Table 1.
Summary of blood samples from r-HAT cases and healthy controls used for RNA sequencing.
Fig 1.
Stratification of Differentially Expressed genes (DEGs) in cases versus controls.
(A) Principal component analysis (PCA) values for r-HAT cases vs healthy controls grouped into males and females which were compared on Principal Component (PC) 3 and PC2. (B) 3D volcano plot showing distribution and relationship of DEGs in Stage 1, Stage 2 and Controls. Grey dots represent non-significant genes, dark blue dots are genes expressed in controls only, red dots are genes expressed in stage 1 only, green dots are genes expressed in stage 2 only, orange are genes expressed in both stage 1and stage 2, purple dots are genes expressed in controls plus stage 1 and light blue dots are genes expressed in controls plus stage 2.
Fig 2.
DEGs and network analysis in Stage 1 case blood.
(A) Volcano plot showing genes that were significant (padj< 0.05) DEG, upregulated (log2FC > 1.0) and downregulated (log2FC < -1). (B) ExpressAnalyst network graph of upregulated protein coding genes. The root of the nodes was color coded according to significance with light yellow representing less significant and red more significant. Translation and immune system process were the most enriched biological pathways in stage 2 blood.
Fig 3.
DEGs and network analysis in blood from Stage 2 case versus healthy controls.
(A) Volcano plot showing significant DEGs (padj< 0.05) that were upregulated (log2FC > 1.0) and downregulated (log2FC < -1.0). (B) ExpressAnalyst network graph of protein coding genes that were upregulated in stage 2 blood relative to controls. The root of the nodes was color coded according to significance with light yellow representing less significant and red more significant. Translation, immune system process and lipid metabolic process were the most enriched biological pathways in stage 2 blood.
Fig 4.
Comparison of protein coding genes differentially expressed in Stage 1 and Stage 2 blood (padj < 0.05).
(A) Number of DE protein coding genes found in both Stage 1 and Stage 2 cases. (B) Hierarchical clustering heatmap of DEGs intersecting in Stage 1 and stage 2 blood. For the heatmap legend color, dark blue represents genes upregulated with log2FC 1 and red represents genes upregulated with log2FC > 5. See S1 and S2 Files for gene names and their corresponding log2 FC.
Fig 5.
Immune system Blood cells activated in r-HAT.
(A and B) Blood cell types that had significantly (p<0.05, t-test) different proportions in stage 1 cases versus controls and stage 2 versus controls respectively. See S3 Table for full cell type names. *****p < 3E-05, ***p < 9E-03 and **p<0.05. (B) Visualized output of innate and adaptive immune system pathways interaction in r-HAT cases based on DEGs loaded into Reactome pathway database (17). Yellow represents more significant and darker yellow less significant. Macrophages, neutrophils and NK cells participate in innate immune response which results in significant activation of cytokine signaling pathway (FDR: 2.94E -4). Dendritic cells link innate immune system and activation of adaptive immune system through activation of CD4+ TH cells. Activated CD4 cells release IL2 and IFN-gamma that activates CD8+ T cells and B cells to differentiate into plasma cells for antibody production.