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Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe 2012; 10:515-26. [PMID: 22100165 DOI: 10.1016/j.chom.2011.09.012] [Citation(s) in RCA: 244] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 07/26/2011] [Accepted: 09/26/2011] [Indexed: 12/11/2022]
Abstract
Primary effusion lymphoma (PEL) is caused by Kaposi's sarcoma-associated herpesvirus (KSHV) and frequently also harbors Epstein-Barr virus (EBV). The expression of KSHV- and EBV-encoded microRNAs (miRNAs) in PELs suggests a role for these miRNAs in latency and lymphomagenesis. Using PAR-CLIP, a technology which allows the direct and transcriptome-wide identification of miRNA targets, we delineate the target sites for all viral and cellular miRNAs expressed in PEL cell lines. The resulting data set revealed that KSHV miRNAs directly target more than 2000 cellular mRNAs, including many involved in pathways relevant to KSHV pathogenesis. Moreover, 58% of these mRNAs are also targeted by EBV miRNAs, via distinct binding sites. In addition to a known viral analog of cellular miR-155, we show that KSHV encodes a viral miRNA that mimics cellular miR-142-3p function. In summary, this study identifies an extensive list of KSHV miRNA targets, which are likely to influence viral replication and pathogenesis.
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52
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Qin Z, Jakymiw A, Findlay V, Parsons C. KSHV-Encoded MicroRNAs: Lessons for Viral Cancer Pathogenesis and Emerging Concepts. Int J Cell Biol 2012; 2012:603961. [PMID: 22505930 PMCID: PMC3296157 DOI: 10.1155/2012/603961] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/05/2011] [Accepted: 12/06/2011] [Indexed: 02/04/2023] Open
Abstract
The human genome contains microRNAs (miRNAs), small noncoding RNAs that orchestrate a number of physiologic processes through regulation of gene expression. Burgeoning evidence suggests that dysregulation of miRNAs may promote disease progression and cancer pathogenesis. Virus-encoded miRNAs, exhibiting unique molecular signatures and functions, have been increasingly recognized as contributors to viral cancer pathogenesis. A large segment of the existing knowledge in this area has been generated through characterization of miRNAs encoded by the human gamma-herpesviruses, including the Kaposi's sarcoma-associated herpesvirus (KSHV). Recent studies focusing on KSHV miRNAs have led to a better understanding of viral miRNA expression in human tumors, the identification of novel pathologic check points regulated by viral miRNAs, and new insights for viral miRNA interactions with cellular ("human") miRNAs. Elucidating the functional effects of inhibiting KSHV miRNAs has also provided a foundation for further translational efforts and consideration of clinical applications. This paper summarizes recent literature outlining mechanisms for KSHV miRNA regulation of cellular function and cancer-associated pathogenesis, as well as implications for interactions between KSHV and human miRNAs that may facilitate cancer progression. Finally, insights are offered for the clinical feasibility of targeting miRNAs as a therapeutic approach for viral cancers.
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Affiliation(s)
- Zhiqiang Qin
- Department of Medicine, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St., Charleston, SC 29425, USA
- Department of Craniofacial Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA
- Key Laboratory of Arrhythmias, Ministry of Education, and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Andrew Jakymiw
- Department of Craniofacial Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA
| | - Victoria Findlay
- Department of Pathology, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St., Charleston, SC 29425, USA
| | - Chris Parsons
- Department of Medicine, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas St., Charleston, SC 29425, USA
- Department of Craniofacial Biology, Medical University of South Carolina, 173 Ashley Avenue, Charleston, SC 29425, USA
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53
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Ziegelbauer JM. Functions of Kaposi's sarcoma-associated herpesvirus microRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:623-30. [PMID: 21616184 DOI: 10.1016/j.bbagrm.2011.05.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/02/2011] [Accepted: 05/06/2011] [Indexed: 01/12/2023]
Abstract
MicroRNAs can modulate gene expression post-transcriptionally by altering mRNA stability and protein translation. Multiple DNA viruses express viral microRNAs and have been shown to modulate expression of host and viral genes. Through various methods of microRNA target identification, we are beginning to understand the various roles of viral miRNAs including viral replication, immune evasion and apoptosis. This review is focused on the roles of microRNAs expressed by Kaposi's sarcoma-associated herpesvirus or human herpesvirus 8. This article is part of a Special Issue entitled: "MicroRNAs in viral gene regulation".
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Lee HR, Lee S, Chaudhary PM, Gill P, Jung JU. Immune evasion by Kaposi's sarcoma-associated herpesvirus. Future Microbiol 2011; 5:1349-65. [PMID: 20860481 DOI: 10.2217/fmb.10.105] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Persistent viral infections are often associated with serious diseases, primarily by altering functions of the host immune system. The hallmark of Kaposi's sarcoma-associated herpesvirus (KSHV) infection is the establishment of a life-long persistent infection, which leads to several clinical, epidemiological and infectious diseases, such as Kaposi's sarcoma, a plasmablastic variant of multicentric Castleman's disease, and primary effusion lymphoma. To sustain an efficient life-long persistency, KSHV dedicates a large portion of its genome to encoding immunomodulatory proteins that antagonize the immune system of its host. In this article, we highlight the strategies KSHV uses to evade, escape and survive its battle against the host's immune system.
