1
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Gupta S, Parveen S. Potential role of microRNAs in personalized medicine against hepatitis: a futuristic approach. Arch Virol 2024; 169:33. [PMID: 38245876 DOI: 10.1007/s00705-023-05955-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/21/2023] [Indexed: 01/23/2024]
Abstract
MicroRNAs (miRNAs) have been the subject of extensive research for many years, primarily in the context of diseases such as cancer. However, our appreciation of their significance in viral infections, particularly in hepatitis, has increased due to the discovery of their association with both the host and the virus. Hepatitis is a major global health concern and can be caused by various viruses, including hepatitis A to E. This review highlights the key factors associated with miRNAs and their involvement in infections with various viruses that cause hepatitis. The review not only emphasizes the expression profiles of miRNAs in hepatitis but also puts a spotlight on their potential for diagnostics and therapeutic interventions. Ongoing extensive studies are propelling the therapeutic application of miRNAs, addressing both current limitations and potential strategies for the future of miRNAs in personalized medicine. Here, we discuss the potential of miRNAs to influence future medical research and an attempt to provide a thorough understanding of their diverse roles in hepatitis and beyond.
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Affiliation(s)
- Sonam Gupta
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025, India.
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2
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Zulian V, Fiscon G, Paci P, Garbuglia AR. Hepatitis B Virus and microRNAs: A Bioinformatics Approach. Int J Mol Sci 2023; 24:17224. [PMID: 38139051 PMCID: PMC10743825 DOI: 10.3390/ijms242417224] [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: 10/12/2023] [Revised: 11/20/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
In recent decades, microRNAs (miRNAs) have emerged as key regulators of gene expression, and the identification of viral miRNAs (v-miRNAs) within some viruses, including hepatitis B virus (HBV), has attracted significant attention. HBV infections often progress to chronic states (CHB) and may induce fibrosis/cirrhosis and hepatocellular carcinoma (HCC). The presence of HBV can dysregulate host miRNA expression, influencing several biological pathways, such as apoptosis, innate and immune response, viral replication, and pathogenesis. Consequently, miRNAs are considered a promising biomarker for diagnostic, prognostic, and treatment response. The dynamics of miRNAs during HBV infection are multifaceted, influenced by host variability and miRNA interactions. Given the ability of miRNAs to target multiple messenger RNA (mRNA), understanding the viral-host (human) interplay is complex but essential to develop novel clinical applications. Therefore, bioinformatics can help to analyze, identify, and interpret a vast amount of miRNA data. This review explores the bioinformatics tools available for viral and host miRNA research. Moreover, we introduce a brief overview focusing on the role of miRNAs during HBV infection. In this way, this review aims to help the selection of the most appropriate bioinformatics tools based on requirements and research goals.
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Affiliation(s)
- Verdiana Zulian
- Virology Laboratory, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
| | - Giulia Fiscon
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (P.P.)
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy; (G.F.); (P.P.)
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy
| | - Anna Rosa Garbuglia
- Virology Laboratory, National Institute for Infectious Diseases “Lazzaro Spallanzani” IRCCS, 00149 Rome, Italy;
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3
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Ruivinho C, Gama-Carvalho M. Small non-coding RNAs encoded by RNA viruses: old controversies and new lessons from the COVID-19 pandemic. Front Genet 2023; 14:1216890. [PMID: 37415603 PMCID: PMC10322155 DOI: 10.3389/fgene.2023.1216890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The recurring outbreaks caused by emerging RNA viruses have fostered an increased interest in the research of the mechanisms that regulate viral life cycles and the pathological outcomes associated with infections. Although interactions at the protein level are well-studied, interactions mediated by RNA molecules are less explored. RNA viruses can encode small non-coding RNAs molecules (sncRNAs), including viral miRNAs (v-miRNAs), that play important roles in modulating host immune responses and viral replication by targeting viral or host transcripts. Starting from the analysis of public databases compiling the known repertoire of viral ncRNA molecules and the evolution of publications and research interests on this topic in the wake of the COVID-19 pandemic, we provide an updated view on the current knowledge on viral sncRNAs, with a focus on v-miRNAs encoded by RNA viruses, and their mechanisms of action. We also discuss the potential of these molecules as diagnostic and prognostic biomarkers for viral infections and the development of antiviral therapies targeting v-miRNAs. This review emphasizes the importance of continued research efforts to characterize sncRNAs encoded by RNA viruses, identifies the most relevant pitfalls in the study of these molecules, and highlights the paradigm changes that have occurred in the last few years regarding their biogenesis, prevalence and functional relevance in the context of host-pathogen interactions.
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4
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Saini S, Khurana S, Saini D, Rajput S, Thakur CJ, Singh J, Jaswal A, Kapoor Y, Kumar V, Saini A. In silico analysis of genomic landscape of SARS-CoV-2 and its variant of concerns (Delta and Omicron) reveals changes in the coding potential of miRNAs and their target genes. Gene 2023; 853:147097. [PMID: 36470485 PMCID: PMC9721428 DOI: 10.1016/j.gene.2022.147097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
COVID-19 related morbidities and mortalities are still continued due to the emergence of new variants of SARS-CoV-2. In the last few years, viral miRNAs have been the centre of study to understand the disease pathophysiology. In this work, we aimed to predict the change in coding potential of the viral miRNAs in SARS-CoV-2's VOCs, Delta and Omicron compared to the Reference (Wuhan origin) strain using bioinformatics tools. After ab-intio based screening by the Vmir tool and validation, we retrieved 22, 6, and 6 pre-miRNAs for Reference, Delta, and Omicron. Most of the predicted unique pre-miRNAs of Delta and Omicron were found to be encoded from the terminal and origin of the genomic sequence, respectively. Mature miRNAs identified by MatureBayes from the unique pre-miRNAs were used for target identification using miRDB. A total of 1786, 216, and 143 high-confidence target genes were captured for GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. The GO and KEGG pathways terms analysis revealed the involvement of Delta miRNAs targeted genes in the pathways such as Human cytomegalovirus infection, Breast cancer, Apoptosis, Neurotrophin signaling, and Axon guidance whereas the Sphingolipid signaling pathway was found for the Omicron. Furthermore, we focussed our analysis on target genes that were validated through GEO's (Gene Expression Omnibus) DEGs (Differentially Expressed Genes) dataset, in which FGL2, TNSF12, OGN, GDF11, and BMP11 target genes were found to be down-regulated by Reference miRNAs and YAE1 and RSU1 by Delta. Few genes were also observed to be validated among in up-regulated gene set of the GEO dataset, in which MMP14, TNFRSF21, SGMS1, and TMEM192 were related to Reference whereas ZEB2 was detected in all three strains. This study thus provides an in-silico based analysis that deciphered the unique pre-miRNAs in Delta and Omicron compared to Reference. However, the findings need future wet lab studies for validation.
