A coordinated transcriptional switching network mediates antigenic variation of human malaria parasites

Abstract

Malaria parasites avoid immune clearance through their ability to systematically alter antigens exposed on the surface of infected red blood cells. This is accomplished by tightly regulated transcriptional control of individual members of a large, multicopy gene family called var and is the key to both the virulence and chronic nature of malaria infections. Expression of var genes is mutually exclusive and controlled epigenetically, however how large populations of parasites coordinate var gene switching to avoid premature exposure of the antigenic repertoire is unknown. Here we provide evidence for a transcriptional network anchored by a universally conserved gene called var2csa that coordinates the switching process. We describe a structured switching bias that shifts overtime and could shape the pattern of var expression over the course of a lengthy infection. Our results provide an explanation for a previously mysterious aspect of malaria infections and shed light on how parasites possessing a relatively small repertoire of variant antigen encoding genes can coordinate switching events to limit antigen exposure, thereby maintaining chronic infections.

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

“…Switching to var2csa has been shown to be favourable and is suggested to be the default var gene of choice upon perturbation to var specific heterochromatin (Ukaegbu et al ., 2015). These studies also suggested var2csa has a unique role in var gene switching and our results are consistent with the role of var2csa as the dominant ‘sink node’ (Zhang et al ., 2022, Ukaegbu et al ., 2015, Ukaegbu et al ., 2014, Mok et al ., 2008). A previous study suggested in vitro cultivation of controlled human malaria infection samples resulted in dramatic changes in var gene expression (Lavstsen et al ., 2005, Peters et al ., 2007).…”

“…These included var2csa , which had increased expression from generation 1 to generation 2. It has previously been suggested that long-term cultured parasites converge to expressing var2csa , but our findings suggest this begins within two cycles of cultivation (Zhang et al ., 2022, Mok et al ., 2008). Switching to var2csa has been shown to be favourable and is suggested to be the default var gene of choice upon perturbation to var specific heterochromatin (Ukaegbu et al ., 2015).…”

Transcriptional plasticity of virulence genes provides malaria parasites with greater adaptive capacity for avoiding host immunity

“…Interestingly, our single cell analysis of var gene expression in the PfSAMS knockdown lines detected activation of a specific subset of var genes, consistent with the hypothesis that certain var genes are more prone to activation than others. This is similar to our previous observations that var activation is biased toward certain subsets of var genes and that this bias shifts overtime, potentially shaping the trajectory of var gene expression over the course of an infection (34). What characteristics determine the likelihood of any particular gene becoming activated remain unknown, although methylation appears to be key to limiting the number of active genes.…”

“…The well-accepted, standard paradigm regarding malaria antigenic variation assumes that at any given time, individual parasites express one and only one member of the var gene family. In recent work from our laboratory, we generated an extensive collection of closely related, isogenic 3D7 and NF54 subclones through limiting dilution, thereby enabling us to examine recently cloned parasite populations expressing alternative var genes (34). To our surprise, not all the clones displayed the predicted pattern of single var gene expression.…”

“…However, no study has yet specifically focused on var gene expression, despite the importance of these genes for parasite survival and pathogenesis. We recently approached the question of var gene choice through the analysis of an extensive library of closely related, recently isolated clonal parasite populations (34). We observed two distinct var expression profiles: either high level expression of a single var gene, as expected for a population of parasites exhibiting mutually exclusive expression of a single dominant var gene, or alternatively low-level expression of a large portion of the var gene family, an unanticipated state that is of unknown significance.…”