1
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Han C, Gui C, Dong S, Lan K. The Interplay between KSHV Infection and DNA-Sensing Pathways. Viruses 2024; 16:749. [PMID: 38793630 PMCID: PMC11125855 DOI: 10.3390/v16050749] [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: 04/19/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
During viral infection, the innate immune system utilizes a variety of specific intracellular sensors to detect virus-derived nucleic acids and activate a series of cellular signaling cascades that produce type I IFNs and proinflammatory cytokines and chemokines. Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic double-stranded DNA virus that has been associated with a variety of human malignancies, including Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman disease. Infection with KSHV activates various DNA sensors, including cGAS, STING, IFI16, and DExD/H-box helicases. Activation of these DNA sensors induces the innate immune response to antagonize the virus. To counteract this, KSHV has developed countless strategies to evade or inhibit DNA sensing and facilitate its own infection. This review summarizes the major DNA-triggered sensing signaling pathways and details the current knowledge of DNA-sensing mechanisms involved in KSHV infection, as well as how KSHV evades antiviral signaling pathways to successfully establish latent infection and undergo lytic reactivation.
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Affiliation(s)
- Chunyan Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430062, China
| | - Chenwu Gui
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430062, China
| | - Shuhong Dong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430062, China
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430062, China
- Department of Infectious Diseases, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
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2
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Skoufos G, Kakoulidis P, Tastsoglou S, Zacharopoulou E, Kotsira V, Miliotis M, Mavromati G, Grigoriadis D, Zioga M, Velli A, Koutou I, Karagkouni D, Stavropoulos S, Kardaras F, Lifousi A, Vavalou E, Ovsepian A, Skoulakis A, Tasoulis S, Georgakopoulos S, Plagianakos V, Hatzigeorgiou A. TarBase-v9.0 extends experimentally supported miRNA-gene interactions to cell-types and virally encoded miRNAs. Nucleic Acids Res 2024; 52:D304-D310. [PMID: 37986224 PMCID: PMC10767993 DOI: 10.1093/nar/gkad1071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/18/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
TarBase is a reference database dedicated to produce, curate and deliver high quality experimentally-supported microRNA (miRNA) targets on protein-coding transcripts. In its latest version (v9.0, https://dianalab.e-ce.uth.gr/tarbasev9), it pushes the envelope by introducing virally-encoded miRNAs, interactions leading to target-directed miRNA degradation (TDMD) events and the largest collection of miRNA-gene interactions to date in a plethora of experimental settings, tissues and cell-types. It catalogues ∼6 million entries, comprising ∼2 million unique miRNA-gene pairs, supported by 37 experimental (high- and low-yield) protocols in 172 tissues and cell-types. Interactions are annotated with rich metadata including information on genes/transcripts, miRNAs, samples, experimental contexts and publications, while millions of miRNA-binding locations are also provided at cell-type resolution. A completely re-designed interface with state-of-the-art web technologies, incorporates more features, and allows flexible and ingenious use. The new interface provides the capability to design sophisticated queries with numerous filtering criteria including cell lines, experimental conditions, cell types, experimental methods, species and/or tissues of interest. Additionally, a plethora of fine-tuning capacities have been integrated to the platform, offering the refinement of the returned interactions based on miRNA confidence and expression levels, while boundless local retrieval of the offered interactions and metadata is enabled.
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Affiliation(s)
- Giorgos Skoufos
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Panos Kakoulidis
- Dept. of Informatics and Telecommunications, National and Kapodistrian Univ. of Athens, Athens, Greece
- Biomedical Research Foundation of the Academy of Athens, 11527Athens, Greece
| | - Spyros Tastsoglou
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Elissavet Zacharopoulou
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Vasiliki Kotsira
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Marios Miliotis
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Galatea Mavromati
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Dimitris Grigoriadis
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Maria Zioga
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Angeliki Velli
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Ioanna Koutou
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Dimitra Karagkouni
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Steve Stavropoulos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Filippos S Kardaras
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Anna Lifousi
- Technical University of Denmark – Department of Health Technology, Copenhagen, Denmark
| | - Eustathia Vavalou
- Department of Biology, National and Kapodistrian University of Athens, 15784Athens, Greece
| | - Armen Ovsepian
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Anargyros Skoulakis
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
| | - Sotiris K Tasoulis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | | | - Vassilis P Plagianakos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Dept. of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
- Hellenic Pasteur Institute, Athens11521, Greece
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3
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Stribling D, Gay LA, Renne R. Hybkit: a Python API and command-line toolkit for hybrid sequence data from chimeric RNA methods. Bioinformatics 2023; 39:btad721. [PMID: 38006335 PMCID: PMC10701094 DOI: 10.1093/bioinformatics/btad721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 11/27/2023] Open
Abstract
SUMMARY Experimental methods using microRNA/target ligation have recently provided significant insights into microRNA functioning through generation of chimeric (hybrid) RNA sequences. Here, we introduce Hybkit, a Python3 API, and command-line toolkit for analysis of hybrid sequence data in the "hyb" file format to enable customizable evaluation and annotation of hybrid characteristics. The Hybkit API includes a suite of python objects for developing custom analyses of hybrid data as well as miRNA-specific analysis methods, built-in plotting of analysis results, and incorporation of predicted miRNA/target interactions in Vienna format. AVAILABILITY AND IMPLEMENTATION Hybkit is provided free and open source under the GNU GPL license at github.com/RenneLab/hybkit and archived on Zenodo (doi.org/10.5281/zenodo.7834299). Hybkit distributions are also provided via PyPI (pypi.org/project/hybkit), Conda (bioconda.github.io/recipes/hybkit/README.html), and Docker (quay.io/repository/biocontainers/hybkit).
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Affiliation(s)
- Daniel Stribling
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, United States
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, United States
| | - Lauren A Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, United States
- UF Genetics Institute, University of Florida, Gainesville, FL 32610, United States
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, United States
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4
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Gouzouasis V, Tastsoglou S, Giannakakis A, Hatzigeorgiou AG. Virus-Derived Small RNAs and microRNAs in Health and Disease. Annu Rev Biomed Data Sci 2023; 6:275-298. [PMID: 37159873 DOI: 10.1146/annurev-biodatasci-122220-111429] [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] [Indexed: 05/11/2023]
Abstract
MicroRNAs (miRNAs) are short noncoding RNAs that can regulate all steps of gene expression (induction, transcription, and translation). Several virus families, primarily double-stranded DNA viruses, encode small RNAs (sRNAs), including miRNAs. These virus-derived miRNAs (v-miRNAs) help the virus evade the host's innate and adaptive immune system and maintain an environment of chronic latent infection. In this review, the functions of the sRNA-mediated virus-host interactions are highlighted, delineating their implication in chronic stress, inflammation, immunopathology, and disease. We provide insights into the latest viral RNA-based research-in silico approaches for functional characterization of v-miRNAs and other RNA types. The latest research can assist toward the identification of therapeutic targets to combat viral infections.
