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Mensah-Bonsu M, Doss C, Gloster C, Muganda P. Identification and Potential Roles of Human MicroRNAs in Ebola Virus Infection and Disease Pathogenesis. Genes (Basel) 2024; 15:403. [PMID: 38674337 PMCID: PMC11049046 DOI: 10.3390/genes15040403] [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: 02/26/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Ebola virus (EBOV) is a highly pathogenic virus that causes a severe illness called Ebola virus disease (EVD). EVD has a high mortality rate and remains a significant threat to public health. Research on EVD pathogenesis has traditionally focused on host transcriptional responses. Limited recent studies, however, have revealed some information on the significance of cellular microRNAs (miRNAs) in EBOV infection and pathogenic mechanisms, but further studies are needed. Thus, this study aimed to identify and validate additional known and novel human miRNAs in EBOV-infected adult retinal pigment epithelial (ARPE) cells and predict their potential roles in EBOV infection and pathogenic mechanisms. We analyzed previously available small RNA-Seq data obtained from ARPE cells and identified 23 upregulated and seven downregulated miRNAs in the EBOV-infected cells; these included two novel miRNAs and 17 additional known miRNAs not previously identified in ARPE cells. In addition to pathways previously identified by others, these miRNAs are associated with pathways and biological processes that include WNT, FoxO, and phosphatidylinositol signaling; these pathways were not identified in the original study. This study thus confirms and expands on the previous study using the same datasets and demonstrates further the importance of human miRNAs in the host response and EVD pathogenesis during infection.
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Affiliation(s)
- Melvin Mensah-Bonsu
- Applied Science and Technology Ph.D. Program, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Christopher Doss
- Department of Electrical and Computer Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Clay Gloster
- Department of Computer Systems Technology, North Carolina A&T State University, Greensboro, NC 27411, USA;
| | - Perpetua Muganda
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
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2
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Rojas-Cruz AF, Bermúdez-Santana CI. Computational Prediction of RNA-RNA Interactions between Small RNA Tracks from Betacoronavirus Nonstructural Protein 3 and Neurotrophin Genes during Infection of an Epithelial Lung Cancer Cell Line: Potential Role of Novel Small Regulatory RNA. Viruses 2023; 15:1647. [PMID: 37631989 PMCID: PMC10458423 DOI: 10.3390/v15081647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Whether RNA-RNA interactions of cytoplasmic RNA viruses, such as Betacoronavirus, might end in the biogenesis of putative virus-derived small RNAs as miRNA-like molecules has been controversial. Even more, whether RNA-RNA interactions of wild animal viruses may act as virus-derived small RNAs is unknown. Here, we address these issues in four ways. First, we use conserved RNA structures undergoing negative selection in the genomes of SARS-CoV, MERS-CoV, and SARS-CoV-2 circulating in different bat species, intermediate animals, and human hosts. Second, a systematic literature review was conducted to identify Betacoronavirus-targeting hsa-miRNAs involved in lung cell infection. Third, we employed sophisticated long-range RNA-RNA interactions to refine the seed sequence homology of hsa-miRNAs with conserved RNA structures. Fourth, we used high-throughput RNA sequencing of a Betacoronavirus-infected epithelial lung cancer cell line (Calu-3) to validate the results. We proposed nine potential virus-derived small RNAs: two vsRNAs in SARS-CoV (Bats: SB-vsRNA-ORF1a-3p; SB-vsRNA-S-5p), one vsRNA in MERS-CoV (Bats: MB-vsRNA-ORF1b-3p), and six vsRNAs in SARS-CoV-2 (Bats: S2B-vsRNA-ORF1a-5p; intermediate animals: S2I-vsRNA-ORF1a-5p; and humans: S2H-vsRNA-ORF1a-5p, S2H-vsRNA-ORF1a-3p, S2H-vsRNA-ORF1b-3p, S2H-vsRNA-ORF3a-3p), mainly encoded by nonstructural protein 3. Notably, Betacoronavirus-derived small RNAs targeted 74 differentially expressed genes in infected human cells, of which 55 upregulate the molecular mechanisms underlying acute respiratory distress syndrome (ARDS), and the 19 downregulated genes might be implicated in neurotrophin signaling impairment. These results reveal a novel small RNA-based regulatory mechanism involved in neuropathogenesis that must be further studied to validate its therapeutic use.
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Affiliation(s)
- Alexis Felipe Rojas-Cruz
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
- Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Clara Isabel Bermúdez-Santana
- Theoretical and Computational RNomics Group, Department of Biology, Faculty of Sciences, Universidad Nacional de Colombia, Bogotá 111321, Colombia;
- Center of Excellence in Scientific Computing, Universidad Nacional de Colombia, Bogotá 111321, Colombia
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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 X 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] [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] Open
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,Corresponding authors at: Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India (S. Saini)
| | - 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,Corresponding authors at: Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32, Chandigarh 160030, India (S. Saini)
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5
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Lu J, Gullett JM, Kanneganti TD. Filoviruses: Innate Immunity, Inflammatory Cell Death, and Cytokines. Pathogens 2022; 11:1400. [PMID: 36558734 PMCID: PMC9785368 DOI: 10.3390/pathogens11121400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Filoviruses are a group of single-stranded negative sense RNA viruses. The most well-known filoviruses that affect humans are ebolaviruses and marburgviruses. During infection, they can cause life-threatening symptoms such as inflammation, tissue damage, and hemorrhagic fever, with case fatality rates as high as 90%. The innate immune system is the first line of defense against pathogenic insults such as filoviruses. Pattern recognition receptors (PRRs), including toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors, AIM2-like receptors, and NOD-like receptors, detect pathogens and activate downstream signaling to induce the production of proinflammatory cytokines and interferons, alert the surrounding cells to the threat, and clear infected and damaged cells through innate immune cell death. However, filoviruses can modulate the host inflammatory response and innate immune cell death, causing an aberrant immune reaction. Here, we discuss how the innate immune system senses invading filoviruses and how these deadly pathogens interfere with the immune response. Furthermore, we highlight the experimental difficulties of studying filoviruses as well as the current state of filovirus-targeting therapeutics.
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6
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Diallo I, Husseini Z, Guellal S, Vion E, Ho J, Kozak RA, Kobinger GP, Provost P. Ebola Virus Encodes Two microRNAs in Huh7-Infected Cells. Int J Mol Sci 2022; 23:ijms23095228. [PMID: 35563619 PMCID: PMC9106010 DOI: 10.3390/ijms23095228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022] Open
Abstract
MicroRNAs (miRNAs) are important gene regulatory molecules involved in a broad range of cellular activities. Although the existence and functions of miRNAs are clearly defined and well established in eukaryotes, this is not always the case for those of viral origin. Indeed, the existence of viral miRNAs is the subject of intense controversy, especially those of RNA viruses. Here, we characterized the miRNA transcriptome of cultured human liver cells infected or not with either of the two Ebola virus (EBOV) variants: Mayinga or Makona; or with Reston virus (RESTV). Bioinformatic analyses revealed the presence of two EBOV-encoded miRNAs, miR-MAY-251 and miR-MAK-403, originating from the EBOV Mayinga and Makona variants, respectively. From the miRDB database, miR-MAY-251 and miR-MAK-403 displayed on average more than 700 potential human host target candidates, 25% of which had a confidence score higher than 80%. By RT-qPCR and dual luciferase assays, we assessed the potential regulatory effect of these two EBOV miRNAs on selected host mRNA targets. Further analysis of Panther pathways unveiled that these two EBOV miRNAs, in addition to general regulatory functions, can potentially target genes involved in the hemorrhagic phenotype, regulation of viral replication and modulation of host immune defense.
