1
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Involvement of host microRNAs in flavivirus-induced neuropathology: An update. J Biosci 2022. [PMID: 36222134 PMCID: PMC9425815 DOI: 10.1007/s12038-022-00288-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flaviviruses are a spectrum of vector-borne RNA viruses that cause potentially severe diseases in humans including encephalitis, acute-flaccid paralysis, cognitive disorders and foetal abnormalities. Japanese encephalitis virus (JEV), Zika virus (ZIKV), West Nile virus (WNV) and Dengue virus (DENV) are globally emerging pathogens that lead to epidemics and outbreaks with continued transmission to newer geographical areas over time. In the past decade, studies have focussed on understanding the pathogenic mechanisms of these viruses in a bid to alleviate their disease burden. MicroRNAs (miRNAs) are short single-stranded RNAs that have emerged as master-regulators of cellular gene expression. The dynamics of miRNAs within a cell have the capacity to modulate hundreds of genes and, consequently, their physiological manifestation. Increasing evidence suggests their role in host response to disease and infection including cell survival, intracellular viral replication and immune activation. In this review, we aim to comprehensively update published evidence on the role of miRNAs in host cells infected with the common neurotropic flaviviruses, with an increased focus on neuropathogenic mechanisms. In addition, we briefly cover therapeutic advancements made in the context of miRNA-based antiviral strategies.
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2
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Cheng J, Lin Y, Xu L, Chen K, Li Q, Xu K, Ning L, Kang J, Cui T, Huang Y, Zhao X, Wang D, Li Y, Su X, Yang B. ViRBase v3.0: a virus and host ncRNA-associated interaction repository with increased coverage and annotation. Nucleic Acids Res 2022; 50:D928-D933. [PMID: 34723320 PMCID: PMC8728225 DOI: 10.1093/nar/gkab1029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/15/2022] Open
Abstract
As a means to aid in the investigation of viral infection mechanisms and identification of more effective antivirus targets, the availability of a source which continually collects and updates information on the virus and host ncRNA-associated interaction resources is essential. Here, we update the ViRBase database to version 3.0 (http://www.virbase.org/ or http://www.rna-society.org/virbase/). This update represents a major revision: (i) the total number of interaction entries is now greater than 820,000, an approximately 70-fold increment, involving 116 virus and 36 host organisms, (ii) it supplements and provides more details on RNA annotations (including RNA editing, RNA localization and RNA modification), ncRNA SNP and ncRNA-drug related information and (iii) it provides two additional tools for predicting binding sites (IntaRNA and PRIdictor), a visual plug-in to display interactions and a website which is optimized for more practical and user-friendly operation. Overall, ViRBase v3.0 provides a more comprehensive resource for virus and host ncRNA-associated interactions enabling researchers a more effective means for investigation of viral infections.
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Affiliation(s)
- Jun Cheng
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital), Foshan 528000, China
| | - Yunqing Lin
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Linfu Xu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kechen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qi Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Kaixin Xu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lin Ning
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Juanjuan Kang
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital), Foshan 528000, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yan Huang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaoyang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
| | - Yanhui Li
- Institute of Cardiovascular Sciences and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Peking University Health Science Center, Beijing, PR China
| | - Xi Su
- Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University (Foshan Maternity & Child Healthcare Hospital), Foshan 528000, China
| | - Bin Yang
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
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3
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da Rosa RL, Yang TS, Tureta EF, de Oliveira LR, Moraes ANS, Tatara JM, Costa RP, Borges JS, Alves CI, Berger M, Guimarães JA, Santi L, Beys-da-Silva WO. SARSCOVIDB-A New Platform for the Analysis of the Molecular Impact of SARS-CoV-2 Viral Infection. ACS OMEGA 2021; 6:3238-3243. [PMID: 33553941 PMCID: PMC7839156 DOI: 10.1021/acsomega.0c05701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/13/2021] [Indexed: 05/07/2023]
Abstract
The COVID-19 pandemic caused by the new coronavirus (SARS-CoV-2) has become a global emergency issue for public health. This threat has led to an acceleration in related research and, consequently, an unprecedented volume of clinical and experimental data that include changes in gene expression resulting from infection. The SARS-CoV-2 infection database (SARSCOVIDB: https://sarscovidb.org/) was created to mitigate the difficulties related to this scenario. The SARSCOVIDB is an online platform that aims to integrate all differential gene expression data, at messenger RNA and protein levels, helping to speed up analysis and research on the molecular impact of COVID-19. The database can be searched from different experimental perspectives and presents all related information from published data, such as viral strains, hosts, methodological approaches (proteomics or transcriptomics), genes/proteins, and samples (clinical or experimental). All information was taken from 24 articles related to analyses of differential gene expression out of 5,554 COVID-19/SARS-CoV-2-related articles published so far. The database features 12,535 genes whose expression has been identified as altered due to SARS-CoV-2 infection. Thus, the SARSCOVIDB is a new resource to support the health workers and the scientific community in understanding the pathogenesis and molecular impact caused by SARS-CoV-2.
