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Abebe JS, Alwie Y, Fuhrmann E, Leins J, Mai J, Verstraten R, Schreiner S, Wilson AC, Depledge DP. Nanopore Guided Annotation of Transcriptome Architectures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587744. [PMID: 38617228 PMCID: PMC11014626 DOI: 10.1101/2024.04.02.587744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
High-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs, without recoding or amplification bias, and resulting data may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails on individual RNA molecules. Existing software solutions for generating high-resolution transcriptome annotations are poorly suited to small gene dense organisms such as viruses due to the challenge of identifying distinct transcript isoforms where alternative splicing and overlapping RNAs are prevalent. To resolve this, we identified key characteristics of DRS datasets and developed a novel approach to transcriptome. We demonstrate, using a combination of synthetic and original datasets, that our novel approach yields a high level of precision and recall when reconstructing both gene sparse and gene dense transcriptomes from DRS datasets. We further apply this approach to generate a new high resolution transcriptome annotation of the neglected pathogen human adenovirus type F 41 for which we identify 77 distinct transcripts encoding at least 23 different proteins.
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Affiliation(s)
- Jonathan S. Abebe
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Yasmine Alwie
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Erik Fuhrmann
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Jonas Leins
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Julia Mai
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Ruth Verstraten
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Sabrina Schreiner
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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2
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Grand RJ. Pathogenicity and virulence of human adenovirus F41: Possible links to severe hepatitis in children. Virulence 2023; 14:2242544. [PMID: 37543996 PMCID: PMC10405776 DOI: 10.1080/21505594.2023.2242544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/08/2023] Open
Abstract
Over 100 human adenoviruses (HAdVs) have been isolated and allocated to seven species, A-G. Species F comprises two members-HAdV-F40 and HAdV-F41. As their primary site of infection is the gastrointestinal tract they have been termed, with species A, enteric adenoviruses. HAdV-F40 and HAdV-F41 are a common cause of gastroenteritis and diarrhoea in children. Partly because of difficulties in propagating the viruses in the laboratory, due to their restrictions on growth in many cell lines, our knowledge of the properties of individual viral proteins is limited. However, the structure of HAdV-F41 has recently been determined by cryo-electron microscopy. The overall structure is similar to those of HAdV-C5 and HAdV-D26 although with some differences. The sequence and arrangement of the hexon hypervariable region 1 (HVR1) and the arrangement of the C-terminal region of protein IX differ. Variations in the penton base and hexon HVR1 may play a role in facilitating infection of intestinal cells by HAdV-F41. A unique feature of HAdV-F40 and F41, among human adenoviruses, is the presence and expression of two fibre genes, giving long and short fibre proteins. This may also contribute to the tropism of these viruses. HAdV-F41 has been linked to a recent outbreak of severe acute hepatitis "of unknown origin" in young children. Further investigation has shown a very high prevalence of adeno-associated virus-2 in the liver and/or plasma of some cohorts of patients. These observations have proved controversial as HAdV-F41 had not been reported to infect the liver and AAV-2 has generally been considered harmless.
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Affiliation(s)
- Roger J. Grand
- Institute for Cancer and Genomic Science, the Medical School, University of Birmingham, Birmingham, UK
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3
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Oliveira ERA, Li L, Bouvier M. Intracellular Sequestration of the NKG2D Ligand MIC B by Species F Adenovirus. Viruses 2021; 13:1289. [PMID: 34372495 PMCID: PMC8310058 DOI: 10.3390/v13071289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/16/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022] Open
Abstract
The enteric human adenoviruses of species F (HAdVs-F), which comprise HAdV-F40 and HAdV-F41, are significant pathogens that cause acute gastroenteritis in children worldwide. The early transcription unit 3 (E3) of HAdVs-F is markedly different from that of all other HAdV species. To date, the E3 proteins unique to HAdVs-F have not been characterized and the mechanism by which HAdVs-F evade immune defenses in the gastrointestinal (GI) tract is poorly understood. Here, we show that HAdV-F41 infection of human intestinal HCT116 cells upregulated the expression of MHC class I-related chain A (MIC A) and MIC B relative to uninfected cells. Our results also showed that, for MIC B, this response did not however result in a significant increase of MIC B on the cell surface. Instead, MIC B was largely sequestered intracellularly. Thus, although HAdV-F41 infection of HCT116 cells upregulated MIC B expression, the ligand remained inside infected cells. A similar observation could not be made for MIC A in these cells. Our preliminary findings represent a novel function of HAdVs-F that may enable these viruses to evade immune surveillance by natural killer (NK) cells in the infected gut, thereby paving the way for the future investigation of their unique E3 proteins.