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Affiliation(s)
- Vasileios Gouzouasis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- Laboratory of Molecular Genetics, Department of Immunology, Hellenic Pasteur Institute, Athens, Greece
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
| | - Spyros Tastsoglou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
| | - Antonis Giannakakis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, Athens, Greece
| | - Artemis G Hatzigeorgiou
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
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5
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Ruan K, Perez GF, Liu J, Kubat M, Hofacker I, Wuchty S, Zhai RG. MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS): a global mechanism for the regulation of alternative splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.536877. [PMID: 37425843 PMCID: PMC10327045 DOI: 10.1101/2023.04.14.536877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
While RNA secondary structures are critical to regulate alternative splicing of long-range pre-mRNA, the factors that modulate RNA structure and interfere with the recognition of the splice sites are largely unknown. Previously, we identified a small, non-coding microRNA that sufficiently affects stable stem structure formation of Nmnat pre-mRNA to regulate the outcomes of alternative splicing. However, the fundamental question remains whether such microRNA-mediated interference with RNA secondary structures is a global molecular mechanism for regulating mRNA splicing. We designed and refined a bioinformatic pipeline to predict candidate microRNAs that potentially interfere with pre-mRNA stem-loop structures, and experimentally verified splicing predictions of three different long-range pre-mRNAs in the Drosophila model system. Specifically, we observed that microRNAs can either disrupt or stabilize stem-loop structures to influence splicing outcomes. Our study suggests that MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS) is a novel regulatory mechanism for the transcriptome-wide regulation of alternative splicing, increases the repertoire of microRNA function and further indicates cellular complexity of post-transcriptional regulation. One-Sentence Summary MicroRNA-Mediated Obstruction of Stem-loop Alternative Splicing (MIMOSAS) is a novel regulatory mechanism for the transcriptome-wide regulation of alternative splicing.
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6
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Fazlalipour M, Ghoreshi ZAS, Molaei HR, Arefinia N. The Role of DNA Viruses in Human Cancer. Cancer Inform 2023; 22:11769351231154186. [PMID: 37363356 PMCID: PMC10286548 DOI: 10.1177/11769351231154186] [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: 09/08/2022] [Accepted: 01/03/2023] [Indexed: 06/28/2023] Open
Abstract
This review discusses the possible involvement of infections-associated cancers in humans, with virus infections contributing 15% to 20% of total cancer cases in humans. DNA virus encoded proteins interact with host cellular signaling pathways and control proliferation, cell death and genomic integrity viral oncoproteins are known to bind cellular Deubiquitinates (DUBs) such as cyclindromatosis tumor suppressor, ubiquitin-specific proteases 7, 11, 15 and 20, and A-20 to improve their intracellular stability and cellular signaling pathways and finally transformation. Human papillomaviruses (cervical carcinoma, oral cancer and laryngeal cancer); human polyomaviruses (mesotheliomas, brain tumors); Epstein-Barr virus (B-cell lymphoproliferative diseases and nasopharyngeal carcinoma); Kaposi's Sarcoma Herpesvirus (Kaposi's Sarcoma and primary effusion lymphomas); hepatitis B (hepatocellular carcinoma (HCC)) cause up to 20% of malignancies around the world.
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Affiliation(s)
- Mehdi Fazlalipour
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran (IPI), Tehran, Iran
- Research Center for Emerging and Reemerging Infectious diseases, Pasteur Institute of Iran (IPI), Tehran, Iran
| | | | - Hamid Reza Molaei
- Department of Medical Bacteriology and Virology, Faculty of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Nasir Arefinia
- Student Research Committee, Jiroft University of Medical Sciences, Jiroft, Iran
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7
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Sheng P, Li L, Li T, Wang Y, Hiers NM, Mejia JS, Sanchez JS, Zhou L, Xie M. Screening of Drosophila microRNA-degradation sequences reveals Argonaute1 mRNA's role in regulating miR-999. Nat Commun 2023; 14:2108. [PMID: 37055443 PMCID: PMC10102002 DOI: 10.1038/s41467-023-37819-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
MicroRNAs (miRNA) load onto AGO proteins to target mRNAs for translational repression or degradation. However, miRNA degradation can be triggered when extensively base-paired with target RNAs, which induces confirmational change of AGO and recruitment of ZSWIM8 ubiquitin ligase to mark AGO for proteasomal degradation. This target RNA-directed miRNA degradation (TDMD) mechanism appears to be evolutionarily conserved, but recent studies have focused on mammalian systems. Here, we performed AGO1-CLASH in Drosophila S2 cells, with Dora (ortholog of vertebrate ZSWIM8) knockout mediated by CRISPR-Cas9 to identify five TDMD triggers (sequences that can induce miRNA degradation). Interestingly, one trigger in the 3' UTR of AGO1 mRNA induces miR-999 degradation. CRISPR-Cas9 knockout of the AGO1 trigger in S2 cells and in Drosophila specifically elevates miR-999, with concurrent repression of the miR-999 targets. AGO1 trigger knockout flies respond poorly to hydrogen peroxide-induced stress, demonstrating the physiological importance of this TDMD event.
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Affiliation(s)
- Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Yuzhi Wang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA
| | - Jennifer S Mejia
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL, 32610, USA
| | - Jossie S Sanchez
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL, 32610, USA
| | - Lei Zhou
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, FL, 32610, USA.
- UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, 32610, USA.
- UF Health Cancer Center, University of Florida, Gainesville, FL, 32610, USA.
- UF Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
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8
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Diggins NL, Hancock MH. Viral miRNA regulation of host gene expression. Semin Cell Dev Biol 2022; 146:2-19. [PMID: 36463091 PMCID: PMC10101914 DOI: 10.1016/j.semcdb.2022.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
Viruses have evolved a multitude of mechanisms to combat barriers to productive infection in the host cell. Virally-encoded miRNAs are one such means to regulate host gene expression in ways that benefit the virus lifecycle. miRNAs are small non-coding RNAs that regulate protein expression but do not trigger the adaptive immune response, making them powerful tools encoded by viruses to regulate cellular processes. Diverse viruses encode for miRNAs but little sequence homology exists between miRNAs of different viral species. Despite this, common cellular pathways are targeted for regulation, including apoptosis, immune evasion, cell growth and differentiation. Herein we will highlight the viruses that encode miRNAs and provide mechanistic insight into how viral miRNAs aid in lytic and latent infection by targeting common cellular processes. We also highlight how viral miRNAs can mimic host cell miRNAs as well as how viral miRNAs have evolved to regulate host miRNA expression. These studies dispel the myth that viral miRNAs are subtle regulators of gene expression, and highlight the critical importance of viral miRNAs to the virus lifecycle.
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Affiliation(s)
- Nicole L Diggins
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR, USA
| | - Meaghan H Hancock
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Portland, OR, USA.
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9
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Herb S, Zeleznjak J, Hennig T, L'Hernault A, Lodha M, Jürges C, Trsan T, Juranic Lisnic V, Jonjic S, Erhard F, Krmpotic A, Dölken L. Two murine cytomegalovirus microRNAs target the major viral immediate early 3 gene. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Human cytomegalovirus is responsible for morbidity and mortality in immune compromised patients and is the leading viral cause of congenital infection. Virus-encoded microRNAs (miRNAs) represent interesting targets for novel antiviral agents. While many cellular targets that augment productive infection have been identified in recent years, regulation of viral genes such as the major viral immediate early protein 72 (IE72) by hcmv-miR-UL112-1 may contribute to both the establishment and the maintenance of latent infection. We employed photoactivated ribonucleotide-enhanced individual nucleotide resolution crosslinking (PAR-iCLIP) to identify murine cytomegalovirus (MCMV) miRNA targets during lytic infection. While the PAR-iCLIP data were of insufficient quality to obtain a comprehensive list of cellular and viral miRNA targets, the most prominent PAR-iCLIP peak in the MCMV genome mapped to the 3′ untranslated region of the major viral immediate early 3 (ie3) transcript. We show that this results from two closely positioned binding sites for the abundant MCMV miRNAs miR-M23-2-3p and miR-m01-2-3p. Their pre-expression significantly impaired viral plaque formation. However, mutation of the respective binding sites did not alter viral fitness during acute or subacute infection in vivo. Furthermore, no differences in the induction of virus-specific CD8+ T cells were observed. Future studies will probably need to go beyond studying immunocompetent laboratory mice housed in pathogen-free conditions to reveal the functional relevance of viral miRNA-mediated regulation of key viral immediate early genes.
