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Nunes Santos L, Sousa Costa ÂM, Nikolov M, Carvalho JE, Coelho Sampaio A, Stockdale FE, Wang GF, Andrade Castillo H, Bortoletto Grizante M, Dudczig S, Vasconcelos M, Rosenthal N, Jusuf PR, Nim HT, de Oliveira P, Guimarães de Freitas Matos T, Nikovits W, Tambones IL, Figueira ACM, Schubert M, Ramialison M, Xavier-Neto J. Unraveling the evolutionary origin of the complex Nuclear Receptor Element (cNRE), a cis-regulatory module required for preferential expression in the atrial chamber. Commun Biol 2024; 7:371. [PMID: 38575811 PMCID: PMC10995137 DOI: 10.1038/s42003-024-05972-6] [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: 07/26/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024] Open
Abstract
Cardiac function requires appropriate proteins in each chamber. Atria requires slow myosin to act as reservoirs, while ventricles demand fast myosin for swift pumping. Myosins are thus under chamber-biased cis-regulation, with myosin gene expression imbalances leading to congenital heart dysfunction. To identify regulatory inputs leading to cardiac chamber-biased expression, we computationally and molecularly dissected the quail Slow Myosin Heavy Chain III (SMyHC III) promoter that drives preferential expression to the atria. We show that SMyHC III gene states are orchestrated by a complex Nuclear Receptor Element (cNRE) of 32 base pairs. Using transgenesis in zebrafish and mice, we demonstrate that preferential atrial expression is achieved by a combinatorial regulatory input composed of atrial activation motifs and ventricular repression motifs. Using comparative genomics, we show that the cNRE might have emerged from an endogenous viral element through infection of an ancestral host germline, revealing an evolutionary pathway to cardiac chamber-specific expression.
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Affiliation(s)
- Luana Nunes Santos
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- Australian Regenerative Medicine Institute, Monash University, VIC Australia - Systems Biology Institute, Melbourne, Australia
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Ângela Maria Sousa Costa
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Martin Nikolov
- Australian Regenerative Medicine Institute, Monash University, VIC Australia - Systems Biology Institute, Melbourne, Australia
| | - João E Carvalho
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Allysson Coelho Sampaio
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
- Faculdade Santa Marcelina - São Paulo, São Paulo, SP, Brazil
| | | | - Gang Feng Wang
- Department of Medicine, Stanford University, Stanford, CA, USA
| | - Hozana Andrade Castillo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
- Australian Regenerative Medicine Institute, Monash University, VIC Australia - Systems Biology Institute, Melbourne, Australia
| | - Mariana Bortoletto Grizante
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Stefanie Dudczig
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Michelle Vasconcelos
- Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Nadia Rosenthal
- The Jackson Laboratory, Bar Harbor, Maine, USA
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Hieu T Nim
- Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Paulo de Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | | | | | - Izabella Luisa Tambones
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center of Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Institut de la Mer de Villefranche, Sorbonne Université, CNRS, Villefranche-sur-Mer, France
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, VIC Australia - Systems Biology Institute, Melbourne, Australia.
- Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - José Xavier-Neto
- Department of Morphology, Federal University of Ceará (UFC), Ceará, CE, Brazil.
- Health Scientist-in-Chief of Ceará State, Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico, Ceará, CE, Brazil.
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Palomäki J, Kalke K, Orpana J, Lund L, Frejborg F, Paavilainen H, Järveläinen H, Hukkanen V. Attenuated Replication-Competent Herpes Simplex Virus Expressing an ECM-Modifying Transgene Hyaluronan Synthase 2 of Naked Mole Rat in Oncolytic Gene Therapy. Microorganisms 2023; 11:2657. [PMID: 38004669 PMCID: PMC10673056 DOI: 10.3390/microorganisms11112657] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Herpes simplex virus (HSV) has proven successful in treating human cancer. Since the approval of talimogene laherparepvec (T-VEC) in 2015, HSV has been thoroughly researched to discover novel mechanisms to combat cancer and treat other diseases. Another HSV-based drug, beremagene geperpavec (B-VEC), received approval in 2023 to treat the rare genetic disease dystrophic epidermolysis bullosa, and was also the first clinically approved HSV vector carrying an extracellular matrix (ECM)-modifying transgene. The ECM is a network of macromolecules surrounding cells, which provides support and regulates cell growth and differentiation, the disruption of which is common in cancer. The naked mole rat (NMR) has a thick ECM and a unique mutation in the hyaluronan synthase 2 (HAS2) gene, which has been linked to the high cancer resistance of the species. To study the effect of this mutation in human cancer, we have developed an attenuated, replication-competent HSV vector expressing the NMR-HAS2 gene. The viral replication, transgene expression and cytotoxic effect of the novel vector was studied in glioma cells. Our results show that an attenuated, replication-competent HSV vector expressing a foreign ECM-modifying transgene, namely HAS2, provides an effective tool to study and combat cancer in humans.
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Affiliation(s)
- Jussi Palomäki
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (J.P.)
| | - Kiira Kalke
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (J.P.)
| | - Julius Orpana
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (J.P.)
| | - Liisa Lund
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (J.P.)
| | - Fanny Frejborg
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (J.P.)
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Henrik Paavilainen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (J.P.)
| | - Hannu Järveläinen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (J.P.)
- Department of Internal Medicine, Satakunta Hospital District, Satasairaala Central Hospital, Sairaalantie 3, 28500 Pori, Finland
| | - Veijo Hukkanen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland; (J.P.)
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Komatsu H, Inui A, Hoshino H, Umetsu S, Fujisawa T. Integration of Viral Genome to Human Genomic DNA in Nails of Patients with Chronic Hepatitis B Virus Infection. JMA J 2023; 6:426-436. [PMID: 37941707 PMCID: PMC10628332 DOI: 10.31662/jmaj.2023-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/11/2023] [Indexed: 11/10/2023] Open
Abstract
Introduction Hepatitis B virus (HBV) DNA and cytomegalovirus (CMV) DNA can be detected in patient genomes. However, it remains unknown whether viral DNA can be integrated into host genomic DNA and detected in fingernails. Methods Nails from patients with chronic HBV infection were investigated. A total of 60 patients (male/female = 20/40, age range from 2 years to 59 years, median 15 years) were included in this study. The viral DNA levels of herpes simplex virus 1 (HSV-1), herpes simplex virus 2 (HSV-2), varicella-zoster virus (VZV), Epstein‒Barr virus (EBV), cytomegalovirus (CMV), human herpes virus 6 (HHV-6), human herpes virus 7 (HHV-7), and HBV in nails were measured with real-time PCR. Viral DNA integration into host genomic DNA was analyzed by capture-based next-generation sequencing (NGS). Moreover, virus/host chimeric sequences, which were detected by capture-based NGS, were confirmed by Sanger sequencing. Results Of the 60 patients, 37 (62%) were positive for nail HBV DNA. All 60 patients were negative for nail HSV-1, HSV-2, VZV, CMV, EBV, or HHV-6 DNA. However, three patients were positive for nail HHV-7 DNA. All three nail HHV-7-positive patients were also positive for nail HBV DNA. The three nail samples that were positive for both HBV and HHV-7 DNA were used for viral integration analysis by capture-based NGS. One of the three nail samples showed HBV/host chimeric sequences. In addition, all three nail samples showed HHV-7/host chimeric sequences. However, these viral integration breakpoints were not confirmed by Sanger sequencing. Conclusions Viral integrations were detected in nails by capture-based NGS. However, Sanger sequencing did not confirm any virus/host chimeric sequences. This study could not show reliable evidence of viral integration in nails.
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Affiliation(s)
- Haruki Komatsu
- Department of Pediatrics, Toho University, Sakura Medical Center, Chiba, Japan
- Komatsu Children's Clinic, Chiba, Japan
| | - Ayano Inui
- Department of Pediatric Hepatology and Gastroenterology, Eastern Yokohama Hospital, Kanagawa, Japan
| | - Hiroki Hoshino
- Department of Pediatrics, Toho University, Sakura Medical Center, Chiba, Japan
| | - Shuichiro Umetsu
- Department of Pediatric Hepatology and Gastroenterology, Eastern Yokohama Hospital, Kanagawa, Japan
| | - Tomoo Fujisawa
- Department of Pediatric Hepatology and Gastroenterology, Eastern Yokohama Hospital, Kanagawa, Japan
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Crawford LB. Hematopoietic stem cells and betaherpesvirus latency. Front Cell Infect Microbiol 2023; 13:1189805. [PMID: 37346032 PMCID: PMC10279960 DOI: 10.3389/fcimb.2023.1189805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/11/2023] [Indexed: 06/23/2023] Open
Abstract
The human betaherpesviruses including human cytomegalovirus (HCMV), human herpesvirus (HHV)-6a and HHV-6b, and HHV-7 infect and establish latency in CD34+ hematopoietic stem and progenitor cells (HPCs). The diverse repertoire of HPCs in humans and the complex interactions between these viruses and host HPCs regulate the viral lifecycle, including latency. Precise manipulation of host and viral factors contribute to preferential maintenance of the viral genome, increased host cell survival, and specific manipulation of the cellular environment including suppression of neighboring cells and immune control. The dynamic control of these processes by the virus regulate inter- and intra-host signals critical to the establishment of chronic infection. Regulation occurs through direct viral protein interactions and cellular signaling, miRNA regulation, and viral mimics of cellular receptors and ligands, all leading to control of cell proliferation, survival, and differentiation. Hematopoietic stem cells have unique biological properties and the tandem control of virus and host make this a unique environment for chronic herpesvirus infection in the bone marrow. This review highlights the elegant complexities of the betaherpesvirus latency and HPC virus-host interactions.
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Affiliation(s)
- Lindsey B Crawford
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE, United States
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Inoue Y, Takeda H. Teratorn and its relatives - a cross-point of distinct mobile elements, transposons and viruses. Front Vet Sci 2023; 10:1158023. [PMID: 37187934 PMCID: PMC10175614 DOI: 10.3389/fvets.2023.1158023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Mobile genetic elements (e.g., transposable elements and plasmids) and viruses display significant diversity with various life cycles, but how this diversity emerges remains obscure. We previously reported a novel and giant (180 kb long) mobile element, Teratorn, originally identified in the genome of medaka, Oryzias latipes. Teratorn is a composite DNA transposon created by a fusion of a piggyBac-like DNA transposon (piggyBac) and a novel herpesvirus of the Alloherpesviridae family. Genomic survey revealed that Teratorn-like herpesviruses are widely distributed among teleost genomes, the majority of which are also fused with piggyBac, suggesting that fusion with piggyBac is a trigger for the life-cycle shift of authentic herpesviruses to an intragenomic parasite. Thus, Teratorn-like herpesvirus provides a clear example of how novel mobile elements emerge, that is to say, the creation of diversity. In this review, we discuss the unique sequence and life-cycle characteristics of Teratorn, followed by the evolutionary process of piggyBac-herpesvirus fusion based on the distribution of Teratorn-like herpesviruses (relatives) among teleosts. Finally, we provide other examples of evolutionary associations between different classes of elements and propose that recombination could be a driving force generating novel mobile elements.