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Affiliation(s)
| | | | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois at Chicago, 909 S Wolcott Avenue, Chicago, IL 60612, USA; (E.R.A.O.); (L.L.)
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4
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Oliveira ERA, Bouvier M. Immune evasion by adenoviruses: a window into host-virus adaptation. FEBS Lett 2019; 593:3496-3503. [PMID: 31736048 DOI: 10.1002/1873-3468.13682] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 11/09/2022]
Abstract
Human adenoviruses (HAdVs) are widespread pathogens that cause a number of partially overlapping, species-specific infections associated with respiratory, urinary, gastrointestinal, and ocular diseases. The early 3 (E3) region of adenoviruses is highly divergent between different species, and it encodes a multitude of proteins with immunomodulatory functions. The study of genetic diversity in the E3 region offers a unique opportunity to gain insight into how the various HAdVs have evolutionarily adapted in response to the selection pressures exerted by host immune defenses. The objective of this review was to discuss subversion of host antiviral immune responses by HAdVs, with a focus on suppression of MHC class I antigen presentation, as a window into host-HAdV adaptation.
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Affiliation(s)
- Edson R A Oliveira
- Department of Microbiology and Immunology, University of Illinois at Chicago, IL, USA
| | - Marlene Bouvier
- Department of Microbiology and Immunology, University of Illinois at Chicago, IL, USA
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Lu ZZ, Zou XH, Lastinger K, Williams A, Qu JG, Estes DM. Enhanced growth of recombinant human adenovirus type 41 (HAdV-41) carrying ADP gene. Virus Res 2013; 176:61-8. [PMID: 23769974 DOI: 10.1016/j.virusres.2013.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 05/09/2013] [Accepted: 05/10/2013] [Indexed: 12/11/2022]
Abstract
Human adenovirus type 41 (HAdV-41) has the potential to be constructed as a gene transfer vector for oral vaccine or gene therapy targeting gastrointestinal tract. Block in release of progeny virus from host cell severely affects the yield during virus amplification. In this study, HAdV-5 adenovirus death protein (ADP) gene was used to replace the open reading frames (ORFs) of the HAdV-41 E3 region to construct a backbone plasmid pAdbone41ADP. Recombinant adenoviral plasmids harboring ADP and GFP genes (pAd41ADP-GFP) were generated. Plaques were formed and HAdV-41-ADP-GFP virus was rescued after transfecting pAd41ADP-GFP into the packaging cell line 293TE32. When amplified on 293TE32 cells, HAdV-41-ADP-GFP virus released to the culture medium was 10-50 times more than control virus HAdV-41-GFP, which did not carry ADP gene. The results demonstrated that incorporation of the ADP gene substantially increased the yield of recombinant HAdV-41 virus through enhancing spread of progeny virus among packaging cells.
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Affiliation(s)
- Zhuo-Zhuang Lu
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, GA 30602, USA
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6
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Chen DL, Dong LX, Li M, Guo XJ, Wang M, Liu XF, Lu ZZ, Hung T. Construction of an infectious clone of human adenovirus type 41. Arch Virol 2012; 157:1313-21. [DOI: 10.1007/s00705-012-1293-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 02/22/2012] [Indexed: 11/28/2022]
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7
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Zou XH, Xiao X, Chen DL, Li ZL, Song JD, Wang M, Qu JG, Lu ZZ, Hung T. An improved HAdV-41 E1B55K-expressing 293 cell line for packaging fastidious adenovirus. J Virol Methods 2011; 175:188-96. [DOI: 10.1016/j.jviromet.2011.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 04/06/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
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Applying genomic and bioinformatic resources to human adenovirus genomes for use in vaccine development and for applications in vector development for gene delivery. Viruses 2010; 2:1-26. [PMID: 21994597 PMCID: PMC3185558 DOI: 10.3390/v2010001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 12/05/2009] [Accepted: 12/17/2009] [Indexed: 12/25/2022] Open
Abstract
Technological advances and increasingly cost-effect methodologies in DNA sequencing and computational analysis are providing genome and proteome data for human adenovirus research. Applying these tools, data and derived knowledge to the development of vaccines against these pathogens will provide effective prophylactics. The same data and approaches can be applied to vector development for gene delivery in gene therapy and vaccine delivery protocols. Examination of several field strain genomes and their analyses provide examples of data that are available using these approaches. An example of the development of HAdV-B3 both as a vaccine and also as a vector is presented.