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Affiliation(s)
- Stefanie Herb
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Jelena Zeleznjak
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Anne L'Hernault
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Manivel Lodha
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Christopher Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Tihana Trsan
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Vanda Juranic Lisnic
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Stipan Jonjic
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
| | - Astrid Krmpotic
- Department of Histology and Embryology/Center for Proteomics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51 000 Rijeka, Croatia
| | - Lars Dölken
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), 97080 Würzburg, Germany
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Versbacherstr. 7, 97078, Würzburg, Germany
- Department of Medicine, University of Cambridge, Box 157, Addenbrookes Hospital, Hills Road, Cambridge CB2 0QQ, UK
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10
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Mills WT, Eadara S, Jaffe AE, Meffert MK. SCRAP: a bioinformatic pipeline for the analysis of small chimeric RNA-seq data. RNA (NEW YORK, N.Y.) 2022; 29:rna.079240.122. [PMID: 36316086 PMCID: PMC9808574 DOI: 10.1261/rna.079240.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (sncRNAs) that function in post-transcriptional gene regulation through imperfect base pairing with mRNA targets which results in inhibition of translation and typically destabilization of bound transcripts. Sequence-based algorithms historically used to predict miRNA targets face inherent challenges in reliably reflecting in vivo interactions. Recent strategies have directly profiled miRNA-target interactions by crosslinking and ligation of sncRNAs to their targets within the RNA-induced silencing complex (RISC), followed by high throughput sequencing of the chimeric sncRNA:target RNAs. Despite the strength of these direct profiling approaches, standardized pipelines for effectively analyzing the resulting chimeric sncRNA:target RNA sequencing data are not readily available. Here we present SCRAP, a robust Small Chimeric RNA Analysis Pipeline for the bioinformatic processing of chimeric sncRNA:target RNA sequencing data. SCRAP consists of two parts, each of which are specifically optimized for the distinctive characteristics of chimeric small RNA sequencing reads: first, read processing and alignment and second, peak calling and annotation. We apply SCRAP to benchmark chimeric sncRNA:target RNA sequencing datasets generated by distinct molecular approaches, and compare SCRAP to existing chimeric RNA analysis pipelines. SCRAP has minimal hardware requirements, is cross-platform, and contains extensive annotation to broaden accessibility for processing small chimeric RNA sequencing data and enable insights about the targets of small non-coding RNAs in regulating diverse biological systems.
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11
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Serfecz JC, Hong Y, Gay LA, Shekhar R, Turner PC, Renne R. DExD/H Box Helicases DDX24 and DDX49 Inhibit Reactivation of Kaposi's Sarcoma Associated Herpesvirus by Interacting with Viral mRNAs. Viruses 2022; 14:2083. [PMID: 36298642 PMCID: PMC9609691 DOI: 10.3390/v14102083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic gammaherpesvirus that is the causative agent of primary effusion lymphoma and Kaposi's sarcoma. In healthy carriers, KSHV remains latent, but a compromised immune system can lead to lytic viral replication that increases the probability of tumorigenesis. RIG-I-like receptors (RLRs) are members of the DExD/H box helicase family of RNA binding proteins that recognize KSHV to stimulate the immune system and prevent reactivation from latency. To determine if other DExD/H box helicases can affect KSHV lytic reactivation, we performed a knock-down screen that revealed DHX29-dependent activities appear to support viral replication but, in contrast, DDX24 and DDX49 have antiviral activity. When DDX24 or DDX49 are overexpressed in BCBL-1 cells, transcription of all lytic viral genes and genome replication were significantly reduced. RNA immunoprecipitation of tagged DDX24 and DDX49 followed by next-generation sequencing revealed that the helicases bind to mostly immediate-early and early KSHV mRNAs. Transfection of expression plasmids of candidate KSHV transcripts, identified from RNA pull-down, demonstrated that KSHV mRNAs stimulate type I interferon (alpha/beta) production and affect the expression of multiple interferon-stimulated genes. Our findings reveal that host DExD/H box helicases DDX24 and DDX49 recognize gammaherpesvirus transcripts and convey an antiviral effect in the context of lytic reactivation.
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Affiliation(s)
- Jacquelyn C. Serfecz
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Yuan Hong
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lauren A. Gay
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Ritu Shekhar
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Peter C. Turner
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
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12
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Fields CJ, Li L, Hiers NM, Li T, Sheng P, Huda T, Shan J, Gay L, Gu T, Bian J, Kilberg MS, Renne R, Xie M. Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. PLoS Genet 2021; 17:e1009934. [PMID: 34914716 PMCID: PMC8675727 DOI: 10.1371/journal.pgen.1009934] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNA) are short non-coding RNAs widely implicated in gene regulation. Most metazoan miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis does not require Drosha. The functional importance of the TSS-miRNA biogenesis is uncertain. To better understand the function of TSS-miRNAs, we applied a modified Crosslinking, Ligation, and Sequencing of Hybrids on Argonaute (AGO-qCLASH) to identify the targets for TSS-miRNAs in HCT116 colorectal cancer cells with or without DROSHA knockout. We observed that miR-320a hybrids dominate in TSS-miRNA hybrids identified by AGO-qCLASH. Targets for miR-320a are enriched for the eIF2 signaling pathway, a downstream component of the unfolded protein response. Consistently, in miR-320a mimic- and antagomir- transfected cells, differentially expressed gene products are associated with eIF2 signaling. Within the AGO-qCLASH data, we identified the endoplasmic reticulum (ER) chaperone calnexin as a direct miR-320a down-regulated target, thus connecting miR-320a to the unfolded protein response. During ER stress, but not amino acid deprivation, miR-320a up-regulates ATF4, a critical transcription factor for resolving ER stress. In summary, our study investigates the targetome of the TSS-miRNAs in colorectal cancer cells and establishes miR-320a as a regulator of unfolded protein response.
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Affiliation(s)
- Christopher J. Fields
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Nicholas M. Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Taha Huda
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Jixiu Shan
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lauren Gay
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Tongjun Gu
- Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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13
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Li L, Sheng P, Li T, Fields CJ, Hiers NM, Wang Y, Li J, Guardia CM, Licht JD, Xie M. Widespread microRNA degradation elements in target mRNAs can assist the encoded proteins. Genes Dev 2021; 35:1595-1609. [PMID: 34819352 PMCID: PMC8653786 DOI: 10.1101/gad.348874.121] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022]
Abstract
Binding of microRNAs (miRNAs) to mRNAs normally results in post-transcriptional repression of gene expression. However, extensive base-pairing between miRNAs and target RNAs can trigger miRNA degradation, a phenomenon called target RNA-directed miRNA degradation (TDMD). Here, we systematically analyzed Argonaute-CLASH (cross-linking, ligation, and sequencing of miRNA-target RNA hybrids) data and identified numerous candidate TDMD triggers, focusing on their ability to induce nontemplated nucleotide addition at the miRNA 3' end. When exogenously expressed in various cell lines, eight triggers induce degradation of corresponding miRNAs. Both the TDMD base-pairing and surrounding sequences are essential for TDMD. CRISPR knockout of endogenous trigger or ZSWIM8, a ubiquitin ligase essential for TDMD, reduced miRNA degradation. Furthermore, degradation of miR-221 and miR-222 by a trigger in BCL2L11, which encodes a proapoptotic protein, enhances apoptosis. Therefore, we uncovered widespread TDMD triggers in target RNAs and demonstrated an example that could functionally cooperate with the encoded protein.