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Affiliation(s)
- Sandeep Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India; Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India.
| | - Savi Khurana
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Dikshant Saini
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Saru Rajput
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Chander Jyoti Thakur
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Jeevisha Singh
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Akanksha Jaswal
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Yogesh Kapoor
- Department of Engineering and Technology, Shoolini University, Solan, Himachal Pradesh, India
| | - Varinder Kumar
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India.
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5
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Wang Y, Lin S, Zhao Z, Xu P, Gao K, Qian H, Zhang Z, Guo X. Functional analysis of a putative Bombyx mori cypovirus miRNA BmCPV-miR-10 and its effect on virus replication. INSECT MOLECULAR BIOLOGY 2021; 30:552-565. [PMID: 34296485 DOI: 10.1111/imb.12725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Bombyx mori cypovirus (BmCPV) is an important pathogen of silkworm (B. mori), the economically beneficial insect. The mechanism of its interaction with host immune defence system in the process of infection is still not yet completely clear. Researches have demonstrated that virus-encoded microRNAs (miRNA) play a crucial role in regulating host-pathogen interaction, but few reports are available so far on miRNAs encoded by insect viruses, especially the RNA viruses. In this study, a putative miRNA encoded by the 10th segment of BmCPV genomic RNA, BmCPV-miR-10, was identified and functionally analysed. The expression of the putative BmCPV-miR-10 could be detected via stem-loop RT-PCR (reverse transcription-Polymerase Chain Reaction) in the midgut of silkworm larvae infected with BmCPV. BmCSDE1 (B. mori cold shock domain E1 protein) gene was predicted to be a candidate target gene for BmCPV-miR-10 with the miRNA binding site located in 3' untranslated region of its mRNA. The regulation effect of the putative BmCPV-miR-10 on BmCSDE1 was verified in HEK293 cells by lentiviral expression system, in BmN cells by transfecting BmCPV-miR-10 mimics. The qRT-PCR (quantitative real-time PCR) results showed that the putative BmCPV-miR-10 could suppress the expression of BmCSDE1. By injection of BmCPV-miR-10 mimics into the silkworm larvae infected with BmCPV, it was further proved that the putative BmCPV-miR-10 could suppress the expression of BmCSDE1 in vivo, then inhibit the expression of BmApaf-1 (B. mori apoptotic protease activating factor 1), while enhance the replication of BmCPV genomic RNAs to a certain extent. These results implied that the putative BmCPV-miR-10 could down-regulate the expression of BmCSDE1, then suppress the expression of BmApaf-1, thereby created a favourable intracellular environment for virus replication and proliferation.
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Affiliation(s)
- Y Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - S Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Z Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - P Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - K Gao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - H Qian
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Z Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - X Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericulture Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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6
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Lin S, Wang Y, Zhao Z, Wu W, Su Y, Zhang Z, Shen M, Wu P, Qian H, Guo X. Two Putative Cypovirus-Encoded miRNAs Co-regulate the Host Gene of GTP-Binding Nuclear Protein Ran and Facilitate Virus Replication. Front Physiol 2021; 12:663482. [PMID: 34421632 PMCID: PMC8373394 DOI: 10.3389/fphys.2021.663482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/13/2021] [Indexed: 01/08/2023] Open
Abstract
microRNA (miRNA) plays important roles in regulating various biological processes, including host-pathogen interaction. Recent studies have demonstrated that virus-encoded miRNAs can manipulate host gene expression to ensure viral effective multiplication. Bombyx mori cypovirus (BmCPV), a double-stranded RNA virus with a segmented genome, is one of the important pathogens for the economically important insect silkworm. Our present study indicated that two putative miRNAs encoded by BmCPV could promote viral replication by inhibiting the gene expression of B. mori GTP-binding nuclear protein Ran (BmRan), an essential component of the exportin-5-mediated nucleocytoplasmic transport of small RNAs. BmCPV-miR-1 and BmCPV-miR-3 are two of the BmCPV-encoded miRNAs identified in our previous studies. BmRan is a common target gene of them with binding sites all located in the 3′-untranslated region (3′-UTR) of its mRNA. The expression levels of the two miRNAs in the midgut of larvae infected with BmCPV gradually increased with the advance of infection, while the expression of the target gene BmRan decreased gradually. The miRNAs and the recombinant target gene consisting of reporter gene mCherry and 3′-UTR of BmRan mRNA were expressed in HEK293T cells for validating the interaction between the miRNAs and the target gene. qRT-PCR results revealed that BmCPV-miR-1 and BmCPV-miR-3 negatively regulate target gene expression not only separately but also cooperatively by binding to the 3′-UTR of BmRan mRNA. By transfecting miRNA mimics into BmN cells and injecting the mimics into the body of silkworm larvae, it was indicated that both BmCPV-miR-1 and BmCPV-miR-3 could repress the expression of BmRan in BmN cells and in the silkworm, and the cooperative action of the two miRNAs could enhance the repression of BmRan expression. Furthermore, the repression of BmRan could facilitate the replication of BmCPV genomic RNAs. It is speculated that BmCPV-miR-1 and BmCPV-miR-3 might reduce the generation of host miRNAs by inhibiting expression of BmRan, thus creating a favorable intracellular environment for virus replication. Our results are helpful to better understand the pathogenic mechanism of BmCPV to the silkworm, and provide insights into one of the evasion strategies used by viruses to counter the host defense for their effective multiplication.