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9
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Molecular cloning and expression of channel catfish, Ictalurus punctatus, complement membrane attack complex inhibitor CD59. Vet Immunol Immunopathol 2007; 120:246-53. [DOI: 10.1016/j.vetimm.2007.07.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 07/11/2007] [Accepted: 07/17/2007] [Indexed: 11/23/2022]
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10
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Lemiale F, Haddada H, Nabel GJ, Brough DE, King CR, Gall JGD. Novel adenovirus vaccine vectors based on the enteric-tropic serotype 41. Vaccine 2006; 25:2074-84. [PMID: 17250935 PMCID: PMC2584667 DOI: 10.1016/j.vaccine.2006.11.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 11/06/2006] [Accepted: 11/13/2006] [Indexed: 10/23/2022]
Abstract
Replication-defective adenovirus vectors, primarily developed from serotype 5 (Ad5) viruses, have been widely used for gene transfer and vaccination approaches. Vectors based on other serotypes of adenovirus could be used in conjunction with, or in place of, Ad5 vectors. In this study, Ad41, an enteric adenovirus usually described as 'non-cultivable' or 'fastidious,' has been successfully cloned, rescued and propagated on 293-ORF6 cells. The complementation capabilities of this cell line allow generation of Ad41 vectors at titers comparable to those obtained for Ad5 vectors. Mice immunized with an Ad41 vector containing an HIV envelope (Env) gene mounted anti-Env cellular and humoral immune responses. Ad41-Env vectors appear to be particularly attractive when used in heterologous prime-boost regimens, where they induce significantly higher cellular immune responses to HIV-Env than Ad5-based regimens. Ad41-based constructs are attractive vaccine vectors alone or in combination with Ad5 adenovectors, since each vector type can provide circumvention of pre-existing immunity to the other.
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Affiliation(s)
- Franck Lemiale
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Hedi Haddada
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | - Gary J. Nabel
- Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland 20892
| | | | | | - Jason G. D. Gall
- GenVec, Inc. Gaithersburg, Maryland, USA, 20878
- Corresponding author. 65 West Watkins Mill Road, Gaithersburg, MD, USA, 20878.
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11
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Burgert HG, Ruzsics Z, Obermeier S, Hilgendorf A, Windheim M, Elsing A. Subversion of host defense mechanisms by adenoviruses. Curr Top Microbiol Immunol 2002; 269:273-318. [PMID: 12224514 DOI: 10.1007/978-3-642-59421-2_16] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Adenoviruses (Ads) cause acute and persistent infections. Alike the much more complex herpesviruses, Ads encode numerous immunomodulatory functions. About a third of the viral genome is devoted to counteract both the innate and the adaptive antiviral immune response. Immediately upon infection, E1A blocks interferon-induced gene expression and the VA-RNA inhibits interferon-induced PKR activity. At the same time, E1A reprograms the cell for DNA synthesis and induces the intrinsic cellular apoptosis program that is interrupted by E1B/19K and E1B/55K proteins, the latter inhibits p53-mediated apoptosis. Most other viral stealth functions are encoded by a separate transcription units, E3. Several E3 products prevent death receptor-mediated apoptosis. E3/14.7K seems to interfere with the cytolytic and pro-inflammatory activities of TNF while E3/10.4K and 14.5K proteins remove Fas and TRAIL receptors from the cell surface by inducing their degradation in lysosomes. These and other functions that may afect granule-mediated cell death might drastically limit lysis by NK cells and cytotoxic T cells (CTL). Moreover, Ads interfere with recognition of infected cell by CTL. The paradigmatic E3/19K protein subverts antigen presentation by MHC class I molecules by inhibiting their transport to the cell surface. In concert, these viral countermeasures ensure prolonged survival in the infected host and, as a consequence, facilitate transmission. Elucidating the molecular mechanisms of Ad-mediated immune evasion has stimulated corresponding research on other viruses. This knowledge will also be instrumental for designing better vectors for gene therapy and vaccination, and may lead to a more rational treatment of life-threatening Ad infections, e.g. in transplantation patients.
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Affiliation(s)
- H G Burgert
- Max von Pettenkofer-Institut, Lehrstuhl Virologie, Genzentrum der Ludwig-Maximilians-Universität, Feodor-Lynen-Str. 25, 81377 München, Germany
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12
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Sparer TE, Gooding LR. Suppression of MHC class I antigen presentation by human adenoviruses. Curr Top Microbiol Immunol 1998; 232:135-47. [PMID: 9557397 DOI: 10.1007/978-3-642-72045-1_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- T E Sparer
- St. Mary's Medical School, Respiratory Medicine, London, UK
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