. Immunofluorescence demonstrated the co-localization of CCT5 and CCND1 protein in LUAD cells. CCT5 expression was detected with both immunohistochemistry (IHC) and bioinformatics analyses. Similar with the expression pattern of CCND1, CCT5 displayed a high level in LUAD tissues compared to non cancerous lung specimens. Patients with high CCT5 expression showed a significant shorter overall survival relative to those with low expression level. Furthermore, upregulated CCT5 exhibited significant positive correlation with TNM stage of LUAD patients in both IHC analyses and bioinformatics. Knocking down CCT5 remarkably inhibited LUAD cell migration and invasion in vitro by inactivating PI3K/AKT and its downstream EMT signals, which could abrogated the accelerated migration and invasion caused by CCND1 overexpression. In summary, our study discovered a highly expressed protein CCT5 in LUAD which interacted with CCND1 and promoted migration and invasion of LUAD cells by positively moderating PI3K/AKT-induced EMT pathway.
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Affiliation(s)
- Yiliang Meng
- Department of Oncology, Baise People's Hospital, Guangxi, Baise, 33000, Guangxi, China
| | - Liu Yang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510095, PR China
| | - Xiao Wei
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510095, PR China
| | | | - Yingying Hu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510095, PR China
| | - Xingyu Tao
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510095, PR China
| | - Jingjing He
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong, 510095, PR China
| | - Xuesong Zheng
- Department of Oncology, Baise People's Hospital, Guangxi, Baise, 33000, Guangxi, China
| | - Qunying Xu
- Department of Oncology, Baise People's Hospital, Guangxi, Baise, 33000, Guangxi, China
| | - Kunxiang Luo
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, BaiSe, 533000, China
| | - Guifang Yu
- Department of Oncology, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Qisheng Luo
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, BaiSe, 533000, China.
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9
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IKKε isoform switching governs the immune response against EV71 infection. Commun Biol 2021; 4:663. [PMID: 34079066 PMCID: PMC8172566 DOI: 10.1038/s42003-021-02187-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/30/2021] [Indexed: 12/19/2022] Open
Abstract
The reciprocal interactions between pathogens and hosts are complicated and profound. A comprehensive understanding of these interactions is essential for developing effective therapies against infectious diseases. Interferon responses induced upon virus infection are critical for establishing host antiviral innate immunity. Here, we provide a molecular mechanism wherein isoform switching of the host IKKε gene, an interferon-associated molecule, leads to alterations in IFN production during EV71 infection. We found that IKKε isoform 2 (IKKε v2) is upregulated while IKKε v1 is downregulated in EV71 infection. IKKε v2 interacts with IRF7 and promotes IRF7 activation through phosphorylation and translocation of IRF7 in the presence of ubiquitin, by which the expression of IFNβ and ISGs is elicited and virus propagation is attenuated. We also identified that IKKε v2 is activated via K63-linked ubiquitination. Our results suggest that host cells induce IKKε isoform switching and result in IFN production against EV71 infection. This finding highlights a gene regulatory mechanism in pathogen-host interactions and provides a potential strategy for establishing host first-line defense against pathogens.
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Nekoua MP, Bertin A, Sane F, Gimeno JP, Fournier I, Salzet M, Engelmann I, Alidjinou EK, Hober D. Persistence of Coxsackievirus B4 in Pancreatic β Cells Disturbs Insulin Maturation, Pattern of Cellular Proteins, and DNA Methylation. Microorganisms 2021; 9:microorganisms9061125. [PMID: 34067388 PMCID: PMC8224704 DOI: 10.3390/microorganisms9061125] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/15/2022] Open
Abstract
Coxsackievirus-B4 (CV-B4) can persist in pancreatic cell lines and impair the phenoytpe and/or gene expressions in these cells; however, the models used to study this phenomenon did not produce insulin. Therefore, we investigated CV-B4 persistence and its consequences in insulin-producing pancreatic β cells. The insulin-secreting rat β cell line, INS-1, was infected with CV-B4. After lysis of a large part of the cell layer, the culture was still maintained and no additional cytopathic effect was observed. The amount of insulin in supernatants of cell cultures persistently infected with CV-B4 was not affected by the infection; in fact, a larger quantity of proinsulin was found. The mRNA expression of pro-hormone convertase 2, an enzyme involved in the maturation of proinsulin into insulin and studied using real-time reverse transcription-polymerase chain reaction, was inhibited in infected cultures. Further, the pattern of 47 cell proteins analyzed using Shotgun mass spectrometry was significantly modified. The DNA of persistently infected cell cultures was hypermethylated unlike that of controls. The persistent infection of INS-1 cells with CV-B4 had a deep impact on these cells, especially on insulin metabolism. Cellular changes caused by persistent CV-B4 infection of β cells can play a role in type 1 diabetes pathogenesis.
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Affiliation(s)
- Magloire Pandoua Nekoua
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Antoine Bertin
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Famara Sane
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Jean-Pascal Gimeno
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (J.-P.G.); (I.F.); (M.S.)
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (J.-P.G.); (I.F.); (M.S.)
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (J.-P.G.); (I.F.); (M.S.)
| | - Ilka Engelmann
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Enagnon Kazali Alidjinou
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Didier Hober
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
- Correspondence: ; Tel.: +33-(0)-3-2044-6688
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11
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Vavouraki N, Tomkins JE, Kara E, Houlden H, Hardy J, Tindall MJ, Lewis PA, Manzoni C. Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. iScience 2021; 24:102484. [PMID: 34113825 PMCID: PMC8169945 DOI: 10.1016/j.isci.2021.102484] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/01/2021] [Accepted: 04/23/2021] [Indexed: 12/14/2022] Open
Abstract
The Hereditary Spastic Paraplegias are a group of neurodegenerative diseases characterized by spasticity and weakness in the lower body. Owing to the combination of genetic diversity and variable clinical presentation, the Hereditary Spastic Paraplegias are a strong candidate for protein-protein interaction network analysis as a tool to understand disease mechanism(s) and to aid functional stratification of phenotypes. In this study, experimentally validated human data were used to create a protein-protein interaction network based on the causative genes. Network evaluation as a combination of topological analysis and functional annotation led to the identification of core proteins in putative shared biological processes, such as intracellular transport and vesicle trafficking. The application of machine learning techniques suggested a functional dichotomy linked with distinct sets of clinical presentations, indicating that there is scope to further classify conditions currently described under the same umbrella-term of Hereditary Spastic Paraplegias based on specific molecular mechanisms of disease.
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Affiliation(s)
- Nikoleta Vavouraki
- School of Pharmacy, University of Reading, Reading, RG6 6AX, UK
- Department of Mathematics and Statistics, University of Reading, Reading, RG6 6AX, UK
| | | | - Eleanna Kara
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- UK Dementia Research Institute at UCL and Department of Neurodegenerative Disease, UCL IoN, UCL London, W1T 7NF UK
- Reta Lila Weston Institute, UCL IoN, 1 Wakefield Street, London, WC1N 1PJ, UK
- UCL Movement Disorders Centre, Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Marcus J. Tindall
- Department of Mathematics and Statistics, University of Reading, Reading, RG6 6AX, UK
- Institute of Cardiovascular and Metabolic Research, University of Reading, Reading, RG6 6AS, UK
| | - Patrick A. Lewis
- School of Pharmacy, University of Reading, Reading, RG6 6AX, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, UK
| | - Claudia Manzoni
- School of Pharmacy, University of Reading, Reading, RG6 6AX, UK
- School of Pharmacy, University College London, London, WC1N 1AX, UK
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12
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Ramchandar N, Coufal NG, Warden AS, Briggs B, Schwarz T, Stinnett R, Xie H, Schlaberg R, Foley J, Clarke C, Waldeman B, Enriquez C, Osborne S, Arrieta A, Salyakina D, Janvier M, Sendi P, Totapally BR, Dimmock D, Farnaes L. Metagenomic Next-Generation Sequencing for Pathogen Detection and Transcriptomic Analysis in Pediatric Central Nervous System Infections. Open Forum Infect Dis 2021; 8:ofab104. [PMID: 34104666 PMCID: PMC8180245 DOI: 10.1093/ofid/ofab104] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/02/2021] [Indexed: 01/08/2023] Open
Abstract
Background Pediatric central nervous system (CNS) infections are potentially life-threatening and may incur significant morbidity. Identifying a pathogen is important, both in terms of guiding therapeutic management and in characterizing prognosis. Usual care testing by culture and polymerase chain reaction is often unable to identify a pathogen. We examined the systematic application of metagenomic next-generation sequencing (mNGS) for detecting organisms and transcriptomic analysis of cerebrospinal fluid (CSF) in children with central nervous system (CNS) infections. Methods We conducted a prospective multisite study that aimed to enroll all children with a CSF pleocytosis and suspected CNS infection admitted to 1 of 3 tertiary pediatric hospitals during the study timeframe. After usual care testing had been performed, the remaining CSF was sent for mNGS and transcriptomic analysis. Results We screened 221 and enrolled 70 subjects over a 12-month recruitment period. A putative organism was isolated from CSF in 25 (35.7%) subjects by any diagnostic modality. Metagenomic next-generation sequencing of the CSF samples identified a pathogen in 20 (28.6%) subjects, which were also all identified by usual care testing. The median time to result was 38 hours. Conclusions Metagenomic sequencing of CSF has the potential to rapidly identify pathogens in children with CNS infections.