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Affiliation(s)
- Idrissa Diallo
- Centre Hospitalier Universitaire de Québec Research Center/CHUL Pavilion, Quebec, QC G1V 4G2, Canada; (I.D.); (Z.H.); (S.G.); (E.V.); (J.H.)
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada
| | - Zeinab Husseini
- Centre Hospitalier Universitaire de Québec Research Center/CHUL Pavilion, Quebec, QC G1V 4G2, Canada; (I.D.); (Z.H.); (S.G.); (E.V.); (J.H.)
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada
| | - Sara Guellal
- Centre Hospitalier Universitaire de Québec Research Center/CHUL Pavilion, Quebec, QC G1V 4G2, Canada; (I.D.); (Z.H.); (S.G.); (E.V.); (J.H.)
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada
| | - Elodie Vion
- Centre Hospitalier Universitaire de Québec Research Center/CHUL Pavilion, Quebec, QC G1V 4G2, Canada; (I.D.); (Z.H.); (S.G.); (E.V.); (J.H.)
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada
| | - Jeffrey Ho
- Centre Hospitalier Universitaire de Québec Research Center/CHUL Pavilion, Quebec, QC G1V 4G2, Canada; (I.D.); (Z.H.); (S.G.); (E.V.); (J.H.)
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada
| | - Robert A. Kozak
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3B 3M9, Canada;
- Division of Microbiology, Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Gary P. Kobinger
- Galveston National Laboratory, Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX 77550, USA;
| | - Patrick Provost
- Centre Hospitalier Universitaire de Québec Research Center/CHUL Pavilion, Quebec, QC G1V 4G2, Canada; (I.D.); (Z.H.); (S.G.); (E.V.); (J.H.)
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada
- Correspondence: ; Tel.: +1-418-525-4444 (ext. 48842)
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ALV-miRNA-p19-01 Promotes Viral Replication via Targeting Dual Specificity Phosphatase 6. Viruses 2022; 14:v14040805. [PMID: 35458535 PMCID: PMC9024826 DOI: 10.3390/v14040805] [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] [Received: 12/29/2021] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of regulatory noncoding RNAs, serving as major regulators with a sequence-specific manner in multifarious biological processes. Although a series of viral families have been proved to encode miRNAs, few reports were available regarding the function of ALV-J-encoded miRNA. Here, we reported a novel miRNA (designated ALV-miRNA-p19-01) in ALV-J-infected DF-1 cells. We found that ALV-miRNA-p19-01 is encoded by the genome of the ALV-J SCAU1903 strain (located at nucleotides site 779 to 801) in a classic miRNA biogenesis manner. The transfection of DF-1 cells with ALV-miRNA-p19-01 enhanced ALV-J replication, while the blockage of ALV-miRNA-p19-01 suppressed ALV-J replication. Furthermore, our data showed that ALV-miRNA-p19-01 promotes ALV-J replication by directly targeting the cellular gene dual specificity phosphatase 6 through regulating ERK2 activity.
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Li J, Yang S, Liu S, Chen Y, Liu H, Su Y, Liu R, Cui Y, Song Y, Teng Y, Wang T. Transcriptomic Profiling Reveals a Role for TREM-1 Activation in Enterovirus D68 Infection-Induced Proinflammatory Responses. Front Immunol 2021; 12:749618. [PMID: 34887856 PMCID: PMC8650217 DOI: 10.3389/fimmu.2021.749618] [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: 07/29/2021] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
Increasing cases related to the pathogenicity of Enterovirus D68 (EV-D68) have made it a growing worldwide public health concern, especially due to increased severe respiratory illness and acute flaccid myelitis (AFM) in children. There are currently no vaccines or medicines to prevent or treat EV-D68 infections. Herein, we performed genome-wide transcriptional profiling of EV-D68-infected human rhabdomyosarcoma (RD) cells to investigate host-pathogen interplay. RNA sequencing and subsequent experiments revealed that EV-D68 infection induced a profound transcriptional dysregulation of host genes, causing significantly elevated inflammatory responses and altered antiviral immune responses. In particular, triggering receptor expressed on myeloid cells 1 (TREM-1) is involved in highly activated TREM-1 signaling processes, acting as an important mediator in EV-D68 infection, and it is related to upregulation of interleukin 8 (IL-8), IL-6, IL-12p70, IL-1β, and tumor necrosis factor alpha (TNF-α). Further results demonstrated that NF-κB p65 was essential for EV-D68-induced TREM-1 upregulation. Moreover, inhibition of the TREM1 signaling pathway by the specific inhibitor LP17 dampened activation of the p38 mitogen-activated protein kinase (MAPK) signaling cascade, suggesting that TREM-1 mainly transmits activation signals to phosphorylate p38 MAPK. Interestingly, treatment with LP17 to inhibit TREM-1 inhibited viral replication and infection. These findings imply the pathogenic mechanisms of EV-D68 and provide critical insight into therapeutic intervention in enterovirus diseases.
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Affiliation(s)
- Jinyu Li
- School of Life Sciences, Tianjin University, Tianjin, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Shan Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Sihua Liu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yulu Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hongyun Liu
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yazhi Su
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Ruicun Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yue Teng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Tao Wang
- School of Life Sciences, Tianjin University, Tianjin, China.,Institute of Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, Tianjin, China
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9
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Identification of putative microRNAs in the complete genome of Mycobacterium avium and their possible interaction with human transcripts. J Appl Genet 2021; 63:169-182. [PMID: 34677783 DOI: 10.1007/s13353-021-00666-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/05/2021] [Accepted: 10/14/2021] [Indexed: 10/20/2022]
Abstract
The grievous adversity regarding Mycobacterium avium is its ubiquitous nature. Isolation of the bacteria from drinking water, house dust, and soil, etc., is an alarming issue for the scientific community. The microRNAs are the molecular influencers of gene expression that act during the process of post transcription. A few reports claimed the existence of microRNAs or microRNA-like molecules in the prokaryotic species. Biogenesis of bacterial miRNAs requires their transport into the host cell. Subsequently, the host-encoded enzymes are exerted for the formation of bacterial mature miRNAs and their regulation. In our study, the screening of complete genome of Mycobacterium avium revealed six putative precursor microRNA sequences bearing typical secondary structures. The mature microRNAs were predicted in both arms of the secondary structures. A total of 12 possible mature microRNAs were identified in this study. The likely targets of the predicted mature miRNAs were searched in human 3' UTR. In the human transcriptome, 193 genes were possibly targeted by 12 mature miRNAs of Mycobacterium avium. The essential functionalities of the target genes included signal transduction, immune system, DNA binding, and response to stress.
