Figure 2

Bexarotene treatment significantly affects genes related to nervous system development, axon guidance and neurites extension.

RNA was isolated from cortices of the same APOE3 mice treated with bexarotene or vehicle as shown on Fig. 1. (A) Scatter plot of transcripts in vehicle and bexarotene treated APOE3 mice. Transcripts identified as significantly differentially expressed at p < 0.05 cut-off are colored in blue (down-regulated) and red (up-regulated). Up-regulated transcripts associated with neurite extension are shown in green and down-regulated genes associated with inflammation in orange. Gene symbols of representative transcripts are shown next to the corresponding values. (B) Most significant common canonical pathways identified by ChIP-seq and RNA-seq in APOE3 mice; (C) Significantly changed levels of RNA expression of genes in categories “neuron differentiation” and “neuron projection”; statistics is by edgeR, p < 0.05, n = 4/group; (D) Validation of RNA-seq results by qPCR; APOE3 mice, n = 4/group; (E) Validation by qPCR in N2a cells: Cells were treated with 1 μM bexarotene or vehicle for 24 hours and 48 hours (details in Materials & Methods). Values are mean ± SEM. For (D,E) statistics is by t-test; n = 3, *p < 0.05, **p < 0.01, ***p <  0.001.