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Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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Viral Vectors in Gene Therapy: Where Do We Stand in 2023? Viruses 2023; 15:v15030698. [PMID: 36992407 PMCID: PMC10059137 DOI: 10.3390/v15030698] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023] Open
Abstract
Viral vectors have been used for a broad spectrum of gene therapy for both acute and chronic diseases. In the context of cancer gene therapy, viral vectors expressing anti-tumor, toxic, suicide and immunostimulatory genes, such as cytokines and chemokines, have been applied. Oncolytic viruses, which specifically replicate in and kill tumor cells, have provided tumor eradication, and even cure of cancers in animal models. In a broader meaning, vaccine development against infectious diseases and various cancers has been considered as a type of gene therapy. Especially in the case of COVID-19 vaccines, adenovirus-based vaccines such as ChAdOx1 nCoV-19 and Ad26.COV2.S have demonstrated excellent safety and vaccine efficacy in clinical trials, leading to Emergency Use Authorization in many countries. Viral vectors have shown great promise in the treatment of chronic diseases such as severe combined immunodeficiency (SCID), muscular dystrophy, hemophilia, β-thalassemia, and sickle cell disease (SCD). Proof-of-concept has been established in preclinical studies in various animal models. Clinical gene therapy trials have confirmed good safety, tolerability, and therapeutic efficacy. Viral-based drugs have been approved for cancer, hematological, metabolic, neurological, and ophthalmological diseases as well as for vaccines. For example, the adenovirus-based drug Gendicine® for non-small-cell lung cancer, the reovirus-based drug Reolysin® for ovarian cancer, the oncolytic HSV T-VEC for melanoma, lentivirus-based treatment of ADA-SCID disease, and the rhabdovirus-based vaccine Ervebo against Ebola virus disease have been approved for human use.
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Inoue Y, Takeda H. Teratorn and Its Related Elements – a Novel Group of Herpesviruses Widespread in Teleost Genomes. Zoolog Sci 2023; 40:83-90. [PMID: 37042688 DOI: 10.2108/zs220069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/12/2022] [Indexed: 03/08/2023]
Abstract
Herpesviruses are a large family of DNA viruses infecting vertebrates and invertebrates, and are important pathogens in the field of aquaculture. In general, herpesviruses do not have the ability to integrate into the host genomes since they do not have a chromosomal integration step in their life cycles. Recently, we identified a novel group of herpesviruses, "Teratorn" and its related elements, in the genomes of various teleost fish species. At least some of the Teratorn-like herpesviruses are fused with a piggyBac-like DNA transposon, suggesting that they have acquired the transposon-like intragenomic lifestyle by hijacking the transposon system. In this review, we describe the sequence characteristics of Teratorn-like herpesviruses and phylogenetic relationships with other herpesviruses. Then we discuss the process of transposon-herpesvirus fusion, their life cycle, and the generality of transposon-virus fusion. Teratorn-like herpesviruses provide a piece of concrete evidence that even non-retroviral elements can become intragenomic parasites retaining replication capacity, by acquiring transposition machinery from other sources.
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Affiliation(s)
- Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Inherited Chromosomally Integrated Human Herpesvirus 6: Laboratory and Clinical Features. Microorganisms 2023; 11:microorganisms11030548. [PMID: 36985122 PMCID: PMC10052293 DOI: 10.3390/microorganisms11030548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Inherited chromosomally integrated human herpesvirus 6 (iciHHV-6) is a condition in which the complete HHV-6 genome is integrated into the chromosomes of the host germ cell and is vertically transmitted. The aims of this study were to identify iciHHV-6 prevalence in hospitalized patients and clinical features in individuals carrying this integration. HHV-6 PCR on hair follicles was used to confirm iciHHV-6 status when the blood viral load was more than 5 Log10 copies/mL. From January 2012 to June 2022, HHV-6 DNAemia was investigated in 2019 patients. In particular, 49 had a viral load higher than 6 Log10 copies/mL and HHV-6 DNA in hair follicles was positive. A viral load between 5.0 and 5.9 Log10 copies/mL was observed in 10 patients: 6 infants with acute HHV-6 infection and 4 patients with leukopenia and HHV-6 integration. Therefore, the iciHHV-6 prevalence in our population was 2.6% (53/2019). Adult patients with integration presented hematological (24%), autoimmune (11%), autoimmune neurological (19%), not-autoimmune neurological (22%), and other diseases (19%), whereas 5% had no clinically relevant disease. Although in our study population a high percentage of iciHHV-6 adult hospitalized patients presented a specific pathology, it is still unknown whether the integration is responsible for, or contributes to, the disease development.
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Vojdani A, Vojdani E, Saidara E, Maes M. Persistent SARS-CoV-2 Infection, EBV, HHV-6 and Other Factors May Contribute to Inflammation and Autoimmunity in Long COVID. Viruses 2023; 15:v15020400. [PMID: 36851614 PMCID: PMC9967513 DOI: 10.3390/v15020400] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/24/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
A novel syndrome called long-haul COVID or long COVID is increasingly recognized in a significant percentage of individuals within a few months after infection with SARS-CoV-2. This disorder is characterized by a wide range of persisting, returning or even new but related symptoms that involve different tissues and organs, including respiratory, cardiac, vascular, gastrointestinal, musculo-skeletal, neurological, endocrine and systemic. Some overlapping symptomatologies exist between long COVID and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Very much like with long ME/CFS, infections with herpes family viruses, immune dysregulation, and the persistence of inflammation have been reported as the most common pattern for the development of long COVID. This review describes several factors and determinants of long COVID that have been proposed, elaborating mainly on viral persistence, reactivation of latent viruses such as Epstein-Barr virus and human herpesvirus 6 which are also associated with the pathology of ME/CFS, viral superantigen activation of the immune system, disturbance in the gut microbiome, and multiple tissue damage and autoimmunity. Based on these factors, we propose diagnostic strategies such as the measurement of IgG and IgM antibodies against SARS-CoV-2, EBV, HHV-6, viral superantigens, gut microbiota, and biomarkers of autoimmunity to better understand and manage this multi-factorial disorder that continues to affect millions of people in the world.
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Affiliation(s)
- Aristo Vojdani
- Immunosciences Lab, Inc., Los Angeles, CA 90035, USA
- Cyrex Laboratories, LLC, Phoenix, AZ 85034, USA
- Correspondence: ; Tel.: +1-310-657-1077
| | | | - Evan Saidara
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | - Michael Maes
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, 1873 Rama 4 Road, Pathumwan, Bangkok 10330, Thailand
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Hogestyn JM, Salois G, Xie L, Apa C, Youngyunpipatkul J, Pröschel C, Mayer-Pröschel M. Expression of the human herpesvirus 6A latency-associated transcript U94A impairs cytoskeletal functions in human neural cells. Mol Cell Neurosci 2022; 123:103770. [PMID: 36055520 PMCID: PMC10124163 DOI: 10.1016/j.mcn.2022.103770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/12/2022] [Accepted: 08/20/2022] [Indexed: 12/30/2022] Open
Abstract
Many neurodegenerative diseases have a multifactorial etiology and variable course of progression that cannot be explained by current models. Neurotropic viruses have long been suggested to play a role in these diseases, although their exact contributions remain unclear. Human herpesvirus 6A (HHV-6A) is one of the most common viruses detected in the adult brain, and has been clinically associated with multiple sclerosis (MS), and, more recently, Alzheimer's disease (AD). HHV-6A is a ubiquitous viral pathogen capable of infecting glia and neurons. Primary infection in childhood is followed by the induction of latency, characterized by expression of the U94A viral transcript in the absence of viral replication. Here we examine the effects of U94A on cells of the central nervous system. We found that U94A expression inhibits the migration and impairs cytoplasmic maturation of human oligodendrocyte precursor cells (OPCs) without affecting their viability, a phenotype that may contribute to the failure of remyelination seen in many patients with MS. A subsequent proteomics analysis of U94A expression OPCs revealed altered expression of genes involved in tubulin associated cytoskeletal regulation. As HHV-6A seems to significantly be associated with early AD pathology, we extended our initially analysis of the impact of U94A on human derived neurons. We found that U94A expression inhibits neurite outgrowth of primary human cortical neurons and impairs synapse maturation. Based on these data we suggest that U94A expression by latent HHV-6A in glial cells and neurons renders them susceptible to dysfunction and degeneration. Therefore, latent viral infections of the brain represent a unique pathological risk factor that may contribute to disease processes.
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Affiliation(s)
- Jessica M Hogestyn
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Department of Neuroscience, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Garrick Salois
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Department of Neuroscience, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Li Xie
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Connor Apa
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Stem cell and Regenerative Medicine Institute, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Justin Youngyunpipatkul
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Christoph Pröschel
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Stem cell and Regenerative Medicine Institute, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA
| | - Margot Mayer-Pröschel
- Department of Biomedical Genetics, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA; Department of Neuroscience, School of Medicine and Dentistry, 601 Elmwood Avenue, Box 633, University of Rochester, Rochester, NY 14642, USA,.
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Santiago JC, Adams SV, Towlerton A, Okuku F, Phipps W, Mullins JI. Genomic changes in Kaposi Sarcoma-associated Herpesvirus and their clinical correlates. PLoS Pathog 2022; 18:e1010524. [PMID: 36441790 PMCID: PMC9731496 DOI: 10.1371/journal.ppat.1010524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 12/08/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022] Open
Abstract
Kaposi sarcoma (KS), a common HIV-associated malignancy, presents a range of clinicopathological features. Kaposi sarcoma-associated herpesvirus (KSHV) is its etiologic agent, but the contribution of viral genomic variation to KS development is poorly understood. To identify potentially influential viral polymorphisms, we characterized KSHV genetic variation in 67 tumors from 1-4 distinct sites from 29 adults with advanced KS in Kampala, Uganda. Whole KSHV genomes were sequenced from 20 tumors with the highest viral load, whereas only polymorphic genes were screened by PCR and sequenced from 47 other tumors. Nine individuals harbored ≥1 tumors with a median 6-fold over-coverage of a region centering on K5 and K6 genes. K8.1 gene was inactivated in 8 individuals, while 5 had mutations in the miR-K10 microRNA coding sequence. Recurring inter-host polymorphisms were detected in K4.2 and K11.2. The K5-K6 region rearrangement breakpoints and K8.1 mutations were all unique, indicating that they arise frequently de novo. Rearrangement breakpoints were associated with potential G-quadruplex and Z-DNA forming sequences. Exploratory evaluations of viral mutations with clinical and tumor traits were conducted by logistic regression without multiple test corrections. K5-K6 over-coverage and K8.1 inactivation were tentatively correlated (p<0.001 and p = 0.005, respectively) with nodular rather than macular tumors, and with individuals that had lesions in ≤4 anatomic areas (both p≤0.01). Additionally, a trend was noted for miR-K10 point mutations and lower survival rates (HR = 4.11, p = 0.053). Two instances were found of distinct tumors within an individual sharing the same viral mutation, suggesting metastases or transmission of the aberrant viruses within the host. To summarize, KSHV genomes in tumors frequently have over-representation of the K5-K6 region, as well as K8.1 and miR-K10 mutations, and each might be associated with clinical phenotypes. Studying their possible effects may be useful for understanding KS tumorigenesis and disease progression.