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Affiliation(s)
- Rafael Lopes da Rosa
- Programa de Pós-Graduação
em Biologia Celular e Molecular, Universidade
Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio
43431, Porto Alegre, Rio
Grande do Sul 91501-970, Brasil
| | - Tung Sheng Yang
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga 2752, Porto
Alegre, Rio Grande do Sul 90610-000, Brasil
| | - Emanuela Fernanda Tureta
- Programa de Pós-Graduação
em Biologia Celular e Molecular, Universidade
Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio
43431, Porto Alegre, Rio
Grande do Sul 91501-970, Brasil
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga 2752, Porto
Alegre, Rio Grande do Sul 90610-000, Brasil
| | | | - Amanda Naiara Silva Moraes
- Programa de Pós-Graduação
em Biologia Celular e Molecular, Universidade
Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio
43431, Porto Alegre, Rio
Grande do Sul 91501-970, Brasil
| | - Juliana Miranda Tatara
- Programa de Pós-Graduação
em Biologia Celular e Molecular, Universidade
Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio
43431, Porto Alegre, Rio
Grande do Sul 91501-970, Brasil
| | - Renata Pereira Costa
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga 2752, Porto
Alegre, Rio Grande do Sul 90610-000, Brasil
| | - Júlia Spier Borges
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga 2752, Porto
Alegre, Rio Grande do Sul 90610-000, Brasil
| | - Camila Innocente Alves
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga 2752, Porto
Alegre, Rio Grande do Sul 90610-000, Brasil
| | - Markus Berger
- Centro de Pesquisa
Experimental, Hospital de Clínicas
de Porto Alegre, Rua
Ramiro Barcelos, 2350, Porto Alegre, Rio Grande do Sul 90035-903, Brasil
| | - Jorge Almeida Guimarães
- Centro de Pesquisa
Experimental, Hospital de Clínicas
de Porto Alegre, Rua
Ramiro Barcelos, 2350, Porto Alegre, Rio Grande do Sul 90035-903, Brasil
| | - Lucélia Santi
- Programa de Pós-Graduação
em Biologia Celular e Molecular, Universidade
Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio
43431, Porto Alegre, Rio
Grande do Sul 91501-970, Brasil
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga 2752, Porto
Alegre, Rio Grande do Sul 90610-000, Brasil
| | - Walter Orlando Beys-da-Silva
- Programa de Pós-Graduação
em Biologia Celular e Molecular, Universidade
Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, prédio
43431, Porto Alegre, Rio
Grande do Sul 91501-970, Brasil
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga 2752, Porto
Alegre, Rio Grande do Sul 90610-000, Brasil
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4
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Chetta M, Tarsitano M, Vicari L, Saracino A, Bukvic N. In Silico Analysis of Possible Interaction between Host Genomic Transcription Factors (TFs) and Zika Virus (ZikaSPH2015) Strain with Combinatorial Gene Regulation; Virus Versus Host-The Game Reloaded. Pathogens 2021; 10:pathogens10010069. [PMID: 33466592 PMCID: PMC7828653 DOI: 10.3390/pathogens10010069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 12/30/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
In silico analysis is a promising approach for understanding biological events in complex diseases. Herein we report on the innovative computational workflow allowed to highlight new direct interactions between human transcription factors (TFs) and an entire genome of virus ZikaSPH2015 strain in order to identify the occurrence of specific motifs on a genomic Zika Virus sequence that is able to bind and, therefore, sequester host’s TFs. The analysis pipeline was performed using different bioinformatics tools available online (free of charge). According to obtained results of this in silico analysis, it is possible to hypothesize that these TFs binding motifs might be able to explain the complex and heterogeneous phenotype presentation in Zika-virus-affected fetuses/newborns, as well as the less severe condition in adults. Moreover, the proposed in silico protocol identified thirty-three different TFs identical to the distribution of TFBSs (Transcription Factor Binding Sites) on ZikaSPH2015 strain, potentially able to influence genes and pathways with biological functions confirming that this approach could find potential answers on disease pathogenesis.