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Affiliation(s)
- Su Lin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Yongsheng Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ze Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Wanming Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Yun Su
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Zhendong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Manman Shen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Heying Qian
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Xijie Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China.,Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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7
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Roy S, Sharma B, Mazid MI, Akhand RN, Das M, Marufatuzzahan M, Chowdhury TA, Azim KF, Hasan M. Identification and host response interaction study of SARS-CoV-2 encoded miRNA-like sequences: an in silico approach. Comput Biol Med 2021; 134:104451. [PMID: 34020131 PMCID: PMC8078050 DOI: 10.1016/j.compbiomed.2021.104451] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023]
Abstract
COVID-19, a global pandemic caused by an RNA virus named SARS-CoV-2 has brought the world to a standstill in terms of infectivity, casualty, and commercial plummet. RNA viruses can encode microRNAs (miRNAs) capable of modulating host gene expression, and with that notion, we aimed to predict viral miRNA like sequences of MERS-CoV, SARS-CoV and SARS-CoV-2, analyze sequence reciprocity and investigate SARS-CoV-2 encoded potential miRNA-human genes interaction using bioinformatics tools. In this study, we retrieved 206 SARS-CoV-2 genomes, executed phylogenetic analysis, and the selected reference genome (MT434792.1) exhibited about 99% similarities among the retrieved genomes. We predicted 402, 137, and 85 putative miRNAs of MERS-CoV (NC_019843.3), SARS-CoV (NC_004718.3), and SARS-CoV-2 (MT434792.1) genome, respectively. Sequence similarity was analyzed among 624 miRNAs which revealed that the predicted miRNAs of SARS-CoV-2 share a cluster with the clad of miRNAs from MERS-CoV and SARS-CoV. Only SARS-CoV-2 derived 85 miRNAs were encountered for target prediction and 29 viral miRNAs seemed to target 119 human genes. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analysis suggested the involvement of respective genes in various pathways and biological processes. Finally, we focused on eight putative miRNAs influencing 14 genes that are involved in the adaptive hypoxic response, neuroinvasion and hormonal regulation, and tumorigenic progression in patients with COVID-19. SARS-CoV-2 encoded miRNAs may cause misexpression of some critical regulators and facilitate viral neuroinvasion, altered hormonal axis, and tumorigenic events in the human host. However, these propositions need validation from future studies.
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Affiliation(s)
- Sawrab Roy
- Department of Microbiology and Immunology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Binayok Sharma
- Department of Medicine, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | | | - Rubaiat Nazneen Akhand
- Department of Biochemistry and Chemistry, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Moumita Das
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | | | - Tanjia Afrin Chowdhury
- Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Kazi Faizul Azim
- Department of Microbial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh,Corresponding author. Department of Pharmaceuticals and Industrial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
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8
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Hepatitis A virus-induced hsa-miR-146a-5p attenuates IFN-β signaling by targeting adaptor protein TRAF6. Arch Virol 2021; 166:789-799. [PMID: 33459883 DOI: 10.1007/s00705-021-04952-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/26/2020] [Indexed: 12/21/2022]
Abstract
Hepatitis A virus (HAV), a unique hepatotropic human picornavirus, is the causative agent of acute hepatitis A in humans. Some studies have shown that HAV antagonizes the innate immune response by disrupting interferon-beta (IFN-β) signaling by viral proteins. However, whether microRNAs (miRNAs), a class of non-coding RNAs, are involved in the antagonism of IFN-β induction upon HAV infection is still unclear. In this study, we investigated the effects and mechanisms by which HAV-induced miRNAs antagonize IFN-β signaling. A variety of analytical methods, including miRNA microarray, RT-qPCR, dual-luciferase reporter assay, and Western blotting, were performed using HAV-infected cells. The results indicated that HAV infection upregulates the expression of hsa-miR-146a-5p, which in turn partially suppresses the induction of IFN-β synthesis, thereby promoting viral replication. Mechanistically, TRAF6 (TNF receptor-associated factor 6), a key adaptor protein in the RIG-I/MDA5-mediated IFN-I signaling pathway, is targeted and degraded by hsa-miR-146a-5p. As TRAF6 is necessary for IFN-β induction, inhibition of this protein attenuates IFN-β signaling. Taken together, the results from this study indicated that HAV disrupts RIG-I/MDA5-mediated IFN-I signaling partially through the cleavage of the essential adaptor molecule TRAF6 via hsa-miR-146a-5p.
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Saini S, Saini A, Thakur CJ, Kumar V, Gupta RD, Sharma JK. Genome-wide computational prediction of miRNAs in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed target genes involved in pulmonary vasculature and antiviral innate immunity. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2020; 9:83-91. [PMID: 32802902 PMCID: PMC7382400 DOI: 10.22099/mbrc.2020.36507.1487] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The current outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China threatened humankind worldwide. The coronaviruses contains the largest RNA genome among all other known RNA viruses, therefore the disease etiology can be understood by analyzing the genome sequence of SARS-CoV-2. In this study, we used an ab-intio based computational tool VMir to scan the complete genome of SARS-CoV-2 to predict pre-miRNAs. The potential pre-miRNAs were identified by ViralMir and mature miRNAs were recognized by Mature Bayes. Additionally, predicted mature miRNAs were analysed against human genome by miRDB server to retrieve target genes. Besides that we also retrieved GO (Gene Ontology) terms for pathways, functions and cellular components. We predicted 26 mature miRNAs from genome of SARS-CoV-2 that targets human genes involved in pathways like EGF receptor signaling, apoptosis signaling, VEGF signaling, FGF receptor signaling. Gene enrichment tool analysis and substantial literature evidences suggests role of genes like BMPR2 and p53 in pulmonary vasculature and antiviral innate immunity respectively. Our findings may help research community to understand virus pathogenesis.