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Affiliation(s)
- Jan Clement Santiago
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Scott V. Adams
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrea Towlerton
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Fred Okuku
- Uganda Cancer Institute, Kampala, Uganda
| | - Warren Phipps
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - James I. Mullins
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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12
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Shimohama S, Iizuka T, Takizawa T, Watanabe N, Tezuka T, Matsuda K, Yamanoi K, Kanazawa N, Kawamura Y, Yoshikawa T, Suzuki T, Takao M, Nakahara J, Izawa Y. Anti‐N‐methyl‐D‐aspartate receptor encephalitis with concurrent human herpes virus‐6A deoxyribonucleic acid detection: An autopsy case. Neuropathology 2022. [DOI: 10.1111/neup.12881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/22/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Sho Shimohama
- Department of Neurology Keio University School of Medicine Tokyo Japan
| | - Takahiro Iizuka
- Department of Neurology Kitasato University School of Medicine Sagamihara Japan
| | - Tsubasa Takizawa
- Department of Neurology Keio University School of Medicine Tokyo Japan
| | - Narumi Watanabe
- Department of Neurology Keio University School of Medicine Tokyo Japan
| | - Toshiki Tezuka
- Department of Neurology Keio University School of Medicine Tokyo Japan
| | - Kosuke Matsuda
- Department of Pathology Keio University School of Medicine Tokyo Japan
| | - Kazuhiro Yamanoi
- Department of Pathology Keio University School of Medicine Tokyo Japan
| | - Naomi Kanazawa
- Department of Neurology Kitasato University School of Medicine Sagamihara Japan
| | - Yoshiki Kawamura
- Department of Pediatrics Fujita Health University School of Medicine Toyoake Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics Fujita Health University School of Medicine Toyoake Japan
| | - Tadaki Suzuki
- Department of Pathology National Institute of Infectious Diseases Tokyo Japan
| | - Masaki Takao
- Department of Clinical Laboratory National Center of Neurology and Psychiatry (NCNP) National Center Hospital Kodaira Japan
| | - Jin Nakahara
- Department of Neurology Keio University School of Medicine Tokyo Japan
| | - Yoshikane Izawa
- Department of Neurology Keio University School of Medicine Tokyo Japan
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13
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Chetty VK, Ghanam J, Anchan S, Reinhardt K, Brenzel A, Gelléri M, Cremer C, Grueso-Navarro E, Schneider M, von Neuhoff N, Reinhardt D, Jablonska J, Nazarenko I, Thakur BK. Efficient Small Extracellular Vesicles (EV) Isolation Method and Evaluation of EV-Associated DNA Role in Cell-Cell Communication in Cancer. Cancers (Basel) 2022; 14:cancers14092068. [PMID: 35565197 PMCID: PMC9099953 DOI: 10.3390/cancers14092068] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Small extracellular vesicles (sEVs) released by all cell types function as a mediator in intercellular communication that can promote cell division and survival to remodel the tumor microenvironment to develop tumor invasion and metastasis. Even though dsDNA baggage is associated with all small EV populations, the functional role of EV-DNA in cancer remains poorly understood. This is due to a lack of methods allowing the efficient separation of small EVs (sEVs) from other non-sEV components. The main aim of our study was to develop an efficient sEV isolation method along with EV-associated DNA (EV-DNA) monitoring tool to evaluate the role of EV-DNA as a mediator of cell–cell communication in cancer. Our detailed small EV-DNA characterization confirmed that isolated sEVs using the TSU method (Tangential flow filtration + Size exclusion chromatography + Ultrafiltration) are free from contaminants such as cell-free and apoptotic bodies DNA, making TSU ideal for performing EV-DNA functional studies. Next, we revealed the exact EV-DNA distribution in the recipient cells using 3D image analysis and the association of EV-DNA with key cellular proteins, which may have an essential role in cancer. In the leukemia model, EV-DNA isolated from leukemia cell lines associated with mesenchymal stromal cells (MSCs), a crucial factor in the bone marrow (BM) microenvironment. Abstract Small extracellular vesicles (sEVs) play essential roles in intercellular signaling both in normal and pathophysiological conditions. Comprehensive studies of dsDNA associated with sEVs are hampered by a lack of methods, allowing efficient separation of sEVs from free-circulating DNA and apoptotic bodies. In this work, using controlled culture conditions, we enriched the reproducible separation of sEVs from free-circulated components by combining tangential flow filtration, size-exclusion chromatography, and ultrafiltration (TSU). EV-enriched fractions (F2 and F3) obtained using TSU also contained more dsDNA derived from the host genome and mitochondria, predominantly localized inside the vesicles. Three-dimensional reconstruction of high-resolution imaging showed that the recipient cell membrane barrier restricts a portion of EV-DNA. Simultaneously, the remaining EV-DNA overcomes it and enters the cytoplasm and nucleus. In the cytoplasm, EV-DNA associates with dsDNA-inflammatory sensors (cGAS/STING) and endosomal proteins (Rab5/Rab7). Relevant to cancer, we found that EV-DNA isolated from leukemia cell lines communicates with mesenchymal stromal cells (MSCs), a critical component in the BM microenvironment. Furthermore, we illustrated the arrangement of sEVs and EV-DNA at a single vesicle level using super-resolution microscopy. Altogether, employing TSU isolation, we demonstrated EV-DNA distribution and a tool to evaluate the exact EV-DNA role of cell–cell communication in cancer.
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Affiliation(s)
- Venkatesh Kumar Chetty
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Jamal Ghanam
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Srishti Anchan
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Katarina Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Alexandra Brenzel
- Imaging Center Essen (IMCES), University Hospital Essen, 45147 Essen, Germany;
| | - Márton Gelléri
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; (M.G.); (C.C.)
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany; (M.G.); (C.C.)
- Max Planck Institutes for Polymer Research and for Chemistry, 55128 Mainz, Germany
| | - Elena Grueso-Navarro
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany; (E.G.-N.); (I.N.)
| | - Markus Schneider
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Nils von Neuhoff
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
| | - Jadwiga Jablonska
- Department of Otorhinolaryngology, University Hospital Essen, 45147 Essen, Germany;
| | - Irina Nazarenko
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany; (E.G.-N.); (I.N.)
- German Cancer Consortium (DKTK), Partner Site Freiburg and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Basant Kumar Thakur
- Department of Pediatrics III, University Hospital Essen, 45147 Essen, Germany; (V.K.C.); (J.G.); (S.A.); (K.R.); (M.S.); (N.v.N.); (D.R.)
- Correspondence: ; Tel.: +49-201-723-2504
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14
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Sánchez‐Ponce Y, Fuentes‐Pananá EM. Molecular and immune interactions between β‐ and γ‐herpesviruses in the immunocompromised host. J Leukoc Biol 2022; 112:79-95. [DOI: 10.1002/jlb.4mr1221-452r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Yessica Sánchez‐Ponce
- Research Unit in Virology and Cancer Children's Hospital of Mexico Federico Gómez Mexico City Mexico
- Postgraduate Program in Biological Science National Autonomous University of Mexico Mexico City Mexico
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15
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Norins LC. Down syndrome and Alzheimer’s disease: Same infectious cause, same preventive? Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2021.110745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Viglietta M, Bellone R, Blisnick AA, Failloux AB. Vector Specificity of Arbovirus Transmission. Front Microbiol 2021; 12:773211. [PMID: 34956136 PMCID: PMC8696169 DOI: 10.3389/fmicb.2021.773211] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 10/19/2021] [Indexed: 12/20/2022] Open
Abstract
More than 25% of human infectious diseases are vector-borne diseases (VBDs). These diseases, caused by pathogens shared between animals and humans, are a growing threat to global health with more than 2.5 million annual deaths. Mosquitoes and ticks are the main vectors of arboviruses including flaviviruses, which greatly affect humans. However, all tick or mosquito species are not able to transmit all viruses, suggesting important molecular mechanisms regulating viral infection, dissemination, and transmission by vectors. Despite the large distribution of arthropods (mosquitoes and ticks) and arboviruses, only a few pairings of arthropods (family, genus, and population) and viruses (family, genus, and genotype) successfully transmit. Here, we review the factors that might limit pathogen transmission: internal (vector genetics, immune responses, microbiome including insect-specific viruses, and coinfections) and external, either biotic (adult and larvae nutrition) or abiotic (temperature, chemicals, and altitude). This review will demonstrate the dynamic nature and complexity of virus–vector interactions to help in designing appropriate practices in surveillance and prevention to reduce VBD threats.
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Affiliation(s)
- Marine Viglietta
- Unit of Arboviruses and Insect Vectors, Institut Pasteur, Sorbonne Université, Paris, France
| | - Rachel Bellone
- Unit of Arboviruses and Insect Vectors, Institut Pasteur, Sorbonne Université, Paris, France
| | - Adrien Albert Blisnick
- Unit of Arboviruses and Insect Vectors, Institut Pasteur, Sorbonne Université, Paris, France
| | - Anna-Bella Failloux
- Unit of Arboviruses and Insect Vectors, Institut Pasteur, Sorbonne Université, Paris, France
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17
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Koonin EV, Dolja VV, Krupovic M, Kuhn JH. Viruses Defined by the Position of the Virosphere within the Replicator Space. Microbiol Mol Biol Rev 2021; 85:e0019320. [PMID: 34468181 PMCID: PMC8483706 DOI: 10.1128/mmbr.00193-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Originally, viruses were defined as miniscule infectious agents that passed through filters that retain even the smallest cells. Subsequently, viruses were considered obligate intracellular parasites whose reproduction depends on their cellular hosts for energy supply and molecular building blocks. However, these features are insufficient to unambiguously define viruses as they are broadly understood today. We outline possible approaches to define viruses and explore the boundaries of the virosphere within the virtual space of replicators and the relationships between viruses and other types of replicators. Regardless of how, exactly, viruses are defined, viruses clearly have evolved on many occasions from nonviral replicators, such as plasmids, by recruiting host proteins to become virion components. Conversely, other types of replicators have repeatedly evolved from viruses. Thus, the virosphere is a dynamic entity with extensive evolutionary traffic across its boundaries. We argue that the virosphere proper, here termed orthovirosphere, consists of a distinct variety of replicators that encode structural proteins encasing the replicators' genomes, thereby providing protection and facilitating transmission among hosts. Numerous and diverse replicators, such as virus-derived but capsidless RNA and DNA elements, or defective viruses occupy the zone surrounding the orthovirosphere in the virtual replicator space. We define this zone as the perivirosphere. Although intense debates on the nature of certain replicators that adorn the internal and external boundaries of the virosphere will likely continue, we present an operational definition of virus that recently has been accepted by the International Committee on Taxonomy of Viruses.
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Affiliation(s)
- Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Valerian V. Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, Maryland, USA
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18
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Thakkar P, Banks JM, Rahat R, Brandini DA, Naqvi AR. Viruses of the oral cavity: Prevalence, pathobiology and association with oral diseases. Rev Med Virol 2021; 32:e2311. [PMID: 34854161 DOI: 10.1002/rmv.2311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/27/2022]
Abstract
The human oral cavity contains a plethora of habitats and tissue environments, such as teeth, tongue, and gingiva, which are home to a rich microbial flora including bacteria, fungi, and viruses. Given the exposed nature of the mouth, oral tissues constantly encounter infectious agents, forming a complex ecological community. In the past, the discussion of microbiological aspects of oral disease has traditionally focused on bacteria and fungi, but viruses are attracting increasing attention as pathogens in oral inflammatory diseases. Therefore, understanding viral prevalence, pathogenicity, and preference regarding oral tissues is critical to understanding the holistic effects of viruses on oral infections. Recent investigations have demonstrated the abundance of certain viruses in oral inflammatory diseases, suggesting an association between viruses and disease. Human herpesviruses are the most extensively studied viruses in different oral inflammatory diseases. However, challenges in viral detection and the lack of reproducible in vitro and in vivo infection models have limited our progress in understanding viruses and their contribution to oral diseases. This review presents a summary of major mammalian viruses and associated diseases in the human oral cavity. The emergence of a recent pathogen SARS-CoV-2 and its tropism for salivary and periodontal tissues further highlights the relevance of the oral cavity in host-pathogen interaction. Understanding how these different viruses present clinically and influence oral health will advance our understanding of multifactorial oral diseases and their association with viruses.