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Affiliation(s)
- Hye-Ra Lee
- Department of Molecular Microbiology & Immunology, University of Southern California, Los Angeles, CA 90033, USA.
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55
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Abstract
Since 2004, more than 200 microRNAs (miRNAs) have been discovered in double-stranded DNA viruses, mainly herpesviruses and polyomaviruses (Nucleic Acids Res 32:D109-D111, 2004). miRNAs are short 22 ± 3 nt RNA molecules that posttranscriptionally regulate gene expression by binding to 3'-untranslated regions (3'UTR) of target mRNAs, thereby inducing translational silencing and/or transcript degradation (Nature 431:350-355, 2004; Cell 116:281-297, 2004). Since miRNAs require only limited complementarity for binding, miRNA targets are difficult to determine (Mol Cell 27:91-105, 2007). To date, targets have only been experimentally verified for relatively few viral miRNAs, which either target viral or host cellular gene expression: For example, SV40 and related polyomaviruses encode miRNAs which target viral large T antigen expression (Nature 435:682-686, 2005; J Virol 79:13094-13104, 2005; Virology 383:183-187, 2009; J Virol 82:9823-9828, 2008) and miRNAs of α-, β-, and γ-herpesviruses have been implicated in regulating the transition from latent to lytic gene expression, a key step in the herpesvirus life cycle. Viral miRNAs have also been shown to target various host cellular genes. Although this field is just beginning to unravel the multiple roles of viral miRNA in biology and pathogenesis, the current data strongly suggest that virally encoded miRNAs are able to regulate fundamental biological processes such as immune recognition, promotion of cell survival, angiogenesis, proliferation, and cell differentiation. This chapter aims to summarize our current knowledge of viral miRNAs, their targets and function, and the challenges lying ahead to decipher their role in viral biology, pathogenesis, and for γ-herepsvirus-encoded miRNAs, potentially tumorigenesis.
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Affiliation(s)
- Karlie Plaisance-Bonstaff
- Department of Molecular Genetics and Microbiology, University of Florida Shands Cancer Center, University of Florida, Gainesville, FL, USA
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56
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Lin Z, Flemington EK. miRNAs in the pathogenesis of oncogenic human viruses. Cancer Lett 2010; 305:186-99. [PMID: 20943311 DOI: 10.1016/j.canlet.2010.08.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/25/2010] [Accepted: 08/26/2010] [Indexed: 12/21/2022]
Abstract
Tumor viruses are a class of pathogens with well established roles in the development of malignant diseases. Numerous bodies of work have highlighted miRNAs (microRNAs) as critical regulators of tumor pathways and it is clear that the dysregulation of cellular miRNA expression can promote tumor formation. Tumor viruses encode their own miRNAs and/or manipulate the expression of cellular miRNAs to modulate their host cell environment, thereby facilitating their respective infection cycles. The modulation of these miRNA responsive pathways, however, often influences certain signal transduction cascades in ways that favor tumorigenesis. In this review, we discuss the roles of virally-encoded and virally-regulated cellular miRNAs in the respective viral life cycles and in virus associated pathogenesis.
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Affiliation(s)
- Zhen Lin
- Department of Pathology, SL-79, Tulane Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA
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57
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Marshall V, Martró E, Labo N, Ray A, Wang D, Mbisa G, Bagni RK, Volfovsky N, Casabona J, Whitby D. Kaposi sarcoma (KS)-associated herpesvirus microRNA sequence analysis and KS risk in a European AIDS-KS case control study. J Infect Dis 2010; 202:1126-35. [PMID: 20715927 PMCID: PMC2932837 DOI: 10.1086/656045] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND We recently identified polymorphisms in Kaposi sarcoma-associated herpesvirus (KSHV)-encoded microRNA (miRNA) sequences from clinical subjects. Here, we examine whether any of these may contribute to KS risk in a European AIDS-KS case-control study. METHODS KSHV load in peripheral blood was determined by real-time quantitative polymerase chain reaction. Samples that had detectable viral loads were used to amplify the 2.8-kb miRNA encoding region plus a 646-bp fragment of the K12/T0.7 gene. Additionally, we characterized an 840-bp fragment of the K1 gene to determine KSHV subtypes. RESULTS KSHV DNA was detected in peripheral blood mononuclear cells of 49.6% of case patients and 6.8% of controls, and viral loads tended to be higher in case patients. Sequences from the miRNA-encoding regions were conserved overall, but distinct polymorphisms were detected, some of which occurred in primary miRNAs, pre-miRNAs, or mature miRNAs. CONCLUSIONS Patients with KS were more likely to have detectable viral loads than were controls without disease. Despite high conservation in KSHV miRNA-encoded sequences, polymorphisms were observed, including some that have been reported elsewhere. Some polymorphisms could affect mature miRNA processing and appear to be associated with KS risk.
