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Sun B, Yang X, Hou F, Yu X, Wang Q, Oh HS, Raja P, Pesola JM, Vanni EAH, McCarron S, Morris-Love J, Ng AHM, Church GM, Knipe DM, Coen DM, Pan D. Regulation of host and virus genes by neuronal miR-138 favours herpes simplex virus 1 latency. Nat Microbiol 2021; 6:682-696. [PMID: 33558653 PMCID: PMC8221016 DOI: 10.1038/s41564-020-00860-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 11/20/2020] [Indexed: 01/30/2023]
Abstract
MicroRNA miR-138, which is highly expressed in neurons, represses herpes simplex virus 1 (HSV-1) lytic cycle genes by targeting viral ICP0 messenger RNA, thereby promoting viral latency in mice. We found that overexpressed miR-138 also represses lytic processes independently of ICP0 in murine and human neuronal cells; therefore, we investigated whether miR-138 has targets besides ICP0. Using genome-wide RNA sequencing/photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation followed by short interfering RNA knockdown of candidate targets, we identified the host Oct-1 and Foxc1 messenger mRNAs as miR-138's targets, whose gene products are transcription factors important for HSV-1 replication in neuronal cells. OCT-1 has a known role in the initiation of HSV transcription. Overexpression of FOXC1, which was not known to affect HSV-1, promoted HSV-1 replication in murine neurons and ganglia. CRISPR-Cas9 knockout of FOXC1 reduced viral replication, lytic gene expression and miR-138 repression in murine neuronal cells. FOXC1 also collaborated with ICP0 to decrease heterochromatin on viral genes and compensated for the defect of an ICP0-null virus. In summary, miR-138 targets ICP0, Oct-1 and Foxc1 to repress HSV-1 lytic cycle genes and promote epigenetic gene silencing, which together enable favourable conditions for latent infection.
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Affiliation(s)
- Boqiang Sun
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Thermo Fisher Scientific, Shanghai, China
| | - Xuewei Yang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Innovent Biologics, Inc., Suzhou, China
| | - Fujun Hou
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaofeng Yu
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiongyan Wang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hyung Suk Oh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Priya Raja
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jean M Pesola
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Emilia A H Vanni
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Seamus McCarron
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jenna Morris-Love
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Graduate Program in Pathobiology, Brown University, Providence, RI, USA
| | - Alex H M Ng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - David M Knipe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Donald M Coen
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Dongli Pan
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, China.
- Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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Vanni EAH, Foley JW, Davison AJ, Sommer M, Liu D, Sung P, Moffat J, Zerboni L, Arvin AM. The latency-associated transcript locus of herpes simplex virus 1 is a virulence determinant in human skin. PLoS Pathog 2020; 16:e1009166. [PMID: 33370402 PMCID: PMC7794027 DOI: 10.1371/journal.ppat.1009166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/08/2021] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) infects skin and mucosal epithelial cells and then travels along axons to establish latency in the neurones of sensory ganglia. Although viral gene expression is restricted during latency, the latency-associated transcript (LAT) locus encodes many RNAs, including a 2 kb intron known as the hallmark of HSV-1 latency. Here, we studied HSV-1 infection and the role of the LAT locus in human skin xenografts in vivo and in cultured explants. We sequenced the genomes of our stock of HSV-1 strain 17syn+ and seven derived viruses and found nonsynonymous mutations in many viral proteins that had no impact on skin infection. In contrast, deletions in the LAT locus severely impaired HSV-1 replication and lesion formation in skin. However, skin replication was not affected by impaired intron splicing. Moreover, although the LAT locus has been implicated in regulating gene expression in neurones, we observed only small changes in transcript levels that were unrelated to the growth defect in skin, suggesting that its functions in skin may be different from those in neurones. Thus, although the LAT locus was previously thought to be dispensable for lytic infection, we show that it is a determinant of HSV-1 virulence during lytic infection of human skin. Herpes simplex virus type 1 (HSV-1) infects and destroys the outer layer of skin cells, producing lesions known as cold sores. Although these lesions heal, the virus persists in the host for the lifetime and can reactivate to cause new lesions. This is possible because the virus enters the axons of neurones in the skin and moves to their cell bodies located in spinal or cranial nerve bundles called ganglia, where the virus becomes dormant (latent). The most abundant viral RNAs expressed during this state are the latency associated transcripts (LATs), which have been considered a hallmark of HSV-1 latency. Here, we studied HSV-1 infection and spread in human skin. Unexpectedly, we found that the LAT locus is necessary for lesion formation in skin. HSV-1 viruses that were genetically mutated to delete the start of the locus could not spread in skin, whereas viruses with many other genetic mutations had this capacity. Our results suggest that an antiviral drug that inhibits transcripts from this region of the viral genome could block viral spread in skin, or a vaccine could possibly be produced by genetically modifying the virus at the LAT locus and by doing so, limit the virus’ ability become latent in neurones.
