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Viruses
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Viruses and miRNAs
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Viruses and miRNAs

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Animal Viruses".

Deadline for manuscript submissions: closed (31 December 2013) | Viewed by 83857

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Prof. Dr. Andrew P. Rice

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Nancy Chang Professor, Rice Lab - Molecular Virology & Microbiology, One Baylor Plaza, Mail Stop BCM-385, Houston, TX 77030, USA
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Keywords

  • viruses
  • miRNAs

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Published Papers (9 papers)

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Research

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783 KiB  
Article
Dysregulated microRNA Expression in Serum of Non-Vaccinated Children with Varicella
by Yuhua Qi, Zheng Zhu, Zhiyang Shi, Yiyue Ge, Kangchen Zhao, Minghao Zhou and Lunbiao Cui
Viruses 2014, 6(4), 1823-1836; https://doi.org/10.3390/v6041823 - 22 Apr 2014
Cited by 25 | Viewed by 6960
Abstract
Circulating microRNAs (miRNAs) may play an important role in pathogen-host interactions and can serve as molecular markers for the detection of infectious diseases. To date, the relationship between circulating miRNAs and varicella-zoster virus (VZV) caused varicella has not been reported. Using TaqMan Low-Density [...] Read more.
Circulating microRNAs (miRNAs) may play an important role in pathogen-host interactions and can serve as molecular markers for the detection of infectious diseases. To date, the relationship between circulating miRNAs and varicella-zoster virus (VZV) caused varicella has not been reported. Using TaqMan Low-Density Array (TLDA) analysis, expression levels of miRNAs in serum samples from 29 patients with varicella and 60 patients with Bordetella pertussis (BP), measles virus (MEV) and enterovirus (EV) were analyzed. The array results showed that 247 miRNAs were differentially expressed in sera of the varicella patients compared with healthy controls (215 up-regulated and 32 down-regulated). Through the following qRT-PCR confirmation and receiver operational characteristic (ROC) curve analysis, five miRNAs (miR-197, miR-629, miR-363, miR-132 and miR-122) were shown to distinguish varicella patients from healthy controls and other microbial infections with moderate sensitivity and specificity. A number of significantly enriched pathways regulated by these circulating miRNAs were predicted, and some of them were involved in inflammatory response, nervous system and respiratory system development. Our results, for the first time, revealed that a number of miRNAs were differentially expressed during VZV infection, and these five serum miRNAs have great potential to serve as biomarkers for the diagnosis of VZV infection in varicella patients. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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951 KiB  
Article
Comprehensive Characterization of Serum MicroRNA Profile in Response to the Emerging Avian Influenza A (H7N9) Virus Infection in Humans
by Zheng Zhu, Yuhua Qi, Aihua Ge, Yefei Zhu, Ke Xu, Hong Ji, Zhiyang Shi, Lunbiao Cui and Minghao Zhou
Viruses 2014, 6(4), 1525-1539; https://doi.org/10.3390/v6041525 - 2 Apr 2014
Cited by 66 | Viewed by 8225
Abstract
A novel avian-origin influenza A (H7N9) virus recently occurred in China and caused 137 human infection cases with a 32.8% mortality rate. Although various detection procedures have been developed, the pathogenesis of this emerging virus in humans remains largely unknown. In this study, [...] Read more.
A novel avian-origin influenza A (H7N9) virus recently occurred in China and caused 137 human infection cases with a 32.8% mortality rate. Although various detection procedures have been developed, the pathogenesis of this emerging virus in humans remains largely unknown. In this study, we characterized serum microRNA (miRNA) profile in response to H7N9 virus infection using TaqMan Low Density Arrays. Upon infection, a total of 395 miRNAs were expressed in the serum pool of patients, far beyond the 221 in healthy controls. Among the 187 commonly expressed miRNAs, 146 were up-regulated and only 7 down-regulated in patients. Further analysis by quantitative RT-PCR revealed that the serum levels of miR-17, miR-20a, miR-106a and miR-376c were significantly elevated in patients compared with healthy individuals (p < 0.05). Receiver operating characteristic (ROC) curves were constructed to show that each miRNA could discriminate H7N9 patients from controls with area under the curve (AUC) values ranging from 0.622 to 0.898, whereas a combination of miR-17, miR-20a, miR-106a and miR-376c obtained a higher discriminating ability with an AUC value of 0.96. Our findings unravel the significant alterations in serum miRNA expression following virus infection and manifest great potential of circulating miRNAs for the diagnosis of viral diseases. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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526 KiB  
Article
miRNA Profiles of Monocyte-Lineage Cells Are Consistent with Complicated Roles in HIV-1 Restriction
by Jeanne M. Sisk, Janice E. Clements and Kenneth W. Witwer
Viruses 2012, 4(10), 1844-1864; https://doi.org/10.3390/v4101844 - 25 Sep 2012
Cited by 28 | Viewed by 7568 | Correction
Abstract
Long-lived HIV-1 reservoirs include tissue macrophages. Monocyte-derived macrophages are more susceptible to infection and more permissive to HIV-1 replication than monocytes for reasons that may include the effects of different populations of miRNAs in these two cell classes. Specifically, miRs-28-3p, -150, -223, -198, [...] Read more.
Long-lived HIV-1 reservoirs include tissue macrophages. Monocyte-derived macrophages are more susceptible to infection and more permissive to HIV-1 replication than monocytes for reasons that may include the effects of different populations of miRNAs in these two cell classes. Specifically, miRs-28-3p, -150, -223, -198, and -382 exert direct or indirect negative effects on HIV-1 and are reportedly downmodulated during monocyte-to-macrophage differentiation. Here, new experimental results are presented along with reviews and analysis of published studies and publicly available datasets, supporting a broader role of miRNAs in HIV-1 restriction than would be suggested by a simple and uniform downregulation of anti-HIV miRNAs during monocyte-to-macrophage differentiation. Although miR-223 is downregulated in macrophages, other putatively antiviral miRNAs are more abundant in macrophages than in monocytes or are rare and/or variably present in both cell classes. Our analyses point to the need for further studies to determine miRNA profiles of monocytes and macrophages, including classic and newly identified subpopulations; examine the sensitivity of miRNA profiling to cell isolation and differentiation protocols; and characterize rigorously the antiviral effects of previously reported and novel predicted miRNA-HIV-1 interactions in cell-specific contexts. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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Review