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Affiliation(s)
- Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Christopher J Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Nicholas M Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Yuzhi Wang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Jianping Li
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Division of Hematology/Oncology, University of Florida, Gainesville, Florida 32610, USA
| | - Casey M Guardia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Jonathan D Licht
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Division of Hematology/Oncology, University of Florida, Gainesville, Florida 32610, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
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14
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Gay LA, Turner PC, Renne R. Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) to Identify MicroRNA Targets. Curr Protoc 2021; 1:e257. [PMID: 34610213 PMCID: PMC8500481 DOI: 10.1002/cpz1.257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This protocol was designed to identify microRNA (miRNA) targetomes from smaller‐input samples by performing a simplified workflow of the Cross‐Linking and Sequencing of Hybrids (CLASH) technique developed in the Tollervey group. In this ribonomics‐based technique, Cross‐Linking and Immunoprecipitation (CLIP) of Argonaute (Ago) is combined with an RNA ligase reaction that yields covalently bound “hybrids” between miRNAs and their target RNAs. While this iteration of CLIP identifies “high‐confidence” or “unambiguous” miRNA targets, the added ligation step is highly inefficient and therefore requires large numbers of cultured cells. To make this powerful approach applicable to smaller cell numbers, we created qCLASH, incorporating a workflow that performs all enzymatic reactions on bead‐bound complexes and omits gel purification of immunoprecipitated Ago complexes associated with major loss of RNA. At a sequencing depth of 100 million reads per library, which is highly feasible with rapidly decreasing sequencing costs, qCLASH, when used with three biological replicates, results in thousands of high‐confidence miRNA targets. qCLASH was first developed to identify viral miRNA targetomes of endothelial cells infected with Kaposi's sarcoma−associated herpesvirus. Since then, qCLASH has been applied to Epstein‐Barr virus− and MHV68‐infected cells, and more recently to metastatic melanoma and breast cancer cells. Currently, protocols are under development to apply qCLASH to human solid tumor specimens. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Quick Cross‐Linking and Sequencing of Hybrids (qCLASH) Support Protocol: Optimization of Ago immunoprecipitation
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Affiliation(s)
- Lauren A Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida
| | - Peter C Turner
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida.,UF Health Cancer Center, University of Florida, Gainesville, Florida.,UF Genetics Institute, University of Florida, Gainesville, Florida
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15
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Powell NR, Zhao H, Ipe J, Liu Y, Skaar TC. Mapping the miRNA-mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes. Clin Pharmacol Ther 2021; 110:1106-1118. [PMID: 34314509 PMCID: PMC9007393 DOI: 10.1002/cpt.2379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/21/2021] [Indexed: 12/21/2022]
Abstract
MiRNAs regulate the expression of hepatic genes involved in pharmacokinetics and pharmacodynamics. Genetic variants affecting miRNA binding (mirSNPs) have been associated with altered drug response, but previously used methods to identify miRNA binding sites and functional mirSNPs in pharmacogenes are indirect and limited by low throughput. We utilized the high-throughput chimeric-eCLIP assay to directly map thousands of miRNA-mRNA interactions and define the miRNA binding sites in primary hepatocytes. We then used the high-throughput PASSPORT-seq assay to functionally test 262 potential mirSNPs with coordinates overlapping the identified miRNA binding sites. Using chimeric-eCLIP, we identified a network of 448 miRNAs that collectively target 11,263 unique genes in primary hepatocytes pooled from 100 donors. Our data provide an extensive map of miRNA binding of each gene, including pharmacogenes, expressed in primary hepatocytes. For example, we identified the hsa-mir-27b-DPYD interaction at a previously validated binding site. A second example is our identification of 19 unique miRNAs that bind to CYP2B6 across 20 putative binding sites on the transcript. Using PASSPORT-seq, we then identified 24 mirSNPs that functionally impacted reporter mRNA levels. To our knowledge, this is the most comprehensive identification of miRNA binding sites in pharmacogenes. Combining chimeric-eCLIP with PASSPORT-seq successfully identified functional mirSNPs in pharmacogenes that may affect transcript levels through altered miRNA binding. These results provide additional insights into potential mechanisms contributing to interindividual variability in drug response.
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Affiliation(s)
- Nicholas R. Powell
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis, Indiana, USA
| | - Harrison Zhao
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, USA
| | - Joseph Ipe
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis, Indiana, USA
| | - Yunlong Liu
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, Indiana, USA
| | - Todd C. Skaar
- Indiana University School of Medicine, Department of Medicine, Division of Clinical Pharmacology, Indianapolis, Indiana, USA
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16
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Stribling D, Lei Y, Guardia CM, Li L, Fields CJ, Nowialis P, Opavsky R, Renne R, Xie M. A noncanonical microRNA derived from the snaR-A noncoding RNA targets a metastasis inhibitor. RNA (NEW YORK, N.Y.) 2021; 27:694-709. [PMID: 33795480 PMCID: PMC8127991 DOI: 10.1261/rna.078694.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/24/2021] [Indexed: 05/04/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that function as critical posttranscriptional regulators in various biological processes. While most miRNAs are generated from processing of long primary transcripts via sequential Drosha and Dicer cleavage, some miRNAs that bypass Drosha cleavage can be transcribed as part of another small noncoding RNA. Here, we develop the target-oriented miRNA discovery (TOMiD) bioinformatic analysis method to identify Drosha-independent miRNAs from Argonaute crosslinking and sequencing of hybrids (Ago-CLASH) data sets. Using this technique, we discovered a novel miRNA derived from a primate specific noncoding RNA, the small NF90 associated RNA A (snaR-A). The miRNA derived from snaR-A (miR-snaR) arises independently of Drosha processing but requires Exportin-5 and Dicer for biogenesis. We identify that miR-snaR is concurrently up-regulated with the full snaR-A transcript in cancer cells. Functionally, miR-snaR associates with Ago proteins and targets NME1, a key metastasis inhibitor, contributing to snaR-A's role in promoting cancer cell migration. Our findings suggest a functional link between a novel miRNA and its precursor noncoding RNA.
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Affiliation(s)
- Daniel Stribling
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- UF Informatics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Yi Lei
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Casey M Guardia
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Christopher J Fields
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Pawel Nowialis
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Rene Opavsky
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- UF Informatics Institute, University of Florida, Gainesville, Florida 32611, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
| | - Mingyi Xie
- UF Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
- UF Health Cancer Center, University of Florida, Gainesville, Florida 32610, USA
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Ungerleider N, Bullard W, Kara M, Wang X, Roberts C, Renne R, Tibbetts S, Flemington EK. EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog 2021; 17:e1009217. [PMID: 33956915 PMCID: PMC8130916 DOI: 10.1371/journal.ppat.1009217] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 12/11/2022] Open
Abstract
The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt’s Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response. Burkitt’s Lymphoma and gastric cancer are both associated with EBV, a prolific DNA tumor virus that latently resides in nearly all human beings. Despite mostly restricting viral gene expression to noncoding RNAs, EBV has important influences on the fitness of infected tumor cells. Here, we show that the miRNA class of viral noncoding RNAs are a major viral contributor to remodeling the tumor cell regulatory machinery in patient tumor samples. First, an assessment of miRNA expression in clinical tumor samples showed that EBV miRNAs are expressed at unexpectedly high levels relative to cell miRNAs. Using a highly specific miRNA target identification approach, CLASH, we comprehensively identified both viral and cellular miRNA targets and the relative abundance of each miRNA-mRNA interaction. We also show that viral miRNAs bind to and alter the expression of their mRNA targets more effectively than their cellular miRNA counterparts. Pathway analysis of the most effectively targeted mRNAs revealed enrichment of immune signaling pathways and we show a corresponding inverse correlation between EBV miRNA expression and infiltrating immune cells in EBV positive primary tumors. Altogether, this study shows that EBV miRNAs are key regulators of the tumor cell phenotype and the immune cell microenvironment.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Whitney Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail: (ST); (EKF)
| | - Erik K. Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
- * E-mail: (ST); (EKF)
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18
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Ungerleider N, Bullard W, Kara M, Wang X, Roberts C, Renne R, Tibbetts S, Flemington EK. EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PLoS Pathog 2021; 17:e1009217. [PMID: 33956915 DOI: 10.1101/2020.12.21.423766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/18/2021] [Accepted: 04/15/2021] [Indexed: 05/21/2023] Open
Abstract
The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt's Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi's sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response.