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Affiliation(s)
- Nanda Ramchandar
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Department of Pediatrics, University of California, San Diego, California, USA
| | - Nicole G Coufal
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,Department of Pediatrics, University of California, San Diego, California, USA.,Rady Children's Hospital San Diego, San Diego, California, USA
| | - Anna S Warden
- Department of Cellular and Molecular Medicine, University of California, San Diego, California, USA
| | | | | | | | - Heng Xie
- IDbyDNA, Salt Lake City, Utah, USA
| | | | - Jennifer Foley
- Rady Children's Hospital San Diego, San Diego, California, USA
| | - Christina Clarke
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Bryce Waldeman
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | | | | | - Antonio Arrieta
- Children's Hospital of Orange County, Orange, California, USA
| | | | | | | | | | - David Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA
| | - Lauge Farnaes
- Rady Children's Institute for Genomic Medicine, San Diego, California, USA.,IDbyDNA, Salt Lake City, Utah, USA
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13
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Kuo RL, Chen YT, Li HA, Wu CC, Chiang HC, Lin JY, Huang HI, Shih SR, Chin-Ming Tan B. Molecular determinants and heterogeneity underlying host response to EV-A71 infection at single-cell resolution. RNA Biol 2021; 18:796-808. [PMID: 33406999 DOI: 10.1080/15476286.2021.1872976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
The pathogenic human enterovirus EV-A71 has raised serious public health concerns. A hallmark of EV-A71 infection is the distortion of host transcriptomes in favour of viral replication. While high-throughput approaches have been exploited to dissect these gene dysregulations, they do not fully capture molecular perturbations at the single-cell level and in a physiologically relevant context. In this study, we applied a single-cell RNA sequencing approach on infected differentiated enterocyte cells (C2BBe1), which model the gastrointestinal epithelium targeted initially by EV-A71. Our single-cell analysis of EV-A71-infected culture provided several lines of illuminating observations: 1) This systems approach demonstrated extensive cell-to-cell variation in a single culture upon viral infection and delineated transcriptomic differences between the EV-A71-infected and bystander cells. 2) By analysing expression profiles of known EV-A71 receptors and entry facilitation factors, we found that ANXA2 was closely correlated in expression with the viral RNA in the infected population, supporting its role in EV-A71 entry in the enteric cells. 3) We further catalogued dysregulated lncRNAs elicited by EV-A71 infection and demonstrated the functional implication of lncRNA CYTOR in promoting EV-A71 replication. Viewed together, our single-cell transcriptomic analysis illustrated at the single-cell resolution the heterogeneity of host susceptibility to EV-A71 and revealed the involvement of lncRNAs in host antiviral response.
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Affiliation(s)
- Rei-Lin Kuo
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yi-Tung Chen
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Huai-An Li
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head & Neck Surgery, Linkou Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Hsiao-Chu Chiang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jhao-Yin Lin
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsing-I Huang
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Division of Hematology/Oncology, Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Clinical Virology Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Bertrand Chin-Ming Tan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Linkou, Taiwan
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14
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Echovirus-30 Infection Alters Host Proteins in Lipid Rafts at the Cerebrospinal Fluid Barrier In Vitro. Microorganisms 2020; 8:microorganisms8121958. [PMID: 33321840 PMCID: PMC7764136 DOI: 10.3390/microorganisms8121958] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 11/17/2022] Open
Abstract
Echovirus-30 (E-30) is a non-polio enterovirus responsible for meningitis outbreaks in children worldwide. To gain access to the central nervous system (CNS), E-30 first has to cross the blood-brain barrier (BBB) or the blood-cerebrospinal fluid barrier (BCSFB). E-30 may use lipid rafts of the host cells to interact with and to invade the BCSFB. To study enteroviral infection of the BCSFB, an established in vitro model based on human immortalized brain choroid plexus papilloma (HIBCPP) cells has been used. Here, we investigated the impact of E-30 infection on the protein content of the lipid rafts at the BCSFB in vitro. Mass spectrometry analysis following E-30 infection versus uninfected conditions revealed differential abundancy in proteins implicated in cellular adhesion, cytoskeleton remodeling, and endocytosis/vesicle budding. Further, we evaluated the blocking of endocytosis via clathrin/dynamin blocking and its consequences for E-30 induced barrier disruption. Interestingly, blocking of endocytosis had no impact on the capacity of E-30 to induce loss of barrier properties in HIBCPP cells. Altogether, these data highlight the impact of E-30 on HIBCPP cells microdomain as an important factor for host cell alteration.
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15
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Li D, Su M, Sun PP, Guo WP, Wang CY, Wang JL, Wang H, Zhang Q, Du LY, Xie GC. Global profiling of the alternative splicing landscape reveals transcriptomic diversity during the early phase of enterovirus 71 infection. Virology 2020; 548:213-225. [PMID: 32763492 DOI: 10.1016/j.virol.2020.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/17/2020] [Accepted: 06/17/2020] [Indexed: 02/04/2023]
Abstract
The alteration of host cell splicing is a major strategy favouring viral replication; however, the interaction between human tonsillar epithelial cells (HTECs) and enterovirus 71 (EV71) has not been fully elucidated. Here, a total of 201 differentially expressed genes (DEGs) and 3266 novel genes with coding potential were identified. A total of 3479 skipped exons (SEs), 515 alternative 3' splice sites (A3SSs), 391 alternative 5' splice sites (A5SSs), 531 mutually exclusive exons (MXEs) and 825 retained introns (RIs) were identified as significantly altered alternative splicing (AS) events. The enriched DEGs were mainly related to the cell cycle, spliceosome, and Toll-like receptor (TLR) signalling pathways. Finally, the replication of EV71 was significantly inhibited by TLR2 heterodimers. Our findings suggest that AS events induced by EV71 increase the transcriptomic diversity of HTECs in response to EV71 infection. Additionally, TLR2 heterodimers have the potential to protect HTECs against EV71.
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Affiliation(s)
- Dan Li
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Meng Su
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Ping-Ping Sun
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Wen-Ping Guo
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Chun-Yang Wang
- Clinical Medical College, Xi'an Medical University, Xi'an, 710021, China
| | - Jiang-Li Wang
- Department of Microbiology Laboratory, Chengde Center for Disease Control and Prevention, Chengde, 067000, China
| | - Hong Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qing Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Luan-Ying Du
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China
| | - Guang-Cheng Xie
- Department of Pathogenic Biology, Chengde Medical University, Chengde, 067000, China.
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16
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Protein Phosphorylation in Serine Residues Correlates with Progression from Precancerous Lesions to Cervical Cancer in Mexican Patients. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5058928. [PMID: 32337254 PMCID: PMC7157794 DOI: 10.1155/2020/5058928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/12/2020] [Indexed: 12/24/2022]
Abstract
Protein phosphorylation is a posttranslational modification that is essential for normal cellular processes; however, abnormal phosphorylation is one of the prime causes for alteration of many structural, functional, and regulatory proteins in disease conditions. In cancer, changes in the states of protein phosphorylation in tyrosine residues have been more studied than phosphorylation in threonine or serine residues, which also undergo alterations with greater predominance. In general, serine phosphorylation leads to the formation of multimolecular signaling complexes that regulate diverse biological processes, but in pathological conditions such as tumorigenesis, anomalous phosphorylation may result in the deregulation of some signaling pathways. Cervical cancer (CC), the main neoplasm associated with human papillomavirus (HPV) infection, is the fourth most frequent cancer worldwide. Persistent infection of the cervix with high-risk human papillomaviruses produces precancerous lesions starting with low-grade squamous intraepithelial lesions (LSIL), progressing to high-grade squamous intraepithelial lesions (HSIL) until CC is generated. Here, we compared the proteomic profile of phosphorylated proteins in serine residues from healthy, LSIL, HSIL, and CC samples. Our data show an increase in the number of phosphorylated proteins in serine residues as the grade of injury rises. These results provide a support for future studies focused on phosphorylated proteins and their possible correlation with the progression of cervical lesions.
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17
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Zhou F, Wan Q, Lu J, Chen Y, Lu G, He ML. Pim1 Impacts Enterovirus A71 Replication and Represents a Potential Target in Antiviral Therapy. iScience 2019; 19:715-727. [PMID: 31476618 PMCID: PMC6726883 DOI: 10.1016/j.isci.2019.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 06/02/2019] [Accepted: 08/02/2019] [Indexed: 12/27/2022] Open
Abstract
Enterovirus A71 (EV-A71) infection causes hand-foot-and-mouth disease (HFMD) and fatal neurological diseases, and there are no effective treatments. Host factors play key roles in establishing viral infection and determining the disease progression and outcome of antiviral therapies. In this study, we found that the expression of Pim1 was significantly upregulated in EV-A71 infection. Ectopic expression or silencing of Pim1 promoted or inhibited EV-A71 replication through two distinct mechanisms. Pim1 enhanced viral IRES activity by increasing viral 2A protease-mediated eIF4G cleavage and blocked AUF1, a suppressor of IRES, translocation from the nucleus to cytosol. More importantly, we discovered that Pim1 inhibitors (SGI-1776, AZD-1208, and CX-6258) reduced EV-A71 reproduction. Particularly, CX-6258 remarkably reduced EV-A71 reproduction more than 1,000 times, providing a potential therapeutic agent for EV-A71 treatment.
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Affiliation(s)
- Fanghang Zhou
- Department of Biomedical Science, City University of Hong Kong, Kowloon, 1A-202, 2/F, Block 1, To Yuen Building, Hong Kong, 518000, China
| | - Qianya Wan
- Department of Biomedical Science, City University of Hong Kong, Kowloon, 1A-202, 2/F, Block 1, To Yuen Building, Hong Kong, 518000, China
| | - Jing Lu
- Guangdong Provincial Institution of Public Health, Guangdong Center for Disease Control and Prevention, Guangzhou 510440, China
| | - Ying Chen
- Department of Biomedical Science, City University of Hong Kong, Kowloon, 1A-202, 2/F, Block 1, To Yuen Building, Hong Kong, 518000, China
| | - Gui Lu
- School of Pharmacology, Sun Yat-sen University, Guangzhou, China
| | - Ming-Liang He
- Department of Biomedical Science, City University of Hong Kong, Kowloon, 1A-202, 2/F, Block 1, To Yuen Building, Hong Kong, 518000, China; CityU Shenzhen Research Institute, Nanshan, Shenzhen, China.
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18
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Frenkel S, Bernstein CN, Sargent M, Kuang Q, Jiang W, Wei J, Thiruvahindrapuram B, Spriggs E, Scherer SW, Hu P. Genome-wide analysis identifies rare copy number variations associated with inflammatory bowel disease. PLoS One 2019; 14:e0217846. [PMID: 31185018 PMCID: PMC6559655 DOI: 10.1371/journal.pone.0217846] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 05/20/2019] [Indexed: 11/30/2022] Open
Abstract
Background Inflammatory bowel disease (IBD) is an idiopathic, chronic disorder of unclear etiology with an underlying genetic predisposition. Recent genome-wide association studies have identified more than 200 IBD susceptibility loci, but the causes of IBD remain poorly defined. We hypothesized that rare (<0.1% population frequency) gene copy number variations (CNVs) could play an important mechanism for risk of IBD. We aimed to examine changes in DNA copy number in a population-based cohort of patients with IBD and search for novel genetic risk factors for IBD. Methods DNA samples from 243 individuals with IBD from the Manitoba IBD Cohort Study and 2988 healthy controls were analyzed using genome-wide SNP microarray technology. Three CNV calling algorithms were applied to maximize sensitivity and specificity of CNV detection. We identified IBD-associated genes affected by rare CNV from comparing the number of overlapping CNVs in IBD samples with the number of overlapping CNVs in controls for each gene. Results 4,402 CNVs detected by two or three algorithms intersected 7,061 genes, in at least one analyzed sample. Four genes (e.g. DUSP22 and IP6K3) intersected by rare deletions and fourteen genes (e.g. SLC25A10, PSPN, GTF2F1) intersected by rare duplications demonstrated significant association with IBD (FDR-adjusted p-value < 0.01). Of these, ten genes were functionally related to immune response and intracellular signalling pathways. Some of these genes were also identified in other IBD related genome-wide association studies. These suggested that the identified genes may play a role in the risk of IBD. Conclusion Our results revealed new genomic loci associated with IBD, which suggested the role of rare CNVs in IBD risk.
