Hit-and-run, hit-and-stay, and commensal bacteria present different peptide content when viewed from the perspective of the T cell.pdfVIP

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Hit-and-run, hit-and-stay, and commensal bacteria present different peptide content when viewed from the perspective of the T cell.pdf

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Hit-and-run, hit-and-stay, and commensal bacteria present different peptide content when viewed from the perspective of the T cell.pdf

Vaccine 33 (2015) 6922–6929 Contents lists available at ScienceDirect Vaccine journal homepage: /locate/vaccine Hit-and-run, hit-and-stay, and commensal bacteria present different peptide content when viewed from the perspective of the T cell Lu He a, Anne S. De Groot b,c, Chris Bailey-Kellogg a,? a Dartmouth Computer Science, Hanover, NH 03755, United States b EpiVax, Inc., Providence, RI 02903, United States c Institute for Immunology and Informatics, University of Rhode Island, Providence, RI 02903, United States article info Article history: Available online 1 October 2015 Keywords: Bacterial immune escape Cross-reactivity analysis Immunogenicity prediction Subcellular localizations T cell epitope abstract Different types of bacteria face different pressures from the immune system, with those that persist (“hit-and-stay”) potentially having to adapt more in order to escape than those prone to short-lived infection (“hit-and-run”), and with commensal bacteria potentially different from both due to additional physical mechanisms for avoiding immune detection. The Janus Immunogenicity Score (JIS) was recently developed to assess the likelihood of T cell recognition of an antigen, using an analysis that considers both binding of a peptide within the antigen by major histocompatability complex (MHC) and recognition of the peptide:MHC complex by cognate T cell receptor (TCR). This score was shown to be predictive of T effector vs. T regulatory or null responses in experimental data, as well as to distinguish viruses representative of the hit-and-stay vs. hit-and-run phenotypes. Here, JIS-based analyses were conducted in order to characterize the extent to which the pressure to avoid T cell recognition is manifested in genomic differences among representative hit-and-run, hit-and-stay, and commensal bacteria. Overall, extracellular proteins were found to have different JIS pro?les from cytoplasmic ones. Contrasting the bacterial groups, extracellular proteins were show