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Affiliation(s)
- Vickie Marshall
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - Elisa Martró
- Microbiology Service, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- CIBER de Epidemiologia y Salud Publica (CIBERESP), Spain
| | - Nazzarena Labo
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - Alex Ray
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - Dian Wang
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - Georginia Mbisa
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - Rachel K. Bagni
- Molecular Detection Group, Protein Expression Laboratory, Advanced Technology Program, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - Natalia Volfovsky
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, NCI-Frederick, Frederick, MD
| | - Jordi Casabona
- Centre dEstudis Epidemiologics sobre l’ HIV/SIDS de Catalunya, Department de Salut, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Denise Whitby
- Viral Oncology Section, AIDS and Cancer Virus Program, SAIC-Frederick, NCI-Frederick, Frederick, MD
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58
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Lin YT, Kincaid RP, Arasappan D, Dowd SE, Hunicke-Smith SP, Sullivan CS. Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs. RNA (NEW YORK, N.Y.) 2010; 16:1540-1558. [PMID: 20566670 PMCID: PMC2905754 DOI: 10.1261/rna.1967910] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 04/27/2010] [Indexed: 05/29/2023]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is a human tumor virus that encodes 12 precursor microRNAs (pre-miRNAs) that give rise to 17 different known approximately 22-nucleotide (nt) effector miRNAs. Like all herpesviruses, KSHV has two modes of infection: (1) a latent mode whereby only a subset of viral genes are expressed and (2) a lytic mode during which the full remaining viral genes are expressed. To date, KSHV miRNAs have been mostly identified via analysis of cells that are undergoing latent infection. Here, we developed a method to profile small RNAs ( approximately 18-75 nt) from populations of cells undergoing predominantly lytic infection. Using two different next-generation sequencing platforms, we cloned and sequenced both pre-miRNAs and derivative miRNAs. Our analysis shows that the vast majority of viral and host 5p miRNAs are co-terminal with the 5' end of the cloned pre-miRNAs, consistent with both being defined by microprocessor cleavage. We report the complete repertoire (25 total) of 5p and 3p derivative miRNAs from all 12 previously described KSHV pre-miRNAs. Two KSHV pre-miRNAs, pre-miR-K12-8 and pre-miR-K12-12, encode abundant derivative miRNAs from the previously unreported strands of the pre-miRNA. We identify several novel small RNAs of low abundance, including viral miRNA-offset-RNAs (moRNAs), and antisense viral miRNAs (miRNA-AS) that are encoded antisense to previously reported KSHV pre-miRNAs. Finally, we observe widespread antisense transcription relative to known coding sequences during lytic replication. Despite the enormous potential to form double-stranded RNA in KSHV-infected cells, we observe no evidence for the existence of abundant viral-derived small interfering RNAs (siRNAs).
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Affiliation(s)
- Yao-Tang Lin
- Molecular Genetics and Microbiology, The University of Texas at Austin, Austin, TX 78712-0162, USA
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59
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Abstract
Latency is a state of cryptic viral infection associated with genomic persistence and highly restricted gene expression. Its hallmark is reversibility: under appropriate circumstances, expression of the entire viral genome can be induced, resulting in the production of infectious progeny. Among the small number of virus families capable of authentic latency, the herpesviruses stand out for their ability to produce such infections in every infected individual and for being completely dependent upon latency as a mode of persistence. Here, we review the molecular basis of latency, with special attention to the gamma-herpesviruses, in which the understanding of this process is most advanced.
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Affiliation(s)
- Samuel H Speck
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
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60
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Dölken L, Malterer G, Erhard F, Kothe S, Friedel CC, Suffert G, Marcinowski L, Motsch N, Barth S, Beitzinger M, Lieber D, Bailer SM, Hoffmann R, Ruzsics Z, Kremmer E, Pfeffer S, Zimmer R, Koszinowski UH, Grässer F, Meister G, Haas J. Systematic analysis of viral and cellular microRNA targets in cells latently infected with human gamma-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe 2010; 7:324-334. [PMID: 20413099 DOI: 10.1016/j.chom.2010.03.008] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 11/25/2009] [Accepted: 03/20/2010] [Indexed: 12/13/2022]
Abstract
The mRNA targets of microRNAs (miRNAs) can be identified by immunoprecipitation of Argonaute (Ago) protein-containing RNA-induced silencing complexes (RISCs) followed by microarray analysis (RIP-Chip). Here we used Ago2-based RIP-Chip to identify transcripts targeted by Kaposi's sarcoma-associated herpesvirus (KSHV) miRNAs (n = 114), Epstein-Barr virus (EBV) miRNAs (n = 44), and cellular miRNAs (n = 2337) in six latently infected or stably transduced human B cell lines. Of the six KSHV miRNA targets chosen for validation, four showed regulation via their 3'UTR, while two showed regulation via binding sites within coding sequences. Two genes governing cellular transport processes (TOMM22 and IPO7) were confirmed to be targeted by EBV miRNAs. A significant number of viral miRNA targets were upregulated in infected cells, suggesting that viral miRNAs preferentially target cellular genes induced upon infection. Transcript half-life both of cellular and viral miRNA targets negatively correlated with recruitment to RISC complexes, indicating that RIP-Chip offers a quantitative estimate of miRNA function.
