Severe malarial anemia (SMA, Hb < 6.0 g/dL) is a leading cause of childhood morbidity and mortality in holoendemic Plasmodium falciparum transmission zones. This study explored the entire expressed human transcriptome in whole blood from 66 Kenyan children with non-SMA (Hb ≥ 6.0 g/dL, n = 41) and SMA (n = 25), focusing on host immune response networks. RNA-seq analysis revealed 6862 differentially expressed genes, with equally distributed up-and down-regulated genes, indicating a complex host immune response. Deconvolution analyses uncovered leukocytic immune profiles indicative of a diminished antigenic response, reduced immune priming, and polarization toward cellular repair in SMA. Weighted gene co-expression network analysis revealed that immune-regulated processes are central molecular distinctions between non-SMA and SMA. A top dysregulated immune response signaling network in SMA was the HSP60-HSP70-TLR2/4 signaling pathway, indicating altered pathogen recognition, innate immune activation, stress responses, and antigen recognition. Validation with high-throughput gene expression from a separate cohort of Kenyan children (n = 50) with varying severities of malarial anemia (n = 38 non-SMA and n = 12 SMA) confirmed the RNA-seq findings. Proteomic analyses in 35 children with matched transcript and protein abundance (n = 19 non-SMA and n = 16 SMA) confirmed dysregulation in the HSP60-HSP70-TLR2/4 signaling pathway. Additionally, glutamine transporter and glutamine synthetase genes were differentially expressed, indicating altered glutamine metabolism in SMA. This comprehensive analysis underscores complex immune dysregulation and novel pathogenic features in SMA.

Malaria remains a leading cause of childhood morbidity and mortality in sub-Saharan Africa, with severe malarial anemia (SMA; hemoglobin (Hb) < 6.0 g/dL) representing one of the life-threatening complications of Plasmodium falciparum infection. While limited studies have examined host transcriptional responses in SMA, parasite transcriptional adaptations remain unexplored. Here, we performed parasite transcriptomic profiling in the same cohort of Kenyan children under five years of age in whom we previously characterized host transcriptional responses to SMA, including children presenting with SMA (n = 20) or non-SMA malaria (n = 40). Differential expression analysis identified 566 P. falciparum genes associated with SMA, predominantly involving up-regulated transcripts linked to proteostasis, translational regulation, stress-response pathways, and metabolic remodeling. Transcriptomic deconvolution indicated greater trophozoite and schizont representation in SMA, with reduced ring-stage and gametocyte signatures. Weighted gene co-expression network analysis and protein-protein interaction network analysis identified coordinated transcriptional programs enriched for proteasomal degradation, ubiquitin-mediated protein turnover, chaperone activity, RNA processing, and metabolic adaptation. XGBoost-SHAP modeling identified a small subset of parasite genes that captured much of the transcriptomic signal, classifying SMA from non-SMA malaria. Collectively, these findings define a distinct parasite transcriptional landscape in SMA characterized by coordinated stress adaptation and metabolic flexibility, highlighting proteostasis-associated pathways for further therapeutic investigation.