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Affiliation(s)
- Svetlana Frenkel
- Department of Biochemistry and Medical Genetics and The George and Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Charles N. Bernstein
- Department of Internal Medicine and the University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Michael Sargent
- Department of Internal Medicine and the University of Manitoba IBD Clinical and Research Centre, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Qin Kuang
- Department of Biochemistry and Medical Genetics and The George and Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Wenxin Jiang
- Department of Biochemistry and Medical Genetics and The George and Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - John Wei
- The Centre for Applied Genomics, Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth Spriggs
- Department of Biochemistry and Medical Genetics, the University of Manitoba and Molecular Diagnostic Laboratory, Diagnostic Services of Manitoba, Winnipeg, Manitoba, Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, the Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics and The George and Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, Manitoba, Canada
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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19
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Liao YW, Ho BC, Chen MH, Yu SL. Host relieves lnc-IRAK3-3-sequestered miR-891b to attenuate apoptosis in Enterovirus 71 infection. Cell Microbiol 2019; 21:e13043. [PMID: 31099182 DOI: 10.1111/cmi.13043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/22/2019] [Accepted: 05/10/2019] [Indexed: 12/11/2022]
Abstract
Enterovirus 71 (EV71) is an emerging life-threatening pathogen particularly in the Asia-Pacific region. Apoptosis is a major pathogenic feature in EV71 infection. However, which molecular mechanism participating in EV71-induced apoptosis is not completely understood. Long noncoding RNAs (lncRNAs), a newly discovered class of regulatory RNA molecules, govern a wide range of biological functions through multiple regulatory mechanisms. Whether lncRNAs involved in EV71-induced apoptosis was investigated in this study. We conducted an apoptosis-oriented approach by integrating lncRNA and mRNA profilings. lnc-IRAK3-3 is down-regulated in EV71 infection and plays an important role in EV71 infection-induced apoptosis. Compensation of lnc-IRAK3-3 in EV71 infection promoted cell apoptosis wherein GADD45β expression was increased and further triggered caspase3 and PARP cleavage. Using bioinformatics analysis and functional assays, lnc-IRAK3-3 could functionally sequester miR-891b and GADD45β 3'UTR whereas miR-891b showed the inhibitory activity on GADD45β expression. Taken together, lnc-IRAK3-3 has the ability capturing miR-891b to enforce GADD45β expression and eventually promotes apoptosis. On the contrary, host cells suppress lnc-IRAK3-3 to relieve lnc-IRAK3-3-sequestered miR-891b, restrain GADD45β, and attenuate apoptosis in EV71 infection that prevent host cells from severe damages. We discover a new molecular mechanism by which host cells counteract EV71-induced apoptosis through the lnc-IRAK3-3/miR-891b/GADD45β axis partially.
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Affiliation(s)
- Yu-Wen Liao
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Bing-Ching Ho
- Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Min-Hsuan Chen
- Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Centers of Genomic and Precision Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
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20
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Yao C, Hu K, Xi C, Li N, Wei Y. Transcriptomic analysis of cells in response to EV71 infection and 2Apro as a trigger for apoptosis via TXNIP gene. Genes Genomics 2018; 41:343-357. [DOI: 10.1007/s13258-018-0760-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/30/2018] [Indexed: 02/07/2023]
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21
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Too IHK, Bonne I, Tan EL, Chu JJH, Alonso S. Prohibitin plays a critical role in Enterovirus 71 neuropathogenesis. PLoS Pathog 2018; 14:e1006778. [PMID: 29324904 PMCID: PMC5764453 DOI: 10.1371/journal.ppat.1006778] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/28/2017] [Indexed: 12/14/2022] Open
Abstract
A close relative of poliovirus, enterovirus 71 (EV71) is regarded as an important neurotropic virus of serious public health concern. EV71 causes Hand, Foot and Mouth Disease and has been associated with neurological complications in young children. Our limited understanding of the mechanisms involved in its neuropathogenesis has hampered the development of effective therapeutic options. Here, using a two-dimensional proteomics approach combined with mass spectrometry, we have identified a unique panel of host proteins that were differentially and dynamically modulated during EV71 infection of motor-neuron NSC-34 cells, which are found at the neuromuscular junctions where EV71 is believed to enter the central nervous system. Meta-analysis with previously published proteomics studies in neuroblastoma or muscle cell lines revealed minimal overlapping which suggests unique host-pathogen interactions in NSC-34 cells. Among the candidate proteins, we focused our attention on prohibitin (PHB), a protein that is involved in multiple cellular functions and the target of anti-cancer drug Rocaglamide (Roc-A). We demonstrated that cell surface-expressed PHB is involved in EV71 entry into neuronal cells specifically, while membrane-bound mitochondrial PHB associates with the virus replication complex and facilitates viral replication. Furthermore, Roc-A treatment of EV71-infected neuronal cells reduced significantly virus yields. However, the inhibitory effect of Roc-A on PHB in NSC-34 cells was not through blocking the CRAF/MEK/ERK pathway as previously reported. Instead, Roc-A treated NSC-34 cells had lower mitochondria-associated PHB and lower ATP levels that correlated with impaired mitochondria integrity. In vivo, EV71-infected mice treated with Roc-A survived longer than the vehicle-treated animals and had significantly lower virus loads in their spinal cord and brain, whereas virus titers in their limb muscles were comparable to controls. Together, this study uncovers PHB as the first host factor that is specifically involved in EV71 neuropathogenesis and a potential drug target to limit neurological complications.
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Affiliation(s)
- Issac Horng Khit Too
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore
| | - Isabelle Bonne
- Electron Microscopy Laboratory, Life Sciences Institute, National University of Singapore, Singapore
| | - Eng Lee Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Centre for Biomedical & Life Sciences, Singapore Polytechnic, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sylvie Alonso
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Immunology Programme, Life Sciences Institute, National University of Singapore, Singapore
- * E-mail:
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22
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Fu F, Zhao J, Xi X. Identification of genes involved in enterovirus 71 infected SK-N-SH cells. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:11588-11595. [PMID: 31966515 PMCID: PMC6966083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 11/28/2017] [Indexed: 06/10/2023]
Abstract
The enterovirus 71 (EV71) is the major pathogen of hand-foot-and-mouth disease (HFMD) and has been associated with severe neurological disease in children under 5 years of age. The molecular mechanisms underlying the response of human neural cells to EV71 infection still remain unclear. In this study, the genome microarray was employed to perform transcriptome profiling analysis in human neuroblastoma SK-N-SH cells infected by EV71. The results indicated that EV71 infection lead to altered expression of 87 human mRNA. The up-regulated gene mainly include the cytokine and chemokine, ubiquitin mediated proteolysis, Toll-like receptor signaling pathway, p53 signaling pathway, apoptosis, leukocyte transendothelial migration, MAPK signaling pathway and Jak-STAT signaling pathway, etc. Finally, the microarray results were validated using real-time RT-PCR and ELISA in the RNA and protein level, respectively. Our results suggested that the high fatality rate of EV71 infection probably derived from a severe immune response caused by cytokines and chemokines. The findings will help to better understand the host responses to EV71 infection and provide the potential strategy for prevention and control of EV71 infection.
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Affiliation(s)
- Fei Fu
- School of Basic Medical Sciences, Hubei University of Medicine Shiyan, Hubei Province
| | - Junjie Zhao
- School of Basic Medical Sciences, Hubei University of Medicine Shiyan, Hubei Province
| | - Xueyan Xi
- School of Basic Medical Sciences, Hubei University of Medicine Shiyan, Hubei Province
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23
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Tassini S, Sun L, Lanko K, Crespan E, Langron E, Falchi F, Kissova M, Armijos-Rivera JI, Delang L, Mirabelli C, Neyts J, Pieroni M, Cavalli A, Costantino G, Maga G, Vergani P, Leyssen P, Radi M. Discovery of Multitarget Agents Active as Broad-Spectrum Antivirals and Correctors of Cystic Fibrosis Transmembrane Conductance Regulator for Associated Pulmonary Diseases. J Med Chem 2017; 60:1400-1416. [DOI: 10.1021/acs.jmedchem.6b01521] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sabrina Tassini
- P4T Group, Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Liang Sun
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Kristina Lanko
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Emily Langron
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, WC1E
6BT London, U.K
| | - Federico Falchi
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
- Department of Pharmacy
and Biotechnology, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Miroslava Kissova
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | | | - Leen Delang
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Carmen Mirabelli
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Johan Neyts
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Marco Pieroni
- P4T Group, Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Andrea Cavalli
- CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, I-16163 Genova, Italy
- Department of Pharmacy
and Biotechnology, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Gabriele Costantino
- P4T Group, Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Paola Vergani
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, WC1E
6BT London, U.K
| | - Pieter Leyssen
- Laboratory
of Virology and Experimental Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Marco Radi
- P4T Group, Dipartimento
di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Viale delle Scienze, 27/A, 43124 Parma, Italy
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24
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Wu KX, Phuektes P, Kumar P, Goh GYL, Moreau D, Chow VTK, Bard F, Chu JJH. Human genome-wide RNAi screen reveals host factors required for enterovirus 71 replication. Nat Commun 2016; 7:13150. [PMID: 27748395 PMCID: PMC5071646 DOI: 10.1038/ncomms13150] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 09/08/2016] [Indexed: 12/31/2022] Open
Abstract
Enterovirus 71 (EV71) is a neurotropic enterovirus without antivirals or vaccine, and its host-pathogen interactions remain poorly understood. Here we use a human genome-wide RNAi screen to identify 256 host factors involved in EV71 replication in human rhabdomyosarcoma cells. Enrichment analyses reveal overrepresentation in processes like mitotic cell cycle and transcriptional regulation. We have carried out orthogonal experiments to characterize the roles of selected factors involved in cell cycle regulation and endoplasmatic reticulum-associated degradation. We demonstrate nuclear egress of CDK6 in EV71 infected cells, and identify CDK6 and AURKB as resistance factors. NGLY1, which co-localizes with EV71 replication complexes at the endoplasmatic reticulum, supports EV71 replication. We confirm importance of these factors for EV71 replication in a human neuronal cell line and for coxsackievirus A16 infection. A small molecule inhibitor of NGLY1 reduces EV71 replication. This study provides a comprehensive map of EV71 host factors and reveals potential antiviral targets. Enterovirus 71 (EV71) infection causes a spectrum of symptoms including neurological disease. To improve our understanding of EV71-host interactions, Wu et al. here perform a genome-wide RNAi screen, which implicates cell cycle regulation and ER-associated degradation as important factors in EV71 replication.