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Affiliation(s)
- Massimiliano Chetta
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
- Correspondence:
| | - Marina Tarsitano
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
| | - Laura Vicari
- U.O.C. Genetica Medica e di Laboratorio, Ospedale Antonio Cardarelli, 80131 Napoli, Italy; (M.T.); (L.V.)
| | - Annalisa Saracino
- Clinica di Malattie Infettive, Dipartimento di Scienze Biomediche ed Oncologia Umana, Università degli Studi “Aldo Moro” di Bari, 70124 Bari, Italy;
| | - Nenad Bukvic
- Genetica Medica, Azienda Ospedaliero Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy;
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5
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Lin Y, Liu T, Cui T, Wang Z, Zhang Y, Tan P, Huang Y, Yu J, Wang D. RNAInter in 2020: RNA interactome repository with increased coverage and annotation. Nucleic Acids Res 2020; 48:D189-D197. [PMID: 31906603 PMCID: PMC6943043 DOI: 10.1093/nar/gkz804] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 01/23/2023] Open
Abstract
Research on RNA-associated interactions has exploded in recent years, and increasing numbers of studies are not limited to RNA-RNA and RNA-protein interactions but also include RNA-DNA/compound interactions. To facilitate the development of the interactome and promote understanding of the biological functions and molecular mechanisms of RNA, we updated RAID v2.0 to RNAInter (RNA Interactome Database), a repository for RNA-associated interactions that is freely accessible at http://www.rna-society.org/rnainter/ or http://www.rna-society.org/raid/. Compared to RAID v2.0, new features in RNAInter include (i) 8-fold more interaction data and 94 additional species; (ii) more definite annotations organized, including RNA editing/localization/modification/structure and homology interaction; (iii) advanced functions including fuzzy/batch search, interaction network and RNA dynamic expression and (iv) four embedded RNA interactome tools: RIscoper, IntaRNA, PRIdictor and DeepBind. Consequently, RNAInter contains >41 million RNA-associated interaction entries, involving more than 450 thousand unique molecules, including RNA, protein, DNA and compound. Overall, RNAInter provides a comprehensive RNA interactome resource for researchers and paves the way to investigate the regulatory landscape of cellular RNAs.
