Blood transcriptomic profiles associated with fatal melioidosis and type 2 diabetes induced susceptibility to intracellular pathogens

Background: Melioidosis is caused by the Gram-negative bacterium Burkholderia pseudomallei, and is a leading cause of death from community-acquired infections in Northeast Thailand with a case fatality rate of up to 50%. Most melioidosis patients have one or more comorbidities, and more than half of patients have diabetes which confers a 12-fold increased susceptibility to melioidosis. A similar, but less marked, relationship is seen in tuberculosis (TB) patients, with a 3-fold increased risk of developing TB in people with diabetes. Little is known regarding the mechanisms underlying the increased susceptibility in diabetes to these intracellular pathogens. Likewise, the host response associated with fatal melioidosis remains to be fully elucidated.
Methods: Whole blood RNA sequencing data were generated from three independent melioidosis cohorts from Northeast Thailand and one global multi-site tuberculosis study. Both supervised and unsupervised data analysis approaches were performed including differential gene expression (DGE) analysis, pathway analyses, upstream regulator analysis, weighted gene co-expression network analysis (WGCNA), and hub gene analysis.
Results: Firstly, principal component analysis (PCA) revealed clear separation between fatal and surviving melioidosis patients. DGE analysis identified profound changes in the transcriptome of fatal melioidosis cases with over 600 up- and 1,000 down-regulated genes compared to survivors. Pathway analyses following DGE analysis identified exaggerated inflammation and up-regulated type 2 immune responses concurrent with massively down-regulated T cell signalling cascades in fatal melioidosis. Upstream regulator analysis identified potential key regulators associated with fatality during melioidosis including TNF, IL4, IL1A, PTGER2, and OSM. Likewise, the unsupervised analysis by WGCNA confirmed that several co-expressed gene modules enriched for inflammatory immune responses driven by the innate immune compartment were associated with 28-day mortality. Furthermore, hub genes associated with fatal melioidosis such as CEACAM1, SERPINB1 and SORT1 may play deleterious roles during melioidosis.
Secondly, the impact of diabetes on the transcriptome was subtle in acute melioidosis, with similar but more pronounced changes in TB, which is a more chronic disease. Diabetes status was associated with enhanced non-specific inflammatory responses for both melioidosis and TB, alongside failure to fully switch on interferon-mediated responses for TB.
Conclusion: The transcriptomic signature in fatal melioidosis is characterised by concomitant excessive inflammation, a pronounced anti-inflammatory response, and a stunted T cell response. These results highlight the pivotal role of adaptive immunity during fatal melioidosis. Furthermore, diabetes is associated with increased activation of innate pathways and reduced interferon responses which may contribute to the increased susceptibility observed for these intracellular pathogens.

Keywords: blood transcriptome
tuberculosis
sepsis
intracellular infection
bulk RNA-seq
diabetes
case fatality
mortality
melioidosis
Advisor: Klenerman, P
Kronsteiner-Dobramysl, B