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10
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Abstract
Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) has emerged as a key upstream regulator of cell death and inflammation. RIPK1-mediated signaling governs the outcome of signaling pathways initiated by tumor necrosis factor receptor 1 (TNFR1), Toll-like receptor 3 (TLR3), TLR4, retinoic acid-inducible gene 1 (RIG-I)/melanoma differentiation-associated protein 5 (MDA-5), and Z-binding protein 1 (ZBP1) by signaling for NF-κB activation, mitogen-associated protein kinase (MAPK) and interferon regulatory factor 3/7 (IRF3/7) phosphorylation, and cell death via apoptosis and necroptosis. Both cell death and inflammatory responses play a major role in controlling virus infections. Therefore, viruses have evolved multifaceted mechanisms to exploit host immune responses by targeting RIPK1. This review focuses on the current understanding of RIPK1-mediated inflammatory and cell death pathways and multiple mechanisms by which viruses manipulate these pathways by targeting RIPK1. We also discuss gaps in our knowledge regarding RIPK1-mediated signaling pathways and highlight potential avenues for future research.
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11
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Nath D, Chakraborty S. Genome wide analysis of Mycobacterium leprae for identification of putative microRNAs and their possible targets in human. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00778-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Al Bitar S, Ballouz T, Doughan S, Gali-Muhtasib H, Rizk N. Potential role of micro ribonucleic acids in screening for anal cancer in human papilloma virus and human immunodeficiency virus related malignancies. World J Gastrointest Pathophysiol 2021; 12:59-83. [PMID: 34354849 PMCID: PMC8316837 DOI: 10.4291/wjgp.v12.i4.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/24/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Despite advances in antiretroviral treatment (ART), human immunodeficiency virus (HIV) continues to be a major global public health issue owing to the increased mortality rates related to the prevalent oncogenic viruses among people living with HIV (PLWH). Human papillomavirus (HPV) is the most common sexually transmitted viral disease in both men and women worldwide. High-risk or oncogenic HPV types are associated with the development of HPV-related malignancies, including cervical, penile, and anal cancer, in addition to oral cancers. The incidence of anal squamous cell cancers is increasing among PLWH, necessitating the need for reliable screening methods in this population at risk. In fact, the currently used screening methods, including the Pap smear, are invasive and are neither sensitive nor specific. Investigators are interested in circulatory and tissue micro ribonucleic acids (miRNAs), as these small non-coding RNAs are ideal biomarkers for early detection and prognosis of cancer. Multiple miRNAs are deregulated during HIV and HPV infection and their deregulation contributes to the pathogenesis of disease. Here, we will review the molecular basis of HIV and HPV co-infections and focus on the pathogenesis and epidemiology of anal cancer in PLWH. The limitations of screening for anal cancer and the need for a reliable screening program that involves specific miRNAs with diagnostic and therapeutic values is also discussed.
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Affiliation(s)
- Samar Al Bitar
- Department of Biology, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Tala Ballouz
- Department of Internal Medicine, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon
| | - Samer Doughan
- Department of Surgery, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon
| | - Hala Gali-Muhtasib
- Department of Biology and Center for Drug Discovery, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Nesrine Rizk
- Department of Internal Medicine, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon
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13
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Nanbo A, Furuyama W, Lin Z. RNA Virus-Encoded miRNAs: Current Insights and Future Challenges. Front Microbiol 2021; 12:679210. [PMID: 34248890 PMCID: PMC8266288 DOI: 10.3389/fmicb.2021.679210] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs are small non-coding RNAs that regulate eukaryotic gene expression at the post-transcriptional level and affect a wide range of biological processes. Over the past two decades, numerous virus-encoded miRNAs have been identified. Some of them are crucial for viral replication, whereas others can help immune evasion. Recent sequencing-based bioinformatics methods have helped identify many novel miRNAs, which are encoded by RNA viruses. Unlike the well-characterized DNA virus-encoded miRNAs, the role of RNA virus-encoded miRNAs remains controversial. In this review, we first describe the current knowledge of miRNAs encoded by various RNA viruses, including newly emerging viruses. Next, we discuss how RNA virus-encoded miRNAs might facilitate viral replication, immunoevasion, and persistence in their hosts. Last, we briefly discuss the challenges in the experimental methodologies and potential applications of miRNAs for diagnosis and therapeutics.
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Affiliation(s)
- Asuka Nanbo
- Molecular and Cellular Virology, Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Wakako Furuyama
- Molecular and Cellular Virology, Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Zhen Lin
- Tulane University Health Sciences Center and Tulane Cancer Center, New Orleans, LA, United States
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14
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Satyam R, Bhardwaj T, Goel S, Jha NK, Jha SK, Nand P, Ruokolainen J, Kamal MA, Kesari KK. miRNAs in SARS-CoV 2: A Spoke in the Wheel of Pathogenesis. Curr Pharm Des 2021; 27:1628-1641. [PMID: 33023438 DOI: 10.2174/1381612826999201001200529] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/28/2020] [Accepted: 08/04/2020] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The rapid emergence of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-- CoV-2) has resulted in an increased mortality rate across the globe. However, the underlying mechanism of SARS-CoV-2 altering human immune response is still elusive. The existing literature on miRNA mediated pathogenesis of RNA virus viz. Dengue virus, West Nile virus, etc. raises a suspicion that miRNA encoded by SARS-CoV-2 might facilitate virus replication and regulate the host's gene expression at the post-transcriptional level. METHODS We investigated this possibility via computational prediction of putative miRNAs encoded by the SARS-CoV-2 genome using a novel systematic pipeline that predicts putative mature-miRNA and their targeted genes transcripts. To trace down if viral-miRNAs targeted the genes critical to the immune pathway, we assessed whether mature miRNA transcripts exhibit effective hybridization with the 3'UTR region of human gene transcripts. Conversely, we also tried to study human miRNA-mediated viral gene regulation to get insight into the miRNA mediated offense and defense mechanism of virus and its host organisms in toto. RESULTS Our analysis led us to shortlist six putative miRNAs that target, majorly, genes related to cell proliferation/ differentiation/signaling, and senescence. Nonetheless, they also target immune-related genes that directly/ indirectly orchestrate immune pathways like TNF (Tumor Necrosis Factor) signaling and Chemokine signaling pathways putatively serving as the nucleus to cytokine storms. CONCLUSION Besides, these six miRNAs were found to be conserved so far across 80 complete genomes of SARS-CoV-2 (NCBI Virus, last assessed 12 April 2020) including Indian strains that are also targeted by 7 human miRNAs and can, therefore, be exploited to develop MicroRNA-Attenuated Vaccines.