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Affiliation(s)
- Pari Thakkar
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jonathan M Banks
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Rani Rahat
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Daniela A Brandini
- Department of Diagnosis and Surgery, School of Dentistry, São Paulo State University (UNESP), Araçatuba, São Paulo, Brazil
| | - Afsar R Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois at Chicago, Chicago, Illinois, USA
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19
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You Y, Vychodil T, Aimola G, Previdelli RL, Göbel TW, Bertzbach LD, Kaufer BB. A Cell Culture System to Investigate Marek's Disease Virus Integration into Host Chromosomes. Microorganisms 2021; 9:microorganisms9122489. [PMID: 34946091 PMCID: PMC8706938 DOI: 10.3390/microorganisms9122489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023] Open
Abstract
Marek’s disease virus (MDV) is a highly oncogenic alphaherpesvirus that causes a devastating neoplastic disease in chickens. MDV has been shown to integrate its genome into the telomeres of latently infected and tumor cells, which is crucial for efficient tumor formation. Telomeric repeat arrays present at the ends of the MDV genome facilitate this integration into host telomeres; however, the integration mechanism remains poorly understood. Until now, MDV integration could only be investigated qualitatively upon infection of chickens. To shed further light on the integration mechanism, we established a quantitative integration assay using chicken T cell lines, the target cells for MDV latency and transformation. We optimized the infection conditions and assessed the establishment of latency in these T cells. The MDV genome was efficiently maintained over time, and integration was confirmed in these cells by fluorescence in situ hybridization (FISH). To assess the role of the two distinct viral telomeric repeat arrays in the integration process, we tested various knockout mutants in our in vitro integration assay. Efficient genome maintenance and integration was thereby dependent on the presence of the telomeric repeat arrays in the virus genome. Taken together, we developed and validated a novel in vitro integration assay that will shed light on the integration mechanism of this highly oncogenic virus into host telomeres.
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Affiliation(s)
- Yu You
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (Y.Y.); (T.V.); (G.A.); (R.L.P.)
| | - Tereza Vychodil
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (Y.Y.); (T.V.); (G.A.); (R.L.P.)
| | - Giulia Aimola
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (Y.Y.); (T.V.); (G.A.); (R.L.P.)
| | - Renato L. Previdelli
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (Y.Y.); (T.V.); (G.A.); (R.L.P.)
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London NW1 0TU, UK
| | - Thomas W. Göbel
- Institute for Animal Physiology, Department of Veterinary Sciences, Ludwig Maximilian University Munich, 80539 Munich, Germany;
| | - Luca D. Bertzbach
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (Y.Y.); (T.V.); (G.A.); (R.L.P.)
- Department of Viral Transformation, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany
- Correspondence: (L.D.B.); (B.B.K.)
| | - Benedikt B. Kaufer
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; (Y.Y.); (T.V.); (G.A.); (R.L.P.)
- Correspondence: (L.D.B.); (B.B.K.)
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20
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Glass MC, Smith JM, Cheng HH, Delany ME. Marek's Disease Virus Telomeric Integration Profiles of Neoplastic Host Tissues Reveal Unbiased Chromosomal Selection and Loss of Cellular Diversity during Tumorigenesis. Genes (Basel) 2021; 12:1630. [PMID: 34681024 PMCID: PMC8536068 DOI: 10.3390/genes12101630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/14/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
The avian α-herpesvirus known as Marek's disease virus (MDV) linearly integrates its genomic DNA into host telomeres during infection. The resulting disease, Marek's disease (MD), is characterized by virally-induced lymphomas with high mortality. The temporal dynamics of MDV-positive (MDV+) transformed cells and expansion of MD lymphomas remain targets for further understanding. It also remains to be determined whether specific host chromosomal sites of MDV telomere integration confer an advantage to MDV-transformed cells during tumorigenesis. We applied MDV-specific fluorescence in situ hybridization (MDV FISH) to investigate virus-host cytogenomic interactions within and among a total of 37 gonad lymphomas and neoplastic splenic samples in birds infected with virulent MDV. We also determined single-cell, chromosome-specific MDV integration profiles within and among transformed tissue samples, including multiple samples from the same bird. Most mitotically-dividing cells within neoplastic samples had the cytogenomic phenotype of 'MDV telomere-integrated only', and tissue-specific, temporal changes in phenotype frequencies were detected. Transformed cell populations composing gonad lymphomas exhibited significantly lower diversity, in terms of heterogeneity of MDV integration profiles, at the latest stages of tumorigenesis (>50 days post-infection (dpi)). We further report high interindividual and lower intraindividual variation in MDV integration profiles of lymphoma cells. There was no evidence of integration hotspots into a specific host chromosome(s). Collectively, our data suggests that very few transformed MDV+ T cell populations present earlier in MDV-induced lymphomas (32-50 dpi), survive, and expand to become the dominant clonal population in more advanced MD lymphomas (51-62 dpi) and establish metastatic lymphomas.
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Affiliation(s)
- Marla C. Glass
- Department of Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Justin M. Smith
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA; (J.M.S.); (M.E.D.)
| | - Hans H. Cheng
- Avian Disease and Oncology Laboratory, United States Department of Agriculture, Agricultural Research Service, East Lansing, MI 48823, USA;
| | - Mary E. Delany
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA; (J.M.S.); (M.E.D.)
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21
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Duggan MR, Torkzaban B, Ahooyi TM, Khalili K. Potential Role for Herpesviruses in Alzheimer's Disease. J Alzheimers Dis 2021; 78:855-869. [PMID: 33074235 DOI: 10.3233/jad-200814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Across the fields of virology and neuroscience, the role of neurotropic viruses in Alzheimer's disease (AD) has received renewed enthusiasm, with a particular focus on human herpesviruses (HHVs). Recent genomic analyses of brain tissue collections and investigations of the antimicrobial responses of amyloid-β do not exclude a role of HHVs in contributing to or accelerating AD pathogenesis. Due to continued expansion in our aging cohort and the lack of effective treatments for AD, this composition examines a potential neuroviral theory of AD in light of these recent data. Consideration reveals a possible viral "Hit-and-Run" scenario of AD, as well as neurobiological mechanisms (i.e., neuroinflammation, protein quality control, oxidative stress) that may increase risk for AD following neurotropic infection. Although limitations exist, this theoretical framework reveals several novel therapeutic targets that may prove efficacious in AD.
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Affiliation(s)
- Michael R Duggan
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Bahareh Torkzaban
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Taha Mohseni Ahooyi
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Kamel Khalili
- Department of Neuroscience and Center for Neurovirology, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
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22
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Harding EF, Russo AG, Yan GJH, Waters PD, White PA. Ancient viral integrations in marsupials: a potential antiviral defence. Virus Evol 2021; 7:veab076. [PMID: 34548931 PMCID: PMC8449507 DOI: 10.1093/ve/veab076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 08/05/2021] [Accepted: 08/31/2021] [Indexed: 12/28/2022] Open
Abstract
Marsupial viruses are understudied compared to their eutherian mammal counterparts, although they may pose severe threats to vulnerable marsupial populations. Genomic viral integrations, termed 'endogenous viral elements' (EVEs), could protect the host from infection. It is widely known past viral infections and EVEs play an active role in antiviral defence in invertebrates and plants. This study aimed to characterise actively transcribed EVEs in Australian marsupial species, because they may play an integral role in cellular defence against viruses. This study screened publicly available RNA sequencing data sets (n = 35) and characterised 200 viral transcripts from thirteen Australian marsupial species. Of the 200 transcripts, 188 originated from either Bornaviridae, Filoviridae, or Parvoviridae EVEs. The other twelve transcripts were from putative active infections from members of the Herpesviridae and Anelloviridae, and Hepadnaviridae. EVE transcripts (n = 188) were mapped to marsupial genomes (where available, n = 5/13) to identify the genomic insertion sites. Of the 188 transcripts, 117 mapped to 39 EVEs within the koala, bare-nosed wombat, tammar wallaby, brushtail possum, and Tasmanian devil genomes. The remaining eight animals had no available genome (transcripts n = 71). Every marsupial has Bornaviridae, Filoviridae, and Parvoviridae EVEs, a trend widely observed in eutherian mammals. Whilst eutherian bornavirus EVEs are predominantly nucleoprotein-derived, marsupial bornavirus EVEs demonstrate a surprising replicase gene bias. We predicted these widely distributed EVEs were conserved within marsupials from ancient germline integrations, as many were over 65 million years old. One bornavirus replicase EVE, present in six marsupial genomes, was estimated to be 160 million years old, predating the American-Australian marsupial split. We considered transcription of these EVEs through small non-coding RNA as an ancient viral defence. Consistent with this, in koala small RNA sequence data sets, we detected Bornaviridae replicase and Filoviridae nucleoprotein produced small RNA. These were enriched in testis tissue, suggesting they could protect marsupials from vertically transmitted viral integrations.
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Affiliation(s)
| | - Alice G Russo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, UNSW Sydney, Sydney, NSW 2052, Australia
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23
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Duckworth A, Longhurst HJ, Paxton JK, Scotton CJ. The Role of Herpes Viruses in Pulmonary Fibrosis. Front Med (Lausanne) 2021; 8:704222. [PMID: 34368196 PMCID: PMC8339799 DOI: 10.3389/fmed.2021.704222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/24/2021] [Indexed: 12/29/2022] Open
Abstract
Pulmonary fibrosis (PF) is a serious lung disease which can result from known genetic or environmental exposures but is more commonly idiopathic (IPF). In familial PF (FPF), the majority of identified causal genes play key roles in the maintenance of telomeres, the protective end structures of chromosomes. Recent evidence suggests that short telomeres may also be implicated causally in a significant proportion of idiopathic cases. The possible involvement of herpes viruses in PF disease incidence and progression has been examined for many years, with some studies showing strong, statistically significant associations and others reporting no involvement. Evidence is thus polarized and remains inconclusive. Here we review the reported involvement of herpes viruses in PF in both animals and humans and present a summary of the evidence to date. We also present several possible mechanisms of action of the different herpes viruses in PF pathogenesis, including potential contributions to telomere attrition and cellular senescence. Evidence for antiviral treatment in PF is very limited but suggests a potential benefit. Further work is required to definitely answer the question of whether herpes viruses impact PF disease onset and progression and to enable the possible use of targeted antiviral treatments to improve clinical outcomes.