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Affiliation(s)
- Sandeep Saini
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
- Department of Biophysics, Panjab University, Sector 25, 160014, Chandigarh, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, 160014, Chandigarh, India
| | - Chander Jyoti Thakur
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Varinder Kumar
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Rishabh Dilip Gupta
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
| | - Jogesh Kumar Sharma
- Department of Bioinformatics, GGDSD College, Sector 32-C, 160030, Chandigarh, India
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10
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Guo JY, Wang YS, Chen T, Jiang XX, Wu P, Geng T, Pan ZH, Shang MK, Hou CX, Gao K, Guo XJ. Functional analysis of a miRNA-like small RNA derived from Bombyx mori cytoplasmic polyhedrosis virus. INSECT SCIENCE 2020; 27:449-462. [PMID: 30869181 DOI: 10.1111/1744-7917.12671] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/14/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) is a major pathogen of the economic insect silkworm, Bombyx mori. Virus-encoded microRNAs (miRNAs) have been proven to play important roles in host-pathogen interactions. In this study we identified a BmCPV-derived miRNA-like 21 nt small RNA, BmCPV-miR-1, from the small RNA deep sequencing of BmCPV-infected silkworm larvae by stem-loop quantitative real-time PCR (qPCR) and investigated its functions with qPCR and lentiviral expression systems. Bombyx mori inhibitor of apoptosis protein (BmIAP) gene was predicted by both target prediction software miRanda and Targetscan to be one of its target genes with a binding site for BmCPV-miR-1 at the 5' untranslated region. It was found that the expression of BmCPV-miR-1 and its target gene BmIAP were both up-regulated in BmCPV-infected larvae. At the same time, it was confirmed that BmCPV-miR-1 could up-regulate the expression of BmIAP gene in HEK293T cells with lentiviral expression systems and in BmN cells by transfecting mimics. Furthermore, BmCPV-miR-1 mimics could up-regulate the expression level of BmIAP gene in midgut and fat body in the silkworm. In the midgut of BmCPV-infected larvae, BmCPV-miR-1 mimics could be further up-regulated and inhibitors could lower the virus-mediated expression of BmIAP gene. With the viral genomic RNA segments S1 and S10 as indicators, BmCPV-miR-1 mimics could up-regulate and inhibitors down-regulate their replication in the infected silkworm. These results implied that BmCPV-miR-1 could inhibit cell apoptosis in the infected silkworm through up-regulating BmIAP expression, providing the virus with a better cell circumstance for its replication.
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Affiliation(s)
- Jian-Yong Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Yong-Sheng Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Tian Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xiao-Xu Jiang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Ping Wu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Tao Geng
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikoou, China
| | - Zhong-Hua Pan
- School of Biology & Basic Medical Science, Soochow University, Suzhou, China
| | - Meng-Ke Shang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Cheng-Xiang Hou
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Kun Gao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
| | - Xi-Jie Guo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, China
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11
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Mishra R, Kumar A, Ingle H, Kumar H. The Interplay Between Viral-Derived miRNAs and Host Immunity During Infection. Front Immunol 2020; 10:3079. [PMID: 32038626 PMCID: PMC6989438 DOI: 10.3389/fimmu.2019.03079] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/17/2019] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs are short non-coding RNAs that play a crucial role in the regulation of gene expression during cellular processes. The host-encoded miRNAs are known to modulate the antiviral defense during viral infection. In the last decade, multiple DNA and RNA viruses have been shown to produce miRNAs known as viral miRNAs (v-miRNAs) so as to evade the host immune response. In this review, we highlight the origin and biogenesis of viral miRNAs during the viral lifecycle. We also explore the role of viral miRNAs in immune evasion and hence in maintaining chronic infection and disease. Finally, we offer insights into the underexplored role of viral miRNAs as potential targets for developing therapeutics for treating complex viral diseases.
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Affiliation(s)
- Richa Mishra
- Laboratory of Immunology and Infectious Disease Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Ashish Kumar
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA, United States
| | - Harshad Ingle
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, United States
| | - Himanshu Kumar
- Laboratory of Immunology and Infectious Disease Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
- Laboratory of Host Defense, WPI Immunology, Frontier Research Centre, Osaka University, Osaka, Japan
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12
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Baruah V, Bose S. Computational identification of hepatitis E virus-encoded microRNAs and their targets in human. J Med Virol 2019; 91:1545-1552. [PMID: 30919453 DOI: 10.1002/jmv.25471] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 02/13/2019] [Accepted: 03/12/2019] [Indexed: 12/26/2022]
Abstract
microRNAs (miRNAs) are small, noncoding RNAs which regulate eukaryotic gene expression via RNA interference pathway. Recently, miRNAs have been identified in a number of viruses with current evidence suggesting that they regulate gene expression in both virus and host. This makes viral miRNAs potential targets of clinical intervention, with the possibility of inhibiting aberrant host gene expression associated with the disease. In this study, computational approaches were taken to scan the hepatitis E virus (HEV) genome for putative pre-miRNA molecules, which were then analyzed for the presence of mature miRNAs. The 3'-untranslated region (3'-UTR) and 5'-UTR sequences targeted by these miRNAs were identified using Miranda computational tool, followed by the functional annotation of the associated messenger RNAs (mRNAs) using Gene Ontology terms and Kyoto Encyclopaedia of Genes and Genomes pathway analysis. We identified a total of nine viral encoded miRNAs in HEV. After functional annotation, the majority of the viral miRNA targets were found to be associated with cell cycle, cell differentiation, nitrogen compound metabolism, transmembrane transport, and chromosome organization. This in-silico study identified putative viral miRNAs encoded by HEV and their potential human mRNAs targets. These viral miRNAs have the potential to affect host gene expression as well as viral life cycle and pathogenesis and can, therefore, serve as potential therapeutic targets during HEV infection.