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Affiliation(s)
- Kan Xing Wu
- Department of Microbiology and Immunology, National University of Singapore, Singapore 117597, Singapore
| | - Patchara Phuektes
- Department of Microbiology and Immunology, National University of Singapore, Singapore 117597, Singapore
| | - Pankaj Kumar
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Germaine Yen Lin Goh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Dimitri Moreau
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Vincent Tak Kwong Chow
- Department of Microbiology and Immunology, National University of Singapore, Singapore 117597, Singapore
| | - Frederic Bard
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, National University of Singapore, Singapore 117597, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore 138673, Singapore
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25
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Qi W, Fu R, Wang H, Liu C, Ren Y, Shao Y, Shao Z. Comparative proteomic analysis of CD34(+) cells in bone marrow between severe aplastic anemia and normal control. Cell Immunol 2016; 304-305:9-15. [PMID: 27086042 DOI: 10.1016/j.cellimm.2016.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/14/2016] [Accepted: 04/06/2016] [Indexed: 11/16/2022]
Abstract
Severe aplastic anemia (SAA) is an autoimmune disease with destruction of hematopoietic cells by activated T lymphocytes. However, the precise mechanism of cytotoxicity T cells recognizing and attacking CD34(+) cells remains unclear. Here, we investigated the proteome of CD34(+) cells in SAA patients to further explore the pathogenesis of SAA. CD34(+) cells from 29 SAA patients and 20 health controls were isolated by magnetic activated cell sorting. The protein of CD34(+) cells were examined by iTRAQ labeling combination of multidimensional liquid chromatography and tandem mass spectrometry. A total of 156 differential expression proteins in CD34(+) cells were identified. Compared with health controls, 53 proteins were up-regulated and 103 proteins were down-regulated in SAA patients. Specifically, abnormal expression of proteasome subunits, histone variants, dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit (DAD1) and ATPase inhibitor, mitochondrial isoform 1 precursor(IF1) may relate to the hyperfunction of immune responses and excessive apoptosis of SAA CD34(+) cells.
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Affiliation(s)
- Weiwei Qi
- Department of Hematology, The General Hospital of Tianjin Medical University, Tianjin 300052, PR China
| | - Rong Fu
- Department of Hematology, The General Hospital of Tianjin Medical University, Tianjin 300052, PR China
| | - Huaquan Wang
- Department of Hematology, The General Hospital of Tianjin Medical University, Tianjin 300052, PR China
| | - Chunyan Liu
- Department of Hematology, The General Hospital of Tianjin Medical University, Tianjin 300052, PR China
| | - Yue Ren
- Department of Hematology, The General Hospital of Tianjin Medical University, Tianjin 300052, PR China
| | - Yuanyuan Shao
- Department of Hematology, The General Hospital of Tianjin Medical University, Tianjin 300052, PR China
| | - Zonghong Shao
- Department of Hematology, The General Hospital of Tianjin Medical University, Tianjin 300052, PR China.
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26
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Jeswin J, Xie XL, Ji QL, Wang KJ, Liu HP. Proteomic analysis by iTRAQ in red claw crayfish, Cherax quadricarinatus, hematopoietic tissue cells post white spot syndrome virus infection. FISH & SHELLFISH IMMUNOLOGY 2016; 50:288-96. [PMID: 26845698 PMCID: PMC7111676 DOI: 10.1016/j.fsi.2016.01.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 01/08/2016] [Accepted: 01/29/2016] [Indexed: 05/23/2023]
Abstract
To elucidate proteomic changes of Hpt cells from red claw crayfish, Cherax quadricarinatus, we have carried out isobaric tags for relative and absolute quantitation (iTRAQ) of cellular proteins at both early (1 hpi) and late stage (12 hpi) post white spot syndrome virus (WSSV) infection. Protein database search revealed 594 protein hits by Mascot, in which 17 and 30 proteins were present as differentially expressed proteins at early and late viral infection, respectively. Generally, these differentially expressed proteins include: 1) the metabolic process related proteins in glycolysis and glucogenesis, DNA replication, nucleotide/amino acid/fatty acid metabolism and protein biosynthesis; 2) the signal transduction related proteins like small GTPases, G-protein-alpha stimulatory subunit, proteins bearing PDZ- or 14-3-3-domains that help holding together and organize signaling complexes, casein kinase I and proteins of the MAP-kinase signal transduction pathway; 3) the immune defense related proteins such as α-2 macroglobulin, transglutaminase and trans-activation response RNA-binding protein 1. Taken together, these protein information shed new light on the host cellular response against WSSV infection in a crustacean cell culture.
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Affiliation(s)
- Joseph Jeswin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Xiao-lu Xie
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Qiao-lin Ji
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China
| | - Ke-jian Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen 361102, Fujian, PR China
| | - Hai-peng Liu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, PR China; Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Fujian Engineering Laboratory of Marine Bioproducts and Technology, Xiamen 361102, Fujian, PR China.
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27
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Zhang LK, Lin T, Zhu SL, Xianyu LZ, Lu SY. Global quantitative proteomic analysis of human glioma cells profiled host protein expression in response to enterovirus type 71 infection. Proteomics 2015; 15:3784-96. [PMID: 26350028 DOI: 10.1002/pmic.201500134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 07/29/2015] [Accepted: 09/04/2015] [Indexed: 01/26/2023]
Abstract
Enterovirus 71 (EV71) is one of the leading causes of hand, foot and mouth disease with neurological complications in some cases. To study the pathogenesis of EV71 infection, large-scale analyses of EV71 infected cells have been performed. However, most of these studies employed rhabdomyosarcoma (RD) cells or used transcriptomic strategy. Here, we performed SILAC-based quantitative proteomic analysis of EV71-infected U251 cells, a human glioma cell line. A total of 3125 host proteins were quantified, in which 451 were differentially regulated as a result of EV71 infection at 8 or 20 hpi or both. Gene Ontology analysis indicates the regulated proteins were enriched in "metabolic process", "biological regulation" and "cellular process", implying that these biological processes were affected by EV71 infection. Furthermore, functional study indicated that TRAF2 and TRAF6 among the up-regulated proteins could inhibit the replication of EV71 at the early phase post infection, and the anti-EV71 function of both proteins was independent of interferon β. Our study not only provided an overview of cellular response to EV71 infection in a human glioma cell line, but also found that TRAF2 and TRAF6 might be potential targets to inhibit the replication of EV71. All MS data have been deposited in the ProteomeXchange with identifier PXD002454 (http://proteomecentral.proteomexchange.org/dataset/PXD002454).
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Affiliation(s)
- Lei-Ke Zhang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Tao Lin
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Sheng-Lin Zhu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Ling-Zhi Xianyu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Song-Ya Lu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, P. R. China
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28
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Li HY, Zhang LK, Zhu XJ, Shang J, Chen X, Zhu Y, Guo L. Analysis of EV71 infection progression using triple-SILAC-based proteomics approach. Proteomics 2015; 15:3629-43. [PMID: 26306425 DOI: 10.1002/pmic.201500180] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/29/2015] [Accepted: 08/19/2015] [Indexed: 11/09/2022]
Abstract
Enterovirus 71 (EV71), a member of Picornaviridae, causes severe neurological and systemic illness in children. To better understand the virus-host cell interactions, we performed a triple-SILAC-based quantitative proteomics study monitoring host cell proteome changes after EV71 infection. Based on the quantitative data for more than 4100 proteins, ∼17% of the proteins were found as significantly changed (p<0.01) at either 8 or 20 hours post infection. Five biological processes and seven protein classes showed significant differences. Functional screening of nine regulated proteins discovered the regulatory role of CHCH2, a mitochondrial protein known as a transcriptional activator for cytochrome c oxidase, in EV71 replication. Further studies showed that CHCH2 served as a negative regulator of innate immune responses. All MS data have been deposited in the ProteomeXchange with identifier PXD002483 (http://proteomecentral.proteomexchange.org/dataset/PXD002483).
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Affiliation(s)
- Hao-Yu Li
- State Key Laboratory of Virology, Wuhan University, Wuhan, P. R. China.,College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Lei-Ke Zhang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Xiu-Juan Zhu
- State Key Laboratory of Virology, Wuhan University, Wuhan, P. R. China.,College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Jun Shang
- State Key Laboratory of Virology, Wuhan University, Wuhan, P. R. China.,College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Xi Chen
- Wuhan Institute of Biotechnology, Wuhan, P. R. China
| | - Ying Zhu
- State Key Laboratory of Virology, Wuhan University, Wuhan, P. R. China.,College of Life Sciences, Wuhan University, Wuhan, P. R. China
| | - Lin Guo
- State Key Laboratory of Virology, Wuhan University, Wuhan, P. R. China.,College of Life Sciences, Wuhan University, Wuhan, P. R. China
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29
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Lei X, Cui S, Zhao Z, Wang J. Etiology, pathogenesis, antivirals and vaccines of hand, foot, and mouth disease. Natl Sci Rev 2015. [DOI: 10.1093/nsr/nwv038] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Abstract
Hand, foot, and mouth disease (HFMD), caused by enteroviruses, is a syndrome characterized by fever with vesicular eruptions mainly on the skin of the hands, feet, and oral cavity. HFMD primarily affects infants and young children. Although infection is usually self-limited, severe neurological complications in the central nervous system can present in some cases, which can lead to death. Widespread infection of HFMD across the Asia-Pacific region over the past two decades has made HFMD a major public health challenge, ranking first among the category C notifiable communicable diseases in China every year since 2008. This review summarizes our understanding of HFMD, focusing on the etiology and pathogenesis of the disease, as well as on progress toward antivirals and vaccines. The review also discusses the implications of these studies as they relate to the control and prevention of the disease.
