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Yang Q, Barbachano-Guerrero A, Fairchild LM, Rowland TJ, Dowell RD, Allen MA, Warren CJ, Sawyer SL. Macrophages derived from human induced pluripotent stem cells (iPSCs) serve as a high-fidelity cellular model for investigating HIV-1, dengue, and influenza viruses. J Virol 2024; 98:e0156323. [PMID: 38323811 PMCID: PMC10949493 DOI: 10.1128/jvi.01563-23] [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: 10/05/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Macrophages are important target cells for diverse viruses and thus represent a valuable system for studying virus biology. Isolation of primary human macrophages is done by culture of dissociated tissues or from differentiated blood monocytes, but these methods are both time consuming and result in low numbers of recovered macrophages. Here, we explore whether macrophages derived from human induced pluripotent stem cells (iPSCs)-which proliferate indefinitely and potentially provide unlimited starting material-could serve as a faithful model system for studying virus biology. Human iPSC-derived monocytes were differentiated into macrophages and then infected with HIV-1, dengue virus, or influenza virus as model human viruses. We show that iPSC-derived macrophages support the replication of these viruses with kinetics and phenotypes similar to human blood monocyte-derived macrophages. These iPSC-derived macrophages were virtually indistinguishable from human blood monocyte-derived macrophages based on surface marker expression (flow cytometry), transcriptomics (RNA sequencing), and chromatin accessibility profiling. iPSC lines were additionally generated from non-human primate (chimpanzee) fibroblasts. When challenged with dengue virus, human and chimpanzee iPSC-derived macrophages show differential susceptibility to infection, thus providing a valuable resource for studying the species-tropism of viruses. We also show that blood- and iPSC-derived macrophages both restrict influenza virus at a late stage of the virus lifecycle. Collectively, our results substantiate iPSC-derived macrophages as an alternative to blood monocyte-derived macrophages for the study of virus biology. IMPORTANCE Macrophages have complex relationships with viruses: while macrophages aid in the removal of pathogenic viruses from the body, macrophages are also manipulated by some viruses to serve as vessels for viral replication, dissemination, and long-term persistence. Here, we show that iPSC-derived macrophages are an excellent model that can be exploited in virology.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | | | - Laurence M. Fairchild
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Teisha J. Rowland
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Robin D. Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome Boulder Branch, BioFrontiers Institute, Boulder, Colorado, USA
- Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mary A. Allen
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome Boulder Branch, BioFrontiers Institute, Boulder, Colorado, USA
| | - Cody J. Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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Chen J, Song HX, Hu JH, Bai JS, Li XH, Sun RC, Zhao BQ, Li MZ, Zhou B. Classical swine fever virus non-structural protein 5B hijacks host METTL14-mediated m6A modification to counteract host antiviral immune response. PLoS Pathog 2024; 20:e1012130. [PMID: 38551978 PMCID: PMC11006178 DOI: 10.1371/journal.ppat.1012130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/10/2024] [Accepted: 03/17/2024] [Indexed: 04/11/2024] Open
Abstract
Classical Swine Fever (CSF), caused by the Classical Swine Fever Virus (CSFV), inflicts significant economic losses on the global pig industry. A key factor in the challenge of eradicating this virus is its ability to evade the host's innate immune response, leading to persistent infections. In our study, we elucidate the molecular mechanism through which CSFV exploits m6A modifications to circumvent host immune surveillance, thus facilitating its proliferation. We initially discovered that m6A modifications were elevated both in vivo and in vitro upon CSFV infection, particularly noting an increase in the expression of the methyltransferase METTL14. CSFV non-structural protein 5B was found to hijack HRD1, the E3 ubiquitin ligase for METTL14, preventing METTL14 degradation. MeRIP-seq analysis further revealed that METTL14 specifically targeted and methylated TLRs, notably TLR4. METTL14-mediated regulation of TLR4 degradation, facilitated by YTHDF2, led to the accelerated mRNA decay of TLR4. Consequently, TLR4-mediated NF-κB signaling, a crucial component of the innate immune response, is suppressed by CSFV. Collectively, these data effectively highlight the viral evasion tactics, shedding light on potential antiviral strategies targeting METTL14 to curb CSFV infection.
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Affiliation(s)
- Jing Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Hui-xin Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Jia-huan Hu
- Guizhou Provincial Center for Disease Control and Prevention, Guiyang, China
| | - Ji-shan Bai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiao-han Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Rui-cong Sun
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Bing-qian Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Mei-zhen Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Henrique Ferreira Sucupira P, Silveira Ferreira M, Santos Coutinho-da-Silva M, Alves Bicalho K, Carolina Campi-Azevedo A, Pedro Brito-de-Sousa J, Peruhype-Magalhães V, Rios M, Konduru K, Teixeira-Carvalho A, Grazziela Alves Coelho-Dos-Reis J, Ribeiro do Valle Antonelli L, Bortolo de Rezende V, Ludolf Ribeiro de Melo F, Couto Garcia C, Carla Silva-Andrade J, Artur da Costa-Rocha I, Alves da Rocha L, Aprigio Silva V, Damasceno Pinto S, Araújo de Melo S, Guimarães Costa A, de Souza Gomes M, Rodrigues Amaral L, Luiz Lima Bertarini P, Cristina da Silva Furtado E, Vieira Pinto da Silva E, Alves Ramos B, Barros Dos Santos É, Nazaré Oliveira Freitas M, Maria Caetano Faria A, Fernando da Costa Vasconcelos P, de Souza Bastos M, Carício Martins L, Assis Martins-Filho O, Sobreira Silva Araújo M. Serotype-associated immune response and network immunoclusters in children and adults during acute Dengue virus infection. Cytokine 2023; 169:156306. [PMID: 37542834 DOI: 10.1016/j.cyto.2023.156306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/24/2023] [Accepted: 07/18/2023] [Indexed: 08/07/2023]
Abstract
The present study was designed as an exploratory investigation to characterize the overall profile of chemokines, growth factors, and pro-inflammatory/regulatory cytokines during acute DENV infection according to DENV-1, DENV-2, DENV-4 serotypes and age: children: <1-10-year-old (yo); adolescents:11-20 yo; adults 21-40 yo; and older adults: 41-75 yo. The levels of soluble immunemediators were measured in serum by high-throughput microbeads array in 636 subjects including 317 DENV-infected and 319 age-matching non-infected control (NI). Overall, most soluble mediators were increased in DENV-infected patients as compared to NI group regardless of age and DENV serotype, with high magnitude order of increase for CCL2, CXCL10, IL-1β, IFN-γ, IL1-Ra (fold change >3x), except PDGF in which no fold change was observed. Moreover, despite the age ranges, DENV-1 and DENV-4 presented increased levels of VEGF, IL-6, and TNF-α in serum but decreased levels of PDGF, while DENV-2 exhibited increased levels of CXCL8, CCL4, and IL-12. Noteworthy was that DENV-2 showed increased levels of IL-12, IL-15, IL-17, IL-4, IL-9, and IL-13, and maintained an unaltered levels of PDGF at younger ages (<1-10 yo and 11-20 yo), whereas in older ages (21-40 yo and 41-75 yo), the results showed increased levels of CCL2, IL-6, and TNF-α, but lower levels of PDGF. In general, DENV infection at younger age groups exhibited more complex network immunoclusters as compared to older age groups. Multivariate analysis revealed a clustering of DENV cases according to age for a set of soluble mediators especially in subjects infected with DENV-2 serotype. Altogether, our findings demonstrate that the profile of circulating soluble mediators differs substantially in acute DENV according to age and DENV serotypes suggesting the participation of serotype-associated immune response, which may represent a potential target for development of therapeutics and could be used to assist medical directive for precise clinical management of severe cases.
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Affiliation(s)
| | | | | | - Kelly Alves Bicalho
- Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ-Minas), Belo Horizonte, MG, Brazil
| | | | | | | | - Maria Rios
- Office of Blood Research and Review (OBRR), Center for Biologics Evaluation and Research (CBER), U.S. Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Krishnamurthy Konduru
- Office of Blood Research and Review (OBRR), Center for Biologics Evaluation and Research (CBER), U.S. Food and Drug Administration (FDA), Silver Spring, MD, USA
| | | | | | | | | | - Fernanda Ludolf Ribeiro de Melo
- Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ-Minas), Belo Horizonte, MG, Brazil; Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Cristiana Couto Garcia
- Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ-Minas), Belo Horizonte, MG, Brazil; Laboratório de Vírus Respiratórios e Sarampo, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | | | - Lucia Alves da Rocha
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, AM, Brazil; Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
| | | | | | | | - Allyson Guimarães Costa
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, AM, Brazil; Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil; Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
| | - Matheus de Souza Gomes
- Laboratório de Bioinformática e Análises Moleculares, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia, Universidade Federal de Uberlândia (UFU), Campus Patos de Minas, Minas Gerais, Brazil; Laboratório de Tecnologias Urbanas e Rurais, Faculdade de Engenharia Elétrica, Universidade Federal de Uberlândia (UFU), Campus Patos de Minas, Minas Gerais, Brazil
| | - Laurence Rodrigues Amaral
- Laboratório de Bioinformática e Análises Moleculares, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia, Universidade Federal de Uberlândia (UFU), Campus Patos de Minas, Minas Gerais, Brazil; Laboratório de Tecnologias Urbanas e Rurais, Faculdade de Engenharia Elétrica, Universidade Federal de Uberlândia (UFU), Campus Patos de Minas, Minas Gerais, Brazil
| | - Pedro Luiz Lima Bertarini
- Laboratório de Bioinformática e Análises Moleculares, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia, Universidade Federal de Uberlândia (UFU), Campus Patos de Minas, Minas Gerais, Brazil; Laboratório de Tecnologias Urbanas e Rurais, Faculdade de Engenharia Elétrica, Universidade Federal de Uberlândia (UFU), Campus Patos de Minas, Minas Gerais, Brazil
| | | | | | - Bruna Alves Ramos
- Instituto Evandro Chagas, Rodovia BR-316 KM 7 S/N, Ananindeua, PA, Brazil
| | | | | | - Ana Maria Caetano Faria
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro Fernando da Costa Vasconcelos
- Instituto Evandro Chagas, Rodovia BR-316 KM 7 S/N, Ananindeua, PA, Brazil; Departamento de Patologia, Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém, PA, Brazil
| | - Michele de Souza Bastos
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, AM, Brazil; Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil.
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Rathnakumar S, Kambhampati NSV, Saiswaroop R, Pradhan SS, Ramkumar G, Beeraka N, Muddu GK, Kumar S, Javvaji SK, Parangoankar A, Sivaramakrishnan V, Ramamurthy SS. Integrated clinical and metabolomic analysis of dengue infection shows molecular signatures associated with host-pathogen interaction in different phases of the disease. Metabolomics 2023; 19:47. [PMID: 37130982 DOI: 10.1007/s11306-023-02011-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/20/2023] [Indexed: 05/04/2023]
Abstract
PURPOSE Dengue is a mosquito vector-borne disease caused by the dengue virus, which affects 125 million people globally. The disease causes considerable morbidity. The disease, based on symptoms, is classified into three characteristic phases, which can further lead to complications in the second phase. Molecular signatures that are associated with the three phases have not been well characterized. We performed an integrated clinical and metabolomic analysis of our patient cohort and compared it with omics data from the literature to identify signatures unique to the different phases. METHODS The dengue patients are recruited by clinicians after standard-of-care diagnostic tests and evaluation of symptoms. Blood from the patients was collected. NS1 antigen, IgM, IgG antibodies, and cytokines in serum were analyzed using ELISA. Targeted metabolomics was performed using LC-MS triple quad. The results were compared with analyzed transcriptomic data from the GEO database and metabolomic data sets from the literature. RESULTS The dengue patients displayed characteristic features of the disease, including elevated NS1 levels. TNF-α was found to be elevated in all three phases compared to healthy controls. The metabolic pathways were found to be deregulated compared to healthy controls only in phases I and II of dengue patients. The pathways represent viral replication and host response mediated pathways. The major pathways include nucleotide metabolism of various amino acids and fatty acids, biotin, etc. CONCLUSION: The results show elevated TNF-α and metabolites that are characteristic of viral infection and host response. IL10 and IFN-γ were not significant, consistent with the absence of any complications.