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Affiliation(s)
- Anna Duckworth
- College of Medicine and Health, University of Exeter, Exeter, United Kingdom
| | - Hilary J. Longhurst
- Department of Medicine, University of Auckland, Auckland, New Zealand
- Dyskeratosis Congenita (DC) Action, London, United Kingdom
| | - Jane K. Paxton
- Dyskeratosis Congenita (DC) Action, London, United Kingdom
| | - Chris J. Scotton
- College of Medicine and Health, University of Exeter, Exeter, United Kingdom
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Auriti C, De Rose DU, Santisi A, Martini L, Piersigilli F, Bersani I, Ronchetti MP, Caforio L. Pregnancy and viral infections: Mechanisms of fetal damage, diagnosis and prevention of neonatal adverse outcomes from cytomegalovirus to SARS-CoV-2 and Zika virus. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166198. [PMID: 34118406 PMCID: PMC8883330 DOI: 10.1016/j.bbadis.2021.166198] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/07/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023]
Abstract
Some maternal infections, contracted before or during pregnancy, can be transmitted to the fetus, during gestation (congenital infection), during labor and childbirth (perinatal infection) and through breastfeeding (postnatal infection). The agents responsible for these infections can be viruses, bacteria, protozoa, fungi. Among the viruses most frequently responsible for congenital infections are Cytomegalovirus (CMV), Herpes simplex 1–2, Herpes virus 6, Varicella zoster. Moreover Hepatitis B and C virus, HIV, Parvovirus B19 and non-polio Enteroviruses when contracted during pregnancy may involve the fetus or newborn at birth. Recently, new viruses have emerged, SARS-Cov-2 and Zika virus, of which we do not yet fully know the characteristics and pathogenic power when contracted during pregnancy. Viral infections in pregnancy can damage the fetus (spontaneous abortion, fetal death, intrauterine growth retardation) or the newborn (congenital anomalies, organ diseases with sequelae of different severity). Some risk factors specifically influence the incidence of transmission to the fetus: the timing of the infection in pregnancy, the order of the infection, primary or reinfection or chronic, the duration of membrane rupture, type of delivery, socio-economic conditions and breastfeeding. Frequently infected neonates, symptomatic at birth, have worse outcomes than asymptomatic. Many asymptomatic babies develop long term neurosensory outcomes. The way in which the virus interacts with the maternal immune system, the maternal-fetal interface and the placenta explain these results and also the differences that are observed from time to time in the fetal‑neonatal outcomes of maternal infections. The maternal immune system undergoes functional adaptation during pregnancy, once thought as physiological immunosuppression. This adaptation, crucial for generating a balance between maternal immunity and fetus, is necessary to promote and support the pregnancy itself and the growth of the fetus. When this adaptation is upset by the viral infection, the balance is broken, and the infection can spread and lead to the adverse outcomes previously described. In this review we will describe the main viral harmful infections in pregnancy and the potential mechanisms of the damages on the fetus and newborn.
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Affiliation(s)
- Cinzia Auriti
- Neonatal Intensive Care Unit, Medical and Surgical Department of Fetus, Newborn and Infant - "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy.
| | - Domenico Umberto De Rose
- Neonatal Intensive Care Unit, Medical and Surgical Department of Fetus, Newborn and Infant - "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy.
| | - Alessandra Santisi
- Neonatal Intensive Care Unit, Medical and Surgical Department of Fetus, Newborn and Infant - "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy.
| | - Ludovica Martini
- Neonatal Intensive Care Unit, Medical and Surgical Department of Fetus, Newborn and Infant - "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy.
| | - Fiammetta Piersigilli
- Department of Neonatology, St-Luc University Hospital, Catholic University of Louvain, Brussels, Belgium.
| | - Iliana Bersani
- Neonatal Intensive Care Unit, Medical and Surgical Department of Fetus, Newborn and Infant - "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy.
| | - Maria Paola Ronchetti
- Neonatal Intensive Care Unit, Medical and Surgical Department of Fetus, Newborn and Infant - "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy.
| | - Leonardo Caforio
- Fetal and Perinatal Medicine and Surgery Unit, Medical and Surgical Department of Fetus, Newborn and Infant - "Bambino Gesù" Children's Hospital IRCCS, Rome, Italy.
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25
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Abstract
The "omics" revolution of recent years has simplified the study of RNA transcripts produced during viral infection and under specific defined conditions. In the quest to find new and differentially expressed transcripts during the course of human Herpesvirus 6B (HHV-6B) infection, we made use of large-scale RNA sequencing to analyze the HHV-6B transcriptome during productive infection of human Molt-3 T-cells. Analyses were performed at different time points following infection and specific inhibitors were used to classify the kinetic class of each open reading frame (ORF) reported in the annotated genome of HHV-6B Z29 strain. The initial search focussed on HHV-6B-specific reads matching new HHV-6B transcripts. Differential expression of new HHV-6B transcripts were observed in all samples analyzed. The presence of many of these new HHV-6B transcripts were confirmed by RT-PCR and Sanger sequencing. Many of these transcripts represented new splice variants of previously reported ORFs, including some transcripts that have yet to be defined. Overall, our work demonstrates the diversity and the complexity of the HHV-6B transcriptome.IMPORTANCERNA sequencing (RNA-seq) is an important tool for studying RNA transcripts, particularly during active viral infection. We made use of RNA-seq to study human Herpesvirus 6B (HHV-6B) infection. Using six different time points, we were able to identify the presence of differentially spliced genes at 6, 9, 12, 24, 48 and 72 hours post-infection. Determination of the RNA profiles in the presence of cycloheximide (CHX) or phosphonoacetic acid (PAA) also permitted identification of the kinetic class of each ORF described in the annotated GenBank file. We also identified new spliced transcripts for certain genes and evaluated their relative expression over time. These data and next-generation sequencing (NGS) of the viral DNA have led us to propose a new version of the HHV-6B Z29 GenBank annotated file, without changing ORF names in order to facilitate trace back and correlate our work with previous studies on HHV-6B.
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Abstract
Herpesviruses infect virtually all humans and establish lifelong latency and reactivate to infect other humans. Latency requires multiple functions: maintaining the herpesvirus genome in the nuclei of cells; partitioning the viral genome to daughter cells in dividing cells; avoiding recognition by the immune system by limiting protein expression; producing noncoding viral RNAs (including microRNAs) to suppress lytic gene expression or regulate cellular protein expression that could otherwise eliminate virus-infected cells; modulating the epigenetic state of the viral genome to regulate viral gene expression; and reactivating to infect other hosts. Licensed antivirals inhibit virus replication, but do not affect latency. Understanding of the mechanisms of latency is leading to novel approaches to destroy latently infected cells or inhibit reactivation from latency.
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Grenda A, Krawczyk P. Cancer trigger or remedy: two faces of the human microbiome. Appl Microbiol Biotechnol 2021; 105:1395-1405. [PMID: 33492450 DOI: 10.1007/s00253-021-11125-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/08/2021] [Accepted: 01/16/2021] [Indexed: 12/12/2022]
Abstract
Currently, increasing attention cancer treatment has focused on molecularly targeted therapies and more recently on immunotherapies targeting immune checkpoints. However, even such advanced treatment may be ineffective. The reasons for this are sought, inter alia, in the human microbiome. In our intestines, there are bacteria that are beneficial to us, but pathogenic microorganisms may also be present. Microbial imbalance (dysbiosis) is now perceived as one of the gateways to cancer. However, it is feasible to use bacteria and their metabolites to restore the natural, beneficial microbiome during oncological treatment. Akkermansia mucinifila, Enterococcus hirae, or Faecalibacterium prausnitzii are bacteria that exhibit this beneficial potential. Greater benefits of therapy can be observed in cancer patients enriched in these bacterial species and treated with anti-PD-1, anti-PD-L1, or anti-CTLA-4 monoclonal antibodies. In this review, we present issues related to the role of bacteria in carcinogenesis and their therapeutic potential "supporting" modern anti-cancer therapies.Key Points• Bacteria can be directly or indirectly a cancer trigger.• Bacterial metabolites regulate the pathways associated with carcinogenesis.• Intestinal bacteria activate the immune system to fight cancer.
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Affiliation(s)
- Anna Grenda
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, Jaczewskiego 8, 20-090, Lublin, Poland.
| | - Paweł Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, Jaczewskiego 8, 20-090, Lublin, Poland
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Brar G, Farhat NA, Sukhina A, Lam AK, Kim YH, Hsu T, Tong L, Lin WW, Ware CF, Blackman MA, Sun R, Wu TT. Deletion of immune evasion genes provides an effective vaccine design for tumor-associated herpesviruses. NPJ Vaccines 2020; 5:102. [PMID: 33298958 PMCID: PMC7644650 DOI: 10.1038/s41541-020-00251-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
Vaccines based on live attenuated viruses often induce broad, multifaceted immune responses. However, they also usually sacrifice immunogenicity for attenuation. It is particularly difficult to elicit an effective vaccine for herpesviruses due to an armament of immune evasion genes and a latent phase. Here, to overcome the limitation of attenuation, we developed a rational herpesvirus vaccine in which viral immune evasion genes were deleted to enhance immunogenicity while also attaining safety. To test this vaccine strategy, we utilized murine gammaherpesvirus-68 (MHV-68) as a proof-of-concept model for the cancer-associated human γ-herpesviruses, Epstein-Barr virus and Kaposi sarcoma-associated herpesvirus. We engineered a recombinant MHV-68 virus by targeted inactivation of viral antagonists of type I interferon (IFN-I) pathway and deletion of the latency locus responsible for persistent infection. This recombinant virus is highly attenuated with no measurable capacity for replication, latency, or persistence in immunocompetent hosts. It stimulates robust innate immunity, differentiates virus-specific memory T cells, and elicits neutralizing antibodies. A single vaccination affords durable protection that blocks the establishment of latency following challenge with the wild type MHV-68 for at least six months post-vaccination. These results provide a framework for effective vaccination against cancer-associated herpesviruses through the elimination of latency and key immune evasion mechanisms from the pathogen.
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Affiliation(s)
- Gurpreet Brar
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Nisar A Farhat
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Alisa Sukhina
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Alex K Lam
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Yong Hoon Kim
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Tiffany Hsu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Leming Tong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Wai Wai Lin
- Laboratory of Molecular Immunology, Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Carl F Ware
- Laboratory of Molecular Immunology, Infectious and Inflammatory Diseases Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | | | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA.
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Abstract
Recombinant viruses are the workhorse of modern neuroscience. Whether one would like to understand a neuron's morphology, natural activity patterns, molecular composition, connectivity or behavioural and physiologic function, most studies begin with the injection of an engineered virus, often an adeno-associated virus or herpes simplex virus, among many other types. Recombinant viruses currently enable some combination of cell type-specific, circuit-selective, activity-dependent and spatiotemporally resolved transgene expression. Viruses are now used routinely to study the molecular and cellular functions of a gene within an identified cell type in the brain, and enable the application of optogenetics, chemogenetics, calcium imaging and related approaches. These advantageous properties of engineered viruses thus enable characterization of neuronal function at unprecedented resolution. However, each virus has specific advantages and disadvantages, which makes viral tool selection paramount for properly designing and executing experiments within the central nervous system. In the current Review, we discuss the key principles and uses of engineered viruses and highlight innovations that are needed moving forward.
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Affiliation(s)
- Alexander R Nectow
- Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA.
| | - Eric J Nestler
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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30
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Yakushina SA, Kisteneva LB. [Epstein-Barr virus ( Herpesviridae: Gammaherpesvirinae: Lymphocryptovirus: Human gammaherpesvirus 4): replication strategies]. Vopr Virusol 2020; 65:191-202. [PMID: 33533222 DOI: 10.36233/0507-4088-2020-65-4-191-202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 01/15/2023]
Abstract
The Epstein-Barr virus (EBV), one of the most common in the human population, is capable of lifelong persistence in resting memory B-cells, in T-cells in case of type 2 EBV, and in some undifferentiated epithelial cells. In most people, EBV persistence is not accompanied by significant symptoms, but frequent virus activations are associated with the increased risks of severe diseases, such as chronic active Epstein-Barr virus infection, hemophagocytic lymphohistiocytosis, multiple sclerosis, systemic lupus erythematosus, gastric and nasopharyngeal carcinomas, and a variety of T- and B-cell lymphomas. Therefore, the molecular viral and host cell processes during asymptomatic or low-symptom EBV persistence are of great interest. This review describes the behavior of the viral DNA in an infected cell and the forms of its existence (linear, circular episome, chromosomally integrated forms), as well as methods of EBV genome copying. Two closely related cycles of viral reproduction are considered. Lytic activation is unfavorable for the survival of a particular viral genome in the cell, and may be a result of differentiation of a latently infected cell, or the arrival of stress signals due to adverse extracellular conditions. The EBV has a large number of adaptive mechanisms for limiting lytic reactivation and reducing hostility of host immune cells. Understanding the molecular aspects of EBV persistence will help in the future develop more effective targeted drugs for the treatment of both viral infection and associated diseases.