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Affiliation(s)
- Yunqing Lin
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Tianyuan Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Tianyu Cui
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhao Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yuncong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Puwen Tan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yan Huang
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, China
| | - Jia Yu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry & Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing 100730, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan 528308, China
- Dermatology Hospital, Southern Medical University, Guangzhou 510091, China
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 611731, China
- To whom correspondence should be addressed. Tel: +86 20 61648279; Fax: +86 20 61648279; or
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6
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Rosa RL, Santi L, Berger M, Tureta EF, Quincozes-Santos A, Souza DO, Guimarães JA, Beys-da-Silva WO. ZIKAVID-Zika virus infection database: a new platform to analyze the molecular impact of Zika virus infection. J Neurovirol 2019; 26:77-83. [PMID: 31512145 DOI: 10.1007/s13365-019-00799-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022]
Abstract
The recent outbreak of Zika virus (ZIKV) in Brazil and other countries globally demonstrated the relevance of ZIKV studies. During and after this outbreak, there was an intense increase in scientific production on ZIKV infections, especially toward alterations promoted by the infection and related to clinical outcomes. Considering this massive amount of new data, mainly thousands of genes and proteins whose expression is impacted by ZIKV infection, the ZIKA Virus Infection Database (ZIKAVID) was created. ZIKAVID is an online database that comprises all genes or proteins, and associated information, for which expression was experimentally measured and found to be altered after ZIKV infection. The database, available at https://zikavid.org, contains 16,984 entries of gene expression measurements from a total of 7348 genes. It allows users to easily perform searches for different experimental hosts (cell lines, tissues, and animal models), ZIKV strains (African, Asian, and Brazilian), and target molecules (messenger RNA [mRNA] and protein), among others, used in differential expression studies regarding ZIKV infection. In this way, the ZIKAVID will serve as an additional and important resource to improve the characterization of the molecular impact and pathogenesis associated with ZIKV infection.
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Affiliation(s)
- Rafael L Rosa
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752 suit 709, Porto Alegre, RS, Brazil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lucélia Santi
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752 suit 709, Porto Alegre, RS, Brazil.,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Markus Berger
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Emanuela F Tureta
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752 suit 709, Porto Alegre, RS, Brazil
| | - André Quincozes-Santos
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Diogo O Souza
- Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Jorge A Guimarães
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Walter O Beys-da-Silva
- Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Av. Ipiranga, 2752 suit 709, Porto Alegre, RS, Brazil. .,Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
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7
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Chesnut M, Muñoz LS, Harris G, Freeman D, Gama L, Pardo CA, Pamies D. In vitro and in silico Models to Study Mosquito-Borne Flavivirus Neuropathogenesis, Prevention, and Treatment. Front Cell Infect Microbiol 2019; 9:223. [PMID: 31338335 PMCID: PMC6629778 DOI: 10.3389/fcimb.2019.00223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/11/2019] [Indexed: 01/07/2023] Open
Abstract
Mosquito-borne flaviviruses can cause disease in the nervous system, resulting in a significant burden of morbidity and mortality. Disease models are necessary to understand neuropathogenesis and identify potential therapeutics and vaccines. Non-human primates have been used extensively but present major challenges. Advances have also been made toward the development of humanized mouse models, but these models still do not fully represent human pathophysiology. Recent developments in stem cell technology and cell culture techniques have allowed the development of more physiologically relevant human cell-based models. In silico modeling has also allowed researchers to identify and predict transmission patterns and discover potential vaccine and therapeutic candidates. This review summarizes the research on in vitro and in silico models used to study three mosquito-borne flaviviruses that cause neurological disease in humans: West Nile, Dengue, and Zika. We also propose a roadmap for 21st century research on mosquito-borne flavivirus neuropathogenesis, prevention, and treatment.
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Affiliation(s)
- Megan Chesnut
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Laura S. Muñoz
- Division of Neuroimmunology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Neuroviruses Emerging in the Americas Study, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Georgina Harris
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Dana Freeman
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Lucio Gama
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Carlos A. Pardo
- Division of Neuroimmunology, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Neuroviruses Emerging in the Americas Study, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David Pamies
- Center for Alternatives to Animal Testing, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States,Department of Physiology, University of Lausanne, Lausanne, Switzerland,*Correspondence: David Pamies
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8
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Gharbaran R, Somenarain L. Putative Cellular and Molecular Roles of Zika Virus in Fetal and Pediatric Neuropathologies. Pediatr Dev Pathol 2019; 22:5-21. [PMID: 30149771 DOI: 10.1177/1093526618790742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the World Health Organization declared an end to the recent Zika virus (ZIKV) outbreak and its association with adverse fetal and pediatric outcome, on November 18, 2016, the virus still remains a severe public health threat. Laboratory experiments thus far supported the suspicions that ZIKV is a teratogenic agent. Evidence indicated that ZIKV infection cripples the host cells' innate immune responses, allowing productive replication and potential dissemination of the virus. In addition, studies suggest potential transplacental passage of the virus and subsequent selective targeting of neural progenitor cells (NPCs). Depletion of NPCs by ZIKV is associated with restricted brain growth. And while microcephaly can result from infection at any gestational stages, the risk is greater during the first trimester. Although a number of recent studies revealed some of specific molecular and cellular roles of ZIKV proteins of this mosquito-borne flavivirus, the mechanisms by which it produces it suspected pathophysiological effects are not completely understood. Thus, this review highlights the cellular and molecular evidence that implicate ZIKV in fetal and pediatric neuropathologies.
