Fig. 2: Microglia are essential for HIV-induced transcriptional changes in neural organoids.

MA plot representing DEGs comparing HIV infection vs mock infection in A NOs and B MNOs (adjusted p < 0.05), bar graphs representing extracellular cytokine levels of C CCL20 and D CCL13 in supernatant of HIV-MNO, mock-MNO, HIV-NO, mock-NO and HIV HI-NO. Data were analyzed with a one-way ANOVA followed by Tukey’s post-hoc test (E) pathway analysis showing significantly altered pathways (adjusted p < 0.05) comparing HIV infection vs. mock infection in NOs and MNOs, F Heatmap representing significantly altered genes with high expression changes (adjusted p < 0.05 and L2FC > |2|) comparing HIV infection vs mock infection in NOs (n = 11) and MNOs (n = 88) representing two samples from three donors in the columns, G Sankey plot showing associations between significantly regulated genes with high expression changes (adjusted p < 0.05 and L2FC > 2) comparing HIV infection vs mock infection and their respective cell type and pathways. Data represent two technical replicates for three batches using three individual hiPSC donors. HIV HIV-1, NO neural organoids, MNOs neural organoids embedded with microglia, mock- mock infected, -HIV HIV infected, -HIV HI inoculated with heat-inactivated HIV.