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Affiliation(s)
- S A Yakushina
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Ministry of Health of Russian Federation
| | - L B Kisteneva
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Ministry of Health of Russian Federation
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31
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Chen X, Kost J, Li D. Comprehensive comparative analysis of methods and software for identifying viral integrations. Brief Bioinform 2020; 20:2088-2097. [PMID: 30102374 DOI: 10.1093/bib/bby070] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022] Open
Abstract
Many viruses are capable of integrating in the human genome, particularly viruses involved in tumorigenesis. Viral integrations can be considered genetic markers for discovering virus-caused cancers and inferring cancer cell development. Next-generation sequencing (NGS) technologies have been widely used to screen for viral integrations in cancer genomes, and a number of bioinformatics tools have been developed to detect viral integrations using NGS data. However, there has been no systematic comparison of the methods or software. In this study, we performed a comprehensive comparative analysis of the designs, performance, functionality and limitations among the existing methods and software for detecting viral integrations. We further compared the sensitivity, precision and runtime of integration detection of four representative tools. Our analyses showed that each of the existing software had its own merits; however, none of them were sufficient for parallel or accurate virome-wide detection. After carefully evaluating the limitations shared by the existing methods, we proposed strategies and directions for developing virome-wide integration detection.
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Affiliation(s)
- Xun Chen
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Jason Kost
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405, USA.,Department of Computer Science, University of Vermont, Burlington, Vermont 05405, USA.,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, Vermont 05405, USA.,Cancer Center, University of Vermont, Burlington, Vermont 05405, USA
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32
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Courtier‐Orgogozo V, Danchin A, Gouyon P, Boëte C. Evaluating the probability of CRISPR-based gene drive contaminating another species. Evol Appl 2020; 13:1888-1905. [PMID: 32908593 PMCID: PMC7463340 DOI: 10.1111/eva.12939] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
The probability D that a given clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drive element contaminates another, nontarget species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = h y b + t r a n s f × e x p r e s s × c u t × f l a n k × i m m u n e × n o n e x t i n c t with hyb = probability of hybridization between the target species and a nontarget species; transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a nontarget species (with no hybridization); express = probability that the Cas9 and guide RNA genes are expressed; cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host; flank = probability that the gene drive cassette inserts at the cut site; immune = probability that the immune system does not reject Cas9-expressing cells; nonextinct = probability of invasion of the drive within the population. We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.
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Affiliation(s)
| | - Antoine Danchin
- Institut Cochin INSERM U1016 – CNRS UMR8104 – Université Paris DescartesParisFrance
| | - Pierre‐Henri Gouyon
- Institut de Systématique, Évolution, BiodiversitéMuséum National d'Histoire NaturelleCNRSSorbonne UniversitéEPHEUAParisFrance
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33
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Mostyn A, Lenihan M, O'Sullivan D, Woods S, O'Hara M, Powell J, Power L, O'Connell NH, Dunne CP. Assessment of the FilmArray® multiplex PCR system and associated meningitis/encephalitis panel in the diagnostic service of a tertiary hospital. Infect Prev Pract 2020; 2:100042. [PMID: 34368693 PMCID: PMC8336197 DOI: 10.1016/j.infpip.2020.100042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/02/2020] [Indexed: 11/19/2022] Open
Abstract
Rapid and accurate diagnosis of meningitis/encephalitis (M/E) is essential for successful patient outcomes. The FilmArray® meningitis/encephalitis Panel (MEP) is a multiplexed PCR test for simultaneous, rapid detection of pathogens directly from cerebrospinal fluid (CSF) samples. 94 prospectively collected CSF specimens from patients with clinical suspicion of infective M/E underwent testing for 14 pathogens simultaneously, including Escherichia coli, Haemophilus influenzae, Neisseria meningitidis, and Varicella zoster. MEP demonstrated 95% agreement with current PCR methods, resulting in 16 diagnosed cases of M/E. Typically, the FilmArray® MEP results were delivered within approximately one hour, contrasting with current practices taking up to 5.6 days. Given the significant morbidity and mortality associated with delayed diagnosis of central nervous system infections, the FilmArray® MEP is a useful addition to the diagnostic capabilities of a clinical microbiology department.
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Affiliation(s)
- Amanda Mostyn
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Marie Lenihan
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Donnchadh O'Sullivan
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
| | - Sara Woods
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Maureen O'Hara
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - James Powell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Lorraine Power
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Nuala H O'Connell
- Department of Clinical Microbiology, University Hospital Limerick, Limerick, Ireland
| | - Colum P Dunne
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
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Le Tortorec A, Matusali G, Mahé D, Aubry F, Mazaud-Guittot S, Houzet L, Dejucq-Rainsford N. From Ancient to Emerging Infections: The Odyssey of Viruses in the Male Genital Tract. Physiol Rev 2020; 100:1349-1414. [PMID: 32031468 DOI: 10.1152/physrev.00021.2019] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The male genital tract (MGT) is the target of a number of viral infections that can have deleterious consequences at the individual, offspring, and population levels. These consequences include infertility, cancers of male organs, transmission to the embryo/fetal development abnormalities, and sexual dissemination of major viral pathogens such as human immunodeficiency virus (HIV) and hepatitis B virus. Lately, two emerging viruses, Zika and Ebola, have additionally revealed that the human MGT can constitute a reservoir for viruses cleared from peripheral circulation by the immune system, leading to their sexual transmission by cured men. This represents a concern for future epidemics and further underlines the need for a better understanding of the interplay between viruses and the MGT. We review here how viruses, from ancient viruses that integrated the germline during evolution through old viruses (e.g., papillomaviruses originating from Neanderthals) and more modern sexually transmitted infections (e.g., simian zoonotic HIV) to emerging viruses (e.g., Ebola and Zika) take advantage of genital tract colonization for horizontal dissemination, viral persistence, vertical transmission, and endogenization. The MGT immune responses to viruses and the impact of these infections are discussed. We summarize the latest data regarding the sources of viruses in semen and the complex role of this body fluid in sexual transmission. Finally, we introduce key animal findings that are relevant for our understanding of viral infection and persistence in the human MGT and suggest future research directions.
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Affiliation(s)
- Anna Le Tortorec
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Giulia Matusali
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Dominique Mahé
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Florence Aubry
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Séverine Mazaud-Guittot
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Laurent Houzet
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
| | - Nathalie Dejucq-Rainsford
- University of Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail)-UMR_S1085, Rennes, France
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35
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Modulation of the extrinsic cell death signaling pathway by viral Flip induces acute-death mediated liver failure. Cell Death Dis 2019; 10:878. [PMID: 31754092 PMCID: PMC6872756 DOI: 10.1038/s41419-019-2115-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 10/24/2019] [Accepted: 11/04/2019] [Indexed: 12/18/2022]
Abstract
During viral infections viruses express molecules that interfere with the host-cell death machinery and thus inhibit cell death responses. For example the viral FLIP (vFLIP) encoded by Kaposi’s sarcoma-associated herpesvirus interacts and inhibits the central cell death effector, Caspase-8. In order to analyze the impact of anti-apoptotic viral proteins, like vFlip, on liver physiology in vivo, mice expressing vFlip constitutively in hepatocytes (vFlipAlbCre+) were generated. Transgenic expression of vFlip caused severe liver tissue injury accompanied by massive hepatocellular necrosis and inflammation that finally culminated in early postnatal death of mice. On a molecular level, hepatocellular death was mediated by RIPK1-MLKL necroptosis driven by an autocrine TNF production. The loss of hepatocytes was accompanied by impaired bile acid production and disruption of the bile duct structure with impact on the liver-gut axis. Notably, embryonic development and tissue homeostasis were unaffected by vFlip expression. In summary our data uncovered that transgenic expression of vFlip can cause severe liver injury in mice, culminating in multiple organ insufficiency and death. These results demonstrate that viral cell death regulatory molecules exhibit different facets of activities beyond the inhibition of cell death that may merit more sophisticated in vitro and in vivo analysis.
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Kaján GL, Doszpoly A, Tarján ZL, Vidovszky MZ, Papp T. Virus-Host Coevolution with a Focus on Animal and Human DNA Viruses. J Mol Evol 2019; 88:41-56. [PMID: 31599342 PMCID: PMC6943099 DOI: 10.1007/s00239-019-09913-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 09/23/2019] [Indexed: 01/21/2023]
Abstract
Viruses have been infecting their host cells since the dawn of life, and this extremely long-term coevolution gave rise to some surprising consequences for the entire tree of life. It is hypothesised that viruses might have contributed to the formation of the first cellular life form, or that even the eukaryotic cell nucleus originates from an infection by a coated virus. The continuous struggle between viruses and their hosts to maintain at least a constant fitness level led to the development of an unceasing arms race, where weapons are often shuttled between the participants. In this literature review we try to give a short insight into some general consequences or traits of virus–host coevolution, and after this we zoom in to the viral clades of adenoviruses, herpesviruses, nucleo-cytoplasmic large DNA viruses, polyomaviruses and, finally, circoviruses.
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Affiliation(s)
- Győző L Kaján
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary.
| | - Andor Doszpoly
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Zoltán László Tarján
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Márton Z Vidovszky
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
| | - Tibor Papp
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest, 1143, Hungary
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Kamel M, El-Sayed A. Utilization of herpesviridae as recombinant viral vectors in vaccine development against animal pathogens. Virus Res 2019; 270:197648. [PMID: 31279828 DOI: 10.1016/j.virusres.2019.197648] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 06/27/2019] [Accepted: 06/28/2019] [Indexed: 02/06/2023]
Abstract
Throughout the past few decades, numerous viral species have been generated as vaccine vectors. Every viral vector has its own distinct characteristics. For example, the family herpesviridae encompasses several viruses that have medical and veterinary importance. Attenuated herpesviruses are developed as vectors to convey heterologous immunogens targeting several serious and crucial pathogens. Some of these vectors have already been licensed for use in the veterinary field. One of their prominent features is their capability to accommodate large amount of foreign DNA, and to stimulate both cell-mediated and humoral immune responses. A better understanding of vector-host interaction builds up a robust foundation for the future development of herpesviruses-based vectors. At the time, many molecular tools are applied to enable the generation of herpesvirus-based recombinant vaccine vectors such as BAC technology, homologous and two-step en passant mutagenesis, codon optimization, and the CRISPR/Cas9 system. This review article highlights the most important techniques applied in constructing recombinant herpesviruses vectors, advantages and disadvantages of each recombinant herpesvirus vector, and the most recent research regarding their use to control major animal diseases.