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Affiliation(s)
- Rajendra Gharbaran
- 1 Department of Biological Sciences, Bronx Community College, The City University of New York, Bronx, New York
| | - Latchman Somenarain
- 1 Department of Biological Sciences, Bronx Community College, The City University of New York, Bronx, New York
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9
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Abstract
One of the most important resources for researchers of noncoding RNAs is the information available in public databases spread over the internet. However, the effective exploration of this data can represent a daunting task, given the large amount of databases available and the variety of stored data. This chapter describes a classification of databases based on information source, type of RNA, source organisms, data formats, and the mechanisms for information retrieval, detailing the relevance of each of these classifications and its usability by researchers. This classification is used to update a 2012 review, indexing now more than 229 public databases. This review will include an assessment of the new trends for ncRNA research based on the information that is being offered by the databases. Additionally, we will expand the previous analysis focusing on the usability and application of these databases in pathogen and disease research. Finally, this chapter will analyze how currently available database schemas can help the development of new and improved web resources.
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10
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Arora N, Banerjee AK, Narasu ML. Zika outbreak aftermath: status, progress, concerns and new insights. Future Virol 2018. [DOI: 10.2217/fvl-2018-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Zika, a neurotrophic virus belonging to Flaviviridae family of viruses and transmitted by vector mosquitoes of Aedes species, took the world by storm during its recent outbreak. Its spread to newer territories, unprecedented pace of transmission, lack of existing therapeutic agents and vaccines and an empty drug pipeline raised an alarm. Uncertainty about full spectrum of diseases and its long-term consequences, newly discovered modes of transmission and controversies over vector status of mosquito species like Culex quinquefasciatus led to layers of complexity and presented new hurdles and challenges in Zika virus research. This review summarizes the progress and updates of efforts, concerns, financial burden and available resources in light of newly acquired knowledge in Zika virus research.
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Affiliation(s)
- Neelima Arora
- Centre for Biotechnology, Institute of Science & Technology (Autonomous), Jawaharlal Nehru Technological University-Hyderabad, Kukatpally, Hyderabad 500085, Telangana, India
| | - Amit K Banerjee
- Biology Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana, India
| | - Mangamoori L Narasu
- Centre for Biotechnology, Institute of Science & Technology (Autonomous), Jawaharlal Nehru Technological University-Hyderabad, Kukatpally, Hyderabad 500085, Telangana, India
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11
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Drury RE, O'Connor D, Pollard AJ. The Clinical Application of MicroRNAs in Infectious Disease. Front Immunol 2017; 8:1182. [PMID: 28993774 PMCID: PMC5622146 DOI: 10.3389/fimmu.2017.01182] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/06/2017] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are short single-stranded non-coding RNA sequences that posttranscriptionally regulate up to 60% of protein encoding genes. Evidence is emerging that miRNAs are key mediators of the host response to infection, predominantly by regulating proteins involved in innate and adaptive immune pathways. miRNAs can govern the cellular tropism of some viruses, are implicated in the resistance of some individuals to infections like HIV, and are associated with impaired vaccine response in older people. Not surprisingly, pathogens have evolved ways to undermine the effects of miRNAs on immunity. Recognition of this has led to new experimental treatments, RG-101 and Miravirsen—hepatitis C treatments which target host miRNA. miRNAs are being investigated as novel infection biomarkers, and they are being used to design attenuated vaccines, e.g., against Dengue virus. This comprehensive review synthesizes current knowledge of miRNA in host response to infection with emphasis on potential clinical applications, along with an evaluation of the challenges still to be overcome.
