Differential expression of mitochondria-associated genes in clinical samples of Plasmodium falciparum showing severe manifestations

The malaria parasite mitochondrial proteins are critical targets for antimalarial drugs, however, the emergence of drug resistance against the existing protein targets necessitates novel therapeutic approaches. In this study, we profiled mitochondrial sense and natural antisense transcripts (NATs) in 22 Plasmodium falciparum clinical isolates, classified into three disease groups - uncomplicated malaria (UNC, n = 6), cerebral malaria (CM, n = 4), and hepatic dysfunction (HD, n = 12), using a custom, strand-aware 60 K microarray, and validated the transcriptome using pooled, strand-specific RNA-seq (uncomplicated pool and complicated pool). Differential gene expression in the CM and HD cohort was obtained by comparing with uncomplicated malaria (UNC) as the control cohort. The analysis revealed distinct disease-specific sense and NATs, encoded by the mitochondrial genome, along with those encoded in the nucleus and targeted to the parasite mitochondria. Although mitochondrial activity is known to be reduced in blood-stage malaria, upregulation of genes linked to tricarboxylic-acid-cycle and electron-transport in the CM cluster indicates disrupted mitochondrial bioenergetics in severe disease. Profiling of sense and antisense mitochondrial transcripts reveal a correlated expression of sense-antisense transcript pairs in both the disease manifestations, indicating a potential regulatory role of NATs in mitochondrial function. These data provide direct evidence of NATs originating from the parasite mitochondrial genome and nominate key NATs against core mitochondrial functions as potential non-conventional antimalarial targets.