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Affiliation(s)
- Sriram Rathnakumar
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - Naga Sai Visweswar Kambhampati
- STAR Laboratory, Central Research Instruments Facility, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - R Saiswaroop
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - Sai Sanwid Pradhan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - G Ramkumar
- Department of General Medicine, Sri Sathya Sai General Hospital, Sri Sathya Sai Institute of Higher Medical Sciences Campus, Whitefield, Bengaluru, Karnataka, 560066, India
| | - Nirmala Beeraka
- Department of General Medicine, Sri Sathya Sai General Hospital, Sri Sathya Sai Institute of Higher Medical Sciences Campus, Whitefield, Bengaluru, Karnataka, 560066, India
| | - Gopi Krishna Muddu
- Department of Pediatrics, Sri Sathya Sai General Hospital, Puttaparthi, Andhra Pradesh, 515134, India
| | - Sandeep Kumar
- Department of General Medicine, Sri Sathya Sai General Hospital, Puttaparthi, Andhra Pradesh, 515134, India
| | - Sai Kiran Javvaji
- Department of Laboratory Medicine and Cardiology, Sri Sathya Sai Institute of Higher Medical Sciences, Whitefield, Bengaluru, Karnataka, 560066, India
| | | | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India.
| | - Sai Sathish Ramamurthy
- STAR Laboratory, Central Research Instruments Facility, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India.
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Ioannidis LJ, Studniberg SI, Eriksson EM, Suwarto S, Denis D, Liao Y, Shi W, Garnham AL, Sasmono RT, Hansen DS. Integrated systems immunology approach identifies impaired effector T cell memory responses as a feature of progression to severe dengue fever. J Biomed Sci 2023; 30:24. [PMID: 37055751 PMCID: PMC10103532 DOI: 10.1186/s12929-023-00916-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/02/2023] [Indexed: 04/15/2023] Open
Abstract
BACKGROUND Typical symptoms of uncomplicated dengue fever (DF) include headache, muscle pains, rash, cough, and vomiting. A proportion of cases progress to severe dengue hemorrhagic fever (DHF), associated with increased vascular permeability, thrombocytopenia, and hemorrhages. Progression to severe dengue is difficult to diagnose at the onset of fever, which complicates patient triage, posing a socio-economic burden on health systems. METHODS To identify parameters associated with protection and susceptibility to DHF, we pursued a systems immunology approach integrating plasma chemokine profiling, high-dimensional mass cytometry and peripheral blood mononuclear cell (PBMC) transcriptomic analysis at the onset of fever in a prospective study conducted in Indonesia. RESULTS After a secondary infection, progression to uncomplicated dengue featured transcriptional profiles associated with increased cell proliferation and metabolism, and an expansion of ICOS+CD4+ and CD8+ effector memory T cells. These responses were virtually absent in cases progressing to severe DHF, that instead mounted an innate-like response, characterised by inflammatory transcriptional profiles, high circulating levels of inflammatory chemokines and with high frequencies of CD4low non-classical monocytes predicting increased odds of severe disease. CONCLUSIONS Our results suggests that effector memory T cell activation might play an important role ameliorating severe disease symptoms during a secondary dengue infection, and in the absence of that response, a strong innate inflammatory response is required to control viral replication. Our research also identified discrete cell populations predicting increased odds of severe disease, with potential diagnostic value.
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Affiliation(s)
- Lisa J Ioannidis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Stephanie I Studniberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Emily M Eriksson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Suhendro Suwarto
- Division of Tropical and Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Universitas Indonesia, Cipto Mangunkusumo National Hospital (RSCM), Jakarta, Indonesia
| | - Dionisius Denis
- Eijkman Research Center for Molecular Biology, Jakarta, Indonesia
| | - Yang Liao
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
| | - Wei Shi
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, Australia
| | - Alexandra L Garnham
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - R Tedjo Sasmono
- Eijkman Research Center for Molecular Biology, Jakarta, Indonesia
| | - Diana S Hansen
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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DDPM: A Dengue Disease Prediction and Diagnosis Model Using Sentiment Analysis and Machine Learning Algorithms. Diagnostics (Basel) 2023; 13:diagnostics13061093. [PMID: 36980401 PMCID: PMC10047105 DOI: 10.3390/diagnostics13061093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/28/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
The aedes mosquito-borne dengue viruses cause dengue fever, an arboviral disease (DENVs). In 2019, the World Health Organization forecasts a yearly occurrence of infections from 100 million to 400 million, the maximum number of dengue cases ever testified worldwide, prompting WHO to label the virus one of the world’s top ten public health risks. Dengue hemorrhagic fever can progress into dengue shock syndrome, which can be fatal. Dengue hemorrhagic fever can also advance into dengue shock syndrome. To provide accessible and timely supportive care and therapy, it is necessary to have indispensable practical instruments that accurately differentiate Dengue and its subcategories in the early stages of illness development. Dengue fever can be predicted in advance, saving one’s life by warning them to seek proper diagnosis and treatment. Predicting infectious diseases such as dengue is difficult, and most forecast systems are still in their primary stages. In developing dengue predictive models, data from microarrays and RNA-Seq have been used significantly. Bayesian inferences and support vector machine algorithms are two examples of statistical methods that can mine opinions and analyze sentiment from text. In general, these methods are not very strong semantically, and they only work effectively when the text passage inputs are at the level of the page or the paragraph; they are poor miners of sentiment at the level of the sentence or the phrase. In this research, we propose to construct a machine learning method to forecast dengue fever.
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Dagenais A, Villalba-Guerrero C, Olivier M. Trained immunity: A “new” weapon in the fight against infectious diseases. Front Immunol 2023; 14:1147476. [PMID: 36993966 PMCID: PMC10040606 DOI: 10.3389/fimmu.2023.1147476] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Innate immune cells can potentiate the response to reinfection through an innate form of immunological memory known as trained immunity. The potential of this fast-acting, nonspecific memory compared to traditional adaptive immunological memory in prophylaxis and therapy has been a topic of great interest in many fields, including infectious diseases. Amidst the rise of antimicrobial resistance and climate change—two major threats to global health—, harnessing the advantages of trained immunity compared to traditional forms of prophylaxis and therapy could be game-changing. Here, we present recent works bridging trained immunity and infectious disease that raise important discoveries, questions, concerns, and novel avenues for the modulation of trained immunity in practice. By exploring the progress in bacterial, viral, fungal, and parasitic diseases, we equally highlight future directions with a focus on particularly problematic and/or understudied pathogens.
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Affiliation(s)
- Amy Dagenais
- Department of Microbiology and Immunology, Faculty of Medicine, Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Carlos Villalba-Guerrero
- Department of Microbiology and Immunology, Faculty of Medicine, Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - Martin Olivier
- Department of Microbiology and Immunology, Faculty of Medicine, Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
- Department of Medicine, Faculty of Medicine, Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, QC, Canada
- *Correspondence: Martin Olivier,
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Garishah FM, Boahen CK, Vadaq N, Pramudo SG, Tunjungputri RN, Riswari SF, van Rij RP, Alisjahbana B, Gasem MH, van der Ven AJAM, de Mast Q. Longitudinal proteomic profiling of the inflammatory response in dengue patients. PLoS Negl Trop Dis 2023; 17:e0011041. [PMID: 36595532 PMCID: PMC9838874 DOI: 10.1371/journal.pntd.0011041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 01/13/2023] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The immunopathogenesis of dengue virus (DENV) infection remains incompletely understood. To increase our understanding of inflammatory response in non-severe dengue, we assessed longitudinal changes in the inflammatory proteome in patients with an acute DENV infection. METHODS Using a multiplex proximity extension assay (PEA), we measured relative levels of 368 inflammatory markers in plasma samples from hospitalized patients with non-severe DENV infection in the acute (n = 43) and convalescence (n = 35) phase of the infection and samples of healthy controls (n = 10). RESULTS We identified 203 upregulated and 39 downregulated proteins in acute versus convalescent plasma samples. The upregulated proteins had a strong representation of interferon (IFN) and IFN-inducible effector proteins, cytokines (e.g. IL-10, IL-33) and cytokine receptors, chemokines, pro-apoptotic proteins (e.g. granzymes) and endothelial markers. A number of differentially expressed proteins (DEPs) have not been reported in previous studies. Functional network analysis highlighted a central role for IFNγ, IL-10, IL-33 and chemokines. We identified different novel associations between inflammatory proteins and circulating concentrations of the endothelial glycocalyx disruption surrogate marker syndecan-1. Conclusion: This unbiased proteome analysis provides a comprehensive insight in the inflammatory response in DENV infection and its association with glycocalyx disruption.
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Affiliation(s)
- Fadel Muhammad Garishah
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Collins K. Boahen
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nadira Vadaq
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Setyo G. Pramudo
- Department of Internal Medicine, Diponegoro National University Hospital, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
- Department of Internal Medicine, William Booth Hospital, Semarang, Indonesia
| | - Rahajeng N. Tunjungputri
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Silvita Fitri Riswari
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ronald P. van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bachti Alisjahbana
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Hussein Gasem
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
- Department of Internal Medicine, Diponegoro National University Hospital, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - André J. A. M. van der Ven
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail:
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9
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Srivastava S, Chaudhary N, Dhembla C, Sundd M, Gupta S, Patel AK. STAT3 inhibition mediated upregulation of multiple immune response pathways in dengue infection. Virology 2023; 578:81-91. [PMID: 36473280 DOI: 10.1016/j.virol.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 11/05/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
Dengue infection is a world-wide public health threat infecting millions of people annually. Till date no specific antiviral or vaccine is available against dengue virus. Recent evidence indicates that targeting host STAT3 could prove to be an effective antiviral therapy against dengue infection. To explore the potential of STAT3 inhibition as an antiviral strategy, we utilized a STAT3 inhibitor stattic as antiviral agent and performed whole proteome analysis of mammalian cells by mass spectrometry. Differentially expressed proteins among the infected and stattic treated groups were sorted based on their fold change expression and their functional annotation studies were carried out to establish their biological networks. The results presented in the current study indicated that treatment with stattic induces several antiviral pathways to counteract dengue infection. Together with this, we also observed that treatment with stattic downregulates pathways involved in viral transcription and translation thus establishing STAT3 as a suitable target for the development of antiviral interventions. This study establishes the role of STAT3 inhibition as an alternative strategy to counteract DENV pathogenesis. Targeting STAT3 by stattic or similar molecules may help in identifying novel therapeutic interventions against DENV and probably other flaviviruses.
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Affiliation(s)
- Shikha Srivastava
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Nidhi Chaudhary
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Chetna Dhembla
- Department of Biochemistry, University of Delhi, South Campus, Benito Juarez Marg, New Delhi, 110021, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110 067, India
| | - Sunny Gupta
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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10
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Losada PX, Bosch I, Frydman GH, Gehrke L, Narváez CF. Dengue and Zika virus differential infection of human megakaryoblast MEG-01 reveals unique cellular markers. Virology 2022; 577:16-23. [PMID: 36257128 DOI: 10.1016/j.virol.2022.10.005] [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: 06/23/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/05/2022]
Abstract
Platelet count is widely used for the diagnosis and follow-up of patients with dengue. Despite its close viral structural and symptomatic homology, ZIKV infection does not typically induce significant thrombocytopenia. To determine the effect of DENV-2 and ZIKV infection on human platelet precursors we utilized MEG-01 cell line to evaluate the viral infection, viability, innate gene expression and release of platelet-like particles (PLPs). DENV-2 induced a higher proportion of cell death at 48-72 h post-infection than ZIKV. The median range of intracellular NS1+/E+ cells was 11.2% (3.3%-25%) and 5% (3%-8.1%) for DENV-2 and ZIKV, respectively (p = 0.03). MEG-01 cells infected with DENV-2 quickly expressed higher levels of IFN-β, indolamine 2,3-dioxygenase and CXCL10 mRNA compared to ZIKV infected cells and DENV-2 but not ZIKV infection reduced the number PLPs from stimulated MEG-01 cells. The results shed light into mechanisms including thrombocytopenia present in patients with DENV but absent in ZIKV infections.
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Affiliation(s)
- Paula X Losada
- División de Inmunología, Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, 410001, Huila, Colombia
| | - Irene Bosch
- Institute for Medical Engineering and Science and the Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Galit H Frydman
- Institute for Medical Engineering and Science and the Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Surgery, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Lee Gehrke
- Institute for Medical Engineering and Science and the Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Carlos F Narváez
- División de Inmunología, Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, 410001, Huila, Colombia.
