Transcriptome profiling reveals functional variation in Plasmodium falciparum parasites from controlled human malaria infection studies

The objective of this study is to characterize the overall transcriptome of P. falciparum NF54 derived from a controlled-human malaria infection (CHMI) study. Healthy, immunologically naïve human volunteers were infected intradermally or intravenously with different dosages of Plasmodium falciparum sporozoites (Sanaria® PfSPZ Challenge). Parasites were isolated from these volunteers and subjected to a range of in vitro culture generation prior to RNA collection. P. falciparum parasites strain NF54 obtained from the dose escalation CHMI of Sanaria® PfSPZ Challenge (TÜCHMI-001-NCT01624961) derived from a single P. falciparum NF54 (PfNF54) working cell bank were subjected to RNA isolation and microarray hybridization. In brief, on the day of positivity in patients enrolled in the trial, 0.25 ml of patient blood was used to establish 10 ml in vitro cultures. As soon as the parasitemia reached 3-4%, the culture were expanded into a 20 ml culture. RNA was harvested as soon as an individual 20 ml parasite culture reached a parasitemia of 3-5%, and then every 2-3 generations thereafter. 20 ml parasite cultures were synchronized twice per day with 5% (v/v) sorbitol in water to obtain ring-stage parasites. A total of 55 RNA samples were collected, including 3 pre-mosquito parental culture at synchronized ring stage. RNA were extracted and synthesis and amplification of cDNA was carried out as previously described in Bozdech, Z., S. Mok & A. P. Gupta, (2013). cDNA generated was used for microarray hybridizations against a common RNA reference pool of P. falciparum 3D7 strain.