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Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Whitney Bullard
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Xia Wang
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Claire Roberts
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, Louisiana, United States of America
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19
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Kaposi's Sarcoma-associated Herpesvirus microRNA mutants modulate cancer hallmark phenotypic differences in human endothelial cells. J Virol 2021; 95:JVI.02022-20. [PMID: 33568509 PMCID: PMC8092706 DOI: 10.1128/jvi.02022-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Kaposi's sarcoma (KS) results from the transformation of Kaposi's sarcoma-associated herpesvirus (KSHV)-infected endothelial cells. The contribution of the KSHV microRNAs (miRNAs) to the process of oncogenesis in endothelial cells has not been fully elucidated. To better understand the contributions of individual miRNAs to oncogenesis-related cellular phenotypes, we used KSHV miRNA knockout mutants, each one lacking one of the twelve miRNA genes. An additional mutant lacked all miRNAs. Since KSHV infection causes a variety of phenotypic changes in endothelial cells, we tested the mutants for their ability to effect such changes in Telomerase-Immortalized Vein Endothelial (TIVE) cells infected with each of the mutant viruses. Wild type- and mutant-infected as well as uninfected cells were evaluated for perturbations to proliferation, migration, tubule formation, and glycolysis. We found broad variation between the different viruses in these aspects. With respect to proliferation rate, ΔmiR-K12-3, ΔmiR-K12-8, and ΔmiR-K12-11 showed significant impairment. Cells infected with ΔmiR-K12-11 had reduced migration. In tubule formation, the ΔmiR-K12-5, -6, and -7 viruses were deficient. At the same time, cells infected with the ΔmiR-K12-10 virus showed dysregulated glycolysis. By combining these observations with previously published KSHV miRNA targetome lists from ribonomics data, we were able to functionally validate a number of new miRNA targets in specific pathways. As proof of concept, miR-K12-3 was shown to target Cathepsin D, a strong promoter of apoptosis. Taken together, the results demonstrate that KSHV miRNAs play different roles in inducing the phenotypic changes which are characteristic of transformed cells.Importance: Kaposi's sarcoma-associated herpesvirus (KSHV) causes Kaposi's sarcoma (KS). The contribution of KSHV microRNAs (miRNAs) to oncogenesis is not fully understood. This is particularly true for human endothelial cells, the cell type from which KS tumors are derived. Here we used a panel of KSHV miRNA knockout viruses in order to shed light on the roles of individual miRNAs in the process of transformation. Latently infected endothelial cells were studied for phenotypic changes related to cancer, including proliferation, migration, angiogenesis, glycolysis, and apoptosis. The mutant-infected cell lines displayed a wide range of phenotypes in these selected measures of oncogenesis which differed from wild type-infected cells and from each other. These results indicate that KSHV miRNAs contribute to different aspects of oncogenesis, and that each one has a unique role to play.
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Kozar I, Philippidou D, Margue C, Gay LA, Renne R, Kreis S. Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells. Cancers (Basel) 2021; 13:cancers13051096. [PMID: 33806450 PMCID: PMC7961530 DOI: 10.3390/cancers13051096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs are key post-transcriptional gene regulators often displaying aberrant expression patterns in cancer. As microRNAs are promising disease-associated biomarkers and modulators of responsiveness to anti-cancer therapies, a solid understanding of their targetome is crucial. Despite enormous research efforts, the success rates of available tools to reliably predict microRNAs (miRNA)-target interactions remains limited. To investigate the disease-associated miRNA targetome, we have applied modified cross-linking ligation and sequencing of hybrids (qCLASH) to BRAF-mutant melanoma cells. The resulting RNA-RNA hybrid molecules provide a comprehensive and unbiased snapshot of direct miRNA-target interactions. The regulatory effects on selected miRNA target genes in predicted vs. non-predicted binding regions was validated by miRNA mimic experiments. Most miRNA-target interactions deviate from the central dogma of miRNA targeting up to 60% interactions occur via non-canonical seed pairing with a strong contribution of the 3' miRNA sequence, and over 50% display a clear bias towards the coding sequence of mRNAs. miRNAs targeting the coding sequence can directly reduce gene expression (miR-34a/CD68), while the majority of non-canonical miRNA interactions appear to have roles beyond target gene suppression (miR-100/AXL). Additionally, non-mRNA targets of miRNAs (lncRNAs) whose interactions mainly occur via non-canonical binding were identified in melanoma. This first application of CLASH sequencing to cancer cells identified over 8 K distinct miRNA-target interactions in melanoma cells. Our data highlight the importance non-canonical interactions, revealing further layers of complexity of post-transcriptional gene regulation in melanoma, thus expanding the pool of miRNA-target interactions, which have so far been omitted in the cancer field.
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Affiliation(s)
- Ines Kozar
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Demetra Philippidou
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Christiane Margue
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Lauren A. Gay
- Department of Molecular Genetics and Microbiology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA; (L.A.G.); (R.R.)
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA; (L.A.G.); (R.R.)
| | - Stephanie Kreis
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
- Correspondence:
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Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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22
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Choi YB, Cousins E, Nicholas J. Novel Functions and Virus-Host Interactions Implicated in Pathogenesis and Replication of Human Herpesvirus 8. Recent Results Cancer Res 2021; 217:245-301. [PMID: 33200369 DOI: 10.1007/978-3-030-57362-1_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Human herpesvirus 8 (HHV-8) is classified as a γ2-herpesvirus and is related to Epstein-Barr virus (EBV), a γ1-herpesvirus. One important aspect of the γ-herpesviruses is their association with neoplasia, either naturally or in animal model systems. HHV-8 is associated with B-cell-derived primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD), endothelial-derived Kaposi's sarcoma (KS), and KSHV inflammatory cytokine syndrome (KICS). EBV is also associated with a number of B-cell malignancies, such as Burkitt's lymphoma, Hodgkin's lymphoma, and posttransplant lymphoproliferative disease, in addition to epithelial nasopharyngeal and gastric carcinomas. Despite the similarities between these viruses and their associated malignancies, the particular protein functions and activities involved in key aspects of virus biology and neoplastic transformation appear to be quite distinct. Indeed, HHV-8 specifies a number of proteins for which counterparts had not previously been identified in EBV, other herpesviruses, or even viruses in general, and these proteins are believed to play vital functions in virus biology and to be involved centrally in viral pathogenesis. Additionally, a set of microRNAs encoded by HHV-8 appears to modulate the expression of multiple host proteins to provide conditions conductive to virus persistence within the host and possibly contributing to HHV-8-induced neoplasia. Here, we review the molecular biology underlying these novel virus-host interactions and their potential roles in both virus biology and virus-associated disease.
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Affiliation(s)
- Young Bong Choi
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans Street, Baltimore, MD, 21287, USA.
| | - Emily Cousins
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans Street, Baltimore, MD, 21287, USA
| | - John Nicholas
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans Street, Baltimore, MD, 21287, USA
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Krawczynski K, Ouyang Y, Mouillet JF, Chu T, Coyne CB, Sadovsky Y. Unc-13 homolog D mediates an antiviral effect of the chromosome 19 microRNA cluster miR-517a. J Cell Sci 2020; 134:jcs246769. [PMID: 33093239 PMCID: PMC7687871 DOI: 10.1242/jcs.246769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/07/2020] [Indexed: 11/20/2022] Open
Abstract
The function of microRNAs (miRNAs) can be cell autonomous or communicated to other cell types and has been implicated in diverse biological processes. We previously demonstrated that miR-517a-3p (miR-517a), a highly expressed member of the chromosome 19 miRNA cluster (C19MC) that is transcribed almost exclusively in human trophoblasts, attenuates viral replication via induction of autophagy in non-trophoblastic recipient cells. However, the molecular mechanisms underlying these effects remain unknown. Here, we identified unc-13 homolog D (UNC13D) as a direct, autophagy-related gene target of miR-517a, leading to repression of UNC13D. In line with the antiviral activity of miR-517a, silencing UNC13D suppressed replication of vesicular stomatitis virus (VSV), whereas overexpression of UNC13D increased VSV levels, suggesting a role for UNC13D silencing in the antiviral activity of miR-517a. We also found that miR-517a activated NF-κB signaling in HEK-293XL cells expressing TLR8, but the effect was not specific to C19MC miRNA. Taken together, our results define mechanistic pathways that link C19MC miRNA with inhibition of viral replication.
