Tuberculous meningitis in children is characterized by compartmentalized immune responses and neural excitotoxicity

Abstract

Tuberculous meningitis (TBM) is the most severe form of TB with high rates of mortality and morbidity. Here we conduct RNA-sequencing on whole blood as well as on ventricular and lumbar cerebrospinal fluid (CSF) of pediatric patients treated for TBM. Differential transcript expression of TBM cases are compared with healthy controls in whole blood and with non-TB cerebral infection controls in CSF. Whole blood RNA-Seq analysis demonstrates a distinct immune response pattern in TBM, with significant increase in both canonical and non-canonical inflammasome activation and decrease in T-cell activation. In ventricular CSF, a significant enrichment associated with neuronal excitotoxicity and cerebral damage is detected in TBM. Finally, compartmental comparison in TBM indicates that the ventricular profile represents brain injury whereas the lumbar profile represents protein translation and cytokine signaling. Together, transcriptomic analysis shows that disease processes differ between the periphery and the central nervous system, and within brain compartments.

Fig. 1

Whole blood transcriptome in pediatric TBM cases and IGRA-negative controls. a Principal component analysis on 2230 differentially expressed genes between TBM and healthy controls. b Deconvolution analysis revealed the in silico cellular composition of whole blood RNA. c Ingenuity canonical pathways overrepresented by differentially expressed genes are shown. The z-score indicates whether the pathway was upregulated (red) or downregulated (blue) in TBM. d Inflammasome signaling pathway is depicted. Molecules colored in red were significantly upregulated in TBM, compared to the controls. e T-cell activation pathway is shown. Molecules colored in blue were significantly downregulated in TBM, relative to the healthy controls

Fig. 2

Transcriptome of ventricular CSF in pediatric TBM and other infection controls (OI). a Principal component analysis based on 312 differentially expressed genes between TBM and OI control is shown. b Reactome pathways enriched in TBM, relative to the controls, are listed. The normalized enrichment score indicates whether the pathway is positively enriched (red) or negatively enriched (blue) in TBM. c Heatmaps depicting the log2-transformed gene expression associated with glutamate release, NMDA receptor binding, or GABA degradation in the TBM group and the OI group. Each row represents one gene. d Heatmaps depicting the log2-transformed gene expression associated with glutamate release, NMDA receptor binding, or GABA degradation in relation to TBM diagnosis. e Reactome pathways enriched in OI-like probable TBM cases (blue), relative to definite or definite-like probable TBM cases (red) are listed

Fig. 3

Transcriptome of ventricular CSF in comparison to lumbar CSF. a A heatmap depicting 389 differentially expressed genes between ventricular and lumbar CSF in pediatric TBM patients. b Deconvolution analysis revealed the in silico leukocyte composition of ventricular and lumbar CSF, respectively. c Reactome pathways enriched in ventricular CSF, relative to the lumbar are shown. The normalized enrichment score indicates whether the pathway is positively enriched (red) or negatively enriched (blue) in the ventricle of TBM patients. d Ingenuity disease network analysis clustered 46 of the differentially expressed genes into a network associated with neurological disease and injury. Molecules colored in red were significantly upregulated in ventricular CSF compared to lumbar CSF, while blue indicates significant downregulation. e A heatmap depicting the log2-transformed gene expression associated with glutamate release, NMDA receptor binding, or GABA degradation in relation to TBM diagnosis in lumbar CSF