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Affiliation(s)
- Lars Dölken
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Georg Malterer
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Florian Erhard
- Institute for Informatics, Ludwig-Maximilians-University Munich, Amalienstrasse 17, 80333 Munich, Germany
| | - Sheila Kothe
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Caroline C Friedel
- Institute for Informatics, Ludwig-Maximilians-University Munich, Amalienstrasse 17, 80333 Munich, Germany
| | - Guillaume Suffert
- Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, Université de Strasbourg, 67084 Strasbourg, France
| | - Lisa Marcinowski
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Natalie Motsch
- Institute of Virology, Haus 47, Universitätsklinikum des Saarlandes, 66421 Homburg/Saar, Germany
| | - Stephanie Barth
- Institute of Virology, Haus 47, Universitätsklinikum des Saarlandes, 66421 Homburg/Saar, Germany
| | - Michaela Beitzinger
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Diana Lieber
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Susanne M Bailer
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Reinhard Hoffmann
- Institute of Medical Microbiology, Technical University Munich, Trogerstrasse 30, 81675 Munich, Germany
| | - Zsolt Ruzsics
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Elisabeth Kremmer
- Helmholtz Zentrum München, Institut für Molekulare Immunologie, Marchioninistraße 25, 81377 Munich, Germany
| | - Sébastien Pfeffer
- Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, Université de Strasbourg, 67084 Strasbourg, France
| | - Ralf Zimmer
- Institute for Informatics, Ludwig-Maximilians-University Munich, Amalienstrasse 17, 80333 Munich, Germany
| | - Ulrich H Koszinowski
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany
| | - Friedrich Grässer
- Institute of Virology, Haus 47, Universitätsklinikum des Saarlandes, 66421 Homburg/Saar, Germany
| | - Gunter Meister
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürgen Haas
- Max von Pettenkofer-Institute, Ludwig-Maximilians-University Munich, Pettenkofer Strasse 9a, 80336 Munich, Germany; Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, UK.
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61
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Ganem D. KSHV and the pathogenesis of Kaposi sarcoma: listening to human biology and medicine. J Clin Invest 2010; 120:939-49. [PMID: 20364091 DOI: 10.1172/jci40567] [Citation(s) in RCA: 274] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The linkage of Kaposi sarcoma (KS) to infection by a novel human herpesvirus (Kaposi sarcoma-associated herpesvirus [KSHV]) is one of the great successes of contemporary biomedical research and was achieved by using advanced genomic technologies in a manner informed by a nuanced understanding of epidemiology and clinical investigation. Ongoing efforts to understand the molecular mechanisms by which KSHV infection predisposes to KS continue to be powerfully influenced by insights emanating from the clinic. Here, recent developments in KS pathogenesis are reviewed, with particular emphasis on clinical, pathologic, and molecular observations that highlight the many differences between this process and tumorigenesis by other oncogenic viruses.
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Affiliation(s)
- Don Ganem
- Department of Medicine and Microbiology, University of California, 513 Parnassus Ave., San Francisco, CA 91413, USA.
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62
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Affiliation(s)
- Bryan R Cullen
- Department of Molecular Genetics & Microbiology and Center for Virology, Duke University Medical Center, Durham, North Carolina, United States of America.
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63
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Bandyopadhyay S, Mitra R, Maulik U, Zhang MQ. Development of the human cancer microRNA network. SILENCE 2010; 1:6. [PMID: 20226080 PMCID: PMC2835996 DOI: 10.1186/1758-907x-1-6] [Citation(s) in RCA: 190] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 02/02/2010] [Indexed: 12/15/2022]
Abstract
BACKGROUND MicroRNAs are a class of small noncoding RNAs that are abnormally expressed in different cancer cells. Molecular signature of miRNAs in different malignancies suggests that these are not only actively involved in the pathogenesis of human cancer but also have a significant role in patients survival. The differential expression patterns of specific miRNAs in a specific cancer tissue type have been reported in hundreds of research articles. However limited attempt has been made to collate this multitude of information and obtain a global perspective of miRNA dysregulation in multiple cancer types. RESULTS In this article a cancer-miRNA network is developed by mining the literature of experimentally verified cancer-miRNA relationships. This network throws up several new and interesting biological insights which were not evident in individual experiments, but become evident when studied in the global perspective. From the network a number of cancer-miRNA modules have been identified based on a computational approach to mine associations between cancer types and miRNAs. The modules that are generated based on these association are found to have a number of common predicted target onco/tumor suppressor genes. This suggests a combinatorial effect of the module associated miRNAs on target gene regulation in selective cancer tissues or cell lines. Moreover, neighboring miRNAs (group of miRNAs that are located within 50 kb of genomic location) of these modules show similar dysregulation patterns suggesting common regulatory pathway. Besides this, neighboring miRNAs may also show a similar dysregulation patterns (differentially coexpressed) in the cancer tissues. In this study, we found that in 67% of the cancer types have at least two neighboring miRNAs showing downregulation which is statistically significant (P < 10-7, Randomization test). A similar result is obtained for the neighboring miRNAs showing upregulation in specific cancer type. These results elucidate the fact that the neighboring miRNAs might be differentially coexpressed in cancer tissues as that of the normal tissue types. Additionally, cancer-miRNA network efficiently detect hub miRNAs dysregulated in many cancer types and identify cancer specific miRNAs. Depending on the expression patterns, it is possible to identify those hubs that have strong oncogenic or tumor suppressor characteristics. CONCLUSIONS Limited work has been done towards revealing the fact that a number of miRNAs can control commonly altered regulatory pathways. However, this becomes immediately evident by accompanying the analysis of cancer-miRNA relationships in the proposed network model. These raise many unaddressed issues in miRNA research that have never been reported previously. These observations are expected to have an intense implication in cancer and may be useful for further research.
