Differential Transcriptome Networks between IDO1-Knockout and Wild-Type Mice in Brain Microglia and Macrophages

Abstract

Microglia in the brain and macrophages in peripheral organs are cell types responsible for immune response to challenges. Indoleamine 2,3-dioxygenase 1 (IDO1) is an immunomodulatory enzyme of the tryptophan pathway that is expressed in the brain. The higher activity of IDO1 in response to immune challenge has been implicated in behavioral disorders. The impact of IDO1 depletion on the microglia transcriptome has not been studied. An investigation of the transcript networks in the brain microglia from IDO1-knockout (IDO1-KO) mice was undertaken, relative to peripheral macrophages and to wild-type (WT) mice under unchallenged conditions. Over 105 transcript isoforms were differentially expressed between WT and IDO1-KO within cell type. Within microglia, Saa3 and Irg1 were over-expressed in IDO1-KO relative to WT. Within macrophages, Csf3 and Sele were over-expressed in IDO1-KO relative to WT. Among the genes differentially expressed between strains, enriched biological processes included ion homeostasis and ensheathment of neurons within microglia, and cytokine and chemokine expression within macrophages. Over 11,110 transcript isoforms were differentially expressed between microglia and macrophages and of these, over 10,800 transcripts overlapped between strains. Enriched biological processes among the genes over- and under-expressed in microglia relative to macrophages included cell adhesion and apoptosis, respectively. Detected only in microglia or macrophages were 421 and 43 transcript isoforms, respectively. Alternative splicing between cell types based on differential transcript isoform abundance was detected in 210 genes including Phf11d, H2afy, and Abr. Across strains, networks depicted a predominance of genes under-expressed in microglia relative to macrophages that may be a precursor for the different response of both cell types to challenges. The detected transcriptome differences enhance the understanding of the role of IDO1 in the microglia transcriptome under unchallenged conditions.

Brain region-dependent gene networks associated with selective breeding for increased voluntary wheel-running behavior

“…Brains were extracted, placed on an iced aluminum platform and the entire Ce and St were dissected, immediately transferred to a centrifuge tube and stored at −80°C [ 15 , 16 ]. Individual brain region samples were homogenized with an RNase-free disposable pellet pestle (Fisher); RNeasy® Lipid Tissue Mini Kit (Qiagen, Valencia, CA) was used for RNA extraction; and DNase I (Qiagen, Valencia, CA) was used to purify the isolated RNA.…”

“…Complementary enrichment analyses were used to obtain a comprehensive understanding of the functional categories over-represented among the differentially expressed genes. The categories studied included Gene Ontology (GO) molecular function (MF) and biological process (BP) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways [ 15 , 23 ]. Gene Set Enrichment Analysis (GSEA) considered the expression profiles of all genes analyzed [ 24 ].…”

“…EASE scores (modified Fisher Exact) were used to assess the statistical significance of the enrichment of the individual categories [ 8 , 26 ]. Functional categories including genes in common were clustered and the statistical significance of these functional clusters is represented by the enrichment score (ES) that is the geometric mean of the EASE scores of the categories in the cluster [ 15 , 26 ]. Further analysis of the enrichment of categories from the Mouse Genome Informatics (MGI) mammalian phenotype database of using Fisher exact test were implemented using the software Enrichr [ 27 ].…”

Interplay Between Amphetamine and Activity Level in Gene Networks of the Mouse Striatum

“…Networks encompassing genes that exhibited significant differential expression in at least one of the three orthogonal contrasts (AC-SC, AO-SO, SC-SO) were reconstructed to uncover gene dysregulation on a system-level basis. 37 , 38 Networks were reconstructed using the BisoGenet package within the Cytoscape environment. 39 – 42 These networks depict gene relationships based on protein-protein interactions annotated in the BIOGRID, HPRD, DIP, BIND, INTACT, and MINT databases.…”

Cerebellum Transcriptome of Mice Bred for High Voluntary Activity Offers Insights into Locomotor Control and Reward-Dependent Behaviors

“…Networks encompass genes exhibiting significant (FDR-adjusted P-value < 0.05) differential expression in at least one of the 3 orthogonal contrasts (CF-HF, CB-HB, HB-HF) to facilitate visual comparison [47]. Networks connecting at least 15 differentially expressed genes directly or indirectly through intermediate genes not differentially expressed were considered.…”