Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections.
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...
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ftdoajarticles:oai:doaj.org/article:e97f4a4757b749a9a3f0afa32c365e78 2023-05-15T15:15:54+02:00 Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. Siddharth Jayaraman Claire Harris Edith Paxton Anne-Marie Donachie Heli Vaikkinen Richard McCulloch James P J Hall John Kenny Luca Lenzi Christiane Hertz-Fowler Christina Cobbold Richard Reeve Tom Michoel Liam J Morrison 2019-04-01T00:00:00Z https://doi.org/10.1371/journal.pntd.0007262 https://doaj.org/article/e97f4a4757b749a9a3f0afa32c365e78 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC6464242?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007262 https://doaj.org/article/e97f4a4757b749a9a3f0afa32c365e78 PLoS Neglected Tropical Diseases, Vol 13, Iss 4, p e0007262 (2019) Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 article 2019 ftdoajarticles https://doi.org/10.1371/journal.pntd.0007262 2022-12-31T08:17:55Z 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. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic PLOS Neglected Tropical Diseases 13 4 e0007262 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
spellingShingle |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 Siddharth Jayaraman Claire Harris Edith Paxton Anne-Marie Donachie Heli Vaikkinen Richard McCulloch James P J Hall John Kenny Luca Lenzi Christiane Hertz-Fowler Christina Cobbold Richard Reeve Tom Michoel Liam J Morrison Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. |
topic_facet |
Arctic medicine. Tropical medicine RC955-962 Public aspects of medicine RA1-1270 |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Siddharth Jayaraman Claire Harris Edith Paxton Anne-Marie Donachie Heli Vaikkinen Richard McCulloch James P J Hall John Kenny Luca Lenzi Christiane Hertz-Fowler Christina Cobbold Richard Reeve Tom Michoel Liam J Morrison |
author_facet |
Siddharth Jayaraman Claire Harris Edith Paxton Anne-Marie Donachie Heli Vaikkinen Richard McCulloch James P J Hall John Kenny Luca Lenzi Christiane Hertz-Fowler Christina Cobbold Richard Reeve Tom Michoel Liam J Morrison |
author_sort |
Siddharth Jayaraman |
title |
Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. |
title_short |
Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. |
title_full |
Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. |
title_fullStr |
Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. |
title_full_unstemmed |
Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. |
title_sort |
application of long read sequencing to determine expressed antigen diversity in trypanosoma brucei infections. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2019 |
url |
https://doi.org/10.1371/journal.pntd.0007262 https://doaj.org/article/e97f4a4757b749a9a3f0afa32c365e78 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
PLoS Neglected Tropical Diseases, Vol 13, Iss 4, p e0007262 (2019) |
op_relation |
http://europepmc.org/articles/PMC6464242?pdf=render https://doaj.org/toc/1935-2727 https://doaj.org/toc/1935-2735 1935-2727 1935-2735 doi:10.1371/journal.pntd.0007262 https://doaj.org/article/e97f4a4757b749a9a3f0afa32c365e78 |
op_doi |
https://doi.org/10.1371/journal.pntd.0007262 |
container_title |
PLOS Neglected Tropical Diseases |
container_volume |
13 |
container_issue |
4 |
container_start_page |
e0007262 |
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