The transcriptional PPARβ/δ network in human macrophages defines a unique agonist-induced activation state.
Bottom Line: Surprisingly, bioinformatic analyses also identified immune stimulatory effects.Comparison with published data revealed a significant overlap of the PPARβ/δ transcriptome with coexpression modules characteristic of both anti-inflammatory and pro-inflammatory cytokines.Our findings indicate that PPARβ/δ agonists induce a unique macrophage activation state with strong anti-inflammatory but also specific immune stimulatory components, pointing to a context-dependent function of PPARβ/δ in immune regulation.
Affiliation: Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany.Show MeSH
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Mentions: We used this experimental system to identify ligand-responsive genes as well as PPARβ/δ and RXR binding sites in macrophages by deep sequencing technologies. RNA-Seq data obtained with MDMs cultured either in R10 or serum-free synthetic X-VIVO 10 medium (XV0) revealed a total of 285 protein-coding genes upregulated by PPARβ/δ agonist L165,041 and 246 genes downregulated by the inverse agonists ST247 or PT-S264; logFC ≥ 0.7; FPKM ≥ 0.3), 29.6% of the latter (n = 73) overlapping with the agonist-induced gene set (Figure 2A; Supplementary Table S2). Our RNA-Seq also identified a large fraction of genes repressed by the agonist L165,041 (n = 388) and upregulated by the inverse agonist ST247 (n = 174), with 40 genes (10.3%) overlapping (Figure 2B; Supplementary Table S2). Diseases and functions annotation of the L165,041-induced gene set showed a strong association with the inhibition of cell death of immune cells and suppression of immune cell functions, including migration, inflammatory response, activation, homing, adhesion, chemotaxis and phagocytosis (Figure 2C; Supplementary Table S3). The gene set representing inflammation clearly overlapped with cell survival, migration/movement, adhesion and recruitment/infiltration/ chemotaxis (Figure 2D), suggesting that these to a large extent represent genes with functions in immune regulation. Interestingly, ‘Inflammation of intestine’ and ‘Colitis’ showed a positive activation z-score (Figure 2C), providing a first hint that the response to L165,041 may not be strictly anti-inflammatory. Likewise, lipid metabolism (‘Concentration of acylglycerol’) was upregulated, consistent with the known metabolic role of PPARβ/δ. Finally, analysis of the known upstream regulators of these genes (signaling molecules and transcription factors) identified two groups: canonically regulated (L165,041-induced) genes known to be activated by PPAR agonists (pirixinic acid, fibrates, glitazones) were upregulated by L165,041, while genes induced by pro-inflammatory signaling via LPS, TNFα, IFNγ, IL-1β, STAT3 or TLR4 were downregulated (inverse target genes).
Affiliation: Institute of Molecular Biology and Tumor Research (IMT), Center for Tumor Biology and Immunology (ZTI), Philipps University, 35043 Marburg, Germany.