Proteogenomic and expression profiling of Marek’s disease virus during fully productive replication in the host

Authors: Spatz, Stephen; JAROSINSKI, KEITH - University Of Illinois; VOLKENING, JEREMY - Base2bio; PONNURAJ, NAGENDRAPRABHU - University Of Illinois; AKBAR, HAJI - University Of Illinois; ARRINGTON, JUSTINE - University Of Illinois

Submitted to: American Society for Virology Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/29/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Efficient transmission of herpesviruses is essential for dissemination in host populations. The herpesvirus-host relationship is relatively benign and has co-evolved over millions of years. Marek’s disease is a devastating herpesviral disease of chickens characterized by wasting, neurological disorders, and rapid proliferation of transformed T cells that manifest as solid lymphomas, predominantly in the viscera, caused by Marek’s disease virus (MDV). MDV is highly cell-associated in cell culture and the host, providing a means to evade the host’s immune response. The only site where cell-free MDV is produced is in feather follicle epithelial (FFE) skin cells, where cell-free virus is produced and required for host-to-host transmission. We enriched for actively replicating virus in FFE cells of live chickens to measure both viral transcription and protein expression using combined RNA sequencing and LC/MS-MS bottom-up proteomics during fully productive viral replication. 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 both intron-spanning sequencing reads, as well as a high-quality junction-spanning peptide identification. We identified peptides representing alternative start codon usage in several genes and novel microORFs at the 5’ ends of two core viral genes, pUL47 and ICP4, and evidence of 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.