The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes

Within the human host, the malaria parasite Plasmodium falciparum is exposed to multiple selection pressures. The host environment changes dramatically in severe malaria, but the extent to which the parasite responds to—or is selected by—this environment remains unclear. From previous studies, the parasites that cause severe malaria appear to increase expression of a restricted but poorly defined subset of the PfEMP1 variant, surface antigens. PfEMP1s are major targets of protective immunity. Here, we used RNA sequencing (RNAseq) to analyse gene expression in 44 parasite isolates that caused severe and uncomplicated malaria in Papuan patients. The transcriptomes of 19 parasite isolates associated with severe malaria indicated that these parasites had decreased glycolysis without activation of compensatory pathways; altered chromatin structure and probably transcriptional regulation through decreased histone methylation; reduced surface expression of PfEMP1; and down-regulated expression of multiple chaperone proteins. Our RNAseq also identified novel associations between disease severity and PfEMP1 transcripts, domains, and smaller sequence segments and also confirmed all previously reported associations between expressed PfEMP1 sequences and severe disease. These findings will inform efforts to identify vaccine targets for severe malaria and also indicate how parasites adapt to—or are selected by—the host environment in severe malaria.Author summary: Infection by Plasmodium falciparum—the parasite responsible for malaria in humans—can result in a severe disease that can be fatal or in an uncomplicated disease that can be resolved by the host immune system. However, whether the parasites causing severe disease differ from those causing uncomplicated disease is unknown. Several strands of evidence have suggested that parasites causing severe disease may express a restricted set of the Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) proteins. PfEMP1 proteins are expressed on the surface of the infected red blood cells and elicit protective immunity. We compared the transcriptomes of parasites causing severe and uncomplicated malaria to determine whether these parasites differed in the genes they expressed. We found that the parasites causing severe malaria had altered expression of genes involved in basic metabolism, nuclear processes, and surface expression of PfEMP1. The parasites causing severe malaria had up-regulated expression of a set of PfEMP1 proteins. Some of these PfEMP1s had been previously implicated in severe malaria, lending support to our data. Multiple associations identified between severe malaria and expressed PfEMP1 sequences were novel. These novel, severe disease–associated PfEMP1 sequences could be useful for informing design of vaccines targeting severe malaria disease.