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11
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Hsu JCC, Laurent-Rolle M, Pawlak JB, Xia H, Kunte A, Hee JS, Lim J, Harris LD, Wood JM, Evans GB, Shi PY, Grove TL, Almo SC, Cresswell P. Viperin triggers ribosome collision-dependent translation inhibition to restrict viral replication. Mol Cell 2022; 82:1631-1642.e6. [PMID: 35316659 PMCID: PMC9081181 DOI: 10.1016/j.molcel.2022.02.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/06/2022] [Accepted: 02/23/2022] [Indexed: 12/31/2022]
Abstract
Innate immune responses induce hundreds of interferon-stimulated genes (ISGs). Viperin, a member of the radical S-adenosyl methionine (SAM) superfamily of enzymes, is the product of one such ISG that restricts the replication of a broad spectrum of viruses. Here, we report a previously unknown antiviral mechanism in which viperin activates a ribosome collision-dependent pathway that inhibits both cellular and viral RNA translation. We found that the radical SAM activity of viperin is required for translation inhibition and that this is mediated by viperin's enzymatic product, 3'-deoxy-3',4'-didehydro-CTP (ddhCTP). Viperin triggers ribosome collisions and activates the MAPKKK ZAK pathway that in turn activates the GCN2 arm of the integrated stress response pathway to inhibit translation. The study illustrates the importance of translational repression in the antiviral response and identifies viperin as a translation regulator in innate immunity.
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Affiliation(s)
- Jack Chun-Chieh Hsu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Maudry Laurent-Rolle
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Joanna B Pawlak
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Amit Kunte
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jia Shee Hee
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jaechul Lim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lawrence D Harris
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand; The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - James M Wood
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand; The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Gary B Evans
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand; The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Institute for Drug Discovery, Galveston, TX 77555, USA
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
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12
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Sinha M, Chakraborty U, Kool A, Chakravarti M, Das S, Ghosh S, Thakur L, Khuranna A, Nayak D, Basu B, Kar S, Ray R, Das S. In-vitro antiviral action of Eupatorium perfoliatum against dengue virus infection: Modulation of mTOR signaling and autophagy. JOURNAL OF ETHNOPHARMACOLOGY 2022; 282:114627. [PMID: 34509603 DOI: 10.1016/j.jep.2021.114627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Dengue virus (DENV) is a re-emerging mosquito-borne flavivirus that has recently engendered large epidemics around the world. Consequently antivirals with effective anti-DENV therapeutic activity are urgently required. In the 18th century, Europeans, as well as native inhabitants of North America, were known to adapt the medicinal property of the common perennial plant Eupatorium perfoliatum L. to treat fever and infections. Previous studies have shown that Eupatorium perfoliatum L. possesses anti-inflammatory, anti-oxidative, anti-plasmodial, anti-bacterial and antiviral activities. However, to the best of our knowledge, no anti-DENV activity of E. perfoliatum L. has been investigated at the molecular level so far. AIM OF STUDY Here, for the first time we have attempted to study the action of E. perfoliatum extract and its few bioactive components i.e., quercetin, caffeic acid and eupafolin against wild primary clinical isolate of DENV-2 infection in an in vitro model. MATERIALS AND METHODS The presence of the bioactive components in the E. perfoliatum extract, were analyzed by HPLC- DAD. Then, CC50 as well as IC50 values of the extract and its bioactive components were measured against DENV in HepG2 cell line. After that, the antiviral activity was studied by Time of addition assay using qRT-PCR. Further, the downstream signalling action of E. perfoliatum extract, was studied by Human phosphorylation MAPK antibody array, followed by immunofluorescence microscopy. Moreover, a molecular docking analysis was done to study the binding affinity of bioactive components of E. perfoliatum extract with TIM-1 transmembrane receptor protein, which is known for viral internalization. RESULT We found that E. perfoliatum extract has marked antiviral activity during pre-treatment against DENV infection in HepG2 cell line. The extract also significantly reduced the DENV induced autophagy in HepG2 cell line as detected by LC3 II localization. The presence of different bioactive compounds in E. perfoliatum extract were confirmed by HPLC-DAD. In the bioactive components, in parallel to earlier studies, quercetin showed the most significant preventive action against DENV infection. Further, in molecular docking analysis also, quercetin showed the strongest binding affinity towards DENV membrane receptor TIM-1 protein. CONCLUSION Our findings suggests that E. perfoliatum extract has significant potential to be an anti-DENV therapeutic agent. Moreover, among the bioactive components, quercetin may have a prophylaxis role in executing the antiviral activity of E. perfoliatum extract against DENV infection.
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Affiliation(s)
- Moonmoon Sinha
- Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata-700019, India; Department of Virology, Dr. Anjali Chatterjee Regional Research Institute, Kolkata-700035, India; Department of Microbiology, Institute of Post Graduate Medical Education and Research, Kolkata-700020, India.
| | - Urmita Chakraborty
- Department of Virology, Dr. Anjali Chatterjee Regional Research Institute, Kolkata-700035, India.
| | - Anirban Kool
- Department of Virology, Dr. Anjali Chatterjee Regional Research Institute, Kolkata-700035, India.
| | - Mousumi Chakravarti
- Department of Virology, Dr. Anjali Chatterjee Regional Research Institute, Kolkata-700035, India.
| | - Souvik Das
- Department of Neuroendocrinology and Experimental Hematology, Chittaranjan National Cancer Institute, Kolkata-700026, India.
| | - Sandip Ghosh
- Department of Neuroendocrinology and Experimental Hematology, Chittaranjan National Cancer Institute, Kolkata-700026, India.
| | - Lovnish Thakur
- School of Biosciences, Apeejay Stya University, Gurugram, Haryana-122103, India.
| | - Anil Khuranna
- Central Council for Research in Homoeopathy, Ministry of AYUSH, Govt. of India, Janakpuri, New Delhi-111058, India.
| | - Debadatta Nayak
- Central Council for Research in Homoeopathy, Ministry of AYUSH, Govt. of India, Janakpuri, New Delhi-111058, India.
| | - Biswarup Basu
- Department of Neuroendocrinology and Experimental Hematology, Chittaranjan National Cancer Institute, Kolkata-700026, India.
| | - Subhabrata Kar
- School of Biosciences, Apeejay Stya University, Gurugram, Haryana-122103, India.
| | - Raja Ray
- Department of Microbiology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata-700019, India; Department of Microbiology, Institute of Post Graduate Medical Education and Research, Kolkata-700020, India.
| | - Satadal Das
- Department of Virology, Dr. Anjali Chatterjee Regional Research Institute, Kolkata-700035, India.
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13
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Sun P, Jani V, Johnson A, Cheng Y, Nagabhushana N, Williams M, Morrison BJ, Defang G. T cell and memory B cell responses in tetravalent DNA, tetravalent inactivated and tetravalent live-attenuated prime-boost dengue vaccines in rhesus macaques. Vaccine 2021; 39:7510-7520. [PMID: 34823910 DOI: 10.1016/j.vaccine.2021.10.017] [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: 04/07/2021] [Revised: 10/07/2021] [Accepted: 10/10/2021] [Indexed: 11/17/2022]
Abstract
We previously reported the efficacy of prime-boost vaccination using three tetravalent (T) dengue vaccines, DNA (TDNA), purified inactivated vaccine (TPIV), and live attenuated vaccine (TLAV). We demonstrated that the TPIV/TLAV prime-boost vaccination yielded the highest and most durable neutralizing antibodies and 100% protection to all 4 serotypes of dengue virus in rhesus macaques. This study compares gene transcription, T and B cell responses elicited by these prime-boost combinations in rhesus macaques. This study shows that the TLAV vaccine increased the expression of the innate immune genes, DDX58 and TLR7, IL1A, IL1B, TNF, CXCL8, CXCL10, IRF1, IRF7, and IFNB, more robustly as compared to TDNA and TPIV vaccines. Overall, two doses of TDNA and one dose of TLAV efficiently elicited a T cell IFNγ response to PrM/E with a comparable magnitude. Compared to TDNA vaccine, the TLAV vaccine elicited additional IFNγ response to C, NS1, NS3, and NS5. The TPIV vaccine alone produced poor IFNγ response; however, the TLAV significantly boosted its IFNγ response. The T cell response repertoire associated with TPIV/TLAV prime-boost was to both the structural C/PrM/E and NS proteins, and the T cells were multifunctional as the CD4+ T cells produced IFNγ, TNF α, and IL2 and the CD8+ cells produced TNF α and IFNγ. Opposite to the pattern of CMI, the TPIV vaccine alone elicited the highest BMem compared to the other two vaccines, which continuously remained as the highest after boosting. In summary, the TDNA and TLAV vaccines elicited a strong T cell response whereas the TPIV vaccine elicited a superior BMem. The T cell response of the TPIV vaccine was significantly boosted by the TLAV vaccine. The elevated T cell response may have provided T cell help for a sustained antibody response for TPIV/TLAV vaccines, which is required for a protective immunity against a live virus challenge.
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Affiliation(s)
- Peifang Sun
- Naval Medical Research Center, Silver Spring, MD, United States.
| | - Vihasi Jani
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Alison Johnson
- Boehringer Ingelheim Pharmaceuticals, Inc, CT, United States
| | | | - Nishith Nagabhushana
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States
| | - Maya Williams
- Chemistry Division, US Naval Research Laboratory, DC, United States
| | | | - Gabriel Defang
- Naval Medical Research Center, Silver Spring, MD, United States
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14
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Ye H, Duan X, Yao M, Kang L, Li Y, Li S, Li B, Chen L. USP18 Mediates Interferon Resistance of Dengue Virus Infection. Front Microbiol 2021; 12:682380. [PMID: 34017322 PMCID: PMC8130619 DOI: 10.3389/fmicb.2021.682380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/07/2021] [Indexed: 01/15/2023] Open
Abstract
Previous studies demonstrated that dengue virus (DENV) infection developed resistance to type-I interferons (IFNα/β). The underlying mechanism remains unclear. USP18 is a negative regulator of IFNα/β signaling, and its expression level is significantly increased following DENV infection in cell lines and patients’ blood. Our previous study revealed that increased USP18 expression contributed to the IFN-α resistance of Hepatitis C Virus (HCV). However, the role of USP18 in DENV replication and resistance to IFN-α is elusive. In this current study, we aimed to explore the role of USP18 in DENV-2 replication and resistance to IFN-α. The level of USP18 was up-regulated by plasmid transfection and down-regulated by siRNA transfection in Hela cells. USP18, IFN-α, IFN-β expression, and DENV-2 replication were monitored by qRT-PCR and Western blot. The activation of the Jak/STAT signaling pathway was assessed at three levels: p-STAT1/p-STAT2 (Western blot), interferon-stimulated response element (ISRE) activity (Dual-luciferase assay), and interferon-stimulated genes (ISGs) expression (qRT-PCR). Our data showed that DENV-2 infection increased USP18 expression in Hela cells. USP18 overexpression promoted DENV-2 replication, while USP18 silence inhibited DENV-2 replication. Silence of USP18 potentiated the anti-DENV-2 activity of IFN-α through activation of the IFN-α-mediated Jak/STAT signaling pathway as shown by increased expression of p-STAT1/p-STAT2, enhanced ISRE activity, and elevated expression of some ISGs. Our data indicated that USP18 induced by DENV-2 infection is a critical host factor utilized by DENV-2 to confer antagonism on IFN-α.
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Affiliation(s)
- Haiyan Ye
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Xiaoqiong Duan
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Min Yao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Lan Kang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Yujia Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Shilin Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China
| | - Bin Li
- Joint - Laboratory of Transfusion-Transmitted Infectious Diseases Between Institute of Blood Transfusion and Nanning Blood Center, Nanning Blood Center, Nanning, China
| | - Limin Chen
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, China.,Joint - Laboratory of Transfusion-Transmitted Infectious Diseases Between Institute of Blood Transfusion and Nanning Blood Center, Nanning Blood Center, Nanning, China.,Toronto General Research Institute, University of Toronto, Toronto, ON, Canada
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15
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[6]-Gingerol Inhibits Chikungunya Virus Infection by Suppressing Viral Replication. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6623400. [PMID: 33855075 PMCID: PMC8019639 DOI: 10.1155/2021/6623400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/22/2021] [Accepted: 03/10/2021] [Indexed: 11/18/2022]
Abstract
Chikungunya (CHIK) is a reemerging arboviral disease caused by chikungunya virus (CHIKV) infection. The disease is clinically hallmarked by prolonged debilitating joint pain. Currently, there is no specific antiviral medication nor commercial vaccine available for treatment of the disease, which makes the discovery or development of specific anti-CHIKV compounds a priority. Ginger (Zingiber officinale Roscoe) is widely known for its various health benefits. The compound [6]-gingerol is the main active ingredient found in ginger. This study sought to determine the potential of [6]-gingerol antiviral activity against CHIKV infection using in vitro human hepatocyte HepG2 cells. The antiviral activity mechanism was investigated using direct virucidal and four indirect (pre-, post-, full-, and prevention) treatment assays. [6]-Gingerol showed weak virucidal activity but significant indirect antiviral activity against CHIKV through post- and full treatment with IC50 of 0.038 mM and 0.031 mM, respectively, without showing cell cytotoxicity. The results indicated that [6]-gingerol inhibits CHIKV infection through suppression of viral replication. Together, this study confirms the potential use of [6]-gingerol for CHIK antiviral compound.