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Affiliation(s)
- Kamil Krawczynski
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
- Department of Obstetrics and Gynecology and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yingshi Ouyang
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
- Department of Obstetrics and Gynecology and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jean-Francois Mouillet
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
- Department of Obstetrics and Gynecology and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Tianjiao Chu
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
- Department of Obstetrics and Gynecology and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Carolyn B Coyne
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Center for Microbial Pathogenesis, Children's Hospital of Pittsburgh of the University of Pittsburgh Medical Center (UPMC), Pittsburgh, PA 15224, USA
| | - Yoel Sadovsky
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
- Department of Obstetrics and Gynecology and Reproductive Science, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213, USA
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The Oncogenic Kaposi's Sarcoma-Associated Herpesvirus Encodes a Mimic of the Tumor-Suppressive miR-15/16 miRNA Family. Cell Rep 2020; 29:2961-2969.e6. [PMID: 31801064 PMCID: PMC6939447 DOI: 10.1016/j.celrep.2019.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/07/2019] [Accepted: 11/01/2019] [Indexed: 12/16/2022] Open
Abstract
Many tumor viruses encode oncogenes of cellular origin. Here, we report an oncoviral mimic of a cellular tumor suppressor. The Kaposi’s sarcoma-associated herpesvirus (KSHV) microRNA (miRNA) miR-K6-5p shares sequence similarity to the tumor-suppressive cellular miR-15/16 miRNA family. We show that miR-K6-5p inhibits cell cycle progression, a hallmark function of miR-16. miR-K6-5p regulates conserved miR-15/16 family miRNA targets, including many cell cycle regulators. Inhibition of miR-K6-5p in KSHV-transformed B cells confers a significant growth advantage. Altogether, our data show that KSHV encodes a functional mimic of miR-15/16 family miRNAs. While it is exceedingly well established that oncogenic viruses encode oncogenes of cellular origin, this is an unusual example of an oncogenic virus that encodes a viral mimic of a cellular tumor suppressor. Encoding a tumor-suppressive miRNA could help KSHV balance viral oncogene expression and thereby avoid severe pathogenesis in the healthy host. Morrison et al. report that the tumor virus KSHV encodes a mimic of a cellular tumor suppressor. KSHV miR-K6-5p phenocopies miR-16-induced cell cycle inhibition, shares mRNA targets and binding sites with miR-16, and negatively regulates proliferation in KSHV-infected cells.
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25
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MicroRNAs and Their Targetomes in Tumor-Immune Communication. Cancers (Basel) 2020; 12:cancers12082025. [PMID: 32722019 PMCID: PMC7465095 DOI: 10.3390/cancers12082025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 01/14/2023] Open
Abstract
The development of cancer is a complex and dynamically regulated multiple-step process that involves many changes in gene expression. Over the last decade, microRNAs (miRNAs), a class of short regulatory non-coding RNAs, have emerged as key molecular effectors and regulators of tumorigenesis. While aberrant expression of miRNAs or dysregulated miRNA-mediated gene regulation in tumor cells have been shown to be capable of directly promoting or inhibiting tumorigenesis, considering the well-reported role of the immune system in cancer, tumor-derived miRNAs could also impact tumor growth through regulating anti-tumor immune responses. Here, we discuss howmiRNAs can function as central mediators that influence the crosstalk between cancer and the immune system. Moreover, we also review the current progress in the development of novel experimental approaches for miRNA target identification that will facilitate our understanding of miRNA-mediated gene regulation in not only human malignancies, but also in other genetic disorders.
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Barrozo ER, Nakayama S, Singh P, Vanni EAH, Arvin AM, Neumann DM, Bloom DC. Deletion of Herpes Simplex Virus 1 MicroRNAs miR-H1 and miR-H6 Impairs Reactivation. J Virol 2020; 94:e00639-20. [PMID: 32295910 PMCID: PMC7375377 DOI: 10.1128/jvi.00639-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 04/07/2020] [Indexed: 12/13/2022] Open
Abstract
During all stages of infection, herpes simplex virus 1 (HSV-1) expresses viral microRNAs (miRNAs). There are at least 20 confirmed HSV-1 miRNAs, yet the roles of individual miRNAs in the context of viral infection remain largely uncharacterized. We constructed a recombinant virus lacking the sequences for miR-H1-5p and miR-H6-3p (17dmiR-H1/H6). The seed sequences for these miRNAs are antisense to each other and are transcribed from divergent noncoding RNAs in the latency-associated transcript (LAT) promoter region. Comparing phenotypes exhibited by the recombinant virus lacking these miRNAs to the wild type (17syn+), we found that during acute infection in cell culture, 17dmiR-H1/H6 exhibited a modest increase in viral yields. Analysis of pathogenesis in the mouse following footpad infection revealed a slight increase in virulence for 17dmiR-H1/H6 but no significant difference in the establishment or maintenance of latency. Strikingly, explant of latently infected dorsal root ganglia revealed a decreased and delayed reactivation phenotype. Further, 17dmiR-H1/H6 was severely impaired in epinephrine-induced reactivation in the rabbit ocular model. Finally, we demonstrated that deletion of miR-H1/H6 increased the accumulation of the LAT as well as several of the LAT region miRNAs. These results suggest that miR-H1/H6 plays an important role in facilitating efficient reactivation from latency.IMPORTANCE While HSV antivirals reduce the severity and duration of clinical disease in some individuals, there is no vaccine or cure. Therefore, understanding the mechanisms regulating latency and reactivation as a potential to elucidate targets for better therapeutics is important. There are at least 20 confirmed HSV-1 miRNAs, yet the roles of individual miRNAs in the context of viral infection remain largely uncharacterized. The present study focuses on two of the miRNAs (miR-H1/H6) that are encoded within the latency-associated transcript (LAT) region, a portion of the genome that has been associated with efficient reactivation. Here, we demonstrate that the deletion of the seed sequences of these miRNAs results in a severe reduction in reactivation of HSV-1 in the mouse and rabbit models. These results suggest a linkage between these miRNAs and reactivation.
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Affiliation(s)
- Enrico R Barrozo
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Sanae Nakayama
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Pankaj Singh
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Emilia A H Vanni
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Ann M Arvin
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Donna M Neumann
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David C Bloom
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
- UF Genetics Institute, University of Florida, Gainesville, Florida, USA
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Murmann AE, Bartom ET, Schipma MJ, Vilker J, Chen S, Peter ME. 6mer Seed Toxicity in Viral microRNAs. iScience 2019; 23:100737. [PMID: 31838022 PMCID: PMC7033618 DOI: 10.1016/j.isci.2019.11.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are short double-stranded noncoding RNAs (19-23 nucleotides) that regulate gene expression by suppressing mRNAs through RNA interference. Targeting is determined by the seed sequence (position 2-7/8) of the mature miRNA. A minimal G-rich seed of just six nucleotides is highly toxic to cells by targeting genes essential for cell survival. A screen of 215 miRNAs encoded by 17 human pathogenic viruses (v-miRNAs) now suggests that a number of v-miRNAs can kill cells through a G-rich 6mer sequence embedded in their seed. Specifically, we demonstrate that miR-K12-6-5p, an oncoviral mimic of the tumor suppressive miR-15/16 family encoded by human Kaposi sarcoma-associated herpes virus, harbors a noncanonical toxic 6mer seed (position 3-8) and that v-miRNAs are more likely than cellular miRNAs to utilize a noncanonical 6mer seed. Our data suggest that during evolution viruses evolved to use 6mer seed toxicity to kill cells. Tumor suppressive miR-15/16-5p with a toxic 6mer seed targets survival genes kshv-miR-K12-6-5p, a paralog of hsa-miR-15/16-5p carries an offset toxic 6mer seed A screen of 215 viral miRNAs identifies miRNAs that contain a toxic 6mer seed Many human viral miRNAs have the capacity to kill through 6mer seed toxicity
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Affiliation(s)
- Andrea E Murmann
- Division Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Matthew J Schipma
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Jacob Vilker
- Division Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Siquan Chen
- Cellular Screening Center, Institute for Genomics & Systems Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Marcus E Peter
- Division Hematology/Oncology, Department of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA.