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Affiliation(s)
- Rohit Satyam
- Department of Biotechnology, Noida Institute of Engineering and Technology (NIET), Greater Noida, India
| | - Tulika Bhardwaj
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Sachin Goel
- Department of Biotechnology, Noida Institute of Engineering and Technology (NIET), Greater Noida, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | - Parma Nand
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, India
| | | | - Mohammad Amjad Kamal
- West China School of Nursing / Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
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15
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Diallo I, Ho J, Laffont B, Laugier J, Benmoussa A, Lambert M, Husseini Z, Soule G, Kozak R, Kobinger GP, Provost P. Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus. Int J Mol Sci 2021; 22:ijms22073792. [PMID: 33917562 PMCID: PMC8038836 DOI: 10.3390/ijms22073792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/27/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ebola virus (EBOV) is a virulent pathogen, notorious for inducing life-threatening hemorrhagic fever, that has been responsible for several outbreaks in Africa and remains a public health threat. Yet, its pathogenesis is still not completely understood. Although there have been numerous studies on host transcriptional response to EBOV, with an emphasis on the clinical features, the impact of EBOV infection on post-transcriptional regulatory elements, such as microRNAs (miRNAs), remains largely unexplored. MiRNAs are involved in inflammation and immunity and are believed to be important modulators of the host response to viral infection. Here, we have used small RNA sequencing (sRNA-Seq), qPCR and functional analyses to obtain the first comparative miRNA transcriptome (miRNome) of a human liver cell line (Huh7) infected with one of the following three EBOV strains: Mayinga (responsible for the first Zaire outbreak in 1976), Makona (responsible for the West Africa outbreak in 2013–2016) and the epizootic Reston (presumably innocuous to humans). Our results highlight specific miRNA-based immunity pathways and substantial differences between the strains beyond their clinical manifestation and pathogenicity. These analyses shed new light into the molecular signature of liver cells upon EBOV infection and reveal new insights into miRNA-based virus attack and host defense strategy.
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Affiliation(s)
- Idrissa Diallo
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Jeffrey Ho
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Benoit Laffont
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Jonathan Laugier
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Abderrahim Benmoussa
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Marine Lambert
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Zeinab Husseini
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
| | - Geoff Soule
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3B 3M9, Canada; (G.S.); (R.K.)
| | - Robert Kozak
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3B 3M9, Canada; (G.S.); (R.K.)
- Division of Microbiology, Department of Laboratory Medicine & Molecular Diagnostics, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada
| | - Gary P. Kobinger
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3B 3M9, Canada; (G.S.); (R.K.)
- Département de Microbiologie Médicale, Université du Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Patrick Provost
- CHU de Québec Research Center, Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec, QC G1V 4G2, Canada; (I.D.); (J.H.); (B.L.); (J.L.); (A.B.); (M.L.); (Z.H.); (G.P.K.)
- CHUQ Research Center/CHUL Pavilion, 2705 Blvd Laurier, Room T1-65, Quebec, QC G1V 4G2, Canada
- Correspondence: ; Tel.: +1-418-525-4444 (ext. 48842)
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Aydemir MN, Aydemir HB, Korkmaz EM, Budak M, Cekin N, Pinarbasi E. Computationally predicted SARS-COV-2 encoded microRNAs target NFKB, JAK/STAT and TGFB signaling pathways. GENE REPORTS 2021; 22:101012. [PMID: 33398248 PMCID: PMC7773562 DOI: 10.1016/j.genrep.2020.101012] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/27/2020] [Accepted: 12/13/2020] [Indexed: 12/13/2022]
Abstract
Recently an outbreak that emerged in Wuhan, China in December 2019, spread to the whole world in a short time and killed >1,410,000 people. It was determined that a new type of beta coronavirus called severe acute respiratory disease coronavirus type 2 (SARS-CoV-2) was causative agent of this outbreak and the disease caused by the virus was named as coronavirus disease 19 (COVID19). Despite the information obtained from the viral genome structure, many aspects of the virus-host interactions during infection is still unknown. In this study we aimed to identify SARS-CoV-2 encoded microRNAs and their cellular targets. We applied a computational method to predict miRNAs encoded by SARS-CoV-2 along with their putative targets in humans. Targets of predicted miRNAs were clustered into groups based on their biological processes, molecular function, and cellular compartments using GO and PANTHER. By using KEGG pathway enrichment analysis top pathways were identified. Finally, we have constructed an integrative pathway network analysis with target genes. We identified 40 SARS-CoV-2 miRNAs and their regulated targets. Our analysis showed that targeted genes including NFKB1, NFKBIE, JAK1-2, STAT3-4, STAT5B, STAT6, SOCS1-6, IL2, IL8, IL10, IL17, TGFBR1-2, SMAD2-4, HDAC1-6 and JARID1A-C, JARID2 play important roles in NFKB, JAK/STAT and TGFB signaling pathways as well as cells' epigenetic regulation pathways. Our results may help to understand virus-host interaction and the role of viral miRNAs during SARS-CoV-2 infection. As there is no current drug and effective treatment available for COVID19, it may also help to develop new treatment strategies.
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Key Words
- ACE-2, angiotensin-converting enzyme 2
- AKT1, AKT serine/threonine kinase 1
- BCL2, BCL2 apoptosis regulator
- CDK1, cyclin dependent kinase 1
- CDKL2, cyclin dependent kinase like 2
- COVID19, new type corona virus disease
- CTNNB1, catenin beta 1
- CXCL1, C-X-C motif chemokine ligand 1
- CXCL10, C-X-C motif chemokine ligand 10
- CXCL11, C-X-C motif chemokine ligand 11
- CXCL16, C-X-C motif chemokine ligand 16
- CXCL9, C-X-C motif chemokine ligand 9
- E2F1, E2F transcription factor 1
- EIF4A1, eukaryotic translation initiation factor 4A1
- GRB2, growth factor receptor bound protein 2
- HDAC1, histone deacetylase 1
- HDAC2, histone deacetylase 2
- HDAC3, histone deacetylase 3
- HIF1A, hypoxia inducible factor 1 subunit alpha
- ICTV, International Committee on Taxonomy of Viruses
- IFNGR2, interferon gamma receptor 2
- IKBKE, inhibitor of nuclear factor kappa B kinase subunit epsilon
- IL10, interleukin 10
- IL13, interleukin 13
- IL15, interleukin 15
- IL16, interleukin 16
- IL17A, interleukin 17 A
- IL2, interleukin 2
- IL21, interleukin 21
- IL22, interleukin 22
- IL24, interleukin 24
- IL25, interleukin 25
- IL33, interleukin 33
- IL5, interleukin 5
- IL7, interleukin 7
- IL8, interleukin 8
- JAK/STAT
- JAK1, Janus kinase 1
- JAK2, Janus kinase 2
- JARID1A, lysine demethylase 5A
- JARID1B, lysine demethylase 5B
- JARID1C, lysine demethylase 5C
- JARID2, Jumonji and AT-rich interaction domain containing 2
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- MAPK1, mitogen-activated protein kinase 1
- MAPK3, mitogen-activated protein kinase 3
- MAPK4, mitogen-activated protein kinase 4
- MAPK6, mitogen-activated protein kinase 6
- MAPK7, mitogen-activated protein kinase 7
- NFKB
- NFKB1, nuclear factor kappa B subunit 1
- NFKBIE, NFKB inhibitor epsilon
- NOS3, nitric oxide synthase 3
- PANTHER, protein analysis through evolutionary relationships
- PIK3CA, phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha
- PTEN, phosphatase and tensin homolog
- RB1, RB transcriptional corepressor 1
- RHOA, ras homolog family member A
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory disease coronavirus type 2
- SMAD2, SMAD family member 2
- SMAD3, SMAD family member 3
- SMAD4, SMAD family member 4
- SOCS1, suppressor of cytokine signaling 1
- SOCS3, suppressor of cytokine signaling 3
- SOCS4, suppressor of cytokine signaling 4
- SOCS5, suppressor of cytokine signaling 5
- SOCS6, suppressor of cytokine signaling 6
- SOS1, SOS Ras/Rac guanine nucleotide exchange factor 1
- SP1, Sp1 transcription factor
- STAT3, signal transducer and activator of transcription 3
- STAT4, signal transducer and activator of transcription 4
- STAT5B, signal transducer and activator of transcription 5B
- STAT6, signal transducer and activator of transcription 6
- SUMO1, small ubiquitin like modifier 1
