RNA-sequencing analysis of the CD4+ T cell response to a first-in-life infection and malaria re-challenge

Human volunteers received either their first, second or third homologous Plasmodium falciparum infection and six days after parasite clearance (at the peak of the adaptive immune response) we flow-sorted naïve, effector memory and regulatory CD4+ T cells for bulk RNA-sequencing. Transcriptional profiling of the T cell response at this time point allowed us to measure the outcome of critical cell-cell interactions within the inflamed spleen during the first three infections of life. T cells were isolated directly ex vivo from the blood of volunteers participating in a controlled human malaria reinfection trial (vac063c: clinicaltrials.gov NCT03906474). Effector memory, naive and regulatory CD4 T cells were flow sorted into Trizol and total RNA was extracted using a modified phenol-chloroform protocol. Libraries were constructed using the Nextera XT DNA Library Preparation kit and sequenced on an Illumina NextSeq 550 platform. - 11 volunteers: n = 3 first, n = 2 second, n = 6 third malaria infection - 2 time points: baseline before malaria infection and 6-days after drug treatment T6 - 3 flow sorted CD4 T cell subsets: effector memory (Tm), naive (Tn) and regulatory (Tr) - RNA-sequencing: 66 samples