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Volkening JD, Spatz SJ, Ponnuraj N, Akbar H, Arrington JV, Vega-Rodriguez W, Jarosinski KW. Viral proteogenomic and expression profiling during productive replication of a skin-tropic herpesvirus in the natural host. PLoS Pathog 2023; 19:e1011204. [PMID: 37289833 DOI: 10.1371/journal.ppat.1011204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/29/2023] [Indexed: 06/10/2023] Open
Abstract
Efficient transmission of herpesviruses is essential for dissemination in host populations; however, little is known about the viral genes that mediate transmission, mostly due to a lack of natural virus-host model systems. Marek's disease is a devastating herpesviral disease of chickens caused by Marek's disease virus (MDV) and an excellent natural model to study skin-tropic herpesviruses and transmission. Like varicella zoster virus that causes chicken pox in humans, the only site where infectious cell-free MD virions are efficiently produced is in epithelial skin cells, a requirement for host-to-host transmission. Here, we enriched for heavily infected feather follicle epithelial skin cells of live chickens to measure both viral transcription and protein expression using combined short- and long-read RNA sequencing and LC/MS-MS bottom-up proteomics. Enrichment produced a previously unseen breadth and depth of viral peptide sequencing. We confirmed protein translation for 84 viral genes at high confidence (1% FDR) and correlated relative protein abundance with RNA expression levels. Using a proteogenomic approach, we confirmed translation of most well-characterized spliced viral transcripts and identified a novel, abundant isoform of the 14 kDa transcript family via IsoSeq transcripts, short-read intron-spanning sequencing reads, and a high-quality junction-spanning peptide identification. We identified peptides representing alternative start codon usage in several genes and putative novel microORFs at the 5' ends of two core herpesviral genes, pUL47 and ICP4, along with strong evidence of independent transcription and translation of the capsid scaffold protein pUL26.5. Using a natural animal host model system to examine viral gene expression provides a robust, efficient, and meaningful way of validating results gathered from cell culture systems.
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Affiliation(s)
| | - Stephen J Spatz
- US National Poultry Research Laboratory, ARS, USDA, Athens, Georgia, United States of America
| | - Nagendraprabhu Ponnuraj
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Haji Akbar
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Justine V Arrington
- Protein Sciences Facility, Roy J. Carver Biotechnology Center, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Widaliz Vega-Rodriguez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Keith W Jarosinski
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Bertzbach LD, Tregaskes CA, Martin RJ, Deumer US, Huynh L, Kheimar AM, Conradie AM, Trimpert J, Kaufman J, Kaufer BB. The Diverse Major Histocompatibility Complex Haplotypes of a Common Commercial Chicken Line and Their Effect on Marek's Disease Virus Pathogenesis and Tumorigenesis. Front Immunol 2022; 13:908305. [PMID: 35693787 PMCID: PMC9186122 DOI: 10.3389/fimmu.2022.908305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/29/2022] [Indexed: 02/05/2023] Open
Abstract
The major histocompatibility complex (MHC) is crucial for appropriate immune responses against invading pathogens. Chickens possess a single predominantly-expressed class I molecule with strong associations between disease resistance and MHC haplotype. For Marek's disease virus (MDV) infections of chickens, the MHC haplotype is one of the major determinants of genetic resistance and susceptibility. VALO specific pathogen free (SPF) chickens are widely used in biomedical research and vaccine production. While valuable findings originate from MDV infections of VALO SPF chickens, their MHC haplotypes and associated disease resistance remained elusive. In this study, we used several typing systems to show that VALO SPF chickens possess MHC haplotypes that include B9, B9:02, B15, B19 and B21 at various frequencies. Moreover, we associate the MHC haplotypes to MDV-induced disease and lymphoma formation and found that B15 homozygotes had the lowest tumor incidence while B21 homozygotes had the lowest number of organs with tumors. Finally, we found transmission at variable levels to all contact birds except B15/B21 heterozygotes. These data have immediate implications for the use of VALO SPF chickens and eggs in the life sciences and add another piece to the puzzle of the chicken MHC complex and its role in infections with this oncogenic herpesvirus.
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Affiliation(s)
| | - Clive A. Tregaskes
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Rebecca J. Martin
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | | | - Lan Huynh
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ahmed M. Kheimar
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Sohag University, Sohag, Egypt
| | | | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Jim Kaufman
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Benedikt B. Kaufer
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
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