- SUMO2, small ubiquitin like modifier 2
- TBP, TATA-box binding protein
- TGFB
- TGFBR1, transforming growth factor beta receptor 1
- TGFBR2, transforming growth factor beta receptor 2
- TMPRSS11A, transmembrane serine protease 11A
- TMPRSS4, transmembrane serine protease 4
- TNFRSF21, TNF receptor superfamily member 21
- WHO, World Health Organization
- miRNA
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Affiliation(s)
- Merve Nur Aydemir
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Habes Bilal Aydemir
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Gaziosmanpaşa University, Tokat, Turkey
| | - Ertan Mahir Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Nilgun Cekin
- Sivas Cumhuriyet University, Faculty of Medicine, Department of Medical Biology, 58140 Sivas, Turkey
| | - Ergun Pinarbasi
- Sivas Cumhuriyet University, Faculty of Medicine, Department of Medical Biology, 58140 Sivas, Turkey
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17
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Zhan S, Wang Y, Chen X. RNA virus-encoded microRNAs: biogenesis, functions and perspectives on application. ACTA ACUST UNITED AC 2020; 2:15. [PMID: 33209991 PMCID: PMC7548135 DOI: 10.1186/s41544-020-00056-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression at the posttranscriptional level and play a crucial role in development and many diseases. The discovery of miRNAs has greatly expanded our understanding of the intricate scenario of genome-wide regulation. Over the last two decades, hundreds of virus-encoded miRNAs have been identified, most of which are from DNA viruses. Although the number of reported RNA virus-derived miRNAs is increasing, current knowledge of their roles in physiological and pathological processes has remained lacking. In this review, we discuss the biogenesis and biological functions of RNA virus- encoded miRNAs and their proposed roles in virus-host interactions and further underscore their potential value in the diagnosis and treatment of viral diseases.
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Affiliation(s)
- Shoubin Zhan
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
| | - Yanbo Wang
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
| | - Xi Chen
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology and Department of Physiology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023 China
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18
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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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Sullivan JA, Stong N, Baugh EH, McDonald MT, Takeuchi A, Shashi V. A pathogenic variant in the SETBP1 hotspot results in a forme-fruste Schinzel-Giedion syndrome. Am J Med Genet A 2020; 182:1947-1951. [PMID: 32445275 DOI: 10.1002/ajmg.a.61630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
Schinzel-Giedion syndrome (SGS; OMIM 269150) is an ultra-rare genetic disorder associated with a distinctive facial gestalt, congenital malformations, severe intellectual disability, and a progressive neurological course. The prognosis for SGS is poor, with survival beyond the first decade rare. Germline, de novo heterozygous variants in the SETBP1 gene cause SGS with the pathogenic variants associated with the SGS phenotype missense and confined to exon 4 of the gene, clustered in a four amino acid (12 bp) hotspot in the SKI homologous region of the SETBP1 protein. We report a patient with a de novo I871S variant within the SKI homologous region, which has been associated with the severe phenotype previously; but our patient has fewer features of SGS and a milder course. This is the first report of a forme-fruste phenotype in a patient with a pathogenic variant within the SGS hotspot on the SETBP1 gene and it highlights the importance of considering atypical clinical presentations in the context of severe ultra-rare genetic disorders.
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Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Akihito Takeuchi
- Department of Neonatology, Okayama Medical Center, National Hospital Organization, Okayama, Japan
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
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20
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Ebola Virus Produces Discrete Small Noncoding RNAs Independently of the Host MicroRNA Pathway Which Lack RNA Interference Activity in Bat and Human Cells. J Virol 2020; 94:JVI.01441-19. [PMID: 31852785 DOI: 10.1128/jvi.01441-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
The question as to whether RNA viruses produce bona fide microRNAs (miRNAs) during infection has been the focus of intense research and debate. Recently, several groups using computational prediction methods have independently reported possible miRNA candidates produced by Ebola virus (EBOV). Additionally, efforts to detect these predicted RNA products in samples from infected animals and humans have produced positive results. However, these studies and their conclusions are predicated on the assumption that these RNA products are actually processed through, and function within, the miRNA pathway. In the present study, we performed the first rigorous assessment of the ability of filoviruses to produce miRNA products during infection of both human and bat cells. Using next-generation sequencing, we detected several candidate miRNAs from both EBOV and the closely related Marburg virus (MARV). Focusing our validation efforts on EBOV, we found evidence contrary to the idea that these small RNA products function as miRNAs. The results of our study are important because they highlight the potential pitfalls of relying on computational methods alone for virus miRNA discovery.IMPORTANCE Here, we report the discovery, via deep sequencing, of numerous noncoding RNAs (ncRNAs) derived from both EBOV and MARV during infection of both bat and human cell lines. In addition to identifying several novel ncRNAs from both viruses, we identified two EBOV ncRNAs in our sequencing data that were near-matches to computationally predicted viral miRNAs reported in the literature. Using molecular and immunological techniques, we assessed the potential of EBOV ncRNAs to function as viral miRNAs. Importantly, we found little evidence supporting this hypothesis. Our work is significant because it represents the first rigorous assessment of the potential for EBOV to encode viral miRNAs and provides evidence contrary to the existing paradigm regarding the biological role of computationally predicted EBOV ncRNAs. Moreover, our work highlights further avenues of research regarding the nature and function of EBOV ncRNAs.
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21
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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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22
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Nehme Z, Pasquereau S, Herbein G. Targeting histone epigenetics to control viral infections. HISTONE MODIFICATIONS IN THERAPY 2020. [PMCID: PMC7453269 DOI: 10.1016/b978-0-12-816422-8.00011-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
During the past decades, many studies have significantly broadened our understanding of complex virus-host interactions to control chromatin structure and dynamics.1, 2 However, the role and impact of such modifications during viral infections is not fully revealed. Indeed, this type of regulation is bidirectional between the virus and the host. While viral replication and gene expression are significantly impacted by histone modifications on the viral chromatin,3 studies have shown that some viral pathogens dynamically manipulate cellular epigenetic factors to enhance their own survival and pathogenesis, as well as escape the immune system defense lines.4 In this dynamic, histone posttranslational modifications (PTMs) appear to play fundamental roles in the regulation of chromatin structure and recruitment of other factors.5 Genuinely, those PTMs play a vital role in lytic infection, latency reinforcement, or, conversely, viral reactivation.6 In this chapter, we will examine and review the involvement of histone modifications as well as their potential manipulation to control infections during various viral life cycle stages, highlighting their prospective implications in the clinical management of human immunodeficiency virus (HIV), herpes simplex virus (HSV), human cytomegalovirus (HCMV), hepatitis B and C viruses (HBV and HCV, respectively), Epstein–Barr virus (EBV), and other viral diseases. Targeting histone modifications is critical in setting the treatment of chronic viral infections with both lytic and latent stages (HIV, HCMV, HSV, RSV), virus-induced cancers (HBV, HCV, EBV, KSHV, HPV), and epidemic/emerging viruses (e.g. influenza virus, arboviruses).