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1009 KiB  
Review
Role of Virus-Encoded microRNAs in Avian Viral Diseases
by Yongxiu Yao and Venugopal Nair
Viruses 2014, 6(3), 1379-1394; https://doi.org/10.3390/v6031379 - 21 Mar 2014
Cited by 43 | Viewed by 7560
Abstract
With total dependence on the host cell, several viruses have adopted strategies to modulate the host cellular environment, including the modulation of microRNA (miRNA) pathway through virus-encoded miRNAs. Several avian viruses, mostly herpesviruses, have been shown to encode a number of novel miRNAs. [...] Read more.
With total dependence on the host cell, several viruses have adopted strategies to modulate the host cellular environment, including the modulation of microRNA (miRNA) pathway through virus-encoded miRNAs. Several avian viruses, mostly herpesviruses, have been shown to encode a number of novel miRNAs. These include the highly oncogenic Marek’s disease virus-1 (26 miRNAs), avirulent Marek’s disease virus-2 (36 miRNAs), herpesvirus of turkeys (28 miRNAs), infectious laryngotracheitis virus (10 miRNAs), duck enteritis virus (33 miRNAs) and avian leukosis virus (2 miRNAs). Despite the closer antigenic and phylogenetic relationship among some of the herpesviruses, miRNAs encoded by different viruses showed no sequence conservation, although locations of some of the miRNAs were conserved within the repeat regions of the genomes. However, some of the virus-encoded miRNAs showed significant sequence homology with host miRNAs demonstrating their ability to serve as functional orthologs. For example, mdv1-miR-M4-5p, a functional ortholog of gga-miR-155, is critical for the oncogenicity of Marek’s disease virus. Additionally, we also describe the potential association of the recently described avian leukosis virus subgroup J encoded E (XSR) miRNA in the induction of myeloid tumors in certain genetically-distinct chicken lines. In this review, we describe the advances in our understanding on the role of virus-encoded miRNAs in avian diseases. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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920 KiB  
Review
Roles of microRNAs in the Hepatitis B Virus Infection and Related Diseases
by Muriel Thirion and Takahiro Ochiya
Viruses 2013, 5(11), 2690-2703; https://doi.org/10.3390/v5112690 - 7 Nov 2013
Cited by 28 | Viewed by 12973
Abstract
The hepatitis B virus (HBV) is a small enveloped DNA virus that belongs to the Hepadnaviridae family. HBV can cause acute and persistent infection which can lead to hepatocellular carcinoma (HCC). MicroRNAs (miRNAs) play a crucial role in the main cellular events. The [...] Read more.
The hepatitis B virus (HBV) is a small enveloped DNA virus that belongs to the Hepadnaviridae family. HBV can cause acute and persistent infection which can lead to hepatocellular carcinoma (HCC). MicroRNAs (miRNAs) play a crucial role in the main cellular events. The dysregulation of their expression has been linked to the development of the cancer as well as to viral interference. This chapter will describe the involvement of miRNAs in the case of HBV infection and their implication in the development of the HBV-related diseases. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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410 KiB  
Review
Involvement of Eukaryotic Small RNA Pathways in Host Defense and Viral Pathogenesis
by Julie Hicks and Hsiao-Ching Liu
Viruses 2013, 5(11), 2659-2678; https://doi.org/10.3390/v5112659 - 30 Oct 2013
Cited by 6 | Viewed by 8728
Abstract
Post-transcriptional gene regulation by small RNAs is now established as an important branch of the gene regulatory system. Many different classes of small RNAs have been discovered; among these are short interfering RNAs (siRNAs) and microRNA (miRNAs). Though differences in the processing and [...] Read more.
Post-transcriptional gene regulation by small RNAs is now established as an important branch of the gene regulatory system. Many different classes of small RNAs have been discovered; among these are short interfering RNAs (siRNAs) and microRNA (miRNAs). Though differences in the processing and function of small RNAs exist between plants and animals, both groups utilize small RNA-mediated gene regulation in response to pathogens. Host encoded miRNAs and siRNAs are generated from viral RNA function in host defense and pathogenic resistance in plants. In animals, miRNAs are key regulators in both immune system development and in immune function. Pathogens, in particular viruses, have evolved mechanisms to usurp the host’s small RNA-mediated regulatory system. Overall, small RNAs are a major component of host defense and immunity in eukaryotes. The goal of this review is to summarize our current knowledge of the involvement of eukaryotic small RNA pathways in host defense and viral pathogenesis. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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2164 KiB  
