Integrative Transcriptomic Analysis Reveals Differential Exon Usage and Virulence Gene Family Dynamics in Plasmodium falciparum during Severe Malaria

Malaria remains a leading cause of child mortality in developing countries, with roughly 610,000 deaths per year. While the disease is caused by five human Plasmodium species, Plasmodium falciparum (Pf ) causes the most severe form. Progression from uncomplicated to severe malaria is characterized by high proliferation of the parasite, severely affecting children under five years old. However, the molecular mechanisms underlying disease progression remain an active area of research. Many multicopy genes have been implicated in Pf virulence. Some of these genes are implicated in cytoadherence, host-cell invasion, immune evasion, sequestration of infected erythrocytes, and antigenic variation. We employed an integrative transcriptomic analysis in this study to elucidate the molecular underpinnings of severe malaria and gene expression patterns, virulence gene dynamics, and the potential contribution of alternative splicing. Results show an overexpression of protein synthesis and ribosomal genes associated with severe malaria. About 86% (n=1865) of all differentially expressed genes (DEGs) were downregulated in severe malaria, and 226 genes exhibited both differential expression and differential exon usage (DEU). Pf virulence genes and antigenic genes such as var (pfEMP1), stevor, surfin, rif (rifin), ptm-2TM, and msp were upregulated in severe malaria compared with uncomplicated malaria, except for rifin. In severe malaria, there was evidence of co-expression and regulation within multigene families, as well as DEU and alternative splicing in virulence genes and antimalarial resistance-related proteins. Pf does not employ a single mechanism for disease progression but suppresses and deregulates nonessential pathways, processes, and genes, which are upregulated virulence genes, DNA replication, mRNA transcription, and protein synthesis. Multicopy genes are co-expressed and regulated to meet the molecular needs of the parasite. The parasite employs alternative splicing and DEU mechanisms for immune invasion and evasion, host-parasite interaction, as well as antimalarial resistance.