Longitudinal profiling of the whole blood transcriptional response of human volunteers to repeated malaria challenge

We took a systems immunology approach to analyse the evolution of the human immune response to the first three infections of life in a re-challenge model of falciparum malaria. Ten volunteers were infected up to three times with Plasmodium falciparum in 4- to 8-month intervals. Remarkably, parasite densities and the dynamics of blood-stage infection were not altered over the course of three homologous infections. To track the development of immunity in real-time we used whole blood RNA-sequencing to analyse each volunteer’s transcriptional response throughout infection and convalescence (up to 9 time points per volunteer per infection). Whole blood samples were collected from volunteers participating in controlled human malaria reinfection trials (vac063a/b: ClinicalTrials.gov NCT02927145, vac063c: ClinicalTrials.gov NCT03906474) and preserved in Tempus reagent. RNA was extracted using the Tempus Spin RNA isolation reagent kit. Libraries were constructed using the TruSeq Stranded mRNA library protocol and sequenced on an Illumina NovaSeq 6000 platform. -- longitudinal study: six volunteers received three malaria infections (1039, 1040, 1061, 1068, 1075, 6032), 4 volunteers two infections (1065, 1067, 806, 818) and 3 volunteers only a single infection (313, 315, 320) -- their whole blood transcriptome was analysed at 5 to 9 time points time per infection covering baseline (before infection), several time points during infection (common time points include 6- and 8-days after malaria challenge (C6 and C8 respectively) and diagnosis), after parasite clearance (6-days after drug treatment, T6) and memory (45-days after challenge)