Transcriptome Analysis of Plasmodium falciparum Isolates From Benin Reveals Specific Gene Expression Associated With Cerebral Malaria

Abstract

Cerebral malaria (CM) is the severest form of Plasmodium falciparum infection. Children under 5 years old are those most vulnerable to CM, and they consequently have the highest risk of malaria-related death. Parasite-associated factors leading to CM are not yet fully elucidated. We therefore sought to characterize the gene expression profile associated with CM, using RNA-seq data from 15 CM and 15 uncomplicated malaria (UM) isolates from Benin. CM parasites displayed reduced circulation times, possibly related to higher cytoadherence capacity. Consistent with the latter, we detected increased var genes abundance in CM isolates. Differential expression analyses showed that distinct transcriptome profiles are signatures of malaria severity. Genes involved in adhesion, excluding variant surface antigens, were dysregulated, supporting the idea of increased cytoadhesion capacity of CM parasites. Finally, we found dysregulated expression of genes in the entry into host pathway that may reflect greater erythrocyte invasion capacity of CM parasites.

Diagnosis of cerebral malaria: Tools to reduce Plasmodium falciparum associated mortality

“…Numerous upregulated genes (for example: eba175 and ama-1 ) involved in entry into host pathway reflects an increased invasion capacity of CM isolates. Finally, genes involved in adhesion, excluding variant surface antigens, were dysregulated, supporting the idea of increased cytoadherence capacity of CM parasites ( Guillochon et al., 2022 ). var A gene transcripts and CIDRα1 domains may therefore be central to the development of an effective CM biomarker ( Table 1 ).…”

A novel computational pipeline forvargene expression augments the discovery of changes in thePlasmodium falciparumtranscriptome during transition fromin vivoto short-termin vitroculture

“…To extend our ability to characterise var gene expression profiles and changes over time in clinical P. falciparum isolates, we set out to improve current assembly methods. Previous methods for assembling var transcripts have focussed on assembling whole transcripts (Tonkin-Hill et al ., 2018, Wichers et al ., 2021, Guillochon et al ., 2022, Andrade et al ., 2020). However, due to the diversity within PfEMP1 domains, their associations with disease severity and the fact different domain types are not inherited together, a method focussing on domain assembly first was developed.…”

“…More recent approaches for var assembly and quantification, based on RNA-sequencing, represent huge advancements compared to qPCR and DBLα-tag analyses. However, they still produce inadequate assembly of the biologically important N-terminal domain region, have a relatively high number of misassemblies and do not provide an adequate solution for handling the conserved var variants (Tonkin-Hill et al ., 2018, Wichers et al ., 2021, Guillochon et al ., 2022).…”

“…While approaches for var assembly and quantification based on RNA-sequencing have recently been proposed (Wichers et al, 2021;Stucke et al, 2021;Andrade et al, 2020;Tonkin-Hill et al, 2018, Duffy et al, 2016, these still produce inadequate assembly of the biologically important Nterminal domain region, have a relatively high number of misassemblies and do not provide an adequate solution for handling the conserved var variants (Table 1). * also used in Wichers et al, 2021;Guillochon et al, 2022 UM: uncomplicated malaria Plasmodium parasites from human blood samples are often adapted to or expanded through in vitro culture to provide sufficient parasites for subsequent investigation of parasite biology and phenotype (Brown & Guler, 2020). This is also the case for several studies assessing the PfEMP1 phenotype of parasites isolated from malaria-infected donors (Pickford et al, 2021, Joste et al, 2020, Storm et al, 2019, Tuikue Ndam et al, 2017, Claessens et al, 2012, Lavstsen et al, 2005, Kirchgatter & Portillo Hdel, 2002, Hoo et al, 2019.…”

“…More recent approaches for var assembly and quantification, based on RNA-sequencing, represent huge advancements compared to qPCR and DBLα-tag analyses. However, they still produce inadequate assembly of the biologically important N-terminal domain region, have a relatively high number of misassemblies and do not provide an adequate solution for handling the conserved var variants (Tonkin-Hill et al, 2018, Wichers et al, 2021, Guillochon et al, 2022. Plasmodium parasites from human blood samples are often adapted to or expanded through in vitro culture to provide sufficient parasites for subsequent investigation of parasite biology and phenotype (Brown & Guler, 2020).…”