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Affiliation(s)
- Xiaobo Lei
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Sheng Cui
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zhendong Zhao
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
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30
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Chan SY, Sam IC, Lai JK, Chan YF. Cellular proteome alterations in response to enterovirus 71 and coxsackievirus A16 infections in neuronal and intestinal cell lines. J Proteomics 2015; 125:121-30. [DOI: 10.1016/j.jprot.2015.05.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/21/2015] [Accepted: 05/13/2015] [Indexed: 12/14/2022]
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31
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Kuo RL, Lin YH, Wang RYL, Hsu CW, Chiu YT, Huang HI, Kao LT, Yu JS, Shih SR, Wu CC. Proteomics analysis of EV71-infected cells reveals the involvement of host protein NEDD4L in EV71 replication. J Proteome Res 2015; 14:1818-30. [PMID: 25785312 DOI: 10.1021/pr501199h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Enterovirus 71 (EV71) is a human enterovirus that has seriously affected the Asia-Pacific area for the past two decades. EV71 infection can result in mild hand-foot-and-mouth disease and herpangina and may occasionally lead to severe neurological complications in children. However, the specific biological processes that become altered during EV71 infection remain unclear. To further explore host responses upon EV71 infection, we identified proteins differentially expressed in EV71-infected human glioblastoma SF268 cells using isobaric mass tag (iTRAQ) labeling coupled with multidimensional liquid chromatography-mass spectrometry (LC-MS/MS). Network analysis of proteins altered in cells infected with EV71 revealed that the changed biological processes are related to protein and ion transport, regulation of protein degradation, and homeostatic processes. We confirmed that the levels of NEDD4L and PSMF1 were increased and reduced, respectively, in EV71-infected cells compared to mock-infected control cells. To determine the physiological relevance of our findings, we investigated the consequences of EV71 infection in cells with NEDD4L or PSMF1 depletion. We found that the depletion of NEDD4L significantly reduced the replication of EV71, whereas PSMF1 knockdown enhanced EV71 replication. Collectively, our findings provide the first evidence of proteome-wide dysregulation by EV71 infection and suggest a novel role for the host protein NEDD4L in the replication of this virus.
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Affiliation(s)
- Rei-Lin Kuo
- †Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,‡Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan
| | - Ya-Han Lin
- †Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,‡Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan
| | - Robert Yung-Liang Wang
- ‡Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,§Department of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan
| | - Chia-Wei Hsu
- ∥Molecular Medicine Research Center, Chang Gung University, Tao-Yuan 333, Taiwan
| | - Yi-Ting Chiu
- †Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan
| | - Hsing-I Huang
- †Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,‡Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan
| | - Li-Ting Kao
- †Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,‡Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan
| | - Jau-Song Yu
- ∥Molecular Medicine Research Center, Chang Gung University, Tao-Yuan 333, Taiwan
| | - Shin-Ru Shih
- †Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,‡Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,⊥Clinical Virology Laboratory, Linkou Chang Gung Memorial Hospital, Tao-Yuan 333, Taiwan
| | - Chih-Ching Wu
- †Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan 333, Taiwan.,∥Molecular Medicine Research Center, Chang Gung University, Tao-Yuan 333, Taiwan
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32
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Zeng S, Zhang H, Ding Z, Luo R, An K, Liu L, Bi J, Chen H, Xiao S, Fang L. Proteome analysis of porcine epidemic diarrhea virus (PEDV)-infected Vero cells. Proteomics 2015; 15:1819-28. [PMID: 25604190 PMCID: PMC7167732 DOI: 10.1002/pmic.201400458] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 12/04/2014] [Accepted: 01/16/2015] [Indexed: 12/16/2022]
Abstract
Porcine epidemic diarrhea virus (PEDV) causes an acute, highly contagious, and devastating viral enteric disease with a high mortality rate in suckling pigs. A large‐scale outbreak of PED occurred in China in 2010, with PEDV emerging in the United States in 2013 and spreading rapidly, posing significant economic and public health concerns. In this study, LC–MS/MS coupled to iTRAQ labeling was used to quantitatively identify differentially expressed cellular proteins in PEDV‐infected Vero cells. We identified 49 differentially expressed cellular proteins, of which 8 were upregulated and 41 downregulated. These differentially expressed proteins were involved in apoptosis, signal transduction, and stress responses. Based on these differentially expressed proteins, we propose that PEDV might utilize apoptosis and extracellular signal regulated kinases pathways for maximum viral replication. Our study is the first attempt to analyze the protein profile of PEDV‐infected cells by quantitative proteomics, and we believe our findings provide valuable information with respect to better understanding the host response to PEDV infection.
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Affiliation(s)
- Songlin Zeng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Huan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Zhen Ding
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Kang An
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Lianzeng Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Jing Bi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P. R. China
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Proteomic analysis of human brain microvascular endothelial cells reveals differential protein expression in response to enterovirus 71 infection. BIOMED RESEARCH INTERNATIONAL 2015; 2015:864169. [PMID: 25821824 PMCID: PMC4363668 DOI: 10.1155/2015/864169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/16/2015] [Indexed: 11/18/2022]
Abstract
2D DIGE technology was employed on proteins prepared from human brain microvascular endothelial cells (HBMEC), to study the differentially expressed proteins in cells at 0 h, 1 h, 16 h, and 24 h after infection. Proteins found to be differentially expressed were identified with matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDITOF/TOF MS) analysis. We identified 43 spots showing changes of at least 2.5 fold up- or downregulated expressions in EV71-infected cells at different time when comparing to control, and 28 proteins could be successfully identified by MALDI TOF/TOF mass spectrometry analysis. 4 proteins were significantly upregulated, and 6 proteins were downregulated, another 18 proteins were different expression at different incubation time. We identified changes in the expression of 12 cellular metabolism-related proteins, 5 molecules involved in cytoskeleton, 3 molecules involved in energy metabolism, 2 molecules involved in signal transduction, 1 molecule involved in the ubiquitin-proteasome pathway, 1 molecule involved in cell cycle, 1 molecule involved in apoptosis-related protein, 1 molecular chaperone, and 2 unknown proteins. These findings build up a comprehensive profile of the HBMEC proteome and provide a useful basis for further analysis of the pathogenic mechanism that underlies EV71 infections to induce severe neural complications.
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Yao C, Yu J, Taylor L, Polgar P, McComb ME, Costello CE. Protein Expression by Human Pulmonary Artery Smooth Muscle Cells Containing a BMPR2 Mutation and the Action of ET-1 as Determined by Proteomic Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 378:347-359. [PMID: 25866469 PMCID: PMC4387548 DOI: 10.1016/j.ijms.2014.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pulmonary arterial hypertension (PAH) is a disease characterized by increased pulmonary vascular resistance and remodeling. Increase in the population of vascular smooth muscle cells is among the key events contributing to the remodeling. Endothelin-1 (ET-1), a potent vasoconstrictor, is linked to the etiology and progression of PAH. Here we analyze changes in protein expressions in response to ET-1 in pulmonary arterial smooth muscle cells (PASMC) from a healthy Control (non-PAH) and a PAH subject presenting a bone morphogenetic protein type II receptor (BMPR2) mutation with exon 1-8 deletion. Protein expressions were analyzed by proteomic mass spectrometry using label-free quantitation and the correlations were subjected to Ingenuity™ Pathway Analysis. The results point to eIF2/mTOR/p70S6K, RhoA/actin cytoskeleton/integrin and protein unbiquitination as canonical pathways whose protein expressions increase with the development of PAH. These pathways have an intimal function in the PAH-related physiology of smooth muscle proliferation, apoptosis, contraction and cellular stress. Exposure of the cells to ET-1 further increases protein expression within these pathways. Thus our results show changes in signaling pathways as a consequence of PAH and the effect of ET-1 interference on Control and PAH-affected cells.
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Affiliation(s)
- Chunxiang Yao
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany St., Boston, MA 02118 USA
| | - Jun Yu
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
| | - Linda Taylor
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
| | - Peter Polgar
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
| | - Mark E. McComb
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany St., Boston, MA 02118 USA
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany St., Boston, MA 02118 USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118 USA
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Chang YL, Ho BC, Sher S, Yu SL, Yang PC. miR-146a and miR-370 coordinate enterovirus 71-induced cell apoptosis through targeting SOS1 and GADD45β. Cell Microbiol 2015; 17:802-18. [PMID: 25469565 DOI: 10.1111/cmi.12401] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 11/20/2014] [Accepted: 11/24/2014] [Indexed: 12/22/2022]
Abstract
Enterovirus 71 (EV71) is an emerging life-threatening pathogen particularly in the Asia-Pacific region. The major pathogenic feature in EV71-infected cells is apoptosis. However, which molecular mechanism mainly contributes to EV71-induced apoptosis is not investigated thoroughly. MicroRNAs (MiRNAs), the newly discovered molecules, govern a wide range of biological functions through post-transcriptional regulation including viral pathogenesis. Whether miRNAs and messenger RNAs (mRNAs) coordinate to trigger host cell apoptosis in EV71 infection was investigated in this study. We conducted an apoptosis-oriented approach using both mRNA and miRNA profiling and bioinformatic analysis. We identified two major apoptosis-associated signalling pathways, Bcl2 antagonist of cell death (BAD) phosphorylation and p53-dependent apoptosis pathways, in which Son of sevenless homolog 1 (SOS1) and Growth arrest and DNA damage-inducible protein 45β (GADD45β) were predicted as targets of miR-146a and miR-370 respectively. Luciferase reporter assays and Western blots demonstrated the negative regulation between miR-146a and SOS1 and between miR-370 and GADD45β. Silencing of miR-146a restored SOS1 expression and partially attenuated EV71 infection-induced apoptosis. Conversely, ectopic expression of miR-370 decreased virus infection-induced GADD45β expression and also diminished apoptosis. Finally, the transfection of antagomiR-146a and miR-370 contributed to attenuating EV71 infection-induced apoptosis. Herein we clearly demonstrate that EV71-induced cell apoptosis is partly governed by altered miRNAs.