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Affiliation(s)
- Ruth E Drury
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, University of Oxford, The Churchill Hospital, Oxford, United Kingdom
| | - Daniel O'Connor
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, University of Oxford, The Churchill Hospital, Oxford, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Centre for Clinical Vaccinology and Tropical Medicine, Department of Paediatrics, University of Oxford, The Churchill Hospital, Oxford, United Kingdom
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Shankar A, Patil AA, Skariyachan S. Recent Perspectives on Genome, Transmission, Clinical Manifestation, Diagnosis, Therapeutic Strategies, Vaccine Developments, and Challenges of Zika Virus Research. Front Microbiol 2017; 8:1761. [PMID: 28959246 PMCID: PMC5603822 DOI: 10.3389/fmicb.2017.01761] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/30/2017] [Indexed: 12/13/2022] Open
Abstract
One of the potential threats to public health microbiology in 21st century is the increased mortality rate caused by Zika virus (ZIKV), a mosquito-borne flavivirus. The severity of ZIKV infection urged World Health Organization (WHO) to declare this virus as a global concern. The limited knowledge on the structure, virulent factors, and replication mechanism of the virus posed as hindrance for vaccine development. Several vector and non-vector-borne mode of transmission are observed for spreading the disease. The similarities of the virus with other flaviviruses such as dengue and West Nile virus are worrisome; hence, there is high scope to undertake ZIKV research that probably provide insight for novel therapeutic intervention. Thus, this review focuses on the recent aspect of ZIKV research which includes the outbreak, genome structure, multiplication and propagation of the virus, current animal models, clinical manifestations, available treatment options (probable vaccines and therapeutics), and the recent advancements in computational drug discovery pipelines, challenges and limitation to undertake ZIKV research. The review suggests that the infection due to ZIKV became one of the universal concerns and an interdisciplinary environment of in vitro cellular assays, genomics, proteomics, and computational biology approaches probably contribute insights for screening of novel molecular targets for drug design. The review tried to provide cutting edge knowledge in ZIKV research with future insights required for the development of novel therapeutic remedies to curtail ZIKV infection.
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Affiliation(s)
- Apoorva Shankar
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar InstitutionsBengaluru, India
| | - Amulya A Patil
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar InstitutionsBengaluru, India
| | - Sinosh Skariyachan
- R&D Centre, Department of Biotechnology Engineering, Dayananda Sagar InstitutionsBengaluru, India.,Visvesvaraya Technological UniversityBelagavi, India
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Zika-Virus-Encoded NS2A Disrupts Mammalian Cortical Neurogenesis by Degrading Adherens Junction Proteins. Cell Stem Cell 2017; 21:349-358.e6. [PMID: 28826723 DOI: 10.1016/j.stem.2017.07.014] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 06/01/2017] [Accepted: 07/21/2017] [Indexed: 11/22/2022]
Abstract
Zika virus (ZIKV) directly infects neural progenitors and impairs their proliferation. How ZIKV interacts with the host molecular machinery to impact neurogenesis in vivo is not well understood. Here, by systematically introducing individual proteins encoded by ZIKV into the embryonic mouse cortex, we show that expression of ZIKV-NS2A, but not Dengue virus (DENV)-NS2A, leads to reduced proliferation and premature differentiation of radial glial cells and aberrant positioning of newborn neurons. Mechanistically, in vitro mapping of protein-interactomes and biochemical analysis suggest interactions between ZIKA-NS2A and multiple adherens junction complex (AJ) components. Functionally, ZIKV-NS2A, but not DENV-NS2A, destabilizes the AJ complex, resulting in impaired AJ formation and aberrant radial glial fiber scaffolding in the embryonic mouse cortex. Similarly, ZIKA-NS2A, but not DENV-NS2A, reduces radial glial cell proliferation and causes AJ deficits in human forebrain organoids. Together, our results reveal pathogenic mechanisms underlying ZIKV infection in the developing mammalian brain.