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Affiliation(s)
| | - Ramkrishna Mitra
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India
| | - Ujjwal Maulik
- Department of Computer Science and Engineering, Jadavpur University, Kolkata, India
| | - Michael Q Zhang
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST, Tsinghua University, Beijing 100084, China
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64
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Qin Z, Kearney P, Plaisance K, Parsons CH. Pivotal advance: Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded microRNA specifically induce IL-6 and IL-10 secretion by macrophages and monocytes. J Leukoc Biol 2010; 87:25-34. [PMID: 20052801 DOI: 10.1189/jlb.0409251] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Macrophages are an important source of inflammatory cytokines generated during the innate immune response,but in the microenvironment of certain tumors,macrophages promote tumor progression through their preferential secretion of cytokines that support tumor cell growth and suppress antitumoral immune responses. KSHV is the causative agent of KS and lymphomas preferentially arising in immuno compromised patients, and specific cytokines, including IL-6 and IL-10, have been implicated in KSHV-associated cancer pathogenesis. However, the contribution of KSHV-infected macrophages to the cytokine milieu within KSHV-related tumors is unclear. We found that individual KSHV-encoded miRNA induce IL-6 and IL-10 secretion independently and additively by murine macrophages and human myelomonocytic cells. Bioinformatics analysis identified KSHV miRNA binding sites formiR-K12-3 and miR-K12-7 within the 3'UTR of the basic region/leucine zipper motif transcription factor C/EBPbeta, a known regulator of IL-6 and IL-10 transcriptional activation.Subsequent immunoblot analyses revealed that miR-K12-3 and miR-K12-7 preferentially reduce expression of C/EBPbeta p20 (LIP), an isoform of C/EBPbeta known to function as a negative transcription regulator. In addition,RNA interference specifically targeting LIP induced basal secretion of IL-6 and IL-10 by macrophages.Taken together, these data support a role for KSHV miRNA in the programming of macrophage cytokine responses in favor of KSHV-related tumor progression.
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Affiliation(s)
- Zhiqiang Qin
- Department of Medicine, Hollings Cancer Center, Medical University of South Carolina,Charleston, South Carolina, USA
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65
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Bellare P, Ganem D. Regulation of KSHV lytic switch protein expression by a virus-encoded microRNA: an evolutionary adaptation that fine-tunes lytic reactivation. Cell Host Microbe 2010; 6:570-5. [PMID: 20006845 PMCID: PMC2822622 DOI: 10.1016/j.chom.2009.11.008] [Citation(s) in RCA: 198] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2009] [Revised: 08/25/2009] [Accepted: 11/24/2009] [Indexed: 12/13/2022]
Abstract
Herpesviruses encode numerous microRNAs (miRNAs), most of whose functions are unknown. The Kaposi's sarcoma-associated herpesvirus (KSHV) encodes 17 known miRNAs as part of its latency program, suggesting that these RNAs might function to regulate the latent state. Here we show that one of these KSHV miRNAs, miRK9( *), targets a sequence in the 3' untranslated region (UTR) of the mRNA encoding the major lytic switch protein (RTA), which controls viral reactivation from latency. Ectopic expression of miRK9( *) impairs RTA synthesis, while its specific antagonism in latently infected cells enhances spontaneous lytic reactivation frequency by 2- to 3-fold. Mutation of the recognition sequence in the RTA 3'UTR abolishes RTA downregulation by miRK9( *). We propose that miRNA targeting of RTA, while not the primary regulator of the lytic switch, functions like a safety mechanism on the trigger of lytic reactivation, preventing stochastic variations in basal RTA transcription from activating inappropriate entry into the lytic cycle.
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Affiliation(s)
- Priya Bellare
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
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66
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Cai Q, Verma SC, Lu J, Robertson ES. Molecular biology of Kaposi's sarcoma-associated herpesvirus and related oncogenesis. Adv Virus Res 2010; 78:87-142. [PMID: 21040832 PMCID: PMC3142360 DOI: 10.1016/b978-0-12-385032-4.00003-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Kaposi's Sarcoma-associated Herpesvirus (KSHV), also known as human herpesvirus 8 (HHV-8), is the most recently identified human tumor virus,and is associated with the pathogenesis of Kaposi's sarcoma and two lymphoproliferative disorders known to occur frequently in AIDS patients-primary effusion lymphoma and multicentric Castleman disease. In the 15 years since its discovery, intense studies have demonstrated an etiologic role for KSHV in the development of these malignancies. Here, we review the recent advances linked to understanding KSHV latent and lytic life cycle and the molecular mechanisms of KSHV-mediated oncogenesis in terms of transformation, cell signaling, cell growth and survival, angiogenesis, immune invasion and response to microenvironmental stress, and highlight the potential therapeutic targets for blocking KSHV tumorigenesis.
