Characterization of the Microglia Transcriptome in IDO1 Knockout and Wild-Type Mice

Inhibition or blockage of Indoleamine 2,3-dioxygenase 1 (IDO1), the important rate-limiting enzyme in the kynurenine pathway, is used to study immunoregulation and other biological processes that involve tryptophan substrates. Gene profile comparisons of IDO1-knockout (IDO1-KO) and wild-type mice in brain macrophages (microglia) are necessary to characterize differences under control, non-inflammatory challenge, conditions.  Microglia from 4 wild-type male mice (C57BL/6J) and 4 IDO1-KO male mice (C57BL/6J background) was enzymatically isolated at 22 weeks of age. The RNA-Seq analysis used the Illumina Genome Analyzer II platform and paired-end reads were mapped to the mouse reference genome (GRCm38/mm10) using Tophat. In total, 14,936 isoform transcripts pertaining to 14,445 genes were identified and 224 isoform transcripts pertaining to 223 genes were identified as differentially expressed (P-value < 0.10) using the Cufflinks. Prolactin (Prl) and growth hormone (Gh) were over-expressed and integrin beta 2 (Itgb2), and 3-phosphoinositide dependent protein kinase 1 (Pdpk1) were under-expressed in IDO1-KO relative to wild-type mice. Functional analysis of the differentially expressed genes using DAVID identified two functional category clusters (Enrichment score > 2): chemokine receptor activity and binding and signaling pathway. The genes in these clusters were over expressed in the microglia of IDO1-KO relative to wild-type mice and confirm the role of IDO1 and the tryptophan pathway on immune response. These results indicate that it is important to account for gene profile differences between IDO1-KO and wild-type mice under normal unchallenged conditions in experiments.