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Fig. 1 | Journal of Neuroinflammation

Fig. 1

From: Neuroinflammatory transcriptional programs induced in rhesus pre-frontal cortex white matter during acute SHIV infection

Fig. 1

Molecular signatures of innate immune surveillance in the brain of uninfected rhesus macaques. A Study schematic: rhesus macaques were infected with SHIV. C.CH505 intravenously (n = 3; 3 females; ages 5.2–5.6 [years.months]) and euthanized at 4 week post-infection. Uninfected animals from opportunistic medical culls (n = 4; 1 male, 3 females; ages 3.6–6.5 [years.months]) were used as controls. 3 mm brain punches were collected from the subcortical white matter of the prefrontal cortex (PFCw) between Bregma + 16 and + 10 mm, the caudate nucleus (CN) between Bregma + 6 and 0 mm, and the superior temporal sulcus (STS) and hippocampus (HP) between Bregma − 14 and − 20 mm. Total RNA was extracted from bulk tissue samples and 3’-tag RNA-seq was performed. B t-Stochastic neighborhood embedding (t-SNE) clustering of gene expression profiles from uninfected control animals. Outlier sample (Animal 43661, pre-frontal cortex white matter control) is removed from the plot. C Cluster dendrogram of gene co-expression modules, indicated by color (Left), and region-specific modules (Right) generated from weighted gene co-expression network analysis of tissue-specific gene expression profiles from uninfected animals. D Regional eigengene expression and corresponding top fifteen most significantly enriched (p < 0.01 by Fisher’s exact test) biological processes GO terms within MEgreen (Left) and MEbrown (Right) modules. Red text indicates terms related to immunological processes. Regional expression levels of genes associated with macrophages/microglia E and anti-viral responses F, G in uninfected animals expressed in Log2 counts per million (CPM). B Circles indicate 95% confidence intervals. Dotted line indicates separation of white matter and gray matter sample clusters. D Box plots indicate quartiles. *P < 0.05 by linear mixed effects models (region effect). E * adjusted p < 0.01 and Log2 fold change (FC) > 1.5 relative other synapse dense regions (STS, CN, and/or HP). Asterisk color corresponds to a region (CN [red]) for which a gene is differentially regulated relative to other synapse dense regions. E–G Data points indicate samples from a single brain region and animal

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