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Affiliation(s)
- Mohamed Kamel
- Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Giza, Egypt.
| | - Amr El-Sayed
- Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Giza, Egypt
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38
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Bartolini L, Theodore WH, Jacobson S, Gaillard WD. Infection with HHV-6 and its role in epilepsy. Epilepsy Res 2019; 153:34-39. [DOI: 10.1016/j.eplepsyres.2019.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/18/2019] [Accepted: 03/24/2019] [Indexed: 01/09/2023]
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39
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Houé V, Bonizzoni M, Failloux AB. Endogenous non-retroviral elements in genomes of Aedes mosquitoes and vector competence. Emerg Microbes Infect 2019; 8:542-555. [PMID: 30938223 PMCID: PMC6455143 DOI: 10.1080/22221751.2019.1599302] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent extensive (re)emergences of arthropod-borne viruses (arboviruses) such as chikungunya (CHIKV), zika (ZIKV) and dengue (DENV) viruses highlight the role of the epidemic vectors, Aedes aegypti and Aedes albopictus, in their spreading. Differences of vector competence to arboviruses highlight different virus/vector interactions. While both are highly competent to transmit CHIKV (Alphavirus,Togaviridae), only Ae. albopictus is considered as a secondary vector for DENV (Flavivirus, Flaviviridae). Among other factors such as environmental temperature, mosquito antiviral immunity and microbiota, the presence of non-retroviral integrated RNA virus sequences (NIRVS) in both mosquito genomes may modulate the vector competence. Here we review the current knowledge on these elements, highlighting the mechanisms by which they are produced and endogenized into Aedes genomes. Additionally, we describe their involvement in antiviral immunity as a stimulator of the RNA interference pathways and in some rare cases, as producer of viral-interfering proteins. Finally, we mention NIRVS as a tool for understanding virus/vector co-evolution. The recent discovery of endogenized elements shows that virus/vector interactions are more dynamic than previously thought, and genetic markers such as NIRVS could be one of the potential targets to reduce arbovirus transmission.
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Affiliation(s)
- Vincent Houé
- a Department of Virology, Arboviruses and Insect Vectors , Institut Pasteur , Paris , France.,b Collège Doctoral , Sorbonne Université , Paris , France
| | | | - Anna-Bella Failloux
- a Department of Virology, Arboviruses and Insect Vectors , Institut Pasteur , Paris , France
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40
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Xia Y, Liu Y, Deng M, Xi R. Detecting virus integration sites based on multiple related sequencing data by VirTect. BMC Med Genomics 2019; 12:19. [PMID: 30704462 PMCID: PMC6357354 DOI: 10.1186/s12920-018-0461-8] [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] [Indexed: 12/14/2022] Open
Abstract
Background Since tumor often has a high level of intra-tumor heterogeneity, multiple tumor samples from the same patient at different locations or different time points are often sequenced to study tumor intra-heterogeneity or tumor evolution. In virus-related tumors such as human papillomavirus- and Hepatitis B Virus-related tumors, virus genome integrations can be critical driving events. It is thus important to investigate the integration sites of the virus genomes. Currently, a few algorithms for detecting virus integration sites based on high-throughput sequencing have been developed, but their insufficient performance in their sensitivity, specificity and computational complexity hinders their applications in multiple related tumor sequencing. Results We develop VirTect for detecting virus integration sites simultaneously from multiple related-sample data. This algorithm is mainly based on the joint analysis of short reads spanning breakpoints of integration sites from multiple samples. To achieve high specificity and breakpoint accuracy, a local precise sandwich alignment algorithm is used. Simulation and real data analyses show that, compared with other algorithms, VirTect is significantly more sensitive and has a similar or lower false discovery rate. Conclusions VirTect can provide more accurate breakpoint position and is computationally much more efficient in terms both memory requirement and computational time. Electronic supplementary material The online version of this article (10.1186/s12920-018-0461-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuchao Xia
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Yun Liu
- School of Mathematical Sciences, Peking University, Beijing, 100871, China
| | - Minghua Deng
- School of Mathematical Sciences, Peking University, Beijing, 100871, China.,Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Ruibin Xi
- School of Mathematical Sciences, Peking University, Beijing, 100871, China. .,Center for Statistical Science, Peking University, Beijing, 100871, China. .,Center for Data Science, Peking University, Beijing, 100871, China.
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41
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Xu M, Zhang WL, Zhu Q, Yao YY, Feng QS, Zhang Z, Peng RJ, Jia WH, He GP, Feng L, Zeng ZL, Luo B, Xu RH, Zeng MS, Zhao WL, Chen SJ, Zeng YX, Jiao Y, Zeng YX, Jiao Y. Genome-wide profiling of Epstein-Barr virus integration by targeted sequencing in Epstein-Barr virus associated malignancies. Theranostics 2019; 9:1115-1124. [PMID: 30867819 PMCID: PMC6401403 DOI: 10.7150/thno.29622] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 01/18/2019] [Indexed: 12/13/2022] Open
Abstract
Rationale: Epstein-Barr virus (EBV) is associated with multiple malignancies with expression of viral oncogenic proteins and chronic inflammation as major mechanisms contributing to tumor development. A less well-studied mechanism is the integration of EBV into the human genome possibly at sites which may disrupt gene expression or genome stability. Methods: We sequenced tumor DNA to profile the EBV sequences by hybridization-based enrichment. Bioinformatic analysis was used to detect the breakpoints of EBV integrations in the genome of cancer cells. Results: We identified 197 breakpoints in nasopharyngeal carcinomas and other EBV-associated malignancies. EBV integrations were enriched at vulnerable regions of the human genome and were close to tumor suppressor and inflammation-related genes. We found that EBV integrations into the introns could decrease the expression of the inflammation-related genes, TNFAIP3, PARK2, and CDK15, in NPC tumors. In the EBV genome, the breakpoints were frequently at oriP or terminal repeats. These breakpoints were surrounded by microhomology sequences, consistent with a mechanism for integration involving viral genome replication and microhomology-mediated recombination. Conclusion: Our finding provides insight into the potential of EBV integration as an additional mechanism mediating tumorigenesis in EBV associated malignancies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,State Key Lab of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College; Collaborative Innovation Center for Cancer Medicine, Beijing, China
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College; Collaborative Innovation Center for Cancer Medicine, Beijing, China
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42
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Guo ZS, Lu B, Guo Z, Giehl E, Feist M, Dai E, Liu W, Storkus WJ, He Y, Liu Z, Bartlett DL. Vaccinia virus-mediated cancer immunotherapy: cancer vaccines and oncolytics. J Immunother Cancer 2019; 7:6. [PMID: 30626434 PMCID: PMC6325819 DOI: 10.1186/s40425-018-0495-7] [Citation(s) in RCA: 176] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/26/2018] [Indexed: 12/11/2022] Open
Abstract
Cancer vaccines and oncolytic immunotherapy are promising treatment strategies with potential to provide greater clinical benefit to patients with advanced-stage cancer. In particular, recombinant vaccinia viruses (VV) hold great promise as interventional agents. In this article, we first summarize the current understanding of virus biology and viral genes involved in host-virus interactions to further improve the utility of these agents in therapeutic applications. We then discuss recent findings from basic and clinical studies using VV as cancer vaccines and oncolytic immunotherapies. Despite encouraging results gleaned from translational studies in animal models, clinical trials implementing VV vectors alone as cancer vaccines have yielded largely disappointing results. However, the combination of VV vaccines with alternate forms of standard therapies has resulted in superior clinical efficacy. For instance, combination regimens using TG4010 (MVA-MUC1-IL2) with first-line chemotherapy in advanced-stage non-small cell lung cancer or combining PANVAC with docetaxel in the setting of metastatic breast cancer have clearly provided enhanced clinical benefits to patients. Another novel cancer vaccine approach is to stimulate anti-tumor immunity via STING activation in Batf3-dependent dendritic cells (DC) through the use of replication-attenuated VV vectors. Oncolytic VVs have now been engineered for improved safety and superior therapeutic efficacy by arming them with immune-stimulatory genes or pro-apoptotic molecules to facilitate tumor immunogenic cell death, leading to enhanced DC-mediated cross-priming of T cells recognizing tumor antigens, including neoantigens. Encouraging translational and early phase clinical results with Pexa-Vec have matured into an ongoing global phase III trial for patients with hepatocellular carcinoma. Combinatorial approaches, most notably those using immune checkpoint blockade, have produced exciting pre-clinical results and warrant the development of innovative clinical studies. Finally, we discuss major hurdles that remain in the field and offer some perspectives regarding the development of next generation VV vectors for use as cancer therapeutics.
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Affiliation(s)
- Zong Sheng Guo
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Binfeng Lu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zongbi Guo
- Fujian Tianjian Pharmaceutical Co. Ltd., Sanming, Fujian, China
| | - Esther Giehl
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mathilde Feist
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Enyong Dai
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Weilin Liu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Walter J Storkus
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Dermatology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yukai He
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Zuqiang Liu
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - David L Bartlett
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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43
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Flamand L. Chromosomal Integration by Human Herpesviruses 6A and 6B. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1045:209-226. [PMID: 29896669 DOI: 10.1007/978-981-10-7230-7_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Upon infection and depending on the infected cell type, human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) can replicate or enter a state of latency. HHV-6A and HHV-6B can integrate their genomes into host chromosomes as one way to establish latency. Viral integration takes place near the subtelomeric/telomeric junction of chromosomes. When HHV-6 infection and integration occur in gametes, the virus can be genetically transmitted. Inherited chromosomally integrated HHV-6 (iciHHV-6)-positive individuals carry one integrated HHV-6 copy per somatic cell. The prevalence of iciHHV-6+ individuals varies between 0.6% and 2%, depending on the geographical region sampled. In this chapter, the mechanisms leading to viral integration and reactivation from latency, as well as some of the biological and medical consequences associated with iciHHV-6, were discussed.
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Affiliation(s)
- Louis Flamand
- Division of Infectious and Immune Diseases, CHU de Québec Research Center, QC, Quebec, Canada. .,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, QC, Quebec, Canada.
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44
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Macaca arctoides gammaherpesvirus 1 (strain herpesvirus Macaca arctoides): virus sequence, phylogeny and characterisation of virus-transformed macaque and rabbit cell lines. Med Microbiol Immunol 2018; 208:109-129. [PMID: 30291474 DOI: 10.1007/s00430-018-0565-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/27/2018] [Indexed: 10/28/2022]
Abstract
Herpesvirus Macaca arctoides (HVMA) has the propensity to transform macaque lymphocytes to lymphoblastoid cells (MAL-1). Inoculation of rabbits with cell-free virus-containing supernatant resulted in the development of malignant lymphomas and allowed isolation of immortalised HVMA-transformed rabbit lymphocytes (HTRL). In this study, the HVMA genome sequence (approx. 167 kbp), its organisation, and novel aspects of virus latency are presented. Ninety-one open reading frames were identified, of which 86 were non-repetitive. HVMA was identified as a Lymphocryptovirus closely related to Epstein-Barr virus, suggesting the designation as 'Macaca arctoides gammaherpesvirus 1' (MarcGHV-1). In situ lysis gel and Southern blot hybridisation experiments revealed that the MAL-1 cell line contains episomal and linear DNA, whereas episomal DNA is predominantly present in HTRL. Integration of viral DNA into macaque and rabbit host cell genomes was demonstrated by fluorescence in situ hybridisation on chromosomal preparations. Analysis of next-generation sequencing data confirmed this finding. Approximately 400 read pairs represent the overlap between macaque and MarcGHV-1 DNA. Both, MAL-1 cells and HTRL show characteristics of a polyclonal tumour with B- and T-lymphocyte markers. Based on analysis of viral gene expression and immunohistochemistry, the persistence of MarcGHV-1 in MAL-1 cells resemble the latency type III, whereas the expression pattern observed in HTRL was more comparable with latency type II. There was no evidence of the presence of STLV-1 proviral DNA in MAL-1 and HTRL. Due to the similarity to EBV-mediated cell transformation, MarcGHV-1 expands the available in vitro models by simian and rabbit cell lines.