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Oliver GF, Orang AV, Appukuttan B, Marri S, Michael MZ, Marsh GA, Smith JR. Expression of microRNA in human retinal pigment epithelial cells following infection with Zaire ebolavirus. BMC Res Notes 2019; 12:639. [PMID: 31570108 PMCID: PMC6771106 DOI: 10.1186/s13104-019-4671-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/19/2019] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Survivors of Ebola virus disease (EVD) are at risk of developing blinding intraocular inflammation-or uveitis-which is associated with retinal pigment epithelial (RPE) scarring and persistence of live Zaire ebolavirus (EBOV) within the eye. As part of a large research project aimed at defining the human RPE cell response to being infected with EBOV, this work focused on the microRNAs (miRNAs) associated with the infection. RESULTS Using RNA-sequencing, we detected 13 highly induced and 2 highly repressed human miRNAs in human ARPE-19 RPE cells infected with EBOV, including hsa-miR-1307-5p, hsa-miR-29b-3p and hsa-miR-33a-5p (up-regulated), and hsa-miR-3074-3p and hsa-miR-27b-5p (down-regulated). EBOV-miR-1-5p was also found in infected RPE cells. Through computational identification of putative miRNA targets, we predicted a broad range of regulatory activities, including effects on innate and adaptive immune responses, cellular metabolism, cell cycle progression, apoptosis and autophagy. The most highly-connected molecule in the miR-target network was leucine-rich repeat kinase 2, which is involved in neuroinflammation and lysosomal processing. Our findings should stimulate new studies on the impact of miRNA changes in EBOV-infected RPE cells to further understanding of intraocular viral persistence and the pathogenesis of uveitis in EVD survivors.
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Affiliation(s)
- Genevieve F Oliver
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Ayla V Orang
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Binoy Appukuttan
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Shashikanth Marri
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Michael Z Michael
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia
| | - Glenn A Marsh
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, 5 Portarlington Rd, Newcomb, VIC, 3219, Australia
| | - Justine R Smith
- Flinders University College of Medicine and Public Health, Flinders Medical Centre Room 4E-431, Flinders Drive, Bedford Park, SA, 5042, Australia.
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Al-Eitan LN, Alghamdi MA, Tarkhan AH, Al-Qarqaz FA. Genome-Wide CpG Island Methylation Profiles of Cutaneous Skin with and without HPV Infection. Int J Mol Sci 2019; 20:E4822. [PMID: 31569353 PMCID: PMC6801420 DOI: 10.3390/ijms20194822] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
HPV infection is one of the most commonly transmitted diseases among the global population. While it can be asymptomatic, non-genital HPV infection often gives rise to cutaneous warts, which are benign growths arising from the epidermal layer of the skin. This study aimed to produce a global analysis of the ways in which cutaneous wart formation affected the CpG island methylome. The Infinium MethylationEPIC BeadChip microarray was utilized in order to quantitatively interrogate CpG island methylation in genomic DNA extracted from 24 paired wart and normal skin samples. Differential methylation analysis was carried out by means of assigning a combined rank score using RnBeads. The 1000 top-ranking CpG islands were then subject to Locus Overlap Analysis (LOLA) for enrichment of genomic ranges, while signaling pathway analysis was carried out on the top 100 differentially methylated CpG islands. Differential methylation analysis illustrated that the most differentially methylated CpG islands in warts lay within the ITGB5, DTNB, RBFOX3, SLC6A9, and C2orf27A genes. In addition, the most enriched genomic region sets in warts were Sheffield's tissue-clustered DNase hypersensitive sites, ENCODE's segmentation and transcription factor binding sites, codex sites, and the epigenome sites from cistrome. Lastly, signaling pathway analysis showed that the GRB2, GNB1, NTRK1, AXIN1, and SKI genes were the most common regulators of the genes associated with the top 100 most differentially methylated CpG islands in warts. Our study shows that HPV-induced cutaneous warts have a clear CpG island methylation profile that sets them apart from normal skin. Such a finding could account for the temporary nature of warts and the capacity for individuals to undergo clinical remission.
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Affiliation(s)
- Laith N Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Mansour A Alghamdi
- Department of Human Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia.
| | - Amneh H Tarkhan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Firas A Al-Qarqaz
- Department of Internal Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan.
- Division of Dermatology, Department of Internal Medicine, King Abdullah University Hospital Jordan University of Science and Technology, Irbid 22110, Jordan.
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25
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Computer-designed orthogonal RNA aptamers programmed to recognize Ebola virus glycoproteins. BIOSAFETY AND HEALTH 2019. [DOI: 10.1016/j.bsheal.2019.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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26
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Wassenaar TM, Wanchai V, Buzard GS, Ussery DW. In silico Selection of Amplification Targets for Rapid Polymorphism Screening in Ebola Virus Outbreaks. Front Microbiol 2019; 10:857. [PMID: 31080442 PMCID: PMC6497787 DOI: 10.3389/fmicb.2019.00857] [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: 01/15/2019] [Accepted: 04/03/2019] [Indexed: 11/13/2022] Open
Abstract
To achieve maximum transmission chain tracking in the current Ebola outbreak, whole genome sequencing (WGS) has been proposed to provide optimal information. However, WGS remains a costly and time-intensive procedure that is poorly suited for the large numbers of samples being generated, especially under severe time and work-environment constraints as in the present DRC outbreak. To better prepare for future outbreaks, where an apparent single outbreak may actually represent overlapping outbreaks caused by independent variants, and where rapid identification of emerging new transmission chains will be essential, a more practical method would be to amplify and sequence genomic areas that reveal the highest information to differentiate EBOV variants. We have identified four highly informative polymorphism PCR sequencing targets, suitable for rapid tracing of transmission chains and identification of new sources of Ebola outbreaks, an approach which will be far more practical in the field than WGS.
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Affiliation(s)
- Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany
| | - Visanu Wanchai
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | | | - David W Ussery
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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27
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Tembo J, Simulundu E, Changula K, Handley D, Gilbert M, Chilufya M, Asogun D, Ansumana R, Kapata N, Ntoumi F, Ippolito G, Zumla A, Bates M. Recent advances in the development and evaluation of molecular diagnostics for Ebola virus disease. Expert Rev Mol Diagn 2019; 19:325-340. [PMID: 30916590 DOI: 10.1080/14737159.2019.1595592] [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] [Indexed: 01/09/2023]
Abstract
INTRODUCTION The 2014-16 outbreak of ebola virus disease (EVD) in West Africa resulted in 11,308 deaths. During the outbreak only 60% of patients were laboratory confirmed and global health authorities have identified the need for accurate and readily deployable molecular diagnostics as an important component of the ideal response to future outbreaks, to quickly identify and isolate patients. Areas covered: Currently PCR-based techniques and rapid diagnostic tests (RDTs) that detect antigens specific to EVD infections dominate the diagnostic landscape, but recent advances in biosensor technologies have led to novel approaches for the development of EVD diagnostics. This review summarises the literature and available performance data of currently available molecular diagnostics for ebolavirus, identifies knowledge gaps and maps out future priorities for research in this field. Expert opinion: While there are now a plethora of diagnostic tests for EVD at various stages of development, there is an acute need for studies to compare their clinical performance, but the sporadic nature of EVD outbreaks makes this extremely challenging, demanding pragmatic new modalities of research funding and ethical/institutional approval, to enable responsive research in outbreak settings. Retrospective head-to-head diagnostic comparisons could also be implemented using biobanked specimens, providing this can be done safely.