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16
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Troost B, Smit JM. Recent advances in antiviral drug development towards dengue virus. Curr Opin Virol 2020; 43:9-21. [PMID: 32795907 DOI: 10.1016/j.coviro.2020.07.009] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 01/29/2023]
Abstract
Despite the high disease burden of dengue virus, there is no approved antiviral treatment or broadly applicable vaccine to treat or prevent dengue virus infection. In the last decade, many antiviral compounds have been identified but only few have been further evaluated in pre-clinical or clinical trials. This review will give an overview of the direct-acting and host-directed antivirals identified to date. Furthermore, important parameters for further development that is, drug properties including efficacy, specificity and stability, pre-clinical animal testing, and combinational drug therapy will be discussed.
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Affiliation(s)
- Berit Troost
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jolanda M Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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17
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Chan KWK, Watanabe S, Jin JY, Pompon J, Teng D, Alonso S, Vijaykrishna D, Halstead SB, Marzinek JK, Bond PJ, Burla B, Torta F, Wenk MR, Ooi EE, Vasudevan SG. A T164S mutation in the dengue virus NS1 protein is associated with greater disease severity in mice. Sci Transl Med 2020; 11:11/498/eaat7726. [PMID: 31243154 DOI: 10.1126/scitranslmed.aat7726] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 10/11/2018] [Accepted: 12/03/2018] [Indexed: 12/14/2022]
Abstract
Dengue viruses cause severe and sudden human epidemics worldwide. The secreted form of the nonstructural protein 1 (sNS1) of dengue virus causes vascular leakage, a hallmark of severe dengue disease. Here, we reverse engineered the T164S mutation of NS1, associated with the severity of dengue epidemics in the Americas, into a dengue virus serotype 2 mildly infectious strain. The T164S mutant virus decreased infectious virus production and increased sNS1 production in mammalian cell lines and human peripheral blood mononuclear cells (PBMCs) without affecting viral RNA replication. Gene expression profiling of 268 inflammation-associated human genes revealed up-regulation of genes induced in response to vascular leakage. Infection of the mosquito vector Aedes aegypti with the T164S mutant virus resulted in increased viral load in the mosquito midgut and higher sNS1 production compared to wild-type virus infection. Infection of type 1 and 2 interferon receptor-deficient AG129 mice with the T164S mutant virus resulted in severe disease coupled with increased complement activation, tissue inflammation, and more rapid mortality compared to AG129 mice infected with wild-type virus. Molecular dynamics simulations predicted that mutant sNS1 formed stable dimers similar to the wild-type protein, whereas the hexameric mutant sNS1 was predicted to be unstable. Immunoaffinity-purified sNS1 from T164S mutant virus-infected mammalian cells was associated with different lipid classes compared to wild-type sNS1. Treatment of human PBMCs with sNS1 purified from T164S mutant virus resulted in a twofold higher production of proinflammatory cytokines, suggesting a mechanism for how mutant sNS1 may cause more severe dengue disease.
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Affiliation(s)
- Kitti Wing Ki Chan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Department of Microbiology and Immunology, 5 Science Drive 2, Singapore 117545, Singapore
| | - Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jocelyn Y Jin
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Julien Pompon
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,MIVEGEC, UMR IRD 224-CNRS5290 Université de Montpellier, Montpellier, France
| | - Don Teng
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia
| | - Sylvie Alonso
- Department of Microbiology and Immunology, 5 Science Drive 2, Singapore 117545, Singapore.,Immunology Programme, Life Science Institute, National University of Singapore, Singapore 117456, Singapore
| | - Dhanasekaran Vijaykrishna
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Victoria 3800, Australia
| | - Scott B Halstead
- Department of Preventive Medicine and Biometrics, Uniformed Services University of the Health Sciences, Bethesda, MD 20817, USA
| | - Jan K Marzinek
- Bioinformatics Institute (A*STAR), 30 Biopolis St., Singapore 138671, Singapore
| | - Peter J Bond
- Bioinformatics Institute (A*STAR), 30 Biopolis St., Singapore 138671, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore.,Department of Microbiology and Immunology, 5 Science Drive 2, Singapore 117545, Singapore
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore. .,Department of Microbiology and Immunology, 5 Science Drive 2, Singapore 117545, Singapore
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18
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Envelope protein ubiquitination drives entry and pathogenesis of Zika virus. Nature 2020; 585:414-419. [PMID: 32641828 PMCID: PMC7501154 DOI: 10.1038/s41586-020-2457-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 04/27/2020] [Indexed: 11/16/2022]
Abstract
Zika virus (ZIKV) belongs to the Flaviviridae family and is related to other viruses that cause human diseases. Unlike other flaviviruses, ZIKV infection can cause congenital neurologic disorders and replicates efficiently in reproductive tissues1–3,. Here, we show that ZIKV envelope (E) protein is K63-linked polyubiquitinated by the E3-ubiquitin ligase TRIM7. Accordingly, ZIKV replicates less efficiently in brain and reproductive tissues of Trim7−/− mice. Ubiquitinated E is present on infectious Zika virions when released from specific cell types and enhances virus attachment and entry into cells. Specifically, K63-linked polyubiquitin chains directly interact with the Tim-1 (HAVCR1) receptor, enhancing virus replication in cells and in vivo in brain tissue. Recombinant ZIKV mutants lacking ubiquitination are attenuated in human cells and in a mouse model, but not in live mosquitoes. Monoclonal antibodies against K63-linked polyubiquitin specifically neutralize ZIKV and reduce viremia in mice. Collectively, the results demonstrate that ubiquitination of ZIKV E is an important determinant of virus entry, tropism and pathogenesis.
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19
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Vila-Sanjurjo A, Juarez D, Loyola S, Torres M, Leguia M. Minority Gene Expression Profiling: Probing the Genetic Signatures of Pathogenesis Using Ribosome Profiling. J Infect Dis 2020; 221:S341-S357. [PMID: 32221545 DOI: 10.1093/infdis/jiz565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Minority Gene Expression Profiling (MGEP) refers to a scenario where the expression profiles of specific genes of interest are concentrated in a small cellular pool that is embedded within a larger, non-expressive pool. An example of this is the analysis of disease-related genes within sub-populations of blood or biopsied tissues. These systems are characterized by low signal-to-noise ratios that make it difficult, if not impossible, to uncover the desired signatures of pathogenesis in the absence of lengthy, and often problematic, technical manipulations. We have adapted ribosome profiling (RP) workflows from the Illumina to the Ion Proton platform and used them to analyze signatures of pathogenesis in an MGEP model system consisting of human cells eliciting <3% productive dengue infection. We find that RP is powerful enough to identify relevant responses of differentially expressed genes, even in the presence of significant noise. We discuss how to deal with sources of unwanted variation, and propose ways to further improve this powerful approach to the study of pathogenic signatures within MGEP systems.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE, Departamento de Bioloxía and Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Diana Juarez
- Genomics Laboratory, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru.,Virology & Emerging Infections Department, U.S. Naval Medical Research Unit No. 6, Lima, Peru
| | - Steev Loyola
- Virology & Emerging Infections Department, U.S. Naval Medical Research Unit No. 6, Lima, Peru
| | - Michael Torres
- Virology & Emerging Infections Department, U.S. Naval Medical Research Unit No. 6, Lima, Peru
| | - Mariana Leguia
- Genomics Laboratory, Pontificia Universidad Católica del Perú (PUCP), Lima, Peru.,Virology & Emerging Infections Department, U.S. Naval Medical Research Unit No. 6, Lima, Peru
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20
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Abstract
Flaviviruses are a genus of mostly arthropod-borne RNA viruses that cause a range of pathologies in humans. Basic knowledge on flaviviruses is rapidly expanding, partly due to their status as frequent emerging or re-emerging pathogens. Flaviviruses include the dengue, Zika, West Nile, tick-borne encephalitis and yellow fever viruses (DENV, ZIKV, WNV, TBEV and YFV, respectively). As is the case with other families of viruses, the success of productive infection of human cells by flaviviruses depends in part on the antiviral activity of a heterogeneous group of cellular antiviral proteins called restriction factors. Restriction factors are the effector proteins of the cell-autonomous innate response against viruses, an immune pathway that also includes virus sensors as well as intracellular and extracellular signal mediators such as type I interferons (IFN-I). In this review, I summarize recent progress toward the identification and characterization of flavivirus restriction factors. In particular, I focus on IFI6, Schlafen 11, FMRP, OAS-RNase L, RyDEN, members of the TRIM family of proteins (TRIM5α, TRIM19, TRIM56, TRIM69 and TRIM79α) and a new mechanism of action proposed for viperin. Recent and future studies on this topic will lead to a more complete picture of the flavivirus restrictome, defined as the ensemble of cellular factors with demonstrated anti-flaviviral activity.
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21
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Murphy Schafer AR, Smith JL, Pryke KM, DeFilippis VR, Hirsch AJ. The E3 Ubiquitin Ligase SIAH1 Targets MyD88 for Proteasomal Degradation During Dengue Virus Infection. Front Microbiol 2020; 11:24. [PMID: 32117091 PMCID: PMC7033647 DOI: 10.3389/fmicb.2020.00024] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/07/2020] [Indexed: 12/27/2022] Open
Abstract
The dengue virus presents a serious threat to human health globally and can cause severe, even life-threatening, illness. Dengue virus (DENV) is endemic on all continents except Antarctica, and it is estimated that more than 100 million people are infected each year. Herein, we further mine the data from a previously described screen for microRNAs (miRNAs) that block flavivirus replication. We use miR-424, a member of the miR-15/16 family, as a tool to further dissect the role of host cell proteins during DENV infection. We observed that miR-424 suppresses expression of the E3 ubiquitin ligase SIAH1, which is normally induced during dengue virus 2 (DENV2) infection through activation of the unfolded protein response (UPR). Specific siRNA-mediated knockdown of SIAH1 also results in inhibition of DENV replication, demonstrating that this target is at least partly responsible for the antiviral activity of miR-424. We further show that SIAH1 binds to and ubiquitinates the innate immune adaptor protein MyD88 and that the antiviral effect of SIAH1 knockdown is reduced in cells in which MyD88 has been deleted by CRISPR/Cas9 gene editing. Additionally, MyD88-dependent signaling, triggered either by DENV2 infection or the Toll-like receptor 7 (TLR7) ligand imiquimod, is increased in cells in which SIAH1 has been knocked down by miR-424 or a SIAH1-specific siRNA. These observations suggest an additional pathway by which DENV2 harnesses aspects of the UPR to dampen the host innate immune response and promote viral replication.
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Affiliation(s)
- Ashleigh R Murphy Schafer
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Jessica L Smith
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Kara M Pryke
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Victor R DeFilippis
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
| | - Alec J Hirsch
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, United States
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22
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Gokhale NS, McIntyre ABR, Mattocks MD, Holley CL, Lazear HM, Mason CE, Horner SM. Altered m 6A Modification of Specific Cellular Transcripts Affects Flaviviridae Infection. Mol Cell 2020; 77:542-555.e8. [PMID: 31810760 PMCID: PMC7007864 DOI: 10.1016/j.molcel.2019.11.007] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/11/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023]
Abstract
The RNA modification N6-methyladenosine (m6A) modulates mRNA fate and thus affects many biological processes. We analyzed m6A across the transcriptome following infection by dengue virus (DENV), Zika virus (ZIKV), West Nile virus (WNV), and hepatitis C virus (HCV). We found that infection by these viruses in the Flaviviridae family alters m6A modification of specific cellular transcripts, including RIOK3 and CIRBP. During viral infection, the addition of m6A to RIOK3 promotes its translation, while loss of m6A in CIRBP promotes alternative splicing. Importantly, viral activation of innate immune sensing or the endoplasmic reticulum (ER) stress response contributes to the changes in m6A in RIOK3 or CIRBP, respectively. Further, several transcripts with infection-altered m6A profiles, including RIOK3 and CIRBP, encode proteins that influence DENV, ZIKV, and HCV infection. Overall, this work reveals that cellular signaling pathways activated during viral infection lead to alterations in m6A modification of host mRNAs to regulate infection.
