Expression patterns of Plasmodium falciparum clonally variant genes at the onset of a blood infection in non-immune humans

Clonally variant genes (CVGs) play fundamental roles in the adaptation of Plasmodium falciparum parasites to the fluctuating conditions of the human host, but their expression patterns under the natural conditions of the blood circulation have been characterized in detail only for a few specific gene families. Here we provide a detailed characterization of the full P. falciparum transcriptome across the full intraerythrocytic development cycle (IDC) at the onset of a blood infection in non-immune human volunteers. We found that the vast majority of transcriptional differences between parasites obtained from the volunteers and the parental parasite line maintained in culture occur for CVGs. Specifically, we observed a major increase in the transcript levels of most members of the pfmc-2tm and gbp families and of specific genes of other families, in addition to previously reported changes in var and clag3 genes. The expression patterns were almost identical between parasites obtained from the different volunteers. Large transcriptional differences correlate with changes in the distribution of histone modifications associated with heterochromatin, confirming their epigenetic nature. The analysis of parasites collected at different points along the infection indicates that when parasites pass through transmission stages, the epigenetic memory at CVG loci is lost, resulting in a reset of their expression state and reestablishment of new epigenetic patterns. Time-course transcriptomic analysis of parental NF54 line (two biological replicates: NF54 I and NF54 II) and of parasites obtained from four different volunteers who participated in a CHMI (V18, V35, V48, V63). Parasites were tightly synchronized to a 5h age window and samples for transcriptomic analysis were collected every 10h at four different time points (10-15h, 20-25h, 30-35h and 40-45h). The reference pool consisted of RNA from NF54 cultures throughout the asexual blood cycle. Total RNA was harvested using the Trizol method. A total number of 24 individual samples were analysed using the microarray design AMADID-085763 (GEO ID: GPL26985).