In vivo transcriptome of Plasmodium falciparum reveals overexpression of transcripts that encode surface proteins

Abstract

Infections with the human parasite Plasmodium falciparum continue to present a great challenge to global health. Fundamental questions regarding the molecular basis of virulence and immune evasion in P. falciparum have been only partially answered. Because of the parasite's intracellular location and complex life cycle, standard genetic approaches to the study of the pathogenesis of malaria have been limited. The present study presents a novel approach to the identification of the biological processes involved in host-pathogen interactions, one that is based on the analysis of in vivo P. falciparum transcripts. We demonstrate that a sufficient quantity of P. falciparum RNA transcripts can be derived from a small blood sample from infected patients for whole-genome microarray analysis. Overall, excellent correlation was observed between the transcriptomes derived from in vivo samples and in vitro samples with ring-stage P. falciparum 3D7 reference strain. However, gene families that encode surface proteins are overexpressed in vivo. Moreover, this analysis has identified a new family of hypothetical genes that may encode surface variant antigens. Comparative studies of the transcriptomes derived from in vivo samples and in vitro 3D7 samples may identify important strategies used by the pathogen for survival in the human host and highlight, for vaccine development, new candidate antigens that were not previously identified through the use of in vitro cultures.

Figure 1

Correlation coefficients comparing the transcriptomes of each in vivo sample with 3D7 stage-specific transcriptomes. ER, early ring; ES, early schizont; ET, early trophozoite; LR, late ring; LS, late schizont; LT, late trophozoite; M, merozoite.

Figure 2

CLUSTALW alignment of PF14_0752 and genes displaying amino acid homology using default settings (E value threshold for TBLASTN, <1 × 10⁻⁷). Coding is as follows: shading denotes identity in at least 5 sequences; the black bar indicates a hydrophobic region; and the boxed sequences represent a host cell targeting signal. Seven genes are expressed in at least 1 sample.

Figure 3

Confirmation of in vivo overexpression of cDNA for PF14_ 0752 in in vivo samples, compared with that in in vitro 3D7 samples with ring-stage parasites.

Figure 4

Graphic representation of the no. of genes expressed in each gene family for each sample. n represents the no. of genes in each family. Each bar represents a gene family member. Red represents detection of transcript, and grey represents unexpressed transcripts. Asterisks denote in vivo samples that contain a significantly greater no. of gene family member transcripts, compared with the no. expressed in in vitro 3D7 (P < .05, Fisher's exact test).