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Affiliation(s)
- Vargab Baruah
- Department of Biotechnology, Gauhati University, Guwahati, Assam, India
| | - Sujoy Bose
- Department of Biotechnology, Gauhati University, Guwahati, Assam, India
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13
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Kim P, Jia P, Zhao Z. Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study. Brief Bioinform 2019; 19:450-460. [PMID: 28013235 DOI: 10.1093/bib/bbw127] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/13/2022] Open
Abstract
Assessing the impact of kinase in gene fusion is essential for both identifying driver fusion genes (FGs) and developing molecular targeted therapies. Kinase domain retention is a crucial factor in kinase fusion genes (KFGs), but such a systematic investigation has not been done yet. To this end, we analyzed kinase domain retention (KDR) status in chimeric protein sequences of 914 KFGs covering 312 kinases across 13 major cancer types. Based on 171 kinase domain-retained KFGs including 101 kinases, we studied their recurrence, kinase groups, fusion partners, exon-based expression depth, short DNA motifs around the break points and networks. Our results, such as more KDR than 5'-kinase fusion genes, combinatorial effects between 3'-KDR kinases and their 5'-partners and a signal transduction-specific DNA sequence motif in the break point intronic sequences, supported positive selection on 3'-kinase fusion genes in cancer. We introduced a degree-of-frequency (DoF) score to measure the possible number of KFGs of a kinase. Interestingly, kinases with high DoF scores tended to undergo strong gene expression alteration at the break points. Furthermore, our KDR gene fusion network analysis revealed six of the seven kinases with the highest DoF scores (ALK, BRAF, MET, NTRK1, NTRK3 and RET) were all observed in thyroid carcinoma. Finally, we summarized common features of 'effective' (highly recurrent) kinases in gene fusions such as expression alteration at break point, redundant usage in multiple cancer types and 3'-location tendency. Collectively, our findings are useful for prioritizing driver kinases and FGs and provided insights into KFGs' clinical implications.
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Affiliation(s)
- Pora Kim
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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14
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Xiao P, Han J, Zhang Y, Li C, Guo X, Wen S, Tian M, Li Y, Wang M, Liu H, Ren J, Zhou H, Lu H, Jin N. Metagenomic Analysis of Flaviviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes From Dengue and Zika Viruses. Front Cell Infect Microbiol 2018; 8:359. [PMID: 30406038 PMCID: PMC6207848 DOI: 10.3389/fcimb.2018.00359] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
More than 6,000 mosquitoes of six species from six sites were collected and tested for their virome using metagenomics sequencing and bioinformatic analysis. The identified viral sequences belonged to more than 50 viral families. The results were verified by PCR of selected viruses in all mosquitoes, followed by phylogenetic analysis. In the present study, we identified the partial dengue virus (DENV), Zika virus (ZIKV), and Japanese encephalitis virus (JEV) sequences in mosquitoes. Metagenomic analysis and the PCR amplification revealed three DENV sequences, one of which encodes a partial envelope protein. Two ZIKV sequences both encoding partial nonstructural protein 3 and one JEV sequence encoding the complete envelope protein were identified. There was variability in the viral titers of the newly isolated virus JEV-China/YN2016-1 of different passage viruses. The newly identified Zika virus gene from ZIKV-China/YN2016-1 was an Asian genotype and shared the highest nucleotide sequence identity (97.1%) with a ZIKV sequence from Thailand isolated in 2004. Phylogenetic analysis of ZIKV-China/YN2016-1 and ZIKV-China/YN2016-2 with known Flavivirus genes indicated that ZIKV has propagated in Yunnan province, China.
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Affiliation(s)
- Pengpeng Xiao
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Jicheng Han
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Chenghui Li
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Xiaofang Guo
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Shubo Wen
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Mingyao Tian
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yiquan Li
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
| | - Maopeng Wang
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Institute of Virology, Wenzhou University, Wenzhou, China
| | - Hao Liu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jingqiang Ren
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Division of Economic Animal Epidemic, Institute of Special Economic Animal and Plant Sciences, Changchun, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Huijun Lu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Ningyi Jin
- Yanbian University Medical College, Yanji, China.,Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China
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15
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Xiao P, Li C, Zhang Y, Han J, Guo X, Xie L, Tian M, Li Y, Wang M, Liu H, Ren J, Zhou H, Lu H, Jin N. Metagenomic Sequencing From Mosquitoes in China Reveals a Variety of Insect and Human Viruses. Front Cell Infect Microbiol 2018; 8:364. [PMID: 30406041 PMCID: PMC6202873 DOI: 10.3389/fcimb.2018.00364] [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: 04/13/2018] [Accepted: 10/01/2018] [Indexed: 12/18/2022] Open
Abstract
We collected 8,700 mosquitoes in three sites in China, which belonged to seven species. Their viromes were tested using metagenomic sequencing and bioinformatic analysis. The abundant viral sequences were detected and annotated belonging to more than 50 viral taxonomic families. The results were verified by PCR, followed by phylogenetic analysis. In the present study, we identified partial viral genes of dengue virus (DENV), a novel circovirus (CCV), densovirus (DNV), Japanese encephalitis virus (JEV), and Wuhan mosquito virus (WMV) in mosquitoes. Metagenomic analysis and PCR amplification revealed three DENV sequences, which were as homologous to the NS3 gene of DENV from Singapore isolated in 2005, with at least 91% nucleotide (nt) identity. Seven fragments of JEV encoding structural proteins were identified belonging to genotype I. They all shared high homology with structural protein genes of JEV isolated from Laos in 2009. The production of infectious virus particles of the newly isolated virus YunnanJEV2017-4 increased after passage from the BHK-21 cell line to the Vero cell line. Novel circovirus-related genes were identified and as being related to an unnamed gene of a mosquito circovirus (MCCV) sequence from the USA isolated in 2011, with at least 41% nt identity: this distant relationship suggests that the parent virus might belong to a novel circovirus genus. Additionally, numerous known viruses and some unknown viruses were also detected in mosquitoes from Yunnan province, China, which will be tested for propagation.
