Malian children infected with Plasmodium ovale and Plasmodium falciparum display very similar gene expression profiles

Abstract

Plasmodium parasites caused 241 million cases of malaria and over 600,000 deaths in 2020. Both P. falciparum and P. ovale are endemic to Mali and cause clinical malaria, with P. falciparum infections typically being more severe. Here, we sequenced RNA from nine pediatric blood samples collected during infections with either P. falciparum or P. ovale, and characterized the host and parasite gene expression profiles. We found that human gene expression varies more between individuals than according to the parasite species causing the infection, while parasite gene expression profiles cluster by species. Additionally, we characterized DNA polymorphisms of the parasites directly from the RNA-seq reads and found comparable levels of genetic diversity in both species, despite dramatic differences in prevalence. Our results provide unique insights into host-pathogen interactions during malaria infections and their variations according to the infecting Plasmodium species, which will be critical to develop better elimination strategies against all human Plasmodium parasites.

Fig 1. Host gene expression differs more between individuals than according to the infecting species.

(A) PCA showing the relationships among the eight infections based on the expression level of 9,884 human genes and colored according to the infecting species (blue–P. falciparum, red–P. ovale). (B) Percentage of the variance in host gene expression explained by the age of the child, the parasitemia of the infection, the individual and the infecting species.

Fig 2. Plasmodium gene expression profiles during symptomatic infections cluster according to the infecting species.

(A) PCA showing the relationships among the eight infections based on the expression level of 2,631 Plasmodium genes and colored according to the infecting species (blue–P. falciparum, red–P. ovale). (B) Percentage of the variance in parasite gene expression explained by the infecting species, the age of the child, the parasitemia of the infection and the individual.

Fig 3. Genetic relationships among the Plasmodium parasites analyzed by RNA-seq.

(A) Neighbor-joining tree showing the relationships among cytochrome B sequences from the P. ovale parasites studied in this study (red) and sequences from NCBI (blue). Note that the sequences from the A2, B1 and B2 infections cluster with P. ovale curtisi sequences while the sequence from infection C2 clusters with P. ovale wallikeri sequences. The number next to each branch indicates the percentage of replicate trees in which the sequences clustered together based on 500 bootstraps. (B) Proportion of pairwise nucleotide differences between pairs of P. falciparum (top) and P. ovale (bottom) infections based on positions covered at >20X. Note the higher proportion of pairwise nucleotide differences in pairs including the C2 infection, consistent with its P. ovale wallikeri determination.