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Affiliation(s)
- Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27705, USA
| | - Alexa B R McIntyre
- Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Melissa D Mattocks
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher L Holley
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27705, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA
| | - Helen M Lazear
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; The HRH Prince Alwaleed Bin Talal Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA; The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27705, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27705, USA.
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23
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Zahid K, Shakoor S, Sajid HA, Afzal S, Ali L, Amin I, Shahid M, Idrees M. Advancements in developing an effective and preventive dengue vaccine. Future Virol 2020. [DOI: 10.2217/fvl-2019-0080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Every year millions of people in various tropical and subtropical regions encounter infection with dengue virus. Within the last few decades, its prevalence has increased up to 30-fold globally and presently these viruses have been transmitted in more than 100 countries. Scientists contributed to the development of tetravalent dengue vaccine by adopting numerous approaches including live vaccine, recombinant protein vaccine, DNA vaccine and virus-vectored vaccines. A vaccine should be genetically stable, equally effective against all serotypes, must be in-expensive and commercially available. Chimeric yellow fever virus-tetravalent dengue vaccine (CYD-TDV) is the first licensed vaccine developed by Sanofi Pasteur in December 2015, but this vaccine is not fully effective against different dengue virus serotypes (Sanofi Pasteur, Lyon, France). This review explores the advancements and challenges involved in the development of dengue vaccine.
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Affiliation(s)
- Khadija Zahid
- Division of Molecular Virology & Infectious Diseases, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Sana Shakoor
- Division of Molecular Virology & Infectious Diseases, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Hina Afzal Sajid
- Division of Molecular Virology & Infectious Diseases, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Division of Molecular Virology & Infectious Diseases, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Liaqat Ali
- Department of Biological Sciences, National University of Modern Sciences, Rawalpindi, Pakistan
| | - Iram Amin
- Division of Molecular Virology & Infectious Diseases, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad Shahid
- Division of Molecular Virology & Infectious Diseases, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- Division of Molecular Virology & Infectious Diseases, Centre of Excellence in Molecular Biology (CEMB), University of the Punjab, Lahore, Pakistan
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24
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Robinson M, Einav S. Towards Predicting Progression to Severe Dengue. Trends Microbiol 2020; 28:478-486. [PMID: 31982232 DOI: 10.1016/j.tim.2019.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/04/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022]
Abstract
There is an urgent need for prognostic assays to predict progression to severe dengue infection, which is a major global threat. While the majority of symptomatic dengue patients experience an acute febrile illness, 5-20% progress to severe infection associated with significant morbidity and mortality. Early monitoring and administration of supportive care reduce mortality and clinically usable biomarkers to predict severe dengue are needed. Here, we review recent discoveries of gene sets, anti-dengue antibody properties, and inflammatory markers with potential utility as predictors of disease progression. Upon larger scale validation and development of affordable sample-to-answer technologies, some of these biomarkers may be utilized to develop the first prognostic assay for improving patient care and allocating healthcare resources more effectively in dengue endemic countries.
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Affiliation(s)
- Makeda Robinson
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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25
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Li M, Liao Z, Xu Z, Zou X, Wang Y, Peng H, Li Y, Ou X, Deng Y, Guo Y, Gan W, Peng T, Chen D, Cai M. The Interaction Mechanism Between Herpes Simplex Virus 1 Glycoprotein D and Host Antiviral Protein Viperin. Front Immunol 2019; 10:2810. [PMID: 31921110 PMCID: PMC6917645 DOI: 10.3389/fimmu.2019.02810] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022] Open
Abstract
Viperin is an interferon-inducible protein that responsible for a variety of antiviral responses to different viruses. Our previous study has shown that the ribonuclease UL41 of herpes simplex virus 1 (HSV-1) can degrade the mRNA of viperin to promote HSV-1 replication. However, it is not clear whether other HSV-1 encoded proteins can regulate the function of viperin. Here, one novel viperin associated protein, glycoprotein D (gD), was identified. To verify the interaction between gD and viperin, gD and viperin expression plasmids were firstly co-transfected into COS-7 cells, and fluorescence microscope showed they co-localized at the perinuclear region, then this potential interaction was confirmed by co-immunoprecipitation (Co-IP) assays. Moreover, confocal microscopy demonstrated that gD and viperin co-localized at the Golgi body and lipid droplets. Furthermore, dual-luciferase reporter and Co-IP assays showed gD and viperin interaction leaded to the increase of IRF7-mediated IFN-β expression through promoting viperin and IRAK1 interaction and facilitating K63-linked IRAK1 polyubiquitination. Nevertheless, gD inhibited TRAF6-induced NF-κB activity by decreasing the interaction of viperin and TRAF6. In addition, gD restrained viperin-mediated interaction between IRAK1 and TRAF6. Eventually, gD and viperin interaction was corroborated to significantly inhibit the proliferation of HSV-1. Taken together, this study would open up new avenues toward delineating the function and physiological significance of gD and viperin during HSV-1 replication cycle.
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Affiliation(s)
- Meili Li
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Zongmin Liao
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China.,Department of Scientific Research and Education, Yuebei People's Hospital, Shaoguan, China
| | - Zuo Xu
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Xingmei Zou
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Yuanfang Wang
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Hao Peng
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Yiwen Li
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Xiaowen Ou
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Yangxi Deng
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Yingjie Guo
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Weidong Gan
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- State Key Laboratory of Respiratory Diseases, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China.,South China Vaccine Corporation Limited, Guangzhou, China
| | - Daixiong Chen
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Mingsheng Cai
- Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Department of Pathogenic Biology and Immunology, School of Basic Medical Science, Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
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26
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Sugiyanto Z, Yohan B, Hadisaputro S, Dharmana E, Suharti C, Djamiatun K, Rahmi FL, Sasmono RT. Inhibitory Effect of Alpha-Mangostin to Dengue Virus Replication and Cytokines Expression in Human Peripheral Blood Mononuclear Cells. NATURAL PRODUCTS AND BIOPROSPECTING 2019; 9:345-349. [PMID: 31538308 PMCID: PMC6814697 DOI: 10.1007/s13659-019-00218-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/10/2019] [Indexed: 05/22/2023]
Abstract
Massive pro-inflammatory cytokines production has been correlated with the pathogenesis of severe dengue disease. The active compound of mangosteen fruit pericarps, α-mangostin, has been commonly used as traditional medicine and dietary supplement. We examined the effect of α-mangostin against dengue virus (DENV) infection in human peripheral blood mononuclear cells (PBMC) by the measurement of virus titer and TNF-α and IFN-γ cytokines concentration post infection. Increasing concentration of α-mangostin inhibited virus replication and reduced inflammatory cytokines expression at 24- and 48-h post infection. Our results support the potential use of α-mangostin as anti-antiviral and anti-inflammatory therapies in the treatment of dengue.
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Affiliation(s)
- Zaenal Sugiyanto
- Faculty of Health Science, Dian Nuswantoro University, Jl. Imam Bonjol 270, Semarang, 50131, Indonesia
- Doctoral Program in Medical and Health Sciences, Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
| | - Benediktus Yohan
- Eijkman Institute for Molecular Biology, Ministry of Research, Technology and Higher Education, Jl. Diponegoro 69, Jakarta, 10430, Indonesia
| | - Soeharyo Hadisaputro
- Doctoral Program in Medical and Health Sciences, Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
- Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
| | - Edi Dharmana
- Doctoral Program in Medical and Health Sciences, Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
- Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
| | - Catharina Suharti
- Doctoral Program in Medical and Health Sciences, Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
- Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
| | - Kis Djamiatun
- Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
| | - Fifin L Rahmi
- Faculty of Medicine, Diponegoro University, Jl. Prof. Sudarto SH, Tembalang, Semarang, 50275, Indonesia
| | - R Tedjo Sasmono
- Eijkman Institute for Molecular Biology, Ministry of Research, Technology and Higher Education, Jl. Diponegoro 69, Jakarta, 10430, Indonesia.
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27
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Neufeldt CJ, Cortese M, Acosta EG, Bartenschlager R. Rewiring cellular networks by members of the Flaviviridae family. Nat Rev Microbiol 2019; 16:125-142. [PMID: 29430005 PMCID: PMC7097628 DOI: 10.1038/nrmicro.2017.170] [Citation(s) in RCA: 230] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Members of the Flaviviridae virus family comprise a large group of enveloped viruses with a single-strand RNA genome of positive polarity. Several genera belong to this family, including the Hepacivirus genus, of which hepatitis C virus (HCV) is the prototype member, and the Flavivirus genus, which contains both dengue virus and Zika virus. Viruses of these genera differ in many respects, such as the mode of transmission or the course of infection, which is either predominantly persistent in the case of HCV or acutely self-limiting in the case of flaviviruses. Although the fundamental replication strategy of Flaviviridae members is similar, during the past few years, important differences have been discovered, including the way in which these viruses exploit cellular resources to facilitate viral propagation. These differences might be responsible, at least in part, for the various biological properties of these viruses, thus offering the possibility to learn from comparisons. In this Review, we discuss the current understanding of how Flaviviridae viruses manipulate and usurp cellular pathways in infected cells. Specifically, we focus on comparing strategies employed by flaviviruses with those employed by hepaciviruses, and we discuss the importance of these interactions in the context of viral replication and antiviral therapies.
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Affiliation(s)
- Christopher J Neufeldt
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
| | - Eliana G Acosta
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120 Heidelberg, Germany.,German Center for Infection Research, Heidelberg Partner Site, 69120 Heidelberg, Germany
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28
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Sri Masyeni DAP, Hadi U, Kuntaman K, Yohan B, Margyaningsih NI, Sasmono RT. Expression of Four Cytokine/Chemokine Genes in Peripheral Blood Mononuclear Cells infected with Dengue Virus. INDONESIAN JOURNAL OF TROPICAL AND INFECTIOUS DISEASE 2019. [DOI: 10.20473/ijtid.v7i4.7860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Overproduction of numerous pro-inflammatory cytokines, during dengue virus (DENV) infection, has been related to plasma leakage in the vascular endothelium and studied elsewhere with conflicting results. The current study objective is to evaluate the expression of four cytokine/chemokine genes following DENV-2 infection within peripheral blood mononuclear cells (PBMC) isolated from a healthy donor. Venous blood was drawn, and PBMCs were isolated using Ficoll density gradient centrifugation. Cells were maintained in culture medium and infected with Indonesian isolate of DENV-2. Cells were harvested and followed by total RNA extraction and reverse-transcription into cDNA using oligo d(T) primers and Reverse Transcriptase enzyme system. The SYBR Green-based quantitative qRT-PCR was used to calculate the relative expression of IL-6, IL-8, IP-10 and MIP-1β- encoding genes during infection time points, compared to uninfected cell controls. The observation of the cytokine was on the 6 and 18 hours post-infection. The different expression profiles of cytokines/chemokines were observed. The up-regulation of gene expression was observed for IL-8 and IP-10. In contrast, the down-regulatory of IL-6 and MIP-1β genes expression was documented during the infection period. The cytokine IL-8 and IP-10 are potent chemoattractants in the recruitment of neutrophil, basophil, and lymphocytes in response to an infection. The highlight of this study is on the up-regulation of IL-8 and IP-10 genes expression which may confirm the roles of these chemokines in the pathogenesis of dengue infection.
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29
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Glover KKM, Gao A, Zahedi-Amiri A, Coombs KM. Vero Cell Proteomic Changes Induced by Zika Virus Infection. Proteomics 2019; 19:e1800309. [PMID: 30578658 DOI: 10.1002/pmic.201800309] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/06/2018] [Indexed: 12/12/2022]
Abstract
The re-emergence and the recent spread of the Zika virus (ZIKV) has raised significant global concerns due to lack of information in patient diagnosis and management. Thus, in addition to gaining more basic information about ZIKV biology, appropriate interventions and management strategies are being sought to control ZIKV-associated diseases and its spread. This study's objective is to identify host cell proteins that are significantly dysregulated during ZIKV infection. SOMAScan, a novel aptamer-based assay, is used to simultaneously screen >1300 host proteins to detect ZIKV-induced host protein dysregulation at multiple time points during infection. A total of 125 Vero cell host proteins, including cytokines such as CXCL11 and CCL5, interferon stimulated gene 15, and translation initiation factors EIF5A and EIF4G2, are significantly dysregulated after ZIKV infection. Bioinformatic analyses of 77 host proteins, that are significantly dysregulated ≥1.25-fold, identify several activated biological processes, including the JAK/STAT, Tec kinase, and complement cascade pathways.