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Park J, Zhu Y, Tao X, Brazill JM, Li C, Wuchty S, Zhai RG. MicroRNA miR-1002 Enhances NMNAT-Mediated Stress Response by Modulating Alternative Splicing. iScience 2019; 19:1048-1064. [PMID: 31522116 PMCID: PMC6745518 DOI: 10.1016/j.isci.2019.08.052] [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: 10/05/2018] [Revised: 05/07/2019] [Accepted: 08/27/2019] [Indexed: 11/30/2022] Open
Abstract
Understanding endogenous regulation of stress resistance and homeostasis maintenance is critical to developing neuroprotective therapies. Nicotinamide mononucleotide adenylyltransferase (NMNAT) is a conserved essential enzyme that confers extraordinary protection and stress resistance in many neurodegenerative disease models. Drosophila Nmnat is alternatively spliced to two mRNA variants, RA and RB. RB translates to protein isoform PD with robust protective activity and is upregulated upon stress to confer enhanced neuroprotection. The mechanisms regulating the alternative splicing and stress response of NMNAT remain unclear. We have discovered a Drosophila microRNA, dme-miR-1002, which promotes the splicing of NMNAT pre-mRNA to RB by disrupting a pre-mRNA stem-loop structure. NMNAT pre-mRNA is preferentially spliced to RA in basal conditions, whereas miR-1002 enhances NMNAT PD-mediated stress protection by binding via RISC component Argonaute1 to the pre-mRNA, facilitating the splicing switch to RB. These results outline a new process for microRNAs in regulating alternative splicing and modulating stress resistance.
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Affiliation(s)
- Joun Park
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Neuroscience, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Yi Zhu
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Xianzun Tao
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jennifer M Brazill
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Chong Li
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
| | - R Grace Zhai
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Neuroscience, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Program in Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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Sethuraman S, Thomas M, Gay LA, Renne R. Computational analysis of ribonomics datasets identifies long non-coding RNA targets of γ-herpesviral miRNAs. Nucleic Acids Res 2019; 46:8574-8589. [PMID: 29846699 PMCID: PMC6144796 DOI: 10.1093/nar/gky459] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/14/2018] [Indexed: 12/16/2022] Open
Abstract
Ribonomics experiments involving crosslinking and immuno-precipitation (CLIP) of Ago proteins have expanded the understanding of the miRNA targetome of several organisms. These techniques, collectively referred to as CLIP-seq, have been applied to identifying the mRNA targets of miRNAs expressed by Kaposi’s Sarcoma-associated herpes virus (KSHV) and Epstein–Barr virus (EBV). However, these studies focused on identifying only those RNA targets of KSHV and EBV miRNAs that are known to encode proteins. Recent studies have demonstrated that long non-coding RNAs (lncRNAs) are also targeted by miRNAs. In this study, we performed a systematic re-analysis of published datasets from KSHV- and EBV-driven cancers. We used CLIP-seq data from lymphoma cells or EBV-transformed B cells, and a crosslinking, ligation and sequencing of hybrids dataset from KSHV-infected endothelial cells, to identify novel lncRNA targets of viral miRNAs. Here, we catalog the lncRNA targetome of KSHV and EBV miRNAs, and provide a detailed in silico analysis of lncRNA–miRNA binding interactions. Viral miRNAs target several hundred lncRNAs, including a subset previously shown to be aberrantly expressed in human malignancies. In addition, we identified thousands of lncRNAs to be putative targets of human miRNAs, suggesting that miRNA–lncRNA interactions broadly contribute to the regulation of gene expression.
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Affiliation(s)
- Sunantha Sethuraman
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Merin Thomas
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Lauren A Gay
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.,UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA.,UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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Bullard WL, Kara M, Gay LA, Sethuraman S, Wang Y, Nirmalan S, Esemenli A, Feswick A, Hoffman BA, Renne R, Tibbetts SA. Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery. PLoS Pathog 2019; 15:e1007843. [PMID: 31393953 PMCID: PMC6687095 DOI: 10.1371/journal.ppat.1007843] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023] Open
Abstract
Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), establish lifelong latent infection in B cells and are associated with a variety of tumors. In addition to protein coding genes, these viruses encode numerous microRNAs (miRNAs) within their genomes. While putative host targets of EBV and KSHV miRNAs have been previously identified, the specific functions of these miRNAs during in vivo infection are largely unknown. Murine gammaherpesvirus 68 (MHV68) is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV genetic elements such as miRNAs in the context of infection and disease. However, the specific targets of MHV68 miRNAs remain completely unknown. Using a technique known as qCLASH (quick crosslinking, ligation, and sequencing of hybrids), we have now identified thousands of Ago-associated, direct miRNA-mRNA interactions during lytic infection, latent infection and reactivation from latency. Validating this approach, detailed molecular analyses of specific interactions demonstrated repression of numerous host mRNA targets of MHV68 miRNAs, including Arid1a, Ctsl, Ifitm3 and Phc3. Notably, of the 1,505 MHV68 miRNA-host mRNA targets identified in B cells, 86% were shared with either EBV or KSHV, and 64% were shared among all three viruses, demonstrating significant conservation of gammaherpesvirus miRNA targeting. Pathway analysis of MHV68 miRNA targets further revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including eIF2 Signaling, mTOR signaling and protein ubiquitination, pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs. Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), establish lifelong infections and are associated with a variety of tumors. These viruses encode numerous molecules called microRNAs (miRNAs) within their genomes, which target and suppress the products of specific genes within infected host cells. However, the function of these miRNAs during in vivo infection is largely unknown. Murine gammaherpesvirus 68 (MHV68) is a natural pathogen of rodents that is genetically related to both EBV and KSHV, and thus serves as an excellent model for the study of EBV and KSHV. Here, we describe the identification and validation of thousands of new MHV68 miRNA targets. Notably, 86% of the MHV68 miRNA targets identified were shared with either EBV or KSHV, and 64% were shared among all three viruses. Further analyses revealed enrichment of cellular pathways involved in protein synthesis and protein modification, including pathways also enriched for targets of EBV and KSHV miRNAs. These findings provide substantial new information about specific targets of MHV68 miRNAs and shed important light on likely conserved functions of gammaherpesvirus miRNAs.
