Jayaraman, S. et al. (2019) Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS Neglected Tropical Diseases, 13(4), e0007262. (doi: 10.1371/journal.pntd.0007262) (PMID:30943202) (PMCID:PMC6464242)
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Abstract
Antigenic variation is employed by many pathogens to evade the host immune response, and Trypanosoma brucei has evolved a complex system to achieve this phenotype, involving sequential use of variant surface glycoprotein (VSG) genes encoded from a large repertoire of ~2,000 genes. T. brucei express multiple, sometimes closely related, VSGs in a population at any one time, and the ability to resolve and analyse this diversity has been limited. We applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from batches of mice sacrificed at time points (days 3, 6, 10 and 12) post-infection with T. brucei TREU927. The data showed that long read sequencing is reliable for resolving variant differences between VSGs, and demonstrated that there is significant expressed diversity (449 VSGs detected across 20 mice) and across the timeframe of study there was a clear semi-reproducible pattern of expressed diversity (median of 27 VSGs per sample at day 3 post infection (p.i.), 82 VSGs at day 6 p.i., 187 VSGs at day 10 p.i. and 132 VSGs by day 12 p.i.). There was also consistent detection of one VSG dominating expression across replicates at days 3 and 6, and emergence of a second dominant VSG across replicates by day 12. The innovative application of ecological diversity analysis to VSG reads enabled characterisation of hierarchical VSG expression in the dataset, and resulted in a novel method for analysing such patterns of variation. Additionally, the long read approach allowed detection of mosaic VSG expression from very few reads–the earliest in infection that such events have been detected. Therefore, our results indicate that long read analysis is a reliable tool for resolving diverse gene expression profiles, and provides novel insights into the complexity and nature of VSG expression in trypanosomes, revealing significantly higher diversity than previously shown and the ability to identify mosaic gene formation early during the infection process.
Item Type: | Articles |
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Status: | Published |
Refereed: | Yes |
Glasgow Author(s) Enlighten ID: | Cobbold, Professor Christina and Vaikkinen, Ms Heli and Reeve, Professor Richard and Harris, Claire and Donachie, Ms Anne Marie and McCulloch, Professor Richard |
Creator Roles: | Harris, C.Formal analysis, Methodology, Writing – original draft Donachie, A.-M.Investigation, Methodology Vaikkinen, H.Investigation, Methodology McCulloch, R.Conceptualization, Writing – original draft Cobbold, C.Conceptualization, Formal analysis, Investigation, Methodology, Supervision, Writing – original draft, Writing – review and editing Reeve, R.Formal analysis, Investigation, Methodology, Supervision, Writing – original draft, Writing – review and editing |
Authors: | Jayaraman, S., Harris, C., Paxton, E., Donachie, A.-M., Vaikkinen, H., McCulloch, R., Hall, J. P.J., Kenny, J., Lenzi, L., Herts-Fowler, C., Cobbold, C., Reeve, R., Micheol, T., and Morrison, L. J. |
College/School: | College of Medical Veterinary and Life Sciences College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Science and Engineering > School of Mathematics and Statistics College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine |
Journal Name: | PLoS Neglected Tropical Diseases |
Publisher: | Public Library of Science |
ISSN: | 1935-2727 |
ISSN (Online): | 1935-2735 |
Published Online: | 03 April 2019 |
Copyright Holders: | Copyright © 2019 Jayaraman et al. |
First Published: | First published in PLoS Neglected Tropical Diseases 13(4):e0007262 |
Publisher Policy: | Reproduced under a Creative Commons license |
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