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Affiliation(s)
- Ya-Ling Chang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Bing-Ching Ho
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,NTU Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Singh Sher
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan.,NTU Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Pathology and Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei, Taiwan.,Center for Optoelectronic Biomedicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pan-Chyr Yang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,NTU Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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Prediction of signaling pathways involved in enterovirus 71 infection by algorithm analysis based on miRNA profiles and their target genes. Arch Virol 2014; 160:173-82. [PMID: 25287131 DOI: 10.1007/s00705-014-2249-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/29/2014] [Indexed: 12/12/2022]
Abstract
Enterovirus 71 (EV71) causes major outbreaks of hand, foot, and mouth disease. Host factors and signaling pathways exhibit important functions in the EV71 life cycle. We conducted algorithm analysis based on miRNA profiles and their target genes to identify the miRNAs and downstream signaling pathways involved in EV71 infection. The miRNA profiles of human rhabdomyosarcoma cells treated with interferon (IFN-)-α or IFN-γ were compared with those of cells infected with EV71. Genes targeted by differentially expressed miRNAs were identified and assigned to different signaling pathways according to public databases. The results showed that host miRNAs specifically responded to the viral infection and IFN treatment. Some miRNAs, including miR-124 and miR-491-3p, were regulated in opposite manners by the IFNs and EV71. Some signaling pathways regulated by both EV71 infection and IFN treatment were also predicted. These pathways included axon guidance, Wingless/Int1 (Wnt) signaling cascade, platelet-derived growth factor receptor (PDGFR)/PDGF, phosphatidylinositol 3-kinase (PI3K), Jun N-terminal kinase (JNK)/mitogen-activated protein kinase (MAPK), transforming growth factor-beta receptor (TGF-βR)/TGF-β, SMAD2/3, insulin/insulin-like growth factor (IGF), bone morphogenetic protein (BMP), CDC42, ERB1, hepatocyte growth factor receptor (c-Met), eukaryotic translation initiation factor 4E (eIF4E), protein kinase A (PKA), and IFN-γ pathways. The identified miRNA and downstream signaling pathways would help to elucidate the interaction between the virus and the host. The genomics method using algorithm analysis also provided a new way to investigate the host factors and signaling pathways critical for viral replication.
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Yang K, Boswell M, Walter DJ, Downs KP, Gaston-Pravia K, Garcia T, Shen Y, Mitchell DL, Walter RB. UVB-induced gene expression in the skin of Xiphophorus maculatus Jp 163 B. Comp Biochem Physiol C Toxicol Pharmacol 2014; 163:86-94. [PMID: 24556253 PMCID: PMC4067948 DOI: 10.1016/j.cbpc.2014.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/15/2014] [Accepted: 01/29/2014] [Indexed: 01/04/2023]
Abstract
Xiphophorus fish and interspecies hybrids represent long-standing models to study the genetics underlying spontaneous and induced tumorigenesis. The recent release of the Xiphophorus maculatus genome sequence will allow global genetic regulation studies of genes involved in the inherited susceptibility to UVB-induced melanoma within select backcross hybrids. As a first step toward this goal, we report results of an RNA-Seq approach to identify genes and pathways showing modulated transcription within the skin of X. maculatus Jp 163 B upon UVB exposure. X. maculatus Jp 163 B were exposed to various doses of UVB followed by RNA-Seq analysis at each dose to investigate overall gene expression in each sample. A total of 357 genes with a minimum expression change of 4-fold (p-adj<0.05) were identified as responsive to UVB. The molecular genetic response of Xiphophorus skin to UVB exposure permitted assessment of; (1) the basal expression level of each transcript for each skin sample, (2) the changes in expression levels for each gene in the transcriptome upon exposure to increasing doses of UVB, and (3) clusters of genes that exhibit similar patterns of change in expression upon UVB exposure. These data provide a foundation for understanding the molecular genetic response of fish skin to UVB exposure.
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Affiliation(s)
- Kuan Yang
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States.
| | - Mikki Boswell
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States.
| | - Dylan J Walter
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States.
| | - Kevin P Downs
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States.
| | - Kimberly Gaston-Pravia
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States.
| | - Tzintzuni Garcia
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States.
| | - Yingjia Shen
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States.
| | - David L Mitchell
- Department of Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, United States.
| | - Ronald B Walter
- Molecular Biosciences Research Group, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, United States.
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Huang HL, Yao HS, Wang Y, Wang WJ, Hu ZQ, Jin KZ. Proteomic identification of tumor biomarkers associated with primary gallbladder cancer. World J Gastroenterol 2014; 20:5511-5518. [PMID: 24833881 PMCID: PMC4017066 DOI: 10.3748/wjg.v20.i18.5511] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/22/2014] [Accepted: 02/20/2014] [Indexed: 02/06/2023] Open
Abstract
AIM: To identify potential biomarkers of primary gallbladder cancer (PGC).
METHODS: Fresh PGC, cholecystitis and normal gallbladder tissue specimens collected from 10 patients, respectively, were subjected to comparative proteomic analysis. The proteomic patterns of PGC were compared with those of cholecystitis and normal gallbladder tissues using two-dimensional gel electrophoresis (2-DE). The differentially expressed proteins were then identified using a MALDI-TOF mass spectrometer (MS) and database searches. To further validate these proteins, 20 samples of PGC tissues and normal tumor-adjacent tissues were collected for Western blot, quantitative real-time PCR, and immunohistochemical staining assay.
RESULTS: Seven differentially expressed protein spots were detected by 2-ED analysis by comparing the average maps of PGC, cholecystitis and normal gallbladder tissues. Six of the seven differentially expressed proteins were identified using MALDI-TOF MS, with three overexpressed and three underexpressed in PGC tissue. Protein levels of annexin A4 (ANXA4) were significantly elevated, and heat shock protein 90-beta (Hsp90β) and dynein cytoplasmic 1 heavy chain 1 (Dync1h1) were decreased in PGC tissues relative to the normal tumor-adjacent tissues as shown by Western blot analysis. However, levels of actin, aortic smooth muscle and gamma-actin were unchanged. In addition, the mRNA levels of all 5 proteins showed similar changes to those of the protein levels (P < 0.01). Further validation by immunohistochemical analysis showed the upregulated expression of ANXA4 and decreased expression of Hsp90β and Dync1h1 in the cytoplasm of PGC tissues relative to the normal tumor-adjacent tissues.
CONCLUSION: Three proteins are identified as potential biomarkers of PGC using proteomic analysis. The functions of these proteins in the carcinogenesis of PGC remain to be studied.
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MESH Headings
- Aged
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Blotting, Western
- Case-Control Studies
- Databases, Protein
- Electrophoresis, Gel, Two-Dimensional
- Female
- Gallbladder Neoplasms/chemistry
- Gallbladder Neoplasms/genetics
- Gallbladder Neoplasms/pathology
- Gene Expression Regulation, Neoplastic
- Humans
- Immunohistochemistry
- Male
- Middle Aged
- Neoplasm Proteins/analysis
- Neoplasm Proteins/genetics
- Predictive Value of Tests
- Proteomics/methods
- RNA, Messenger/analysis
- Real-Time Polymerase Chain Reaction
- Reproducibility of Results
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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Lui YLE, Tan TL, Timms P, Hafner LM, Tan KH, Tan EL. Elucidating the host-pathogen interaction between human colorectal cells and invading Enterovirus 71 using transcriptomics profiling. FEBS Open Bio 2014; 4:426-31. [PMID: 24918057 PMCID: PMC4050184 DOI: 10.1016/j.fob.2014.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 04/16/2014] [Accepted: 04/17/2014] [Indexed: 01/08/2023] Open
Abstract
Enterovirus 71 (EV71) is one of the main etiological agents for Hand, Foot and Mouth Disease (HFMD). Types I, II and III interferon may be a key antiviral response against EV71. We examine the transcriptomic changes in human colorectal cells during EV71 infection. The intestinal epithelial immune system plays a key role in the progression of HFMD.
Enterovirus 71 (EV71) is one of the main etiological agents for Hand, Foot and Mouth Disease (HFMD) and has been shown to be associated with severe clinical manifestation. Currently, there is no antiviral therapeutic for the treatment of HFMD patients owing to a lack of understanding of EV71 pathogenesis. This study seeks to elucidate the transcriptomic changes that result from EV71 infection. Human whole genome microarray was employed to monitor changes in genomic profiles between infected and uninfected cells. The results reveal altered expression of human genes involved in critical pathways including the immune response and the stress response. Together, data from this study provide valuable insights into the host–pathogen interaction between human colorectal cells and EV71.
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Affiliation(s)
- Yan Long Edmund Lui
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Queensland, Australia ; Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia ; School of Chemical and Life Sciences, Singapore Polytechnic, Singapore ; Centre for Biomedical and Life Sciences, Singapore Polytechnic, Singapore
| | - Tuan Lin Tan
- School of Chemical and Life Sciences, Singapore Polytechnic, Singapore
| | - Peter Timms
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Queensland, Australia ; Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia ; Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Queensland, Australia
| | - Louise Marie Hafner
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Queensland, Australia ; Institute of Health and Biomedical Innovation, Queensland University of Technology, Queensland, Australia
| | - Kian Hwa Tan
- School of Chemical and Life Sciences, Singapore Polytechnic, Singapore
| | - Eng Lee Tan
- Centre for Biomedical and Life Sciences, Singapore Polytechnic, Singapore ; Department of Paediatrics, University Children's Medical Institute, National University Hospital, Singapore
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40
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Liu X, Yang Y, Zhao M, Bode L, Zhang L, Pan J, Lv L, Zhan Y, Liu S, Zhang L, Wang X, Huang R, Zhou J, Xie P. Proteomics reveal energy metabolism and mitogen-activated protein kinase signal transduction perturbation in human Borna disease virus Hu-H1-infected oligodendroglial cells. Neuroscience 2014; 268:284-96. [PMID: 24637096 PMCID: PMC7116963 DOI: 10.1016/j.neuroscience.2014.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/01/2014] [Accepted: 03/06/2014] [Indexed: 12/19/2022]
Abstract
A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells). Energy metabolism was the most significantly altered pathway in BDV Hu-H1-infected OL cells. The Raf/MEK/ERK signaling cascade was significantly perturbed in BDV Hu-H1-infected OL cells. BDV Hu-H1caused constitutive activation of the ERK1/2 pathway, but cell proliferation was down-regulated at the same time. BDV Hu-H1 manages to down-regulate cell proliferation, in the presence of activated but not translocated ERK–RSK complex.
Borna disease virus (BDV) is a neurotropic, non-cytolytic RNA virus which replicates in the cell nucleus targeting mainly hippocampal neurons, but also astroglial and oligodendroglial cells in the brain. BDV is associated with a large spectrum of neuropsychiatric pathologies in animals. Its relationship to human neuropsychiatric illness still remains controversial. We could recently demonstrate that human BDV strain Hu-H1 promoted apoptosis and inhibited cell proliferation in a human oligodendroglial cell line (OL cells) whereas laboratory BDV strain V acted contrariwise. Here, differential protein expression between BDV Hu-H1-infected OL cells and non-infected OL cells was assessed through a proteomics approach, using two-dimensional electrophoresis followed by matrix-assisted laser desorption ionization-time of flight tandem mass spectrometry. A total of 63 differential host proteins were identified in BDV Hu-H1-infected OL cells compared to non-infected OL cells. We found that most changes referred to alterations related to the pentose phosphate pathway, glyoxylate and dicarboxylate metabolism, the tricarboxylic acid (TCA) cycle, and glycolysis /gluconeogenesis. By manual querying, two differential proteins were found to be associated with mitogen-activated protein kinase (MAPK) signal transduction. Five key signaling proteins of this pathway (i.e., p-Raf, p-MEK, p-ERK1/2, p-RSK, and p-MSK) were selected for Western blotting validation. p-ERK1/2 and p-RSK were found to be significantly up-regulated, and p-MSK was found to be significantly down-regulated in BDV Hu-H1-infected OL cells compared to non-infected OL cell. Although BDV Hu-H1 constitutively activated the ERK–RSK pathway, host cell proliferation and nuclear translocation of activated pERK in BDV Hu-H1-infected OL cells were impaired. These findings indicate that BDV Hu-H1 infection of human oligodendroglial cells significantly perturbs host energy metabolism, activates the downstream ERK–RSK complex of the Raf/MEK/ERK signaling cascade, and disturbs host cell proliferation possibly through impaired nuclear translocation of pERK, a finding which warrants further research.
