Integrated pathogen load and dual transcriptome analysis of systemic host-pathogen interactions in severe malaria

Abstract

The pathogenesis of infectious diseases depends on the interaction of host and pathogen. In Plasmodium falciparum malaria, host and parasite processes can be assessed by dual RNA-sequencing of blood from infected patients. Here we performed dual transcriptome analyses on samples from 46 malaria-infected Gambian children to reveal mechanisms driving the systemic pathophysiology of severe malaria. Integrating these transcriptomic data with estimates of parasite load and detailed clinical information allowed consideration of potentially confounding effects due to differing leukocyte proportions in blood, parasite developmental stage, and whole-body pathogen load. We report hundreds of human and parasite genes differentially expressed between severe and uncomplicated malaria, with distinct profiles associated with coma, hyperlactatemia, and thrombocytopenia. High expression of neutrophil granule-related genes was consistently associated with all severe malaria phenotypes. We observed severity-associated variation in the expression of parasite genes which determine cytoadhesion to vascular endothelium, rigidity of infected erythrocytes, and parasite growth rate. Up to 99% of human differential gene expression in severe malaria was driven by differences in parasite load, whereas parasite gene expression showed little association with parasite load. Co-expression analyses revealed interactions between human and P. falciparum, with prominent co-regulation of translation genes in severe malaria between host and parasite. Multivariate analyses suggested that increased expression of granulopoiesis and interferon-γ related genes, together with inadequate suppression of type-1 interferon signalling, best explained severity of infection. These findings provide a framework for understanding the contributions of host and parasite to the pathogenesis of severe malaria and identifying targets for adjunctive therapy.

Neutrophil extracellular traps drive inflammatory pathogenesis in malaria

“…On the other hand, several studies have linked activation of these cells to pathogenesis and severe disease [17,18,27]. For instance, a recent blood transcriptomic analysis comparing severe and uncomplicated malaria identified a granulocyte colony stimulating factor (GCSF)-regulated neutrophil granulopoiesis signature as a specific feature of severe malaria [18] . Granulopoiesis refers to production of neutrophils from progenitor cells in the bone marrow; this blood signature therefore identifies increased neutrophil abundance as a pathogenic factor in malaria.…”

“…and cerebral malaria[17,18]. Whether NETs can also upregulate ICAM-1 on human brain endothelium remains to be verified.NET components are also required for pathology and parasite sequestration in the lungs of infected animals, demonstrating that this mechanism may be broadly generalizable to different vascular beds.…”

New Pathogenesis Mechanisms and Translational Leads Identified by Multidimensional Analysis of Necrotizing Myositis in Primates

“…In the present study, we used a well-described NHP model of necrotizing myositis (27,45,46) and dual RNA-seq to study the relationship between pathogen and host transcripts. Until now, a limited number of studies have been conducted using dual RNA-seq under in vivo conditions (41,42,(47)(48)(49)(50)(51)(52)(53). In a very recent study, dual RNA-seq was performed on human tissue biopsiy samples obtained from necrotizing soft tissue infections (54).…”

Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

“…Gene expression analyses at the whole transcriptome level have also shed light on fundamental aspects of host and parasite biology [e.g. 7,8] and hostparasite interactions [9][10][11][12]. In addition, novel insights into the dynamics of host-parasite interactions at the molecular level are increasingly gained also by analysing sequence data that were traditionally deemed to be invaluable and hence excluded [13].…”