Figure 5. iMGLs gene profiles are responsive to neuronal environment.

(A) Schematic of iMGL co-culture with or without rat hippocampal neurons. (B) iMGLs co-cultured with neurons were collected, isolated by flow cytometry and transcriptomes evaluated via RNA-sequencing. (C) Heat map of iMGLs and iMGL-HC gene expression highlights uniquely enriched genes. (D) Differential gene expression analysis highlights 156 upregulated and 244 downregulated genes in iMGL-HCs. (E) Scatter plot of differentially expressed genes [> 2 Log₂(FPKM+1)] highlight TRIM14, CABLES1, MMP2, SIGLEC 11 and 12, MITF, and SLC2A5 being enriched in iMGL-HCs, suggesting that iMGLs respond appropriately to a neuronal environment. Cells cultured alone are enriched for COMT, EGR2, EGR3, and FFAR2 suggesting a primed microglia phenotype. (F) GO and pathway terms from differential gene expression analysis of iMGLs cultured with hippocampal neurons. Genes upregulated in iMGL-HC are associated with 20 statistically significant pathway modules (green histogram) including positive cholesterol efflux, lipid transport, positive regulation of immune response, negative regulation of leukocyte differentiation and cell adhesion molecules. Cells cultured in absence of neurons had a complimentary gene profile with 20 statistically significant biological modules (blue histogram) including hallmark cholesterol homeostasis, hallmark TNFα signaling via NF-κB, leukocyte differentiation, and regulation of IL-1β secretion.