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Affiliation(s)
- X Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Y Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - M Zhao
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - L Bode
- Bornavirus Research Group affiliated to the Free University of Berlin, Berlin, Germany
| | - L Zhang
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - J Pan
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - L Lv
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - Y Zhan
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - S Liu
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - L Zhang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - X Wang
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - R Huang
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China; Department of Rehabilitation, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - J Zhou
- Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China
| | - P Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China; Chongqing Key Laboratory of Neurobiology, Chongqing Medical University, Chongqing, China; Institute of Neuroscience, Chongqing Medical University, Chongqing, China.
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Wu X, Wang S, Yu Y, Zhang J, Sun Z, Yan Y, Zhou J. Subcellular proteomic analysis of human host cells infected with H3N2 swine influenza virus. Proteomics 2013; 13:3309-26. [PMID: 24115376 DOI: 10.1002/pmic.201300180] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/25/2013] [Accepted: 08/28/2013] [Indexed: 11/10/2022]
Abstract
Cross-species transmissions of swine influenza viruses (SIVs) raise great public health concerns. In this study, subcellular proteomic profiles of human A549 cells inoculated with H3N2 subtype SIV were used to characterize dynamic cellular responses to infection. By 2DE and MS, 27 differentially expressed (13 upregulated, 14 downregulated) cytoplasmic proteins and 20 differentially expressed (13 upregulated, 7 downregulated) nuclear proteins were identified. Gene ontology analysis suggested that these differentially expressed proteins were mainly involved in cell death, stress response, lipid metabolism, cell signaling, and RNA PTMs. Moreover, 25 corresponding genes of the differentially expressed proteins were quantitated by real time RT-PCR to examine the transcriptional profiles between mock- and virus-infected A549 cells. Western blot analysis confirmed that changes in abundance of identified cellular proteins heterogeneous nuclear ribonucleoprotein (hnRNP) U, hnRNP C, ALDH1A1, tryptophanyl-tRNA synthetase, IFI35, and HSPB1 in H3N2 SIV-infected cells were consistent with results of 2DE analysis. By confocal microscopy, nucleus-to-cytoplasm translocation of hnRNP C and colocalization between the viral nonstructural protein 1 and hnRNP C as well as N-myc (and STAT) interactor were observed upon infection. Ingenuity Pathway Analysis revealed that cellular proteins altered during infection were grouped mainly into NFκB and interferon signaling networks. Collectively, these identified subcellular constituents provide an important framework for understanding host/SIV interactions and underlying mechanisms of SIV cross-species infection and pathogenesis.
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Affiliation(s)
- Xiaopeng Wu
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, P. R. China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou, P. R. China
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Global transcriptomic analysis of human neuroblastoma cells in response to enterovirus type 71 infection. PLoS One 2013; 8:e65948. [PMID: 23861741 PMCID: PMC3702535 DOI: 10.1371/journal.pone.0065948] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 04/30/2013] [Indexed: 01/27/2023] Open
Abstract
Human enterovirus type 71 (EV71) is the major pathogen of hand-foot-and-mouth disease (HFMD) and has been associated with severe neurological disease and even death in infants and young children. The pathogenesis of EV71 infection in the human central nervous system remains unclear. In this study, human whole genome microarray was employed to perform transcriptome profiling in SH-SY5Y human neuroblastoma cells infected with EV71. The results indicated that EV71 infection lead to altered expression of 161 human mRNAs, including 74 up-regulated genes and 87 down-regulated genes. Bioinformatics analysis indicated the possible roles of the differentially regulated mRNAs in selected pathways, including cell cycle/proliferation, apoptosis, and cytokine/chemokine responses. Finally, the microarray results were validated using real-time RT-PCR with high identity. Overall, our results provided fundamental information regarding the host response to EV71 infection in human neuroblastoma cells, and this finding will help explain the pathogenesis of EV71 infection and virus-host interaction.
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Liu L, Li Q, Lin L, Wang M, Lu Y, Wang W, Yuan J, Li L, Liu X. Proteomic analysis of epithelioma papulosum cyprini cells infected with spring viremia of carp virus. FISH & SHELLFISH IMMUNOLOGY 2013; 35:26-35. [PMID: 23583725 DOI: 10.1016/j.fsi.2013.03.367] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 03/20/2013] [Accepted: 03/20/2013] [Indexed: 06/02/2023]
Abstract
Spring viremia of carp (SVC), caused by spring viremia of carp virus (SVCV) is an important disease due to its drastic effects on carp fisheries in many countries. To better understand molecular responses to SVCV infection, two dimensional electrophoresis (2-DE) and MALDI-TOF/TOF were performed to investigate altered proteins in epithelioma papulosum cyprini cells (EPCs). Differentially expressed proteins in mock-infected EPCs and SVCV-infected EPCs were compared. A total of 54 differentially expressed spots were successfully identified (33 up-regulated spots and 21 down-regulated spots) which include cytoskeleton proteins, macromolecular biosynthesis-associated proteins, stress response proteins, signal transduction proteins, energy metabolism, and ubiquitin proteasome pathway-associated proteins. Moreover, 7 corresponding genes of the differentially expressed proteins were quantified using real time RT-PCR to examine their transcriptional profiles. The presence of four selected cellular proteins (beta-actin, gamma1-actin, heat shock cognate 71 kDa protein and annexin A2) associated with the spring viremia of carp virus (SVCV) particles was validated by Western blot assay. This study provides dynamic and useful protein-related information to further understand the underlying pathogenesis of SVCV infection.
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Affiliation(s)
- Liyue Liu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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Li W, Liu S, Wang Y, Deng F, Yan W, Yang K, Chen H, He Q, Charreyre C, Audoneet JC. Transcription analysis of the porcine alveolar macrophage response to porcine circovirus type 2. BMC Genomics 2013; 14:353. [PMID: 23711280 PMCID: PMC3680065 DOI: 10.1186/1471-2164-14-353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 05/11/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Porcine circovirus type 2 (PCV2) is the causal agent of postweaning multisystemic wasting syndrome (PMWS), which has severely impacted the swine industry worldwide. PCV2 triggers a weak and atypical innate immune response, but the key genes and mechanisms by which the virus interferes with host innate immunity have not yet been elucidated. In this study, genes that control the response of primary porcine alveolar macrophages (PAMs), the main target of PCV2, were profiled in vitro. RESULTS PAMs were successfully infected by PCV2-WH strain, as evidenced quantitative real-time polymerase chain reaction (qPCR) and immunofluorescence assay (IFA) results. Infection-related differential gene expression was investigated using pig microarrays from the US Pig Genome Coordination Program and validated by real-time PCR and enzyme-linked immunosorbent assay (ELISA). Microarray analysis at 24 and 48 hours post-infection (HPI) revealed 266 and 175 unique genes, respectively, that were differentially expressed (false discovery rate <0.05; fold-change >2). Only six genes were differentially expressed between 24 and 48 HPI. The up-regulated genes were principally related to immune response, cytokine activity, locomotion, regulation of cell proliferation, apoptosis, cell growth arrest, and antigen procession and presentation. The down-regulated genes were mainly involved in terpenoid biosynthesis, carbohydrate metabolism, translation, proteasome degradation, signal transducer activity, and ribosomal proteins, which were representative of the reduced vital activity of PCV2-infected cells. CONCLUSIONS PCV2 infection of PAMs causes up-regulation of genes related to inflammation, indicating that PCV2 may induce systematic inflammation. PCV2 persistently induced cytokines, mainly through the Toll-like receptor (TLR) 1 and TLR9 pathways, which may promote high levels of cytokine secretion. PCV2 may prevent apoptosis in PAMs by up-regulating SERPINB9 expression, possibly to lengthen the duration of PCV2 replication-permissive conditions. The observed gene expression profile may provide insights into the underlying immunological response and pathological changes that occur in pigs following PCV2 infection.
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Affiliation(s)
- Wentao Li
- Division of Animal Infectious Disease, State Key Laboratory of Agricultural Microbiology College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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Differential proteome analysis of chikungunya virus infection on host cells. PLoS One 2013; 8:e61444. [PMID: 23593481 PMCID: PMC3622599 DOI: 10.1371/journal.pone.0061444] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 03/10/2013] [Indexed: 11/19/2022] Open
Abstract
Background Chikungunya virus (CHIKV) is an emerging mosquito-borne alphavirus that has caused multiple unprecedented and re-emerging outbreaks in both tropical and temperate countries. Despite ongoing research efforts, the underlying factors involved in facilitating CHIKV replication during early infection remains ill-characterized. The present study serves to identify host proteins modulated in response to early CHIKV infection using a proteomics approach. Methodology and Principal Findings The whole cell proteome profiles of CHIKV-infected and mock control WRL-68 cells were compared and analyzed using two-dimensional gel electrophoresis (2-DGE). Fifty-three spots were found to be differentially modulated and 50 were successfully identified by MALDI-TOF/TOF. Eight were significantly up-regulated and 42 were down-regulated. The mRNA expressions of 15 genes were also found to correlate with the corresponding protein expression. STRING network analysis identified several biological processes to be affected, including mRNA processing, translation, energy production and cellular metabolism, ubiquitin-proteasome pathway (UPP) and cell cycle regulation. Conclusion/Significance This study constitutes a first attempt to investigate alteration of the host cellular proteome during early CHIKV infection. Our proteomics data showed that during early infection, CHIKV affected the expression of proteins that are involved in mRNA processing, host metabolic machinery, UPP, and cyclin-dependent kinase 1 (CDK1) regulation (in favour of virus survival, replication and transmission). While results from this study complement the proteomics results obtained from previous late host response studies, functional characterization of these proteins is warranted to reinforce our understanding of their roles during early CHIKV infection in humans.
