Temporal organization of the Plasmodium falciparum transcriptome prioritises genetic polymorphisms associated with artemisinin response

Artemisinin-based combination therapies (ACTs) have substantially reduced the global burden of malaria, but the emergence and spread of artemisinin partial resistance (ART-R) threatens these gains. Although mutations in Plasmodium falciparum kelch13 (pfk13) are established mediators of ART-R, they do not fully explain variation in parasite responses, highlighting the need for complementary markers. We integrated six independent intra-erythrocytic developmental cycle (IDC) transcriptomic datasets by harmonic regression and random-effects meta-analysis, followed by network analyses, protein structural modelling, population genomics and ex vivo dihydroartemisinin susceptibility data, to identify candidate P. falciparum polymorphisms associated with artemisinin response. The meta-analysis identified 2,842 of 5,292 genes as significantly rhythmic across the 48-hour IDC, including those encoding PfK13 and PfMDR1. Integration with whole-genome sequences of Ugandan field isolates prioritized 13 nonsynonymous variants across 10 genes, encoding PfAP2-G, PfPX1, PfACS7, PfACS1a, PfRESA3, PfDRPC and PfA8IJP together with three proteins of unknown function, all transcriptionally co-timed with pfk13. Polymorphisms in pfpx1 have independently been implicated in artemisinin susceptibility, consistent with our prioritization. These candidates are potential complementary mediators of artemisinin response. Beyond them, the pipeline itself is transferable to other resistance phenotypes and periodic transcriptional programmes.