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

Andradi-Brown, C. et al. (2024) 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. eLife, 12, RP87726. (doi: 10.7554/elife.87726) (PMID:38270586)

Abstract

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.

• Item Type: Articles
• Additional Information: CAB received support from the Wellcome Trust (4- year PhD programme, grant number 220123/Z/20/Z). Infrastructure support for this research was provided by the NIHR Imperial Biomedical Research Centre and Imperial College Research Computing Service, DOI: 10.14469/hpc/2232. JSWM, YDH, and AB were funded by the German Research Foundation (DFG) grants BA 5213/3- 1 (project #323759012) and BA 5213/6- 1 (project #433302244). TO is supported by the Wellcome Trust grant 104111/Z/14/ ZR. JB acknowledges support from Wellcome (100993/Z/13/Z).
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Otto, Professor Thomas

Creator Roles

Otto, T.: Conceptualization, Methodology, Supervision, Writing – original draft, Writing – review and editing

• Authors: Andradi-Brown, C., Wichers-Misterek, J. S., von Thien, H., Höppner, Y. D., Scholz, J. A.M., Hansson, H., Filtenborg Hocke, E., Gilberger, T. W., Duffy, M. F., Lavstsen, T., Baum, J., Otto, T. D., Cunnington, A. J., and Bachmann, A.
• College/School: College of Medical Veterinary and Life Sciences > School of Infection & Immunity
• Journal Name: eLife
• Publisher: eLife Sciences Publications, Ltd
• ISSN: 2050-084X
• ISSN (Online): 2050-084X
• Copyright Holders: Copyright © 2023 Andradi- Brown et al.
• First Published: First published in eLife 12:RP87726
• Publisher Policy: Reproduced under a creative commons licence

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
170547		The Wellcome Centre for Molecular Parasitology ( Core Support )	Andrew Waters	Wellcome Trust (WELLCOTR)	104111/Z/14/Z	SII - Parasitology