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Affiliation(s)
- Pengpeng Xiao
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China.,Institute of Virology, Wenzhou University, Wenzhou, China
| | - Chenghui Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Ying Zhang
- College of Veterinary Medicine, College of Animal Science, Jilin University, Changchun, China
| | - Jicheng Han
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Xiaofang Guo
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Lv Xie
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Mingyao Tian
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Yiquan Li
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
| | - Maopeng Wang
- Institute of Virology, Wenzhou University, Wenzhou, China
| | - Hao Liu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Jingqiang Ren
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Division of Economic Animal Epidemic, Institute of Special Economic Animal and Plant Sciences, Changchun, China
| | - Hongning Zhou
- Yunnan Institute of Parasitic Diseases, Simao, China
| | - Huijun Lu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
| | - Ningyi Jin
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China.,Yanbian University Medical College, Yanji, China
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16
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McLinden JH, Bhattarai N, Stapleton JT, Chang Q, Kaufman TM, Cassel SL, Sutterwala FS, Haim H, Houtman JC, Xiang J. Yellow Fever Virus, but Not Zika Virus or Dengue Virus, Inhibits T-Cell Receptor-Mediated T-Cell Function by an RNA-Based Mechanism. J Infect Dis 2017; 216:1164-1175. [PMID: 28968905 PMCID: PMC5853456 DOI: 10.1093/infdis/jix462] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/13/2017] [Indexed: 01/03/2023] Open
Abstract
The Flavivirus genus within the Flaviviridae family is comprised of many important human pathogens including yellow fever virus (YFV), dengue virus (DENV), and Zika virus (ZKV), all of which are global public health concerns. Although the related flaviviruses hepatitis C virus and human pegivirus (formerly named GBV-C) interfere with T-cell receptor (TCR) signaling by novel RNA and protein-based mechanisms, the effect of other flaviviruses on TCR signaling is unknown. Here, we studied the effect of YFV, DENV, and ZKV on TCR signaling. Both YFV and ZKV replicated in human T cells in vitro; however, only YFV inhibited TCR signaling. This effect was mediated at least in part by the YFV envelope (env) protein coding RNA. Deletion mutagenesis studies demonstrated that expression of a short, YFV env RNA motif (vsRNA) was required and sufficient to inhibit TCR signaling. Expression of this vsRNA and YFV infection of T cells reduced the expression of a Src-kinase regulatory phosphatase (PTPRE), while ZKV infection did not. YFV infection in mice resulted in impaired TCR signaling and PTPRE expression, with associated reduction in murine response to experimental ovalbumin vaccination. Together, these data suggest that viruses within the flavivirus genus inhibit TCR signaling in a species-dependent manner.
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Affiliation(s)
- James H McLinden
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
| | - Nirjal Bhattarai
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
| | - Jack T Stapleton
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
- Department of Microbiology, University of Iowa, Iowa City
| | - Qing Chang
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
| | - Thomas M Kaufman
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
| | - Suzanne L Cassel
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
| | - Fayyaz S Sutterwala
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
| | - Hillel Haim
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
| | - Jon C Houtman
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
- Department of Microbiology, University of Iowa, Iowa City
| | - Jinhua Xiang
- Research Service, Iowa City Veterans Affairs Medical Center
- Department of Internal Medicine, University of Iowa, Iowa City
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17
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Stenfeldt C, Arzt J, Smoliga G, LaRocco M, Gutkoska J, Lawrence P. Proof-of-concept study: profile of circulating microRNAs in Bovine serum harvested during acute and persistent FMDV infection. Virol J 2017; 14:71. [PMID: 28388926 PMCID: PMC5384155 DOI: 10.1186/s12985-017-0743-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 03/29/2017] [Indexed: 02/07/2023] Open
Abstract
Background Changes in the levels of circulating microRNAs (miRNAs) in the serum of humans and animals have been detected as a result of infection with a variety of viruses. However, to date, such a miRNA profiling study has not been conducted for foot-and-mouth disease virus (FMDV) infection. Methods The relative abundance of 169 miRNAs was measured in bovine serum collected at three different phases of FMDV infection in a proof-of-concept study using miRNA PCR array plates. Results Alterations in specific miRNA levels were detected in serum during acute, persistent, and convalescent phases of FMDV infection. Subclinical FMDV persistence produced a circulating miRNA profile distinct from cattle that had cleared infection. bta-miR-17-5p was highest expressed during acute infection, whereas bta-miR-31 was the highest during FMDV persistence. Interestingly, miR-1281was significantly down-regulated during both acute and persistent infection. Cattle that cleared infection resembled the baseline profile, adding support to applying serum miRNA profiling for identification of sub-clinically infected FMDV carriers. Significantly regulated miRNAs during acute or persistent infection were associated with cellular proliferation, apoptosis, modulation of the immune response, and lipid metabolism. Conclusions These findings suggest a role for non-coding regulatory RNAs in FMDV infection of cattle. Future studies will delineate the individual contributions of the reported miRNAs to FMDV replication, determine if this miRNA signature is applicable across all FMDV serotypes, and may facilitate development of novel diagnostic applications. Electronic supplementary material The online version of this article (doi:10.1186/s12985-017-0743-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Carolina Stenfeldt
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - Jonathan Arzt
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - George Smoliga
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - Michael LaRocco
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - Joseph Gutkoska
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA
| | - Paul Lawrence
- Plum Island Animal Disease Center, USDA/ARS/NAA/FADRU, P.O. Box 848, Greenport, NY, 11944-0848, USA.