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Affiliation(s)
- Kathleen K M Glover
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E OJ9, Canada.,Manitoba Centre for Proteomics & Systems Biology, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Ang Gao
- Manitoba Centre for Proteomics & Systems Biology, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Ali Zahedi-Amiri
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E OJ9, Canada.,Manitoba Centre for Proteomics & Systems Biology, Winnipeg, Manitoba, R3E 3P4, Canada
| | - Kevin M Coombs
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, R3E OJ9, Canada.,Manitoba Centre for Proteomics & Systems Biology, Winnipeg, Manitoba, R3E 3P4, Canada.,Children's Hospital Research Institute of Manitoba, Buhler Research Centre, Winnipeg, Manitoba, R3E 3P4, Canada
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NAULITA TURNIP OKTAVIANI, FITRI HAYATI RAHMA, ALAWIYAH RIZKA, YOHAN BENEDIKTUS, DENIS DIONISIUS, BOWOLAKSONO ANOM, SOEBANDRIO AMIN, SASMONO RTEDJO. Growth Characteristics of Chikungunya Virus Isolate from Indonesia in Various Human Cell Lines in vitro. MICROBIOLOGY INDONESIA 2019. [DOI: 10.5454/mi.13.1.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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31
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Virus-inclusive single-cell RNA sequencing reveals the molecular signature of progression to severe dengue. Proc Natl Acad Sci U S A 2018; 115:E12363-E12369. [PMID: 30530648 PMCID: PMC6310786 DOI: 10.1073/pnas.1813819115] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
A fraction of the 400 million people infected with dengue annually progresses to severe dengue (SD). Yet, there are currently no biomarkers to predict disease progression. We profiled the landscape of host transcripts and viral RNA in thousands of single blood cells from dengue patients prior to progressing to SD. We discovered cell type-specific immune activation and candidate predictive biomarkers. We also determined preferential virus association with specific cell populations, particularly naive B cells and monocytes. We explored immune activation of bystander cells, clonality and somatic evolution of adaptive immune repertoires, as well as viral genomics. This multifaceted approach could advance understanding of pathogenesis of any viral infection, map an atlas of infected cells, and promote the development of prognostics. Dengue virus (DENV) infection can result in severe complications. However, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that contain DENV RNA in vivo. Accordingly, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here, we applied virus-inclusive single-cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls and to characterize distinct leukocyte subtypes that harbor viral RNA (vRNA). Multiple IFN response genes, particularly MX2 in naive B cells and CD163 in CD14+ CD16+ monocytes, were up-regulated in a cell-specific manner before progression to SD. The majority of vRNA-containing cells in the blood of two patients who progressed to SD were naive IgM B cells expressing the CD69 and CXCR4 receptors and various antiviral genes, followed by monocytes. Bystander, non-vRNA–containing B cells also demonstrated immune activation, and IgG1 plasmablasts from two patients exhibited clonal expansions. Lastly, assembly of the DENV genome sequence revealed diversity at unexpected sites. This study presents a multifaceted molecular elucidation of natural dengue infection in humans with implications for any tissue and viral infection and proposes candidate biomarkers for prediction of SD.
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Zhou W, Altman RB. Data-driven human transcriptomic modules determined by independent component analysis. BMC Bioinformatics 2018; 19:327. [PMID: 30223787 PMCID: PMC6142401 DOI: 10.1186/s12859-018-2338-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 08/28/2018] [Indexed: 12/20/2022] Open
Abstract
Background Analyzing the human transcriptome is crucial in advancing precision medicine, and the plethora of over half a million human microarray samples in the Gene Expression Omnibus (GEO) has enabled us to better characterize biological processes at the molecular level. However, transcriptomic analysis is challenging because the data is inherently noisy and high-dimensional. Gene set analysis is currently widely used to alleviate the issue of high dimensionality, but the user-defined choice of gene sets can introduce biasness in results. In this paper, we advocate the use of a fixed set of transcriptomic modules for such analysis. We apply independent component analysis to the large collection of microarray data in GEO in order to discover reproducible transcriptomic modules that can be used as features for machine learning. We evaluate the usability of these modules across six studies, and demonstrate (1) their usage as features for sample classification, and also their robustness in dealing with small training sets, (2) their regularization of data when clustering samples and (3) the biological relevancy of differentially expressed features. Results We identified 139 reproducible transcriptomic modules, which we term fundamental components (FCs). In studies with less than 50 samples, FC-space classification model outperformed their gene-space counterparts, with higher sensitivity (p < 0.01). The models also had higher accuracy and negative predictive value (p < 0.01) for small data sets (less than 30 samples). Additionally, we observed a reduction in batch effects when data is clustered in the FC-space. Finally, we found that differentially expressed FCs mapped to GO terms that were also identified via traditional gene-based approaches. Conclusions The 139 FCs provide biologically-relevant summarization of transcriptomic data, and their performance in low sample settings suggest that they should be employed in such studies in order to harness the data efficiently. Electronic supplementary material The online version of this article (10.1186/s12859-018-2338-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weizhuang Zhou
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Russ B Altman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. .,Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
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Kumar VE, Cherupanakkal C, Catherine M, Kadhiravan T, Parameswaran N, Rajendiran S, Pillai AB. Endogenous gene selection for relative quantification PCR and IL6 transcript levels in the PBMC's of severe and non-severe dengue cases. BMC Res Notes 2018; 11:550. [PMID: 30071880 PMCID: PMC6071388 DOI: 10.1186/s13104-018-3620-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
Objectives Dengue viral infection ranges from dengue fever to dengue haemorrhagic fever and lethal dengue shock syndrome. Currently no means are available to monitor the progression of disease. Real time PCR based gene expression analyses are used to find potential molecular markers for effective prediction of dengue clinical outcome. The accuracy of qPCR analysis is strongly dependent on transcript normalization using stably expressed endogenous genes, which if selected imprecisely can lead to misinterpreted results. We aimed to determine the best fit for endogenous gene among six genes namely COX, ACTB, GAPDH, HMBS, HPRT and B2M for dengue viral infection cases. Gene stability was inferred from qPCR data by normalizing with two algorithms geNorm and Normfinder and the rankings generated were validated by gene expression analysis against target gene IL-6. Results Both the algorithms showed ACTB, HPRT, GAPDH as most stable genes. Normalizing with the stable genes revealed a significant fold change (p < .05) in IL-6 levels of .32, .52, .69, and .62 in non-dengue febrile illness, non severe, severe and All Dengue groups respectively compared to healthy controls. based on our study, we suggest ACTB with HPRT/GAPDH combination for normalization in qPCR for precise quantification of transcripts in dengue infected studies. Electronic supplementary material The online version of this article (10.1186/s13104-018-3620-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vigneshwari Easwar Kumar
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India
| | - Cleetus Cherupanakkal
- Department of Biochemistry, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Minna Catherine
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India
| | - Tamilarasu Kadhiravan
- Department of Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | - Narayanan Parameswaran
- Department of Pediatrics, Jawaharlal Institute of, Postgraduate Medical Education and Research, Puducherry, India
| | - Soundravally Rajendiran
- Department of Biochemistry, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India.
| | - Agieshkumar Balakrishna Pillai
- Central Inter-Disciplinary Research Facility, Sri Balaji Vidyapeeth (Deemed to be University), Puducherry, 607402, India.
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Watanabe S, Low JGH, Vasudevan SG. Preclinical Antiviral Testing for Dengue Virus Infection in Mouse Models and Its Association with Clinical Studies. ACS Infect Dis 2018; 4:1048-1057. [PMID: 29756760 DOI: 10.1021/acsinfecdis.8b00054] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
At present, there is no licensed antiviral drug against dengue virus (DENV) infection. Mouse models of DENV infection have been widely used for preclinical evaluation of antivirals. However, only in a few instances so far have the data obtained from preclinical mouse model testing been associated with data from clinical studies in humans. In this Review, we focus on the antiviral drugs targeting viral replication that have been tested in animals/humans and discuss how preclinical drug evaluation in suitable mouse/animal models may be more fruitfully used to inform early phase clinical testing.
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Affiliation(s)
- Satoru Watanabe
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Jenny Guek-Hong Low
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
- Department of Infectious Diseases, Singapore General Hospital, 20 College Road, Singapore 169856
| | - Subhash G. Vasudevan
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
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36
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Guy B. Which Dengue Vaccine Approach Is the Most Promising, and Should We Be Concerned about Enhanced Disease after Vaccination? Questions Raised by the Development and Implementation of Dengue Vaccines: Example of the Sanofi Pasteur Tetravalent Dengue Vaccine. Cold Spring Harb Perspect Biol 2018; 10:a029462. [PMID: 28716892 PMCID: PMC5983191 DOI: 10.1101/cshperspect.a029462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Dengue is a still-growing public health concern in many tropical and subtropical regions of the world. The development and implementation of an effective dengue vaccine in these regions is a high priority. This insight focuses on the expected characteristics of a safe and efficacious vaccine, referring to the clinical experience obtained during the development of the first tetravalent dengue vaccine from Sanofi Pasteur, now licensed in several endemic countries. Safety and efficacy data from both short- and long-term follow-up of large-scale efficacy studies will be discussed, as well as the next steps following vaccine introduction.
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Affiliation(s)
- Bruno Guy
- Research and Development, Sanofi Pasteur, 69007 Lyon, France
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37
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Dukhovny A, Shlomai A, Sklan EH. The antiviral protein Viperin suppresses T7 promoter dependent RNA synthesis-possible implications for its antiviral activity. Sci Rep 2018; 8:8100. [PMID: 29802323 PMCID: PMC5970183 DOI: 10.1038/s41598-018-26516-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 05/11/2018] [Indexed: 12/28/2022] Open
Abstract
Viperin is a multifunctional interferon-inducible broad-spectrum antiviral protein. Viperin belongs to the S-Adenosylmethionine (SAM) superfamily of enzymes known to catalyze a wide variety of radical-mediated reactions. However, the exact mechanism by which viperin exerts its functions is still unclear. Interestingly, for many RNA viruses viperin was shown to inhibit viral RNA accumulation by interacting with different viral non-structural proteins. Here, we show that viperin inhibits RNA synthesis by bacteriophage T7 polymerase in mammalian cells. This inhibition is specific and occurs at the RNA level. Viperin expression significantly reduced T7-mediated cytoplasmic RNA levels. The data showing that viperin inhibits the bacteriophage T7 polymerase supports the conservation of viperin’s antiviral activity between species. These results highlight the possibility that viperin might utilize a broader mechanism of inhibition. Accordingly, our results suggest a novel mechanism involving polymerase inhibition and provides a tractable system for future mechanistic studies of viperin.
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Affiliation(s)
- Anna Dukhovny
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Amir Shlomai
- Department of Medicine D and the Liver Institute, Rabin Medical Center, Beilinson Hospital, Petach-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ella H Sklan
- Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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38
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Experimental in vitro and in vivo systems for studying the innate immune response during dengue virus infections. Arch Virol 2018. [PMID: 29520688 DOI: 10.1007/s00705-018-3784-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Dengue is the most prevalent arboviral disease in humans and leads to significant morbidity and socioeconomic burden in tropical and subtropical areas. Dengue is caused by infection with any of the four closely related serotypes of dengue virus (DENV1-4) and usually manifests as a mild febrile illness, but may develop into fatal dengue hemorrhagic fever and shock syndrome. There are no specific antiviral therapies against dengue because understanding of DENV biology is limited. A tetravalent chimeric dengue vaccine, Dengvaxia, has finally been licensed for use, but its efficacy was significantly lower against DENV-2 infections and in dengue-naïve individuals. The identification of mechanisms underlying the interactions between DENV and immune responses will help to determine efficient therapeutic and preventive options. It has been well established how the innate immune system responds to DENV infection and how DENV overcomes innate antiviral defenses, however further progress in this field remains hampered by the absence of appropriate experimental dengue models. Herein, we review the available in vitro and in vivo approaches to study the innate immune responses to DENV.