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Affiliation(s)
- Mobeen H Rathore
- University of Florida Center for HIV/AIDS Research, Education and Service (UF CARES), 910 North Jefferson Street, Jacksonville, FL 32209, USA; Infectious Diseases and Immunology, Wolfson Children's Hospital, 800 Prudential Drive, Jacksonville, FL 32207, USA.
| | - Jonathan Runyon
- Nicklaus Children's Hospital, 3100 SW 62nd Avenue, Miami, FL 33155, USA
| | - Tanveer-Ul Haque
- Infectious Diseases and Immunology, Wolfson Children's Hospital, 800 Prudential Drive, Jacksonville, FL 32207, USA
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Pawitwar SS, Dhar S, Tiwari S, Ojha CR, Lapierre J, Martins K, Rodzinski A, Parira T, Paudel I, Li J, Dutta RK, Silva MR, Kaushik A, El-Hage N. Overview on the Current Status of Zika Virus Pathogenesis and Animal Related Research. J Neuroimmune Pharmacol 2017; 12:371-388. [PMID: 28444557 DOI: 10.1007/s11481-017-9743-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/23/2017] [Indexed: 11/28/2022]
Abstract
There is growing evidence that Zika virus (ZIKV) infection is linked with activation of Guillan-Barré syndrome (GBS) in adults infected with the virus and microcephaly in infants following maternal infection. With the recent outpour in publications by numerous research labs, the association between microcephaly in newborns and ZIKV has become very apparent in which large numbers of viral particles were found in the central nervous tissue of an electively aborted microcephalic ZIKV-infected fetus. However, the underlying related mechanisms remain poorly understood. Thus, development of ZIKV-infected animal models are urgently required. The need to develop drugs and vaccines of high efficacy along with efficient diagnostic tools for ZIKV treatment and management raised the demand for a very selective animal model for exploring ZIKV pathogenesis and related mechanisms. In this review, we describe recent advances in animal models developed for studying ZIKV pathogenesis and evaluating potential interventions against human infection, including during pregnancy. The current research directions and the scientific challenges ahead in developing effective vaccines and therapeutics are also discussed.
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Affiliation(s)
- Shashank S Pawitwar
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Supurna Dhar
- Department of Human and Molecular Genetics, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Sneham Tiwari
- Deparment of Immunology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Chet Raj Ojha
- Deparment of Immunology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Jessica Lapierre
- Deparment of Immunology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Kyle Martins
- Department of Human and Molecular Genetics, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Alexandra Rodzinski
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Tiyash Parira
- Deparment of Immunology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Iru Paudel
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Jiaojiao Li
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Rajib Kumar Dutta
- Deparment of Immunology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Monica R Silva
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Ajeet Kaushik
- Deparment of Immunology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Nazira El-Hage
- Deparment of Immunology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA.
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Abstract
PURPOSE OF REVIEW The purpose of this review is to present what is known about the Zika virus (ZIKV) at the time of writing this review. The viral structure and its phylogeny, as well as the limitations of current available techniques used for diagnosis, are discussed. RECENT FINDINGS Crystallography and cryo-electron microscopy of the whole ZIKV, or a few of its proteins, are confirming its overall antigenic relatedness to other flaviviruses. Sequencing has revealed its dynamic genetic variation and has placed the Western cluster of Zika isolates within the Asian phylogenic tree. Genetic codon mutations, although highly prevalent, do not usually translate into modifications at amino acid or proteomic levels, revealing conserved enzymatic functions that could potentially be addressed therapeutically. Clinical characterization of ZIKV infection is complicated because of symptoms similar to dengue and chikungunya. Diagnosis requires specialized laboratories with costly reagents and highly trained personnel. Although commercial labs are now offering ZIKV diagnostic tests, most of them are not fully tested in comparison with standard molecular techniques standardized at CDC and local health departments. We are still in desperate need of simpler diagnostic tests that better discriminate ZIKV from coendemic arboviruses. SUMMARY The area of better Zika diagnostic assays is a rapidly developing field with the public attention directed to this epidemic. Academic interest in this topic is driving fast disclosure of information in peer-reviewed journals and grey papers via web-based forums. We expect in the near future that new promising strategies for improved Zika diagnostics will translate into preventive and therapeutic tools.