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18
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Identification and characterization of two putative microRNAs encoded by Bombyx mori cypovirus. Virus Res 2017; 233:86-94. [DOI: 10.1016/j.virusres.2017.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/03/2017] [Accepted: 03/04/2017] [Indexed: 01/23/2023]
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19
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Gutkoska J, LaRocco M, Ramirez-Medina E, de Los Santos T, Lawrence P. Host microRNA-203a Is antagonistic to the progression of foot-and-mouth disease virus infection. Virology 2017; 504:52-62. [PMID: 28152384 DOI: 10.1016/j.virol.2017.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/22/2017] [Accepted: 01/23/2017] [Indexed: 12/11/2022]
Abstract
Sam68 was previously shown to be a critical host factor for foot-and-mouth disease virus (FMDV) replication. MicroRNA (miR) miR-203a is reportedly a negative regulator of Sam68 expression both in vitro and in vivo. Here, transfection of miR-203a-3p and miR-203a-5p mimics separately and in combination in a porcine cell line followed by FMDV infection resulted in diminished viral protein synthesis and a 4 and 6log reduction in virus titers relative to negative controls, respectively. Unexpectedly, Sam68 expression was increased by miR-203a-5p transfection, but not miR-203a-3p. miR-203a-5p also down-regulated Survivin expression, which was predicted to play a role in FMDV infection. Moreover, miR-203a-5p but not miR-203a-3p affected a reduction in FMDV viral RNA. These effects were not replicated with a related Picornavirus, suggesting FMDV specificity. Importantly, miR-203a-3p and miR-203a-5p impaired FMDV infection across multiple FMDV serotypes. We concluded that miR-203a-3p and miR-203a-5p represent attractive potential naturally occurring bio-therapeutics against FMDV.
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Affiliation(s)
- Joseph Gutkoska
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States
| | - Michael LaRocco
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States
| | - Elizabeth Ramirez-Medina
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States
| | - Teresa de Los Santos
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States
| | - Paul Lawrence
- Plum Island Animal Disease Center Foreign Animal Disease Research Unit (FADRU) Agricultural Research Service (ARS), United States Department of Agriculture (USDA), 40550 Route 25, Orient Point, NY 11957, United States.
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20
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Liu Y, Sun J, Zhang H, Wang M, Gao GF, Li X. Ebola virus encodes a miR-155 analog to regulate importin-α5 expression. Cell Mol Life Sci 2016; 73:3733-44. [PMID: 27094387 PMCID: PMC11108478 DOI: 10.1007/s00018-016-2215-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 01/12/2023]
Abstract
The 2014 outbreak of Ebola virus caused more than 10,000 human deaths. Current knowledge of suitable drugs, clinical diagnostic biomarkers and molecular mechanisms of Ebola virus infection is either absent or insufficient. By screening stem-loop structures from the viral genomes of four virulence species, we identified a novel, putative viral microRNA precursor that is specifically expressed by the Ebola virus. The sequence of the microRNA precursor was further confirmed by mining the existing RNA-Seq database. Two putative mature microRNAs were predicted and subsequently validated in human cell lines. Combined with this prediction of the microRNA target, we identified importin-α5, which is a key regulator of interferon signaling following Ebola virus infection, as one putative target. We speculate that this microRNA could facilitate the evasion of the host immune system by the virus. Moreover, this microRNA might be a potential clinical therapeutic target or a diagnostic biomarker for Ebola virus.
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Affiliation(s)
- Yuanwu Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2, Yuanmingyuan West Rd, 100193, Beijing, China
| | - Jing Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2, Yuanmingyuan West Rd, 100193, Beijing, China
| | - Hongwen Zhang
- Department of General Surgery, The 306th Hospital of PLA, Beijing, China
| | - Mingming Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2, Yuanmingyuan West Rd, 100193, Beijing, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, No. 2, Yuanmingyuan West Rd, 100193, Beijing, China.
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21
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Bovine Leukemia Virus Small Noncoding RNAs Are Functional Elements That Regulate Replication and Contribute to Oncogenesis In Vivo. PLoS Pathog 2016; 12:e1005588. [PMID: 27123579 PMCID: PMC4849745 DOI: 10.1371/journal.ppat.1005588] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/31/2016] [Indexed: 01/16/2023] Open
Abstract
Retroviruses are not expected to encode miRNAs because of the potential problem of self-cleavage of their genomic RNAs. This assumption has recently been challenged by experiments showing that bovine leukemia virus (BLV) encodes miRNAs from intragenomic Pol III promoters. The BLV miRNAs are abundantly expressed in B-cell tumors in the absence of significant levels of genomic and subgenomic viral RNAs. Using deep RNA sequencing and functional reporter assays, we show that miRNAs mediate the expression of genes involved in cell signaling, cancer and immunity. We further demonstrate that BLV miRNAs are essential to induce B-cell tumors in an experimental model and to promote efficient viral replication in the natural host.
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22
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Najib A, Kim MS, Choi SH, Kang YJ, Kim KH. Changes in microRNAs expression profile of olive flounder (Paralichthys olivaceus) in response to viral hemorrhagic septicemia virus (VHSV) infection. FISH & SHELLFISH IMMUNOLOGY 2016; 51:384-391. [PMID: 26975411 DOI: 10.1016/j.fsi.2016.03.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/03/2016] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
To know the effect of viral hemorrhagic septicemia virus (VHSV) infection on the cellular microRNA expression profile in olive flounder (Paralichthys olivaceus), fish were infected with VHSV, and cellular microRNAs expression was analyzed at 0 (control), 6, 12, 24, 48 and 72 h post-infection (h.p.i.) by the high-throughput sequencing. A total of 372 mature miRNAs were identified, and, among them, 63 miRNAs were differentially expressed during VHSV infection. The differentially expressed microRNAs number was greatly increased from 24 h.p.i. compared to the number at 6 and 12 h.p.i., suggesting that the alteration of microRNAs expression by VHSV infection may be related to the progression of VHSV disease. The target prediction analysis, the GO enrichment analysis, and the KEGG pathway analysis of the predicted target genes showed that various biological pathways could be affected by VHSV infection through the down-regulation or up-regulation of host miRNAs. The present results provide a basic information on the microRNAs related to VHSV infection in olive flounder. Considering broad effects of microRNAs on various biological pathways, data in this study can be used to interpret the mechanism of VHSV pathogenesis, which, vice versa, can be used to develop control measures against VHSV.
