Imperial College London
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Dr Aubrey Cunnington

Faculty of Medicine, Department of Infectious Disease

Professor of Paediatric Infectious Disease
 
 
 
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Contact

 

+44 (0)20 7594 3695a.cunnington

 
 
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Location

 

244Norfolk PlaceSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Andradi-Brown:2024:10.7554/eLife.87726,
author = {Andradi-Brown, C and Wichers-Misterek, JS and von, Thien H and Höppner, YD and Scholz, JAM and Hansson, H and Filtenborg, Hocke E and Gilberger, TW and Duffy, MF and Lavstsen, T and Baum, J and Otto, TD and Cunnington, AJ and Bachmann, A},
doi = {10.7554/eLife.87726},
journal = {Elife},
title = {A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture.},
url = {http://dx.doi.org/10.7554/eLife.87726},
volume = {12},
year = {2024}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - The pathogenesis of severe Plasmodium falciparum malaria involves cytoadhesive microvascular sequestration of infected erythrocytes, mediated by P. falciparum erythrocyte membrane protein 1 (PfEMP1). PfEMP1 variants are encoded by the highly polymorphic family of var genes, the sequences of which are largely unknown in clinical samples. Previously, we published new approaches for var gene profiling and classification of predicted binding phenotypes in clinical P. falciparum isolates (Wichers et al., 2021), which represented a major technical advance. Building on this, we report here a novel method for var gene assembly and multidimensional quantification from RNA-sequencing that outperforms the earlier approach of Wichers et al., 2021, on both laboratory and clinical isolates across a combination of metrics. Importantly, the tool can interrogate the var transcriptome in context with the rest of the transcriptome and can be applied to enhance our understanding of the role of var genes in malaria pathogenesis. We applied this new method to investigate changes in var gene expression through early transition of parasite isolates to in vitro culture, using paired sets of ex vivo samples from our previous study, cultured for up to three generations. In parallel, changes in non-polymorphic core gene expression were investigated. Modest but unpredictable var gene switching and convergence towards var2csa were observed in culture, along with differential expression of 19% of the core transcriptome between paired ex vivo and generation 1 samples. Our results cast doubt on the validity of the common practice of using short-term cultured parasites to make inferences about in vivo phenotype and behaviour.
AU  - Andradi-Brown,C
AU  - Wichers-Misterek,JS
AU  - von,Thien H
AU  - Höppner,YD
AU  - Scholz,JAM
AU  - Hansson,H
AU  - Filtenborg,Hocke E
AU  - Gilberger,TW
AU  - Duffy,MF
AU  - Lavstsen,T
AU  - Baum,J
AU  - Otto,TD
AU  - Cunnington,AJ
AU  - Bachmann,A
DO  - 10.7554/eLife.87726
PY  - 2024///
TI  - A novel computational pipeline for var gene expression augments the discovery of changes in the Plasmodium falciparum transcriptome during transition from in vivo to short-term in vitro culture.
T2  - Elife
UR  - http://dx.doi.org/10.7554/eLife.87726
UR  - https://www.ncbi.nlm.nih.gov/pubmed/38270586
VL  - 12
ER  -
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