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Affiliation(s)
- Emilia A. H. Vanni
- Departments of Pediatrics and Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Joseph W. Foley
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Andrew J. Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Marvin Sommer
- Departments of Pediatrics and Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Dongmei Liu
- Department of Microbiology and Immunology, State University of New York-Upstate Medical University, Syracuse, New York, United States of America
| | - Phillip Sung
- Departments of Pediatrics and Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jennifer Moffat
- Department of Microbiology and Immunology, State University of New York-Upstate Medical University, Syracuse, New York, United States of America
| | - Leigh Zerboni
- Departments of Pediatrics and Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Ann M. Arvin
- Departments of Pediatrics and Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sen P, Wilkie AR, Ji F, Yang Y, Taylor IJ, Velazquez-Palafox M, Vanni EAH, Pesola JM, Fernandez R, Chen H, Morsett LM, Abels ER, Piper M, Lane RJ, Hickman SE, Means TK, Rosenberg ES, Sadreyev RI, Li B, Coen DM, Fishman JA, El Khoury J. Linking indirect effects of cytomegalovirus in transplantation to modulation of monocyte innate immune function. Sci Adv 2020; 6:eaax9856. [PMID: 32494628 PMCID: PMC7176434 DOI: 10.1126/sciadv.aax9856] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 01/30/2020] [Indexed: 05/08/2023]
Abstract
Cytomegalovirus (CMV) is an important cause of morbidity and mortality in the immunocompromised host. In transplant recipients, a variety of clinically important "indirect effects" are attributed to immune modulation by CMV, including increased mortality from fungal disease, allograft dysfunction and rejection in solid organ transplantation, and graft-versus-host-disease in stem cell transplantation. Monocytes, key cellular targets of CMV, are permissive to primary, latent and reactivated CMV infection. Here, pairing unbiased bulk and single cell transcriptomics with functional analyses we demonstrate that human monocytes infected with CMV do not effectively phagocytose fungal pathogens, a functional deficit which occurs with decreased expression of fungal recognition receptors. Simultaneously, CMV-infected monocytes upregulate antiviral, pro-inflammatory chemokine, and inflammasome responses associated with allograft rejection and graft-versus-host disease. Our study demonstrates that CMV modulates both immunosuppressive and immunostimulatory monocyte phenotypes, explaining in part, its paradoxical "indirect effects" in transplantation. These data could provide innate immune targets for the stratification and treatment of CMV disease.
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Affiliation(s)
- Pritha Sen
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Transplant Infectious Disease and Compromised Host Program, Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Adrian R. Wilkie
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Yiming Yang
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Emilia A. H. Vanni
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jean M. Pesola
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Rosio Fernandez
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Han Chen
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Liza M. Morsett
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Erik R. Abels
- Department of Neurology and Center for Molecular Imaging Research, Department of Radiology, Massachusetts General Hospital and Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Mary Piper
- Harvard Bioinformatics Core, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Rebekah J. Lane
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Transplant Infectious Disease and Compromised Host Program, Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Suzanne E. Hickman
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Terry K. Means
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Autoimmunity Cluster, Immunology and Inflammation Research Therapeutic Area, Sanofi, Cambridge, MA, USA
| | - Eric S. Rosenberg
- Transplant Infectious Disease and Compromised Host Program, Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ruslan I. Sadreyev
- Department of Molecular Biology and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Bo Li
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Donald M. Coen
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jay A. Fishman
- Transplant Infectious Disease and Compromised Host Program, Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Joseph El Khoury
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Transplant Infectious Disease and Compromised Host Program, Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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