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Affiliation(s)
- Abdellaoui Najib
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 608-737, South Korea
| | - Min Sun Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 608-737, South Korea
| | - Seung Hyuk Choi
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 608-737, South Korea
| | - Yue Jai Kang
- Department of Aquatic Life and Medical Sciences, Sun Moon University, Asan-si, Chungnam, 336-708, South Korea
| | - Ki Hong Kim
- Department of Aquatic Life Medicine, Pukyong National University, Busan, 608-737, South Korea.
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23
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Zhou Y, Wu J, Geng P, Kui X, Xie Y, Zhang L, Liu Y, Yin N, Zhang G, Yi S, Li H, Sun M. MicroRNA profile analysis of host cells before and after wild human rotavirus infection. J Med Virol 2016; 88:1497-510. [PMID: 26890217 DOI: 10.1002/jmv.24500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2016] [Indexed: 01/05/2023]
Abstract
Rotavirus infection is an important cause of acute gastroenteritis in children, but the interaction between rotavirus and host cells is not completely understood. We isolated a wildtype (wt) rotavirus strain, ZTR-68(P [8] G1), which is derived from an infant with diarrhea in southwest China in 2010. In this study, we investigated host cellular miRNA expression profiles changes in response to ZTR-68 in early stage of infection to investigate the role of miRNAs upon rotavirus infection. Differentially expressed miRNAs were identified by deep sequencing and qRT-PCR and the function of their targets predicted by Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. A total of 36 candidate miRNAs were identified. Comparative analysis indicated that 29 miRNAs were significantly down-regulated and 7 were up-regulated after infection. The data were provided contrasting the types of microRNAs in two different permissive cell lines (HT29 and MA104). The target assays results showed that mml-miR-7 and mml-miR-125a are involved in anti-rotavirus and virus-host interaction in host cells. These results offer clues for identifying potential candidates in vector-based antiviral strategies. J. Med. Virol. 88:1497-1510, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yan Zhou
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Jinyuan Wu
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Panpan Geng
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Xiang Kui
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Yuping Xie
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Lei Zhang
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Yaling Liu
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Na Yin
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Guangming Zhang
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Shan Yi
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Hongjun Li
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
| | - Maosheng Sun
- Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Disease, Kunming, China
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24
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Shi J, Sun J, Wu M, Hu N, Hu Y. Hepatitis A virus-encoded miRNAs attenuate the accumulation of viral genomic RNAs in infected cells. Virus Genes 2016; 52:317-24. [DOI: 10.1007/s11262-016-1306-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/16/2016] [Indexed: 11/30/2022]
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25
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Systematic Genome-wide Screening and Prediction of microRNAs in EBOV During the 2014 Ebolavirus Outbreak. Sci Rep 2015; 5:9912. [PMID: 26011078 PMCID: PMC4603304 DOI: 10.1038/srep09912] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/23/2015] [Indexed: 12/15/2022] Open
Abstract
Recently, several thousand people have been killed by the Ebolavirus disease (EVD) in West Africa, yet no current antiviral medications and treatments are available. Systematic investigation of ebolavirus whole genomes during the 2014 outbreak may shed light on the underlying mechanisms of EVD development. Here, using the genome-wide screening in ebolavirus genome sequences, we predicted four putative viral microRNA precursors (pre-miRNAs) and seven putative mature microRNAs (miRNAs). Combing bioinformatics analysis and prediction of the potential ebolavirus miRNA target genes, we suggest that two ebolavirus coding possible miRNAs may be silence and down-regulate the target genes NFKBIE and RIPK1, which are the central mediator of the pathways related with host cell defense mechanism. Additionally, the ebolavirus exploits the miRNAs to inhibit the NF-kB and TNF factors to evade the host defense mechanisms that limit replication by killing infected cells, or to conversely trigger apoptosis as a mechanism to increase virus spreading. This is the first study to use the genome-wide scanning to predict microRNAs in the 2014 outbreak EVD and then to apply systematic bioinformatics to analyze their target genes. We revealed a potential mechanism of miRNAs in ebolavirus infection and possible therapeutic targets for Ebola viral infection treatment.
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26
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Liang H, Zhou Z, Zhang S, Zen K, Chen X, Zhang C. Identification of Ebola virus microRNAs and their putative pathological function. SCIENCE CHINA-LIFE SCIENCES 2014; 57:973-81. [PMID: 25266153 DOI: 10.1007/s11427-014-4759-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 09/13/2014] [Indexed: 11/29/2022]
Abstract
Ebola virus (EBOV), a member of the filovirus family, is an enveloped negative-sense RNA virus that causes lethal infections in humans and primates. Recently, more than 1000 people have been killed by the Ebola virus disease in Africa, yet no specific treatment or diagnostic tests for EBOV are available. In this study, we identified two putative viral microRNA precursors (pre-miRNAs) and three putative mature microRNAs (miRNAs) derived from the EBOV genome. The production of the EBOV miRNAs was further validated in HEK293T cells transfected with a pcDNA6.2-GW/EmGFP-EBOV-pre-miRNA plasmid, indicating that EBOV miRNAs can be produced through the cellular miRNA processing machinery. We also predicted the potential target genes of these EBOV miRNAs and their possible biological functions. Overall, this study reports for the first time that EBOV may produce miRNAs, which could serve as non-invasive biomarkers for the diagnosis and prognosis of EBOV infection and as therapeutic targets for Ebola viral infection treatment.
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Affiliation(s)
- HongWei Liang
- Jiangsu Engineering Research Center for microRNA Biology and Biotechnology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
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