Fig. 5: Global transcriptome analysis of HIV latently infected U1 cells treated with basal ganglia derived ECs. | Molecular Psychiatry

Fig. 5: Global transcriptome analysis of HIV latently infected U1 cells treated with basal ganglia derived ECs.

From: Extracellular condensates (ECs) are endogenous modulators of HIV transcription and latency reactivation

Fig. 5

A) Scatter plot of all transcripts from biological triplicates with transcripts per million mapped reads (TPM) > 1, p-value (unpaired t-test) <= 1.0, and fold-change >= 0.0 are displayed. B) 3-way Venn diagram of DEGs meeting the following criteria: i) pooled-adjusted p-value (FDR) < 0.05 and ii) (log2 fold change >1 or <-1). C) Heatmap of the genes corresponding to the 13 common DEGs identified by the 3-way Venn diagram. D) Overrepresentation analysis of gene ontology biological processes of the 13 common DEG identified by the 3-way Venn diagram. The y-axis represents biological process (noRedundant) and the x-axis represents enrichment ratios. E) IPA network diagrams representing the regulatory effects with top consistency scores found associated with neuroinflammation signaling, with the top network representing FC: VEH  ECs/PBS, middle network representing FC: VEH | SIV  ECs/PBS, and bottom network representing FC: THC | SIV  ECs/PBS. FC = Fold Change. F) Gene to function analysis of THC | SIV  ECs/VEH | SIV  ECs DEGs. G) Histogram of the 92 canonical pathways regulated by treatment with THC | SIV ECs. The left y-axis represents the canonical pathways, and the x-axis represents -log (P-value) of the canonical pathways, where neutrophil degranulation is upregulated, and mitochondrial dysfunction is downregulated. Each bar indicates the value of -log10 (P-value). H) IPA network diagram representing top consistency scores with links to NF-kB activation by viruses and signaling, as well as KRAB-ZNF (Krüppel-associated box domain zinc finger) gene cluster. I) Differences in ZNF514 and ZNF747 represented as counts (left) and log2 fold change (right). J) Gene ontology gene set enrichment analysis (GSEA). The left y-axis represents normalized GO enrichment scores, and the x-axis represents GO biological process (noRedundant). K) DEGs validated with RT-qPCR analysis. Statistical differences were assessed by ordinary one-way ANOVA with Tukey’s correction and by Binary Student’s t tests (Welch’s correction). **** p < 0.001, *** p < 0.005, ** p < 0.01, * p < 0.05, and ns = non-significant.

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