Quantitative temporal viromics: an approach to investigate host-pathogen interaction.
Bottom Line: QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets.Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined.QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.
Affiliation: Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK. Electronic address: email@example.com.Show MeSH
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Mentions: The k-means method is useful to cluster proteins into a specified number of classes based on the similarity of temporal profiles. We clustered all 7,491 proteins from experiment WCL2 and 1,184 proteins from PM2 into three classes (corresponding to upregulation, downregulation, and no change) to identify novel pathways dysregulated during HCMV infection (Figure 3B). We then applied DAVID software (Huang et al., 2009) to determine which KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were enriched in each class (Figures 3C and S3A). We made the discovery that multiple members of the TLR signaling pathway were downregulated (Figures S3A and S3B; Table S4A), suggesting that HCMV might employ a number of strategies to avoid this intrinsic immune mechanism. Fatty acid metabolism and oxidative phosphorylation were upregulated during infection (Figure 3C; Table S4A), corresponding to published literature (Koyuncu et al., 2013).
Affiliation: Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK. Electronic address: firstname.lastname@example.org.