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Affiliation(s)
- Qiliang Cai
- Department of Microbiology, Abramson, Comprehensive Cancer Center, University of Pennsylvania Medical School, Philadelphia, Pennsylvania, USA
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67
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In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J Virol 2009; 84:695-703. [PMID: 19889781 DOI: 10.1128/jvi.02013-09] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We have used deep sequencing to analyze the pattern of viral microRNA (miRNA) expression observed in the B-cell line BC-3, which is latently infected with Kaposi's sarcoma-associated herpesvirus (KSHV). We recovered 14.6 x 10(6) total miRNA cDNA reads, of which a remarkable 92% were of KSHV origin. We detected 11 KSHV miRNAs as well as all 11 predicted miRNA or passenger strands from the miRNA duplex intermediate. One previously reported KSHV miRNA, miR-K9, was found to be mutationally inactivated. This analysis revealed that the 5' ends of 10 of the 11 KSHV miRNAs were essentially invariant, with significantly more variation being observed at the 3' end, a result which is consistent with the proposal that the 5'-proximal region of miRNAs is critical for target mRNA recognition. However, one KSHV miRNA, miR-K10-3p, was detected in two isoforms differing by 1 nucleotide (nt) at the 5' end that were present at comparable levels, and these two related KSHV miRNAs are therefore likely to target at least partially distinct mRNA populations. Finally, we also report the first detection of miRNA offset RNAs (moRs) in vertebrate somatic cells. moRs, which derive from primary miRNA (pri-miRNA) sequences that immediately flank the mature miRNA and miRNA strands, were identified flanking one or both sides of nine of the KSHV miRNAs. These data provide new insights into the pattern of miRNA processing in mammalian cells and indicate that this process is highly conserved during animal evolution.
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68
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A global analysis of evolutionary conservation among known and predicted gammaherpesvirus microRNAs. J Virol 2009; 84:716-28. [PMID: 19889779 DOI: 10.1128/jvi.01302-09] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs which posttranscriptionally regulate gene expression. The current release of the miRNA registry lists 16 viruses which encode a total of 146 miRNA hairpins. Strikingly, 139 of these are encoded by members of the herpesvirus family, suggesting an important role for miRNAs in the herpesvirus life cycle. However, with the exception of 7 miRNA hairpins known to be shared by Epstein-Barr virus (EBV) and the closely related rhesus lymphocryptovirus (rLCV), the known herpesvirus miRNAs show little evidence of evolutionary conservation. We have performed a global analysis of miRNA conservation among gammaherpesviruses which is not limited to family members known to encode miRNAs but includes also those which have not been previously analyzed. For this purpose, we have performed a computational prediction of miRNA candidates of all fully sequenced gammaherpesvirus genomes, followed by sequence/structure alignments. Our results indicate that gammaherpesvirus miRNA conservation is limited to two pairs of viral genomes. One is the already-known case of EBV and rLCV. These viruses, however, share significantly more miRNAs than previously thought, as we identified and experimentally verified 10 novel conserved as well as 7 novel nonconserved rLCV pre-miRNA hairpins. The second case consists of rhesus rhadinovirus (RRV), which is predicted to share at least 9 pre-miRNAs with the closely related Japanese macaque herpesvirus (JMHV). Although several other gammaherpesviruses are predicted to encode large numbers of clustered miRNAs at conserved genomic loci, no further examples of evolutionarily conserved miRNA sequences were found.
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69
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Role of virus-encoded microRNAs in herpesvirus biology. Trends Microbiol 2009; 17:544-53. [PMID: 19828316 DOI: 10.1016/j.tim.2009.09.002] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 09/03/2009] [Accepted: 09/11/2009] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNAs) are short RNAs of about 22 nucleotides in length that post-transcriptionally regulate gene expression by binding to 3' untranslated regions of mRNAs, thereby inducing translational silencing. Recently, more than 140 miRNAs have been identified in the genomes of herpesviruses. Deciphering their role in viral biology requires the identification of target genes, a challenging task because miRNAs require only limited complementarity. The subject of this review will be the herpesvirus miRNAs and their respective target genes that have been determined experimentally to date. These miRNAs regulate fundamental cellular processes including immunity, angiogenesis, apoptosis, and key steps in the herpesvirus life cycle, latency and the switch from latent to lytic replication.
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70
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Wen KW, Damania B. Kaposi sarcoma-associated herpesvirus (KSHV): molecular biology and oncogenesis. Cancer Lett 2009; 289:140-50. [PMID: 19651473 DOI: 10.1016/j.canlet.2009.07.004] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 07/10/2009] [Accepted: 07/13/2009] [Indexed: 11/17/2022]
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) is a double-stranded DNA herpesvirus belonging to the gamma-herpesvirinae subfamily. KSHV has been associated with the development of three neoplastic diseases: Kaposi sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman disease (MCD). In this review, we discuss the three KSHV-associated malignancies, KSHV genome, latent and lytic aspects of the viral lifecycle, putative viral oncogenes, as well as therapeutic regimens used for the treatment of KS, PEL, and MCD.