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Affiliation(s)
- Whitney L. Bullard
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Mehmet Kara
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lauren A. Gay
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Sunantha Sethuraman
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Yiping Wang
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Shreya Nirmalan
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Alim Esemenli
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - April Feswick
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Brett A. Hoffman
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Scott A. Tibbetts
- Dept. of Molecular Genetics and Microbiology, UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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A Gammaherpesvirus MicroRNA Targets EWSR1 (Ewing Sarcoma Breakpoint Region 1) In Vivo To Promote Latent Infection of Germinal Center B Cells. mBio 2019; 10:mBio.00996-19. [PMID: 31363027 PMCID: PMC6667617 DOI: 10.1128/mbio.00996-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV), directly contribute to the genesis of multiple types of malignancies. In vivo, these viruses infect B cells and manipulate B cell biology to establish lifelong infection. To accomplish this, gammaherpesviruses employ an array of gene products, including miRNAs, short noncoding RNAs that bind to and repress protein synthesis from specific target mRNAs. The in vivo relevance of repression of targets of gammaherpesvirus miRNAs remains highly elusive. Here, we identified a murine gammaherpesvirus miRNA as critical for in vivo infection and validated the host mRNA EWSR1 (Ewing sarcoma breakpoint region 1) as the predominant target for this miRNA. Using a novel technology, we demonstrated that repression of EWSR1 was essential for in vivo infection of the critical B cell reservoir. These findings provide the first in vivo demonstration of the significance of repression of a specific host mRNA by a gammaherpesvirus miRNA. Gammaherpesviruses, including the human pathogens Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV), directly contribute to the genesis of multiple types of malignancies, including B cell lymphomas. In vivo, these viruses infect B cells and manipulate B cell biology to establish lifelong latent infection. To accomplish this, gammaherpesviruses employ an array of gene products, including microRNAs (miRNAs). Although numerous host mRNA targets of gammaherpesvirus miRNAs have been identified, the in vivo relevance of repression of these targets remains elusive due to species restriction. Murine gammaherpesvirus 68 (MHV68) provides a robust virus-host system to dissect the in vivo function of conserved gammaherpesvirus genetic elements. We identified here MHV68 mghv-miR-M1-7-5p as critical for in vivo infection and then validated host EWSR1 (Ewing sarcoma breakpoint region 1) as the predominant target for this miRNA. Using novel, target-specific shRNA-expressing viruses, we determined that EWSR1 repression in vivo was essential for germinal center B cell infection. These findings provide the first in vivo demonstration of the biological significance of repression of a specific host mRNA by a gammaherpesvirus miRNA.
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Zhang J, Pu XM, Xiong Y. kshv-mir-k12-1-5p promotes cell growth and metastasis by targeting SOCS6 in Kaposi's sarcoma cells. Cancer Manag Res 2019; 11:4985-4995. [PMID: 31213914 PMCID: PMC6549767 DOI: 10.2147/cmar.s198411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/07/2019] [Indexed: 12/13/2022] Open
Abstract
Background: Kaposi’s sarcoma (KS) is a highly disseminated angiogenic tumour of endothelial cells. Many deregulated miRNAs, including kshv-mir-k12-1-5p, have been identified in KS. kshv-mir-k12-1-5p plays important roles in KS. However, the underlying mechanism is not fully understood. The aim of this study was to investigate the exact functions of kshv-mir-k12-1-5p in KS cells. Materials and methods: The biological functions of kshv-mir-k12-1-5p were studied using CCK-8, apoptosis, migration and invasion assays. Bioinformatics software was used to identify the target gene (SOCS6) of kshv-mir-k12-1-5p. A dual luciferase assay, Western blot (WB) and quantitative real-time polymerase chain reaction (q-PCR) were performed to further verify the target gene. The underlying molecular mechanisms of kshv-mir-k12-1-5p in KS cells were also explored. Results: kshv-mir-k12-1-5p can promote the proliferation, migration and invasion of KS cells and inhibit cell apoptosis. Suppressor of cytokine signalling 6 (SOCS6) was identified as a direct target of kshv-mir-k12-1-5p, and kshv-mir-k12-1-5p can downregulate SOCS6 expression. In addition, knockdown of SOCS6 rescued the effects of kshv-mir-k12-1-5p inhibitor. Hence, a direct relationship between kshv-mir-k12-1-5p and SOCS6 was confirmed. Conclusions: kshv-mir-k12-1-5p promotes the malignant phenotype of KS cells by targeting SOCS6, suggesting that kshv-mir-k12-1-5p could be a potential therapeutic target for KS.
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Affiliation(s)
- Jing Zhang
- Postgraduate College of Xinjiang Medical University, Urumqi, Xinjiang, People's Republic of China.,Department of Pathology, Affiliated Traditional Chinese Medicine Hospital, Xinjiang Medical University, Urumqi, Xinjiang, People's Republic of China
| | - Xiong-Ming Pu
- Department of Dermatology and Venereology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang, People's Republic of China
| | - Yan Xiong
- Department of Pathology, Peking University First Hospital, Beijing, People's Republic of China
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Bondada MS, Yao Y, Nair V. Multifunctional miR-155 Pathway in Avian Oncogenic Virus-Induced Neoplastic Diseases. Noncoding RNA 2019; 5:ncrna5010024. [PMID: 30871221 PMCID: PMC6468363 DOI: 10.3390/ncrna5010024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/02/2019] [Accepted: 03/08/2019] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that fine-tune the responses of the cell by modulating the cell transcriptome and gene expression. MicroRNA 155 (miR-155) is a conserved multifunctional miRNA involved in multiple roles including the modulation of the immune responses. When deregulated, miR-155 can also contribute to cancer as has been demonstrated in several human malignancies such as diffuse large B cell lymphoma, chronic lymphocytic leukemia, as well as in Epstein⁻Barr virus (EBV)-induced B cell transformation. Avian oncogenic viruses such as Marek's disease virus (MDV), avian leukosis virus (ALV), and reticuloendotheliosis virus (REV) that account for more than 90% of cancers in avian species, also make use of the miR-155 pathway during oncogenesis. While oncogenic retroviruses, such as ALV, activate miR-155 by insertional activation, acutely transforming retroviruses use transduced oncogenes such as v-rel to upregulate miR-155 expression. MDV on the other hand, encodes a functional miR-155 ortholog mdv1-miR-M4, similar to the miR-155 ortholog kshv-miR-K11 present in Kaposi's sarcoma-associated herpesvirus (KSHV). We have shown that mdv1-miR-M4 is critical for the induction of MDV-induced lymphomas further demonstrating the oncogenic potential of miR-155 pathway in cancers irrespective of the diverse etiology. In this review, we discuss on our current understanding of miR-155 function in virus-induced lymphomas focusing primarily on avian oncogenic viruses.
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Affiliation(s)
- Megha Sravani Bondada
- Avian Oncogenic Viruses, The Pirbright Institute and the UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
| | - Yongxiu Yao
- Avian Oncogenic Viruses, The Pirbright Institute and the UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
| | - Venugopal Nair
- Avian Oncogenic Viruses, The Pirbright Institute and the UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, United Kingdom..
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Contemporary Ribonomics Methods for Viral microRNA Target Analysis. Noncoding RNA 2018; 4:ncrna4040031. [PMID: 30424002 PMCID: PMC6316675 DOI: 10.3390/ncrna4040031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 12/31/2022] Open
Abstract
Numerous cellular processes are regulated by microRNAs (miRNAs), both cellular and viral. Elucidating the targets of miRNAs has become an active area of research. An important method in this field is cross-linking and immunoprecipitation (CLIP), where cultured cells or tissues are UV-irradiated to cross-link protein and nucleic acid, the RNA binding protein of interest is immunoprecipitated, and the RNAs pulled down with the protein are isolated, reverse-transcribed, and analyzed by sequencing. CLIP using antibody against Argonaute (Ago), which binds to both miRNA and mRNA as they interact in RISC, has allowed researchers to uncover a large number of miRNA targets. Coupled with high-throughput sequencing, CLIP has been useful for revealing miRNA targetomes for the γ-herpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). Variants on the CLIP protocol are described, with the benefits and drawbacks of each. In particular, the most recent methods involving RNA⁻RNA ligation to join the miRNA and its RNA target have aided in target identification. Lastly, data supporting biologically meaningful interactions between miRNAs and long non-coding RNAs (lncRNAs) are reviewed. In summary, ribonomics-based miRNA targetome analysis has expanded our understanding of miRNA targeting and has provided a rich resource for EBV and KSHV research with respect to pathogenesis and tumorigenesis.
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