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de Carvalho NS, de Carvalho BF, Dóris B, Silverio Biscaia E, Arias Fugaça C, de Noronha L. Zika virus and pregnancy: An overview. Am J Reprod Immunol 2017; 77. [PMID: 28045216 DOI: 10.1111/aji.12616] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 11/10/2016] [Indexed: 12/22/2022] Open
Abstract
In May 2015, the first episodes of Zika virus infection of the Latin America were confirmed in Brazil, where currently 196 976 cases were reported. The main route of transmission occurs by Aedes mosquitoes, and the most common symptoms are maculopapular rash, fever, conjunctivitis, polyarthralgia, and periarticular edema. However, the infection is asymptomatic in 80% of the cases. The congenital infection is characterized when the transmission to the fetus occurs during pregnancy, but the mechanisms of how the virus infects the placenta remain unclear. Anatomopathological findings were described in first- and third-trimester human placentas; however, the major affected tissue of the baby is the neural. Several clinical situations were listed in these fetuses, such as neurological, ophthalmological, auditory, and articular alterations. The World Health Organization proposed a new congenital syndrome caused by Zika virus. The virus has an important neurotropism and the main manifestation observed in the syndrome is microcephaly, which is usually severe and associated with other neurological injuries. The appearance of sudden rash in pregnant women determines immediate investigation through RT-PCR and serological analysis. Moreover, the prevention consists in using repellents and avoiding endemic areas, considering that the vaccine is still under development.
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Affiliation(s)
- Newton Sérgio de Carvalho
- Department of Gynecology and Obstetrics, Infectious Diseases in Gynecology and Obstetrics Sector, Clinics Hospital, Federal University of Parana, Curitiba, PR, Brazil
| | | | - Bruna Dóris
- Pontifical Catholic University of Parana, Curitiba, PR, Brazil
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Klase ZA, Khakhina S, Schneider ADB, Callahan MV, Glasspool-Malone J, Malone R. Zika Fetal Neuropathogenesis: Etiology of a Viral Syndrome. PLoS Negl Trop Dis 2016; 10:e0004877. [PMID: 27560129 PMCID: PMC4999274 DOI: 10.1371/journal.pntd.0004877] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The ongoing Zika virus epidemic in the Americas and the observed association with both fetal abnormalities (primary microcephaly) and adult autoimmune pathology (Guillain-Barré syndrome) has brought attention to this neglected pathogen. While initial case studies generated significant interest in the Zika virus outbreak, larger prospective epidemiology and basic virology studies examining the mechanisms of Zika viral infection and associated pathophysiology are only now starting to be published. In this review, we analyze Zika fetal neuropathogenesis from a comparative pathology perspective, using the historic metaphor of "TORCH" viral pathogenesis to provide context. By drawing parallels to other viral infections of the fetus, we identify common themes and mechanisms that may illuminate the observed pathology. The existing data on the susceptibility of various cells to both Zika and other flavivirus infections are summarized. Finally, we highlight relevant aspects of the known molecular mechanisms of flavivirus replication.
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Affiliation(s)
- Zachary A Klase
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Svetlana Khakhina
- Department of Biological Sciences, University of the Sciences, Philadelphia, Pennsylvania, United States of America
| | - Adriano De Bernardi Schneider
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
| | - Michael V Callahan
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Zika Foundation, College Station, Texas, United States of America
| | - Jill Glasspool-Malone
- Atheric Pharmaceutical, Scottsville, Virginia, United States of America
- Global Clinical Scholars Research Training Program, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert Malone
- Atheric Pharmaceutical, Scottsville, Virginia, United States of America
- Global Clinical Scholars Research Training Program, Harvard Medical School, Boston, Massachusetts, United States of America
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