Fig. 2.

Gene expression and ontology analysis reveal significant alterations in both adaptive and innate immunity and microglial-enriched genes. (A) Affymetrix gene expression analysis revealed 2,552 significantly altered genes between Rag-5xfAD (light green) and WT-5xfAD (dark green) groups. In contrast, only 553 genes were different between WT-5xfAD and WT-WT (dark blue) groups. Thus, the combination of AD transgenes and immune deficiency leads to a profound alteration in gene expression within the brain, well beyond that produced by AD pathology alone. (B) Hierarchical cluster analysis of these 2,552 differentially expressed genes confirmed that each genotype could be grouped together based on similar gene expression profiles (red, up-regulated; green, down-regulated). (C) Next, gene ontology (GO) enrichment was performed, identifying numerous examples of significantly altered pathways involving adaptive or innate immunity as well as antigen presentation and Ig binding. (D and E) Based on the GO analysis, we further examined subsets of microglial-enriched (D) or neuronal-enriched (E) genes (26) via unsupervised hierarchical clustering. This analysis again further implicated innate immune system disruption as the Rag-5xfAD and WT-5xfAD groups clustered very well via microglial-specific genes, but not via neuronal genes. In contrast, WT-WT (dark blue) and Rag-WT (light blue) groups did not cluster well together for either microglial or neuronal transcripts. P < 0.05 was defined as the cutoff to identify the statistical significance of enrichment analyses in C.