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Affiliation(s)
- Kwun Wah Wen
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
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71
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Conrad NK. Posttranscriptional gene regulation in Kaposi's sarcoma-associated herpesvirus. ADVANCES IN APPLIED MICROBIOLOGY 2009; 68:241-61. [PMID: 19426857 DOI: 10.1016/s0065-2164(09)01206-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma, primary effusion lymphoma and some cases of multicentric Castleman's disease. To understand the pathogenesis and life cycle of KSHV, significant focus has been placed on determining how KSHV factors influence viral and cellular gene expression. The importance of transcriptional regulation by KSHV is well documented, but several KSHV posttranscriptional regulators are also essential for KSHV replication and pathogenesis. KSHV miRNAs regulate translation and stability of cellular mRNAs that may be important for tumorigenesis. The ORF57 protein has been reported to enhance several posttranscriptional processes including viral mRNA export, RNA stability and pre-mRNA splicing. SOX, Kaposin B and the PAN-ENE regulate the stability of viral or cellular transcripts. Together, these observations point to the importance of posttranscriptional regulation in KSHV. With the growing appreciation of posttranscriptional regulation in cellular gene expression, it seems likely that the list of viral posttranscriptional regulatory schemes will expand as new details of KSHV gene regulation are uncovered.
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Affiliation(s)
- Nicholas K Conrad
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9048, USA.
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72
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Silencing viral microRNA as a novel antiviral therapy? J Biomed Biotechnol 2009; 2009:419539. [PMID: 19704916 PMCID: PMC2688686 DOI: 10.1155/2009/419539] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2008] [Accepted: 03/20/2009] [Indexed: 12/16/2022] Open
Abstract
Viruses are intracellular parasites that ensure their existence by converting host cells into viral particle producing entities or into hiding places rendering the virus invisible to the host immune system. Some viruses may also survive by transforming the infected cell into an immortal tumour cell. MicroRNAs are small non-coding transcripts that function as posttranscriptional regulators of gene expression. Viruses encode miRNAs that regulate expression of both cellular and viral genes, and contribute to the pathogenic properties of viruses. Hence, neutralizing the action of viral miRNAs expression by complementary single-stranded oligonucleotides or so-called anti-miRNAs may represent a strategy to combat viral infections and viral-induced pathogenesis. This review describes the miRNAs encoded by human viruses, and discusses the possible therapeutic applications of anti-miRNAs against viral diseases.
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73
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O'Hara AJ, Chugh P, Wang L, Netto EM, Luz E, Harrington WJ, Dezube BJ, Damania B, Dittmer DP. Pre-micro RNA signatures delineate stages of endothelial cell transformation in Kaposi sarcoma. PLoS Pathog 2009; 5:e1000389. [PMID: 19381257 PMCID: PMC2663814 DOI: 10.1371/journal.ppat.1000389] [Citation(s) in RCA: 57] [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: 11/04/2008] [Accepted: 03/20/2009] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNA) have emerged as key regulators of cell lineage differentiation and cancer. We used precursor miRNA profiling by a novel real-time QPCR method (i) to define progressive stages of endothelial cell transformation cumulating in Kaposi sarcoma (KS) and (ii) to identify specific miRNAs that serve as biomarkers for tumor progression. We were able to compare primary patient biopsies to well-established culture and mouse tumor models. Loss of mir-221 and gain of mir-15 expression demarked the transition from merely immortalized to fully tumorigenic endothelial cells. Mir-140 and Kaposi sarcoma–associated herpesvirus viral miRNAs increased linearly with the degree of transformation. Mir-24 emerged as a biomarker specific for KS. MicroRNAs are key regulators of cancer and development. We can use their pattern of expression to classify different cancers or in our case different stages in cancer development. We used a novel method to define progressive stages for Kaposi sarcoma (KS), which is a cancer of the endothelial cells. We identified specific precursor-miRNAs that accurately identify stages of KS tumor progression. For the first time, we were able to profile KS patient material. This is difficult to come by, but it is more closely related to the human cancer than even the best cell culture models. Our work statistically defined clusters of pre-miRNAs, each signifying one step in cancer progression. This is the first time that precursor miRNAs profiling was used to define cancer stages. It is also the first time that we have defined makers of any kind that allow us to distinguish between different types of the endothelial cancer KS. Loss of mir-221 precursor miRNA and gain of mir-15 precursor miRNA expression demarked the transition from merely immortal to fully tumorigenic cells. Mir-140 and Kaposi sarcoma–associated herpesvirus viral microRNAs increased progressively with the degree of transformation, i.e. more aggressive stages expressed higher levels of these biomarkers. High levels of the precursor microRNA mir-24 emerged as a biomarker only in patient derived KS samples, not in any of the culture models.
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Affiliation(s)
- Andrea J. O'Hara
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research at the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Pauline Chugh
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research at the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ling Wang
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research at the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Estrella Luz
- Federal University of Bahia, Salvador, Bahia, Brazil
| | - William J. Harrington
- The Viral Oncology Program, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Bruce J. Dezube
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Blossom Damania
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research at the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Dirk P. Dittmer
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research at the University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved genomic locations and are virus-specific. Virology 2009; 388:128-36. [PMID: 19328516 DOI: 10.1016/j.virol.2009.02.043] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 02/10/2009] [Accepted: 02/16/2009] [Indexed: 01/04/2023]
Abstract
Many herpesviruses, including Marek's disease viruses (MDV1 and MDV2), encode microRNAs. In this study, we report microRNAs of two related herpesviruses, infectious laryngotracheitis virus (ILTV) and herpesvirus of turkeys (HVT), as well as additional MDV2 microRNAs. The genome locations, but not microRNA sequences, are conserved among all four of these avian herpesviruses. Most are clustered in the repeats flanking the unique long region (I/TR(L)), except in ILTV which lacks these repeats. Two abundant ILTV microRNAs are antisense to the immediate early gene ICP4. A homologue of host microRNA, gga-miR-221, was found among the HVT microRNAs. Additionally, a cluster of HVT microRNAs was found in a region containing two locally duplicated segments, resulting in paralogous HVT microRNAs with 96-100% identity. The prevalence of microRNAs in the genomic repeat regions as well as in local repeats suggests the importance of genetic plasticity in herpesviruses for microRNA evolution and preservation of function.