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Affiliation(s)
- John Tembo
- a HerpeZ , University Teaching hospital , Lusaka , Zambia
| | - Edgar Simulundu
- b Department of Disease Control , University of Zambia School of Veterinary Medicine , Lusaka , Zambia
| | - Katendi Changula
- b Department of Disease Control , University of Zambia School of Veterinary Medicine , Lusaka , Zambia
| | - Dale Handley
- c School of Life Sciences , University of Lincoln , Lincoln , UK
| | - Matthew Gilbert
- c School of Life Sciences , University of Lincoln , Lincoln , UK
| | - Moses Chilufya
- a HerpeZ , University Teaching hospital , Lusaka , Zambia
| | - Danny Asogun
- d Lassa fever research institute , Irrua University Teaching Hospital , Irrua , Nigeria
| | | | - Nathan Kapata
- f Zambia National Public Health Institute , Lusaka , Zambia
| | - Francine Ntoumi
- g Fondation Congolaise pour la Recherche Médicale , Brazzaville , Republic of Congo
| | - Giuseppe Ippolito
- h National Institute for Infectious Diseases , Lazzaro Spallanzani, IRCCS , Rome , Italy
| | - Alimuddin Zumla
- i Centre for Clinical Microbiology, Division of Infection and Immunity , University College London (UCL) , London , UK.,j National Institute of Health and Research Biomedical Research Centre , UCL Hospitals National Health Service Foundation Trust , London , UK
| | - Matthew Bates
- a HerpeZ , University Teaching hospital , Lusaka , Zambia.,c School of Life Sciences , University of Lincoln , Lincoln , UK.,i Centre for Clinical Microbiology, Division of Infection and Immunity , University College London (UCL) , London , UK
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28
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Duy J, Honko AN, Altamura LA, Bixler SL, Wollen-Roberts S, Wauquier N, O'Hearn A, Mucker EM, Johnson JC, Shamblin JD, Zelko J, Botto MA, Bangura J, Coomber M, Pitt ML, Gonzalez JP, Schoepp RJ, Goff AJ, Minogue TD. Virus-encoded miRNAs in Ebola virus disease. Sci Rep 2018; 8:6480. [PMID: 29691416 PMCID: PMC5915558 DOI: 10.1038/s41598-018-23916-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Ebola virus (EBOV) is a negative-strand RNA virus that replicates in the cytoplasm and causes an often-fatal hemorrhagic fever. EBOV, like other viruses, can reportedly encode its own microRNAs (miRNAs) to subvert host immune defenses. miRNAs are short noncoding RNAs that can regulate gene expression by hybridizing to multiple mRNAs, and viral miRNAs can enhance viral replication and infectivity by regulating host or viral genes. To date, only one EBOV miRNA has been examined in human infection. Here, we assayed mouse, rhesus macaque, cynomolgus macaque, and human samples infected with three EBOV variants for twelve computationally predicted viral miRNAs using RT-qPCR. Ten miRNAs aligned to EBOV variants and were detectable in the four species during disease with several viral miRNAs showing presymptomatic amplification in animal models. miRNA abundances in both the mouse and nonhuman primate models mirrored the human cohort, with miR-1-5p, miR-1-3p, and miR-T3-3p consistently at the highest levels. These striking similarities in the most abundant miRNAs during infection with different EBOV variants and hosts indicate that these miRNAs are potential valuable diagnostic markers and key effectors of EBOV pathogenesis.
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Affiliation(s)
- Janice Duy
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Anna N Honko
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Louis A Altamura
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Sandra L Bixler
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Suzanne Wollen-Roberts
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Nadia Wauquier
- Metabiota, Kenema, Sierra Leone.,MRIGlobal - Global Health Surveillance and Diagnostics, Gaithersburg, MD, USA
| | - Aileen O'Hearn
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Eric M Mucker
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Joshua C Johnson
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Joshua D Shamblin
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Justine Zelko
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Miriam A Botto
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | | | | | - M Louise Pitt
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Jean-Paul Gonzalez
- Metabiota, Washington, DC, USA.,Center of Excellence for Emerging & Zoonotic Animal Disease, Kansas State University, Manhattan, KS, USA
| | - Randal J Schoepp
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Arthur J Goff
- Virology Division, U.S. Army Medical Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Timothy D Minogue
- Diagnostic Systems Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA.
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29
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Hsu PC, Chiou BH, Huang CM. On revealing the gene targets of Ebola virus microRNAs involved in the human skin microbiome. PeerJ 2018; 6:e4138. [PMID: 29312814 PMCID: PMC5757418 DOI: 10.7717/peerj.4138] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/15/2017] [Indexed: 01/23/2023] Open
Abstract
Ebola virus, a negative-sense single-stranded RNA virus, causes severe viral hemorrhagic fever and has a high mortality rate. Histopathological and immunopathological analyses of Ebola virus have revealed that histopathological changes in skin tissue are associated with various degrees of endothelial cell swelling and necrosis. The interactions of microbes within or on a host are a crucial for the skin immune shield. The discovery of microRNAs (miRNAs) in Ebola virus implies that immune escape, endothelial cell rupture, and tissue dissolution during Ebola virus infection are a result of the effects of Ebola virus miRNAs. Keratinocytes obtained from normal skin can attach and spread through expression of the thrombospondin family of proteins, playing a role in initiation of cell-mediated immune responses in the skin. Several miRNAs have been shown to bind the 3′ untranslated region of thrombospondin mRNA, thereby controlling its stability and translational activity. In this study, we discovered short RNA sequences that may act as miRNAs from Propionibacterium acnes using a practical workflow of bioinformatics methods. Subsequently, we deciphered the common target gene. These RNA sequences tended to bind to the same thrombospondin protein, THSD4, emphasizing the potential importance of the synergistic binding of miRNAs from Ebola virus, Propionibacterium acnes, and humans to the target. These results provide important insights into the molecular mechanisms of thrombospondin proteins and miRNAs in Ebola virus infection.