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45
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Turbett SE, Tsiaras WG, McDermott S, Eng G. Case 26-2018: A 48-Year-Old Man with Fever, Chills, Myalgias, and Rash. N Engl J Med 2018; 379:775-785. [PMID: 30134139 DOI: 10.1056/nejmcpc1807494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Sarah E Turbett
- From the Departments of Medicine (S.E.T.), Radiology (S.M.), and Pathology (G.E.), Massachusetts General Hospital, the Department of Dermatology, Brigham and Women's Hospital (W.G.T.), and the Departments of Medicine (S.E.T.), Dermatology (W.G.T.), Radiology (S.M.), and Pathology (G.E.), Harvard Medical School - all in Boston
| | - William G Tsiaras
- From the Departments of Medicine (S.E.T.), Radiology (S.M.), and Pathology (G.E.), Massachusetts General Hospital, the Department of Dermatology, Brigham and Women's Hospital (W.G.T.), and the Departments of Medicine (S.E.T.), Dermatology (W.G.T.), Radiology (S.M.), and Pathology (G.E.), Harvard Medical School - all in Boston
| | - Shaunagh McDermott
- From the Departments of Medicine (S.E.T.), Radiology (S.M.), and Pathology (G.E.), Massachusetts General Hospital, the Department of Dermatology, Brigham and Women's Hospital (W.G.T.), and the Departments of Medicine (S.E.T.), Dermatology (W.G.T.), Radiology (S.M.), and Pathology (G.E.), Harvard Medical School - all in Boston
| | - George Eng
- From the Departments of Medicine (S.E.T.), Radiology (S.M.), and Pathology (G.E.), Massachusetts General Hospital, the Department of Dermatology, Brigham and Women's Hospital (W.G.T.), and the Departments of Medicine (S.E.T.), Dermatology (W.G.T.), Radiology (S.M.), and Pathology (G.E.), Harvard Medical School - all in Boston
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46
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Baheti S, Tang X, O'Brien DR, Chia N, Roberts LR, Nelson H, Boughey JC, Wang L, Goetz MP, Kocher JPA, Kalari KR. HGT-ID: an efficient and sensitive workflow to detect human-viral insertion sites using next-generation sequencing data. BMC Bioinformatics 2018; 19:271. [PMID: 30016933 PMCID: PMC6050683 DOI: 10.1186/s12859-018-2260-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Background Transfer of genetic material from microbes or viruses into the host genome is known as horizontal gene transfer (HGT). The integration of viruses into the human genome is associated with multiple cancers, and these can now be detected using next-generation sequencing methods such as whole genome sequencing and RNA-sequencing. Results We designed a novel computational workflow, HGT-ID, to identify the integration of viruses into the human genome using the sequencing data. The HGT-ID workflow primarily follows a four-step procedure: i) pre-processing of unaligned reads, ii) virus detection using subtraction approach, iii) identification of virus integration site using discordant and soft-clipped reads and iv) HGT candidates prioritization through a scoring function. Annotation and visualization of the events, as well as primer design for experimental validation, are also provided in the final report. We evaluated the tool performance with the well-understood cervical cancer samples. The HGT-ID workflow accurately detected known human papillomavirus (HPV) integration sites with high sensitivity and specificity compared to previous HGT methods. We applied HGT-ID to The Cancer Genome Atlas (TCGA) whole-genome sequencing data (WGS) from liver tumor-normal pairs. Multiple hepatitis B virus (HBV) integration sites were identified in TCGA liver samples and confirmed by HGT-ID using the RNA-Seq data from the matched liver pairs. This shows the applicability of the method in both the data types and cross-validation of the HGT events in liver samples. We also processed 220 breast tumor WGS data through the workflow; however, there were no HGT events detected in those samples. Conclusions HGT-ID is a novel computational workflow to detect the integration of viruses in the human genome using the sequencing data. It is fast and accurate with functions such as prioritization, annotation, visualization and primer design for future validation of HGTs. The HGT-ID workflow is released under the MIT License and available at http://kalarikrlab.org/Software/HGT-ID.html.
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Affiliation(s)
- Saurabh Baheti
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xiaojia Tang
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Daniel R O'Brien
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nicholas Chia
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Heidi Nelson
- Department of Surgery, Mayo Clinic, Rochester, MN, USA
| | | | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Matthew P Goetz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Department of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jean-Pierre A Kocher
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Krishna R Kalari
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.
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47
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Mahas A, Mahfouz M. Engineering virus resistance via CRISPR-Cas systems. Curr Opin Virol 2018; 32:1-8. [PMID: 30005359 DOI: 10.1016/j.coviro.2018.06.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/25/2018] [Indexed: 12/15/2022]
Abstract
In prokaryotes, CRISPR/Cas adaptive immunity systems target and destroy nucleic acids derived from invading bacteriophages and other foreign genetic elements. In eukaryotes, the native function of these systems has been exploited to combat viruses in mammals and plants. Rewired CRISPR/Cas9 and CRISPR/Cas13 systems have been used to confer resistance against DNA and RNA viruses, respectively. Here, we discuss recent approaches employing CRISPR/Cas systems to combat viruses in eukaryotes, highlight key challenges, and provide future perspectives. Moreover, we discuss the application of CRISPR/Cas systems in genome-wide screens to identify key host factors for virus infection to enhance our understanding of basic virus biology and to identify and study virus-host interactions.
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Affiliation(s)
- Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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48
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Miura H, Kawamura Y, Hattori F, Kozawa K, Ihira M, Ohye T, Kurahashi H, Yoshikawa T. Chromosomally integrated human herpesvirus 6 in the Japanese population. J Med Virol 2018; 90:1636-1642. [DOI: 10.1002/jmv.25244] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Hiroki Miura
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
| | - Yoshiki Kawamura
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
| | - Fumihiko Hattori
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
| | - Kei Kozawa
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
| | - Masaru Ihira
- Faculty of Clinical Engineering, Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | - Tamae Ohye
- Department of Clinical Laboratory Medicine; Graduate School of Health Sciences, Fujita Health University; Toyoake Aichi Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics; Institute for Comprehensive Medical Science, Fujita Health University; Toyoake Aichi Japan
| | - Tetsushi Yoshikawa
- Department of Pediatrics; Fujita Health University School of Medicine; Toyoake Aichi Japan
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49
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Bartolini L, Libbey JE, Ravizza T, Fujinami RS, Jacobson S, Gaillard WD. Viral Triggers and Inflammatory Mechanisms in Pediatric Epilepsy. Mol Neurobiol 2018; 56:1897-1907. [PMID: 29978423 DOI: 10.1007/s12035-018-1215-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022]
Abstract
Experimental and clinical findings suggest a crucial role for inflammation in the onset of pediatric seizures; this mechanism is not targeted by conventional antiepileptic drugs and may contribute to refractory epilepsy. Several triggers, including infection with neurotropic viruses such as human herpesvirus 6 (HHV-6), other herpesviruses, and picornaviruses, appear to induce activation of the innate and adaptive immune systems, which results in several neuroinflammatory responses, leading to enhanced neuronal excitability, and ultimately contributing to epileptogenesis. This review discusses the proposed mechanisms by which infection with herpesviruses, and particularly with HHV-6, and ensuing inflammation may lead to seizure generation, and later development of epilepsy. We also examine the evidence that links herpesvirus and picornavirus infections with acute seizures and chronic forms of epilepsy. Understanding the mechanisms by which specific viruses may trigger a cascade of alterations in the CNS ultimately leading to epilepsy appears critical for the development of therapeutic agents that may target the virus or inflammatory mechanisms early and prevent progression of epileptogenesis.
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Affiliation(s)
- Luca Bartolini
- Clinical Epilepsy Section, National Institute of Neurological Disorders and Stroke, NIH, Building 10, room 7-5680, 10 Center Drive, Bethesda, MD, 20814, USA. .,Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, NIH, 10 Center Drive, Bethesda, MD, 20892, USA. .,Center for Neuroscience, Children's National Medical Center, George Washington University, 111 Michigan Ave NW, Washington, DC, 20010, USA.
| | - Jane E Libbey
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, 2600 EEJMRB, Salt Lake City, UT, 84112, USA
| | - Teresa Ravizza
- Neuroscience Department, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156, Milan, Italy
| | - Robert S Fujinami
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, 2600 EEJMRB, Salt Lake City, UT, 84112, USA
| | - Steven Jacobson
- Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, NIH, 10 Center Drive, Bethesda, MD, 20892, USA
| | - William D Gaillard
- Center for Neuroscience, Children's National Medical Center, George Washington University, 111 Michigan Ave NW, Washington, DC, 20010, USA
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50
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Greninger AL, Roychoudhury P, Makhsous N, Hanson D, Chase J, Krueger G, Xie H, Huang ML, Saunders L, Ablashi D, Koelle DM, Cook L, Jerome KR. Copy Number Heterogeneity, Large Origin Tandem Repeats, and Interspecies Recombination in Human Herpesvirus 6A (HHV-6A) and HHV-6B Reference Strains. J Virol 2018; 92:e00135-18. [PMID: 29491155 PMCID: PMC5923074 DOI: 10.1128/jvi.00135-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 02/21/2018] [Indexed: 12/17/2022] Open
Abstract
Quantitative PCR is a diagnostic pillar for clinical virology testing, and reference materials are necessary for accurate, comparable quantitation between clinical laboratories. Accurate quantitation of human herpesvirus 6A/B (HHV-6A/B) is important for detection of viral reactivation and inherited chromosomally integrated HHV-6A/B in immunocompromised patients. Reference materials in clinical virology commonly consist of laboratory-adapted viral strains that may be affected by the culture process. We performed next-generation sequencing to make relative copy number measurements at single nucleotide resolution of eight candidate HHV-6A and seven HHV-6B reference strains and DNA materials from the HHV-6 Foundation and Advanced Biotechnologies Inc. Eleven of 17 (65%) HHV-6A/B candidate reference materials showed multiple copies of the origin of replication upstream of the U41 gene by next-generation sequencing. These large tandem repeats arose independently in culture-adapted HHV-6A and HHV-6B strains, measuring 1,254 bp and 983 bp, respectively. The average copy number measured was between 5 and 10 times the number of copies of the rest of the genome. We also report the first interspecies recombinant HHV-6A/B strain with a HHV-6A backbone and a >5.5-kb region from HHV-6B, from U41 to U43, that covered the origin tandem repeat. Specific HHV-6A reference strains demonstrated duplication of regions at U1/U2, U87, and U89, as well as deletion in the U12-to-U24 region and the U94/U95 genes. HHV-6A/B strains derived from cord blood mononuclear cells from different laboratories on different continents with fewer passages revealed no copy number differences throughout the viral genome. These data indicate that large origin tandem duplications are an adaptation of both HHV-6A and HHV-6B in culture and show interspecies recombination is possible within the Betaherpesvirinae.IMPORTANCE Anything in science that needs to be quantitated requires a standard unit of measurement. This includes viruses, for which quantitation increasingly determines definitions of pathology and guidelines for treatment. However, the act of making standard or reference material in virology can alter its very accuracy through genomic duplications, insertions, and rearrangements. We used deep sequencing to examine candidate reference strains for HHV-6, a ubiquitous human virus that can reactivate in the immunocompromised population and is integrated into the human genome in every cell of the body for 1% of people worldwide. We found large tandem repeats in the origin of replication for both HHV-6A and HHV-6B that are selected for in culture. We also found the first interspecies recombinant between HHV-6A and HHV-6B, a phenomenon that is well known in alphaherpesviruses but to date has not been seen in betaherpesviruses. These data critically inform HHV-6A/B biology and the standard selection process.
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Affiliation(s)
- Alexander L Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
| | - Negar Makhsous
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Derek Hanson
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Jill Chase
- HHV-6 Foundation, Santa Barbara, California, USA
| | - Gerhard Krueger
- Department of Pathology and Laboratory Medicine, University of Houston, Houston, Texas, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Lindsay Saunders
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | | | - David M Koelle
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Linda Cook
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Institute, Seattle, Washington, USA
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