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lncRNA expression signatures in response to enterovirus 71 infection. Biochem Biophys Res Commun 2012; 430:629-33. [PMID: 23220233 PMCID: PMC7092842 DOI: 10.1016/j.bbrc.2012.11.101] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 11/25/2012] [Indexed: 11/30/2022]
Abstract
Outbreaks of hand, foot, and mouth disease caused by enterovirus 71 (EV71) have become considerable threats to the health of infants and young children. To identify the cellular long noncoding RNAs (lncRNAs) involved in the host response to EV71 infection, we performed comprehensive lncRNA and mRNA profiling in EV71-infected rhabdomyosarcoma cells through microarray. We observed the differential expression of more than 4800 lncRNAs during infection. Further analysis showed 160 regulated enhancer-like lncRNA and nearby mRNA pairs, as well as 313 regulated Rinn’s lncRNA [M. Guttman I. Amit, M. Garber, C. French, M.F. Lin, D. Feldser, M. Huarte, O. Zuk, B.W. Carey, J.P. Cassady, M.N. Cabili, R. Jaenisch, T.S. Mikkelsen, T. Jacks, N. Hacohen, B.E. Bernstein, M. Kellis, A. Regev, J.L. Rinn, E.S. Lander. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458 (2009) 223–227, A.M. Khalil, M. Guttman, M. Huarte, M. Garber, A. Raj, D. Rivea Morales, K. Thomas, A. Presser, B.E. Bernstein, A. van Oudenaarden, A. Regev, E.S. Lander, J.L. Rinn. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 106 (2009) 11667–11672] and nearby mRNA pairs. The results provided information for further research on the prevention and treatment of EV71 infection, as well as on distinguishing severe and mild EV71 cases.
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Shi W, Li X, Hou X, Peng H, Jiang Q, Shi M, Ji Y, Liu X, Liu J. Differential apoptosis gene expressions of rhabdomyosarcoma cells in response to enterovirus 71 infection. BMC Infect Dis 2012. [PMID: 23191987 PMCID: PMC3536580 DOI: 10.1186/1471-2334-12-327] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Enterovirus 71 (EV71) infection can induce the apoptosis of infected cells. The aim of this study is to explore the effect of EV71 infection on apoptosis mechanisms in virus-infected human rhabdomyosarcoma (RD) cells. Methods The apoptosis of RD cells was examined using annexin V-FITC/PI by flow cytometry and cytokines were detected by ELISA. Cellular RNA was extracted and transcribed to cDNA. PCR array was employed to analyze the expressions of 84 apoptotic genes from EV71-infected RD cells at 8 and 20 h postinfection, respectively. In addition, the expressions of FasL, caspase, AKT2, JNK1/2, c-Jun and NF-κB proteins were detected by western blotting. Results Flow cytometry demonstrated that the apoptosis or death of EV71-infected RD cells was increased by 37.1% with a multiplicity of infection (MOI) of 5 at 20 h postinfection. The production of IL-4, IL-10 and TNF-α was enhanced by the subsequent EV71 infection. PCR array revealed significant changes in the expressions of apoptotic genes. Among 84 genes, 42 genes were down-regulated after EV71 infection at 8 h, whereas 32 genes were up-regulated at 20 h postinfection. Moreover, the ligands of TNF superfamily such as FasL, CD40L and TNF-α were significantly up-regulated and enhanced the expressions of apoptosis-related cysteine peptidases, including caspase-10, -8, -7 and -3. In addition, EV71 infection induces the phosphorylation of AKT2, JNK1/2, c-Jun and NF-κB at 20 h postinfection. Conclusion PCR array for the determination of apoptosis gene expressions is an informative assay in elucidating biological pathways. During the early stage of EV71 infection, the apoptotic process of RD cells is significantly delayed. EV71 infection can also induce the expressions of FasL, TNF-α and CD40L, which contribute to the apoptosis of RD cells.
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Affiliation(s)
- Weifeng Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Suzhou University, Changzhou, Jiangsu, 213003, China.
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Bek EJ, McMinn PC. The Pathogenesis and Prevention of Encephalitis due to Human Enterovirus 71. Curr Infect Dis Rep 2012; 14:397-407. [PMID: 22639066 DOI: 10.1007/s11908-012-0267-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human enterovirus 71 (HEV71) has emerged as a major cause of viral encephalitis in Southeast Asia, with increased epidemic activity observed since 1997. This is reflected in a large increase in scientific publications relating directly to HEV71. New research is elucidating details of the viral life cycle, confirming similarities between HEV71 and other enteroviruses. Scavenger receptor B2 (SCARB2) is a receptor for HEV71, although other receptors are likely to be identified. Currently, the only strategies to prevent HEV71-associated disease are early diagnosis and aggressive supportive management of identified cases. As more information emerges regarding the molecular processes of HEV71 infection, further advances may lead to the development of effective antiviral treatments and ultimately a vaccine-protection strategy. The protective efficacies of several inactivated HEV71 vaccines have been confirmed in animal models, suggesting that an effective vaccine may become available in the next decade.
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Affiliation(s)
- Emily Jane Bek
- Infectious Diseases and Immunology, Sydney Medical School, The University of Sydney, Blackburn Building D06, Sydney, NSW, 2006, Australia
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Tan KS, Olfat F, Phoon MC, Hsu JP, Howe JLC, Seet JE, Chin KC, Chow VTK. In vivo and in vitro studies on the antiviral activities of viperin against influenza H1N1 virus infection. J Gen Virol 2012; 93:1269-1277. [DOI: 10.1099/vir.0.040824-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Influenza A virus has caused a number of pandemics in past decades, including the recent H1N1-2009 pandemic. Viperin is an interferon (IFN)-inducible protein of innate immunity, and acts as a broad-spectrum antiviral protein. We explored the antiviral activities and mechanisms of viperin during influenza virus (IFV) infection in vitro and in vivo. Wild-type (WT) HeLa and viperin-expressing HeLa cells were infected with influenza A/WSN/33/H1N1 (WSN33) virus, and subjected to virological, light and electron microscopic analyses. Viperin expression reduced virus replication and titres, and restricted viral budding. Young and old viperin-knockout (KO) mice and WT control animals were challenged with influenza WSN33 at lethal doses of 103 and 104 p.f.u. via the intratracheal route. Lungs were subjected to histopathological, virological and molecular studies. Upon lethal IFV challenge, both WT and KO mice revealed similar trends of infection and recovery with similar mortality rates. Viral quantification assay and histopathological evaluation of lungs from different time points showed no significant difference in viral loads and lung damage scores between the two groups of mice. Although the in vitro studies demonstrated the ability of viperin to restrict influenza H1N1 virus replication, the viperin-deficient mouse model indicated that absence of viperin enhanced neither the viral load nor pulmonary damage in the lungs of infected mice. This may be due to the compensation of IFN-stimulated genes in the lungs and/or the influenza non-structural protein 1-mediated IFN antagonism dampening the IFN response, thereby rendering the loss of viperin insignificant. Nevertheless, further investigations that exploit the antiviral mechanisms of viperin as prophylaxis are still warranted.
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Affiliation(s)
- Kai Sen Tan
- Infectious Diseases Interdisciplinary Research Group, Singapore–Massachusetts Institute of Technology Alliance in Research and Technology, Singapore 117456
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Kent Ridge, Singapore 117597
| | - Farzad Olfat
- Infectious Diseases Interdisciplinary Research Group, Singapore–Massachusetts Institute of Technology Alliance in Research and Technology, Singapore 117456
| | - Meng Chee Phoon
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Kent Ridge, Singapore 117597
| | - Jung Pu Hsu
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Kent Ridge, Singapore 117597
| | - Josephine L. C. Howe
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Kent Ridge, Singapore 117597
| | - Ju Ee Seet
- Department of Pathology, National University Hospital, Singapore 119074
| | - Keh Chuang Chin
- Singapore Immunology Network, Immunos, Biopolis, Singapore 138648
| | - Vincent T. K. Chow
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Kent Ridge, Singapore 117597
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Lee JW, Yeo SG, Kang BH, Lee HK, Kim JW, Lee SH, Kim KS, Cheon DS. Echovirus 30 induced neuronal cell death through TRIO-RhoA signaling activation. PLoS One 2012; 7:e36656. [PMID: 22586486 PMCID: PMC3346726 DOI: 10.1371/journal.pone.0036656] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 04/05/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Echovirus 30 (Echo30) is one of the most frequently identified human enteroviruses (EVs) causing aseptic meningitis and encephalitis. However the mechanism underlying the pathogenesis of Echo30 infection with significant clinical outcomes is not completely understood. The aim of this investigation is to illustrate molecular pathologic alteration in neuronal cells induced by Echo30 infection using clinical isolate from young patient with neurologic involvement. METHODOLOGY/PRINCIPAL FINDINGS To characterize the neuronal cellular response to Echo30 infection, we performed a proteomic analysis based on two-dimensional gel electrophoresis (2-DE) and MALDI-TOF/TOF Mass Spectrophotometric (MS) analysis. We identified significant alteration of several protein expression levels in Echo30-infected SK-N-SH cells. Among these proteins, we focused on an outstanding up-regulation of Triple functional domain (TRIO) in Echo30-infected SK-N-SH cells. Generally, TRIO acts as a key component in the regulation of axon guidance and cell migration. In this study, we determined that TRIO plays a role in the novel pathways in Echo30 induced neuronal cell death. CONCLUSIONS/SIGNIFICANCE Our finding shows that TRIO plays a critical role in neuronal cell death by Echo30 infection. Echo30 infection activates TRIO-guanine nucleotide exchange factor (GEF) domains (GEFD2) and RhoA signaling in turn. These results suggest that Echo30 infection induced neuronal cell death by activation of the TRIO-RhoA signaling. We expect the regulation of TRIO-RhoA signaling may represent a new therapeutic approach in treating aseptic meningitis and encephalitis induced by Echo30.
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Affiliation(s)
- June-Woo Lee
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institutes of Health, Osong, Korea
| | - Sang-Gu Yeo
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institutes of Health, Osong, Korea
| | - Byung-Hak Kang
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institutes of Health, Osong, Korea
| | - Hoe-Kyu Lee
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institutes of Health, Osong, Korea
| | - Jin-Won Kim
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institutes of Health, Osong, Korea
| | - Sun-Hwa Lee
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institutes of Health, Osong, Korea
| | - Ki-Sang Kim
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institutes of Health, Osong, Korea
| | - Doo-Sung Cheon
- Division of Enteric and Hepatitis Viruses, Center for Infectious Diseases, National Institutes of Health, Osong, Korea
- * E-mail:
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