Review
MicroRNAs, Hepatitis C Virus, and HCV/HIV-1 Co-Infection: New Insights in Pathogenesis and Therapy
by Archana Gupta, Gokul Swaminathan, Julio Martin-Garcia and Sonia Navas-Martin
Viruses 2012, 4(11), 2485-2513; https://doi.org/10.3390/v4112485 - 26 Oct 2012
Cited by 36 | Viewed by 12992
Abstract
MicroRNAs (miRNAs) can exert a profound effect on Hepatitis C virus (HCV) replication. The interaction of HCV with the highly liver-enriched miRNA, miR-122 represents one such unique example of viruses having evolved mechanism(s) to usurp the host miRNA machinery to support viral life [...] Read more.
MicroRNAs (miRNAs) can exert a profound effect on Hepatitis C virus (HCV) replication. The interaction of HCV with the highly liver-enriched miRNA, miR-122 represents one such unique example of viruses having evolved mechanism(s) to usurp the host miRNA machinery to support viral life cycle. Furthermore, HCV infection can also trigger changes in the cellular miRNA profile, which may ultimately contribute to the outcome of viral infection. Accumulating knowledge on HCV-host miRNA interactions has ultimately influenced the design of therapeutic interventions against chronic HCV infection. The importance of microRNA modulation in Human Immunodeficiency Virus (HIV-1) replication has been reported, albeit only in the context of HIV-1 mono-infection. The development of HCV infection is dramatically influenced during co-infection with HIV-1. Here, we review the current knowledge on miRNAs in HCV mono-infection. In addition, we discuss the potential role of some miRNAs, identified from the analyses of public data, in HCV/HIV-1 co-infection. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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2594 KiB  
Review
Emerging Themes from EBV and KSHV microRNA Targets
by Dhivya Ramalingam, Philippe Kieffer-Kwon and Joseph M. Ziegelbauer
Viruses 2012, 4(9), 1687-1710; https://doi.org/10.3390/v4091687 - 21 Sep 2012
Cited by 49 | Viewed by 9071
Abstract
EBV and KSHV are both gamma-herpesviruses which express multiple viral microRNAs. Various methods have been used to investigate the functions of these microRNAs, largely through identification of microRNA target genes. Surprisingly, these related viruses do not share significant sequence homology in their microRNAs. [...] Read more.
EBV and KSHV are both gamma-herpesviruses which express multiple viral microRNAs. Various methods have been used to investigate the functions of these microRNAs, largely through identification of microRNA target genes. Surprisingly, these related viruses do not share significant sequence homology in their microRNAs. A number of reports have described functions of EBV and KSHV microRNA targets, however only three experimentally validated target genes have been shown to be targeted by microRNAs from both viruses. More sensitive methods to identify microRNA targets have predicted approximately 60% of host targets could be shared by EBV and KSHV microRNAs, but by targeting different sequences in the host targets. In this review, we explore the similarities of microRNA functions and targets of these related viruses. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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2176 KiB  
Review
MicroRNA-Mediated Restriction of HIV-1 in Resting CD4+ T Cells and Monocytes
by Karen Chiang and Andrew P. Rice
Viruses 2012, 4(9), 1390-1409; https://doi.org/10.3390/v4091390 - 29 Aug 2012
Cited by 37 | Viewed by 8903
Abstract
In contrast to activated CD4+ T cells and differentiated macrophages, resting CD4+ T cells and monocytes are non-permissive for HIV-1 replication. The mediators which regulate the resting or quiescent phenotype are often actively involved in the restriction of viral replication and [...] Read more.
In contrast to activated CD4+ T cells and differentiated macrophages, resting CD4+ T cells and monocytes are non-permissive for HIV-1 replication. The mediators which regulate the resting or quiescent phenotype are often actively involved in the restriction of viral replication and the establishment and maintenance of viral latency. Recently, certain microRNAs which are highly expressed in resting cells have been implicated in this capacity, inhibiting the expression of cellular proteins that are also viral co-factors; following activation these microRNAs exhibit decreased expression, while their targets are correspondingly up-regulated, contributing to a favorable milieu for virus replication. Other microRNAs exhibiting a similar expression pattern in resting and activated cells have been shown to directly target the HIV-1 genome. In this review we will discuss the resting state and the causes behind viral restriction in resting cells, with emphasis on the role of microRNAs. Full article
(This article belongs to the Special Issue Viruses and miRNAs)
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