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RSAD2 and AIM2 Modulate Coxsackievirus A16 and Enterovirus A71 Replication in Neuronal Cells in Different Ways That May Be Associated with Their 5' Nontranslated Regions. J Virol 2018; 92:JVI.01914-17. [PMID: 29263272 DOI: 10.1128/jvi.01914-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 12/30/2022] Open
Abstract
Coxsackievirus A16 (CV-A16) and enterovirus A71 (EV-A71) are closely related enteroviruses that cause the same hand, foot, and mouth disease (HFMD), but neurological complications occur only very rarely in CV-A16 compared to EV-A71 infections. To elucidate host responses that may be able to explain these differences, we performed transcriptomic analysis and real-time quantitative PCR (RT-qPCR) in CV-A16-infected neuroblastoma cells (SK-N-SH), and the results showed that the radical S-adenosylmethionine domain containing 2 (RSAD2) was the highest upregulated gene in the antimicrobial pathway. Increased RSAD2 expression was correlated with reduced viral replication, while RSAD2 knockdown cells were correlated with increased replication. EV-A71 replication showed no apparent correlation to RSAD2 expressions. Absent in melanoma 2 (AIM2), which is associated with pyroptotic cell death, was upregulated in EV-A71-infected neurons but not in CV-A16 infection, suggesting that the AIM2 inflammasome played a significant role in suppressing EV-A71 replication. Chimeric viruses derived from CV-A16 and EV-A71 but containing swapped 5' nontranslated regions (5' NTRs) showed that RSAD2 expression/viral replication and AIM2 expression/viral replication patterns may be linked to the 5' NTRs of parental viruses. Differences in secondary structure of internal ribosomal entry sites within the 5' NTR may be responsible for these findings. Overall, our results suggest that CV-A16 and EV-A71 elicit different host responses to infection, which may help explain the apparent lower incidence of CV-A16-associated neurovirulence in HFMD outbreaks compared to EV-A71 infection.IMPORTANCE Although coxsackievirus A16 (CV-A16) and enterovirus A17 (EV-A71) both cause hand, foot, and mouth disease, EV-A71 has emerged as a leading cause of nonpolio, enteroviral fatal encephalomyelitis among young children. The significance of our research is in the identification of the possible differing and novel mechanisms of CV-A16 and EV-A71 inhibition in neuronal cells that may impact viral neuropathogenesis. We further showed that viral 5' NTRs may play significant roles in eliciting different host response mechanisms.
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Zanini F, Pu SY, Bekerman E, Einav S, Quake SR. Single-cell transcriptional dynamics of flavivirus infection. eLife 2018; 7:32942. [PMID: 29451494 PMCID: PMC5826272 DOI: 10.7554/elife.32942] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/08/2018] [Indexed: 12/25/2022] Open
Abstract
Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage and shock or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.
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Affiliation(s)
- Fabio Zanini
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Szu-Yuan Pu
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Elena Bekerman
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Shirit Einav
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Applied Physics, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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Giraldo MI, Vargas-Cuartas O, Gallego-Gomez JC, Shi PY, Padilla-Sanabria L, Castaño-Osorio JC, Rajsbaum R. K48-linked polyubiquitination of dengue virus NS1 protein inhibits its interaction with the viral partner NS4B. Virus Res 2017; 246:1-11. [PMID: 29294313 DOI: 10.1016/j.virusres.2017.12.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/22/2017] [Accepted: 12/29/2017] [Indexed: 01/08/2023]
Abstract
Dengue virus (DENV) is a member of the Flaviviridae family, which is transmitted to mammalian species through arthropods, and causes dengue fever or severe dengue fever in humans. The DENV genome encodes for multiple nonstructural (NS) proteins including NS1. NS1 plays an essential role in replication by interacting with other viral proteins including NS4B, however how these interactions are regulated during virus infection is not known. By using bioinformatics, mass spectrometry analysis, and co-immunoprecipitation assays, here we show that DENV-NS1 is ubiquitinated on multiples lysine residues during DENV infection, including K189, a lysine residue previously shown to be important for efficient DENV replication. Data from in vitro and cell culture experiments indicate that dengue NS1 undergoes modification with K48-linked polyubiquitin chains, which usually target proteins to the proteasome for degradation. Furthermore, ubiquitinated NS1 was detected in lysates as well as in supernatants of human and mosquito infected cells. Ubiquitin deconjugation of NS1 using the deubiquitinase OTU resulted in increased interaction with the viral protein NS4B suggesting that ubiquitinated NS1 has reduced affinity for NS4B. In support of these data, a K189R mutation on NS1, which abrogates ubiquitination on amino acid residue 189 of NS1, also increased NS1-NS4B interactions. Our work describes a new mechanism of regulation of NS1-NS4B interactions and suggests that ubiquitination of NS1 may affect DENV replication.
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Affiliation(s)
- Maria Isabel Giraldo
- Centro de Investigaciones Biomédicas, Universidad del Quindío, Cra 15 Cl 12N, Armenia, Colombia; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Oscar Vargas-Cuartas
- Centro de Investigaciones Biomédicas, Universidad del Quindío, Cra 15 Cl 12N, Armenia, Colombia.
| | - Juan Carlos Gallego-Gomez
- Grupo de Medicina Molecular y de Traslación, Universidad de Antioquia, Cra. 51 D No. 62-29, Medellin, Colombia.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | | | | | - Ricardo Rajsbaum
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
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42
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Jadhav M, Nayak M, Kumar S, Venkatesh A, Patel SK, Kumar V, Sharma S, Samanta B, Deb S, Karak A, Verma S, Talukdar A, Kochar SK, Mansukhani P, Gandhi M, Srivastava S. Clinical Proteomics and Cytokine Profiling for Dengue Fever Disease Severity Biomarkers. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:665-677. [PMID: 29091011 DOI: 10.1089/omi.2017.0135] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Dengue fever (DF) is a major global health burden with a pathophysiology that is still incompletely understood. Biomarkers that predict and explain susceptibility to DF and its progression to its more severe hemorrhagic form are much needed. DF is endemic in tropical and subtropical regions of the world, with a rapidly increasing incidence of disease severity. We conducted a clinical biomarker discovery study using both a case-control and longitudinal study design. Plasma proteome alterations in patients with DF (n = 12) and dengue hemorrhagic fever (DHF, n = 24) were analyzed in comparison to healthy controls (HCs, n = 16), using the isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomics methodology (false discovery rate of 1%, ≥2 peptides). Several proteins such as the alpha-2 macroglobulin, angiotensinogen, apolipoprotein B-100, serotransferrin, and ceruloplasmin were upregulated (fold change >1.2) in all DHF cases, and downregulated in DF (fold change <0.83), compared with HCs. Plasma cytokine profiling (8 DF, 8 DHF, and 8 HC) on two consecutive time points, at day 0 (day of admission) and days 5-7, found significant elevation in IL-1RA, IL-7, TNF-α, MCP1-MCAF, and MIP-1β levels, but only in the DHF cases, which is the severe disease, and not in DF, compared with HCs (p < 0.05). These new observations on changes in the plasma proteome and cytokine profiles in patients with dengue infection identify several putative molecular leads for future biomarker development and precision medicine in relation to forecasting DF disease severity.
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Affiliation(s)
- Manali Jadhav
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Monalisha Nayak
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Swati Kumar
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Apoorva Venkatesh
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Sandip K Patel
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Vipin Kumar
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Sarthak Sharma
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Biaus Samanta
- 2 Department of Medicine, Medical College Hospital Kolkata , Kolkata, India
| | - Satarupa Deb
- 2 Department of Medicine, Medical College Hospital Kolkata , Kolkata, India
| | - Avik Karak
- 2 Department of Medicine, Medical College Hospital Kolkata , Kolkata, India
| | - Sumit Verma
- 2 Department of Medicine, Medical College Hospital Kolkata , Kolkata, India
| | - Arunansu Talukdar
- 2 Department of Medicine, Medical College Hospital Kolkata , Kolkata, India
| | - Sanjay K Kochar
- 3 Department of Medicine, Malaria Research Center , S.P. Medical College, Bikaner, India
| | - Preeti Mansukhani
- 4 P.D. Hinduja National Hospital & Medical Research Center , Mumbai, India
| | - Mayuri Gandhi
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
| | - Sanjeeva Srivastava
- 1 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India
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Transcriptional Profiling Confirms the Therapeutic Effects of Mast Cell Stabilization in a Dengue Disease Model. J Virol 2017; 91:JVI.00617-17. [PMID: 28659489 PMCID: PMC5571258 DOI: 10.1128/jvi.00617-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/22/2017] [Indexed: 12/28/2022] Open
Abstract
There are no approved therapeutics for the treatment of dengue disease despite the global prevalence of dengue virus (DENV) and its mosquito vectors. DENV infections can lead to vascular complications, hemorrhage, and shock due to the ability of DENV to infect a variety of immune and nonimmune cell populations. Increasingly, studies have implicated the host response as a major contributor to severe disease. Inflammatory products of various cell types, including responding T cells, mast cells (MCs), and infected monocytes, can contribute to immune pathology. In this study, we show that the host response to DENV infection in immunocompetent mice recapitulates transcriptional changes that have been described in human studies. We found that DENV infection strongly induced metabolic dysregulation, complement signaling, and inflammation. DENV also affected the immune cell content of the spleen and liver, enhancing NK, NKT, and CD8+ T cell activation. The MC-stabilizing drug ketotifen reversed many of these responses without suppressing memory T cell formation and induced additional changes in the transcriptome and immune cell composition of the spleen, consistent with reduced inflammation. This study provides a global transcriptional map of immune activation in DENV target organs of an immunocompetent host and supports the further development of targeted immunomodulatory strategies to treat DENV disease.IMPORTANCE Dengue virus (DENV), which causes febrile illness, is transmitted by mosquito vectors throughout tropical and subtropical regions of the world. Symptoms of DENV infection involve damage to blood vessels and, in rare cases, hemorrhage and shock. Currently, there are no targeted therapies to treat DENV infection, but it is thought that drugs that target the host immune response may be effective in limiting symptoms that result from excessive inflammation. In this study, we measured the host transcriptional response to infection in multiple DENV target organs using a mouse model of disease. We found that DENV infection induced metabolic dysregulation and inflammatory responses and affected the immune cell content of the spleen and liver. The use of the mast cell stabilization drug ketotifen reversed many of these responses and induced additional changes in the transcriptome and immune cell repertoire that contribute to decreased dengue disease.
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Hung CH, Huang CH, Wang L, Huang CC, Wu MC, Chin YY, Lin CY, Chang K, Wu DC, Chen YH. IL-28 and IL-29 as protective markers in subject with dengue fever. Med Microbiol Immunol 2017; 206:217-223. [PMID: 28238051 DOI: 10.1007/s00430-017-0498-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/09/2017] [Indexed: 12/28/2022]
Abstract
About 400 million people every year are estimated to contract dengue virus infection, which causes prolonged morbidity and sometimes mortality. Interleukin (IL)-28 and IL-29 are relatively newly discovered cytokines and play an important role in our immune defense against pathogens, especially for viral infection. In the present study, we investigated serum IL-28 and IL-29 expression and the relationship to clinical and laboratory parameters in patients with dengue virus infection. Adult patients with dengue (n = 45) and control group (n = 24) were included prospectively. Clinical symptoms and laboratory data were collected from every patient. We investigated IL-28 and IL-29 levels in serum by ELISA. The concentrations of serum IL-28 and IL-29 were significantly higher in subjects with dengue when compared to those of control group. The patients with higher serum IL-28 and IL-29 levels had significantly lower ALAT and peripheral blood neutrophil percentage, but higher peripheral platelet, total white blood cell (WBC), monocyte, and lymphocyte counts. Patients with higher serum IL-28 and IL-29 levels also had more flu-like symptoms, but less vomiting. Increased level of IL-28 and IL-29 was associated with better liver function, platelet and WBC numbers and clinical symptom in subjects with dengue and could potentially serve as a protective marker.
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Affiliation(s)
- Chih-Hsing Hung
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Pediatrics, Faculty of Pediatrics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Pediatrics, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung, Taiwan, Republic of China
| | - Chung-Hao Huang
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
| | - Lin Wang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan, Republic of China
- Chang Gung University College of Medicine, Kaohsiung, Taiwan, Republic of China
| | - Chun-Chi Huang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Laboratory Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung, Taiwan, Republic of China
- Department of Public Health, College of Health Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
| | - Meng-Chieh Wu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung, Taiwan, Republic of China
| | - Yi-Ying Chin
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Dermatology, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung, Taiwan, Republic of China
| | - Chun-Yu Lin
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Internal medicine, Faculty of Pediatrics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
| | - Ko Chang
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China.
- Department of Internal medicine, Faculty of Pediatrics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China.
- Department of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung, Taiwan, Republic of China.
