Transcriptomic analysis of the malaria parasite during the red blood cycle

Background: The World Health Organization has estimated that in 2015 there were 214 million cases of malaria that led to approximately 438,000 deaths. Effective drug treatments for malaria have been available, but resistance to these treatments has emerged and there is growing evidence that even the most recently developed antimalarials are losing their effectiveness. The development of novel therapeutics largely relies on a better understanding of parasite biology and pathogenesis. Materials & Methods: In order to unveil temporal-specific patterns of parasite gene expression, we conducted a transcriptomic analysis of the RNA-Seq data collected at seven time points during the red blood cell cycle, using CLC Genomics Workbench Version 8.0. All sequence reads were mapped to the latest reference genome sequence of the malaria parasite Plasmodium falciparum, PF3D7v3.0. Differential expression analysis was conducted for pair-wise comparisons across time points using the Exact Test as implemented in the EdgeR Bioconductor package. The Bonferroni method and the Benjamini and Hochberg's algorithm were used for multiple testing correction. Gene Ontology enrichment analysis was conducted to identify over-represented functional categories. Results: Our analyses identified developmental-stage specific genes: in the ring and early trophozoite stage, genes encoding enzymes that regulate hemoglobin degradation and transcription were highly expressed and 247 genes associated with glycolysis, gluconeogenesis, pathogenesis and pentose-phosphate shut were up-regulated; In the trophozoite and early schizont stage, genes encoding enzymes that regulate cellular biogenic amine biosynthesis and glycolysis maintained a high-level expression and 1,483 genes involved in TCA cycle, mitochondrion organization, deoxyribonucleotide metabolic process, DNA replication and DNA repair were induced; In the schizont stage, 785 genes associated with entry into host cell, actin filament organization, protein phosphorylation were over-expressed. Conclusions: Transcriptomic analysis of the intraerythrocytic developmental cycle revealed an orchestrated transcriptional machinery and a "just-in-time" mechanism for transcriptional regulation in the malaria parasite.