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Affiliation(s)
- Pei-Chun Hsu
- Department of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Bin-Hao Chiou
- Department of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan
| | - Chun-Ming Huang
- Department of Medicine, Division of Dermatology, University of California, San Diego, CA, United States of America
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Wang ZY, Guo ZD, Li JM, Zhao ZZ, Fu YY, Zhang CM, Zhang Y, Liu LN, Qian J, Liu LN. Genome-Wide Search for Competing Endogenous RNAs Responsible for the Effects Induced by Ebola Virus Replication and Transcription Using a trVLP System. Front Cell Infect Microbiol 2017; 7:479. [PMID: 29209594 PMCID: PMC5702449 DOI: 10.3389/fcimb.2017.00479] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 11/03/2017] [Indexed: 11/18/2022] Open
Abstract
Understanding how infected cells respond to Ebola virus (EBOV) and how this response changes during the process of viral replication and transcription are very important for establishing effective antiviral strategies. In this study, we conducted a genome-wide screen to identify long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), micro RNAs (miRNAs), and mRNAs differentially expressed during replication and transcription using a tetracistronic transcription and replication-competent virus-like particle (trVLP) system that models the life cycle of EBOV in 293T cells. To characterize the expression patterns of these differentially expressed RNAs, we performed a series cluster analysis, and up- or down-regulated genes were selected to establish a gene co-expression network. Competing endogenous RNA (ceRNA) networks based on the RNAs responsible for the effects induced by EBOV replication and transcription in human cells, including circRNAs, lncRNAs, miRNAs, and mRNAs, were constructed for the first time. Based on these networks, the interaction details of circRNA-chr19 were explored. Our results demonstrated that circRNA-chr19 targeting miR-30b-3p regulated CLDN18 expression by functioning as a ceRNA. These findings may have important implications for further studies of the mechanisms of EBOV replication and transcription. These RNAs potentially have important functions and may be promising targets for EBOV therapy.
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Affiliation(s)
- Zhong-Yi Wang
- Academy of Military Medical Sciences, Beijing, China
| | - Zhen-Dong Guo
- Academy of Military Medical Sciences, Beijing, China
| | - Jia-Ming Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, China
| | | | - Ying-Ying Fu
- Academy of Military Medical Sciences, Beijing, China
| | | | - Yi Zhang
- Academy of Military Medical Sciences, Beijing, China
| | - Li-Na Liu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun, China
| | - Jun Qian
- Academy of Military Medical Sciences, Beijing, China
| | - Lin-Na Liu
- Academy of Military Medical Sciences, Beijing, China
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31
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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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32
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Computational analysis of Ebolavirus data: prospects, promises and challenges. Biochem Soc Trans 2016; 44:973-8. [DOI: 10.1042/bst20160074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 12/22/2022]
Abstract
The ongoing Ebola virus (also known as Zaire ebolavirus, a member of the Ebolavirus family) outbreak in West Africa has so far resulted in >28000 confirmed cases compared with previous Ebolavirus outbreaks that affected a maximum of a few hundred individuals. Hence, Ebolaviruses impose a much greater threat than we may have expected (or hoped). An improved understanding of the virus biology is essential to develop therapeutic and preventive measures and to be better prepared for future outbreaks by members of the Ebolavirus family. Computational investigations can complement wet laboratory research for biosafety level 4 pathogens such as Ebolaviruses for which the wet experimental capacities are limited due to a small number of appropriate containment laboratories. During the current West Africa outbreak, sequence data from many Ebola virus genomes became available providing a rich resource for computational analysis. Here, we consider the studies that have already reported on the computational analysis of these data. A range of properties have been investigated including Ebolavirus evolution and pathogenicity, prediction of micro RNAs and identification of Ebolavirus specific signatures. However, the accuracy of the results remains to be confirmed by wet laboratory experiments. Therefore, communication and exchange between computational and wet laboratory researchers is necessary to make maximum use of computational analyses and to iteratively improve these approaches.
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Pylro VS, Oliveira FS, Morais DK, Cuadros-Orellana S, Pais FSM, Medeiros JD, Geraldo JA, Gilbert J, Volpini AC, Fernandes GR. ZIKV - CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms. PLoS Negl Trop Dis 2016; 10:e0004817. [PMID: 27332714 PMCID: PMC4917180 DOI: 10.1371/journal.pntd.0004817] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/07/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In early 2015, a ZIKA Virus (ZIKV) infection outbreak was recognized in northeast Brazil, where concerns over its possible links with infant microcephaly have been discussed. Providing a causal link between ZIKV infection and birth defects is still a challenge. MicroRNAs (miRNAs) are small noncoding RNAs (sncRNAs) that regulate post-transcriptional gene expression by translational repression, and play important roles in viral pathogenesis and brain development. The potential for flavivirus-mediated miRNA signalling dysfunction in brain-tissue development provides a compelling hypothesis to test the perceived link between ZIKV and microcephaly. METHODOLOGY/PRINCIPAL FINDINGS Here, we applied in silico analyses to provide novel insights to understand how Congenital ZIKA Syndrome symptoms may be related to an imbalance in miRNAs function. Moreover, following World Health Organization (WHO) recommendations, we have assembled a database to help target investigations of the possible relationship between ZIKV symptoms and miRNA-mediated human gene expression. CONCLUSIONS/SIGNIFICANCE We have computationally predicted both miRNAs encoded by ZIKV able to target genes in the human genome and cellular (human) miRNAs capable of interacting with ZIKV genomes. Our results represent a step forward in the ZIKV studies, providing new insights to support research in this field and identify potential targets for therapy.
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Affiliation(s)
- Victor Satler Pylro
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Francislon Silva Oliveira
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Daniel Kumazawa Morais
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Sara Cuadros-Orellana
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Fabiano Sviatopolk-Mirsky Pais
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Julliane Dutra Medeiros
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Assis Geraldo
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Jack Gilbert
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
- Argonne National Laboratory, Institute for Genomic and Systems Biology, Argonne, Illinois, United States of America
- Department of Surgery, The University of Chicago, Chicago, Illinois, United States of America
| | - Angela Cristina Volpini
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Rocha Fernandes
- Biosystems Informatics and Genomics Group, René Rachou Research Center (CPqRR-FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
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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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Conserved differences in protein sequence determine the human pathogenicity of Ebolaviruses. Sci Rep 2016; 6:23743. [PMID: 27009368 PMCID: PMC4806318 DOI: 10.1038/srep23743] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 03/14/2016] [Indexed: 12/23/2022] Open
Abstract
Reston viruses are the only Ebolaviruses that are not pathogenic in humans. We analyzed 196 Ebolavirus genomes and identified specificity determining positions (SDPs) in all nine Ebolavirus proteins that distinguish Reston viruses from the four human pathogenic Ebolaviruses. A subset of these SDPs will explain the differences in human pathogenicity between Reston and the other four ebolavirus species. Structural analysis was performed to identify those SDPs that are likely to have a functional effect. This analysis revealed novel functional insights in particular for Ebolavirus proteins VP40 and VP24. The VP40 SDP P85T interferes with VP40 function by altering octamer formation. The VP40 SDP Q245P affects the structure and hydrophobic core of the protein and consequently protein function. Three VP24 SDPs (T131S, M136L, Q139R) are likely to impair VP24 binding to human karyopherin alpha5 (KPNA5) and therefore inhibition of interferon signaling. Since VP24 is critical for Ebolavirus adaptation to novel hosts, and only a few SDPs distinguish Reston virus VP24 from VP24 of other Ebolaviruses, human pathogenic Reston viruses may emerge. This is of concern since Reston viruses circulate in domestic pigs and can infect humans, possibly via airborne transmission.
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