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, No. 100, Tz-You 1st Road, Kaohsiung, Taiwan, Republic of China.
| | - Deng-Chyang Wu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China.
- Department of Internal medicine, Faculty of Pediatrics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China.
- Department of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung, Taiwan, Republic of China.
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, No. 100 Tz-You 1st road, Kaohsiung, 807, Taiwan, Republic of China.
| | - Yen-Hsu Chen
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Internal medicine, Faculty of Pediatrics, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China
- Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
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Cyclooxygenase-2 facilitates dengue virus replication and serves as a potential target for developing antiviral agents. Sci Rep 2017; 7:44701. [PMID: 28317866 PMCID: PMC5357798 DOI: 10.1038/srep44701] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/13/2017] [Indexed: 12/20/2022] Open
Abstract
Cyclooxygenase-2 (COX-2) is one of the important mediators of inflammation in response to viral infection, and it contributes to viral replication, for example, cytomegalovirus or hepatitis C virus replication. The role of COX-2 in dengue virus (DENV) replication remains unclear. In the present study, we observed an increased level of COX-2 in patients with dengue fever compared with healthy donors. Consistent with the clinical data, an elevated level of COX-2 expression was also observed in DENV-infected ICR suckling mice. Using cell-based experiments, we revealed that DENV-2 infection significantly induced COX-2 expression and prostaglandin E2 (PGE2) production in human hepatoma Huh-7 cells. The exogenous expression of COX-2 or PGE2 treatment dose-dependently enhanced DENV-2 replication. In contrast, COX-2 gene silencing and catalytic inhibition sufficiently suppressed DENV-2 replication. In an ICR suckling mouse model, we identified that the COX-2 inhibitor NS398 protected mice from succumbing to life-threatening DENV-2 infection. By using COX-2 promoter-based analysis and specific inhibitors against signaling molecules, we identified that NF-κB and MAPK/JNK are critical factors for DENV-2-induced COX-2 expression and viral replication. Altogether, our results reveal that COX-2 is an important factor for DENV replication and can serve as a potential target for developing therapeutic agents against DENV infection.
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Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein. Proc Natl Acad Sci U S A 2017; 114:2018-2023. [PMID: 28159892 DOI: 10.1073/pnas.1614623114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hepatitis C virus (HCV) encodes mechanisms to evade the multilayered antiviral actions of the host immune system. Great progress has been made in elucidating the strategies HCV employs to down-regulate interferon (IFN) production, impede IFN signaling transduction, and impair IFN-stimulated gene (ISG) expression. However, there is a limited understanding of the mechanisms governing how viral proteins counteract the antiviral functions of downstream IFN effectors due to the lack of an efficient approach to identify such interactions systematically. To study the mechanisms by which HCV antagonizes the IFN responses, we have developed a high-throughput profiling platform that enables mapping of HCV sequences critical for anti-IFN function at high resolution. Genome-wide profiling performed with a 15-nt insertion mutant library of HCV showed that mutations in the p7 region conferred high levels of IFN sensitivity, which could be alleviated by the expression of WT p7 protein. This finding suggests that p7 protein of HCV has an immune evasion function. By screening a liver-specific ISG library, we identified that IFI6-16 significantly inhibits the replication of p7 mutant viruses without affecting WT virus replication. In contrast, knockout of IFI6-16 reversed the IFN hypersensitivity of p7 mutant virus. In addition, p7 was found to be coimmunoprecipitated with IFI6-16 and to counteract the function of IFI6-16 by depolarizing the mitochondria potential. Our data suggest that p7 is a critical immune evasion protein that suppresses the antiviral IFN function by counteracting the function of IFI6-16.
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Oliveira RADS, Silva MMCD, Calzavara-Silva CE, Silva AM, Cordeiro MT, Moura PMMFD, Baptista PN, Marques ETDA, Gil LHVG. Primary dengue haemorrhagic fever in patients from northeast of Brazil is associated with high levels of interferon-β during acute phase. Mem Inst Oswaldo Cruz 2017; 111:378-84. [PMID: 27223651 PMCID: PMC4909036 DOI: 10.1590/0074-02760150453] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/29/2016] [Indexed: 01/05/2023] Open
Abstract
Dengue is an acute febrile disease caused by the mosquito-borne dengue virus (DENV) that according to clinical manifestations can be classified as asymptomatic, mild or severe dengue. Severe dengue cases have been associated with an unbalanced immune response characterised by an over secretion of inflammatory cytokines. In the present study we measured type I interferon (IFN-I) transcript and circulating levels in primary and secondary DENV infected patients. We observed that dengue fever (DF) and dengue haemorrhagic fever (DHF) patients express IFN-I differently. While DF and DHF patients express interferon-α similarly (52,71 ± 7,40 and 49,05 ± 7,70, respectively), IFN- β were associated with primary DHF patients. On the other hand, secondary DHF patients were not able to secrete large amounts of IFN- β which in turn may have influenced the high-level of viraemia. Our results suggest that, in patients from our cohort, infection by DENV serotype 3 elicits an innate response characterised by higher levels of IFN- β in the DHF patients with primary infection, which could contribute to control infection evidenced by the low-level of viraemia in these patients. The present findings may contribute to shed light in the role of innate immune response in dengue pathogenesis.
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Affiliation(s)
- Renato Antônio Dos Santos Oliveira
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife PE , Brasil, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
| | - Mayara Marques Carneiro da Silva
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife PE , Brasil, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
| | - Carlos Eduardo Calzavara-Silva
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Centro de Pesquisas René Rachou, Departamento de Imunologia, Laboratório de Imunologia Celular e Molecular, Belo Horizonte MG , Brasil, Fundação Oswaldo Cruz, Centro de Pesquisas René Rachou, Departamento de Imunologia, Laboratório de Imunologia Celular e Molecular, Belo Horizonte, MG, Brasil
| | - Ana Maria Silva
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife PE , Brasil, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
| | - Marli Tenório Cordeiro
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife PE , Brasil, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
| | - Patrícia Muniz Mendes Freire de Moura
- Universidade de Pernambuco, Universidade de Pernambuco, Instituto de Ciências Biológicas, Recife PE , Brasil, Universidade de Pernambuco, Instituto de Ciências Biológicas, Recife, PE, Brasil
| | - Paulo Neves Baptista
- Universidade de Pernambuco, Universidade de Pernambuco, Faculdade de Ciências Médicas, Recife PE , Brasil, Universidade de Pernambuco, Faculdade de Ciências Médicas, Recife, PE, Brasil
| | - Ernesto Torres de Azevedo Marques
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife PE , Brasil, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil.,University of Pittsburgh, Center for Vaccine Research, Department of Infectious Diseases and Microbiology, Pittsburgh PA , US, University of Pittsburgh, Center for Vaccine Research, Department of Infectious Diseases and Microbiology, Pittsburgh, PA, US
| | - Laura Helena Vega Gonzales Gil
- Fundação Oswaldo Cruz, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife PE , Brasil, Fundação Oswaldo Cruz, Centro de Pesquisas Aggeu Magalhães, Departamento de Virologia, Recife, PE, Brasil
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Giovannoni F, Hemmerich P, García CC. How do host restriction factors influence dengue virus replication? Future Virol 2016. [DOI: 10.2217/fvl-2016-0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Federico Giovannoni
- Laboratorio de Estrategias Antivirales, Departamento de Química Biológica (QB), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA) – Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Peter Hemmerich
- Leibniz Institute on Aging – Fritz-Lipman-Institut, Jena, Germany
| | - Cybele Carina García
- Laboratorio de Estrategias Antivirales, Departamento de Química Biológica (QB), Facultad de Ciencias Exactas y Naturales (FCEyN), Universidad de Buenos Aires (UBA) – Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Rabelo K, Trugilho MRO, Costa SM, Pereira BAS, Moreira OC, Ferreira ATS, Carvalho PC, Perales J, Alves AMB. The effect of the dengue non-structural 1 protein expression over the HepG2 cell proteins in a proteomic approach. J Proteomics 2016; 152:339-354. [PMID: 27826075 DOI: 10.1016/j.jprot.2016.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 10/14/2016] [Accepted: 11/01/2016] [Indexed: 01/01/2023]
Abstract
Dengue is an important mosquito borne viral disease in the world. Dengue virus (DENV) encodes a polyprotein, which is cleaved in ten proteins, including the non-structural protein 1 (NS1). In this work, we analyzed the effect of NS1 expression in one hepatic cell line, HepG2, through a shotgun proteomic approach. Cells were transfected with pcENS1 plasmid, which encodes the DENV2 NS1 protein, or the controls pcDNA3 (negative control) and pMAXGFP (GFP, a protein unrelated to dengue). Expression of NS1 was detected by immunofluorescence, western blot and flow cytometry. We identified 14,138 peptides that mapped to 4,756 proteins in all analyzed conditions. We found 41 and 81 differentially abundant proteins when compared to cells transfected with plasmids pcDNA3 and pMAXGFP, respectively. Besides, 107 proteins were detected only in the presence of NS1. We identified clusters of proteins involved mainly in mRNA process and viral RNA replication. Down regulation expression of one protein (MARCKS), identified by the proteomic analysis, was also confirmed by real time PCR in HepG2 cells infected with DENV2. Identification of proteins modulated by the presence of NS1 may improve our understanding of its role in virus infection and pathogenesis, contributing to development of new therapies and vaccines. BIOLOGICAL SIGNIFICANCE Dengue is an important viral disease, with epidemics in tropical and subtropical regions of the world. The disease is complex, with different manifestations, in which the liver is normally affected. The NS1 is found in infected cells associated with plasma membrane and secreted into the circulation as a soluble multimer. This protein is essential for virus viability, although its function is not elucidated. Some reports indicate that the NS1 can be used as a protective antigen for the development of a dengue vaccine, while others suggest its involvement in viral pathogenesis. In this work, we report an in-depth comprehensive proteomic profiling resulting from the presence of NS1 in HepG2 cells. These results can contribute to a better understanding of the NS1 role during infection.
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Affiliation(s)
- Kíssila Rabelo
- Laboratory of Biotechnology and Physiology of Viral Infections, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Monique R O Trugilho
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Simone M Costa
- Laboratory of Biotechnology and Physiology of Viral Infections, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Bernardo A S Pereira
- Laboratory of Biotechnology and Physiology of Viral Infections, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Otacílio C Moreira
- Laboratory of Molecular Biology and Endemic Diseases, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - André T S Ferreira
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Paulo C Carvalho
- Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil
| | - Jonas Perales
- Laboratory of Toxinology, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Ada M B Alves
- Laboratory of Biotechnology and Physiology of Viral Infections, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
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Afroz S, Giddaluru J, Abbas MM, Khan N. Transcriptome meta-analysis reveals a dysregulation in extra cellular matrix and cell junction associated gene signatures during Dengue virus infection. Sci Rep 2016; 6:33752. [PMID: 27651116 PMCID: PMC5030657 DOI: 10.1038/srep33752] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 09/02/2016] [Indexed: 12/28/2022] Open
Abstract
Dengue Viruses (DENVs) cause one of the most prevalent arthropod-borne viral diseases affecting millions of people worldwide. Identification of genes involved in DENV pathogenesis would help in deciphering molecular mechanisms responsible for the disease progression. Here, we carried out a meta-analysis of publicly available gene expression data of dengue patients and further validated the meta-profile using in-vitro infection in THP-1 cells. Our findings reveal that DENV infection modulates expression of several genes and signalling pathways including interferons, detoxification of ROS and viral assembly. Interestingly, we have identified novel gene signatures comprising of INADL/PATJ and CRTAP (Cartilage Associated Protein), which were significantly down-regulated across all patient data sets as well as in DENV infected THP-1 cells. PATJ and CRTAP genes are involved in maintaining cell junction integrity and collagen assembly (extracellular matrix component) respectively, which together play a crucial role in cell-cell adhesion. Our results categorically reveal that overexpression of CRTAP and PATJ genes restrict DENV infection, thereby suggesting a critical role of these genes in DENV pathogenesis. Conclusively, these findings emphasize the utility of meta-analysis approach in identifying novel gene signatures that might provide mechanistic insights into disease pathogenesis and possibly lead towards the development of better therapeutic interventions.
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Affiliation(s)
- Sumbul Afroz
- School of Life Sciences, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Jeevan Giddaluru
- School of Life Sciences, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Mohd Manzar Abbas
- School of Life Sciences, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad-500046, Telangana, India
| | - Nooruddin Khan
- School of Life Sciences, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad-500046, Telangana, India
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