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75
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MicroRNAs of Kaposi's sarcoma-associated herpes virus. Semin Cancer Biol 2008; 18:437-40. [DOI: 10.1016/j.semcancer.2008.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 10/16/2008] [Indexed: 11/18/2022]
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76
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Morgan R, Anderson A, Bernberg E, Kamboj S, Huang E, Lagasse G, Isaacs G, Parcells M, Meyers BC, Green PJ, Burnside J. Sequence conservation and differential expression of Marek's disease virus microRNAs. J Virol 2008; 82:12213-20. [PMID: 18842708 PMCID: PMC2593341 DOI: 10.1128/jvi.01722-08] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2008] [Accepted: 09/30/2008] [Indexed: 02/01/2023] Open
Abstract
Marek's disease virus (MDV), a herpesvirus that causes a lymphoproliferative disorder in chickens, encodes a number of microRNAs derived primarily from two locations in the MDV genome. One cluster of microRNA genes flanks the meq oncogene, and a second cluster is found within the latency-associated transcript (LAT) region. The sequences of MDV microRNAs from a collection of field and reference strains with various levels of virulence were compared and found to be highly conserved. However, microRNAs from the meq cluster were detected at higher levels in lymphomas caused by a form of the virus designated very virulent plus (vv+; strain 615K, also known as T. King) than in those caused by a less virulent (very virulent [vv]) form (RB1B). For example, levels of mdv1-miR-M4, which shares a seed sequence with miR-155, a microRNA implicated in B-cell lymphoma, were threefold higher and levels of mdv1-miR-M2*/3p were more than sixfold higher in vv+ MDV-induced tumors than in vv MDV-induced tumors. In contrast, levels of the microRNAs from the LAT cluster were equivalent in tumors produced by vv and vv+ strains. Additionally, mdv1-miR-M4 is the MDV microRNA most highly expressed in tumors, where it accounts for 72% of all MDV microRNAs, as determined by deep sequencing. These data suggest that the meq cluster microRNAs play an important role in the pathogenicity of MDV.
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Affiliation(s)
- Robin Morgan
- Department of Animal and Food Sciences, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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77
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Abstract
The two human herpesviruses that are causally associated with cancer are Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus (KSHV). Both are lymphocryptoviruses that establish latency in B lymphocytes and persist for the lifetime of the host. EBV and KSHV are both linked to a variety of lymphomas. EBV is also a causative agent or cofactor in epithelial malignancies such as nasopharyngeal carcinoma whereas Kaposi's sarcoma is of endothelial cell origin. Both viruses encode a limited number of proteins during latent replication that are important for growth transformation and evasion of the immune system. In addition, they express noncoding RNAs during both latent and lytic infection. Many of these RNAs have been highly conserved during evolution and are expressed in a wide variety of clinical settings, suggesting their fundamental importance in the viral life cycle. The function of some of these RNAs such as the nuclear EBV EBER RNAs remains elusive although they are some of the most abundant transcripts produced by each virus. Both EBV and KSHV also have recently been shown to encode and express microRNAs. The study of these viral microRNAs is just beginning although several of their cellular and viral gene targets have been established. Viral microRNAs appear to be involved in both modulation of the immune response as well as oncogenesis. Because each target gene may have many microRNAs acting on its mRNA, and each microRNA may have more than one target, there are likely to be many new discoveries regarding the complex interactions of viral microRNAs and host cell genes.
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Affiliation(s)
- Sankar Swaminathan
- University of Florida Shands Cancer Center, Gainesville, Florida 32610, USA.
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78
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O'Hara AJ, Vahrson W, Dittmer DP. Gene alteration and precursor and mature microRNA transcription changes contribute to the miRNA signature of primary effusion lymphoma. Blood 2008; 111:2347-53. [PMID: 18079361 PMCID: PMC2234063 DOI: 10.1182/blood-2007-08-104463] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Accepted: 12/05/2007] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are regulated by gene alteration, transcription, and processing. Thus far, few studies have simultaneously assessed all 3 levels of regulation. Using real-time quantitative polymerase chain reaction (QPCR)-based arrays, we determined changes in gene copy number, pre-miRNA, and mature miRNA levels for the largest set of primary effusion lymphomas (PELs) to date. We detected PEL-specific miRNA gene amplifications, and concordant changes in pre-miRNA and mature miRNA. We identified 68 PEL-specific miRNAs. This defines the miRNA signature of PEL and shows that transcriptional regulation of pre-miRNA as well as mature miRNA levels contribute nonredundant information that can be used for the classification of human tumors.
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Affiliation(s)
- Andrea J O'Hara
- Department of Microbiology and Immunology, Lineberger Comprehensive Cancer Center, Center for AIDS Research, and Curriculum in Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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