Network Integration of Parallel Metabolic and Transcriptional Data Reveals Metabolic Modules that Regulate Macrophage Polarization

Abstract

Macrophage polarization involves a coordinated metabolic and transcriptional rewiring that is only partially understood. By using an integrated high-throughput transcriptional-metabolic profiling and analysis pipeline, we characterized systemic changes during murine macrophage M1 and M2 polarization. M2 polarization was found to activate glutamine catabolism and UDP-GlcNAc-associated modules. Correspondingly, glutamine deprivation or inhibition of N-glycosylation decreased M2 polarization and production of chemokine CCL22. In M1 macrophages, we identified a metabolic break at Idh, the enzyme that converts isocitrate to alpha-ketoglutarate, providing mechanistic explanation for TCA cycle fragmentation. (13)C-tracer studies suggested the presence of an active variant of the aspartate-arginosuccinate shunt that compensated for this break. Consistently, inhibition of aspartate-aminotransferase, a key enzyme of the shunt, inhibited nitric oxide and interleukin-6 production in M1 macrophages, while promoting mitochondrial respiration. This systems approach provides a highly integrated picture of the physiological modules supporting macrophage polarization, identifying potential pharmacologic control points for both macrophage phenotypes.

Highly Dynamic Transcriptional Signature of Distinct Macrophage Subsets during Sterile Inflammation, Resolution, and Tissue Repair

“…This was preceded by an early upregulation, between days 1 and 2, of the pathways associated with oxidative phosphorylation and TCA cycle, suggesting that macrophages first started to shift their metabolic profile before shifting their inflammatory status. Finally, we observed a strong upregulation of genes involved in glutamine metabolism, associated with oxidative metabolism, which is characteristic of M2(IL-4) macrophages in vitro (15), during the late steps of muscle regeneration (days 4-8). These results suggest that metabolic shift precedes inflammatory shift in macrophages and that a specific metabolic signature characterizes recovery macrophages during the repair phase.…”

“…Gene set enrichment analysis (GSEA) was performed as described previously (14) using the KEGG pathway database (http://www.genome.jp/ kegg/pathway.html) as in Jha et al (15) and for 49 gene sets associated with macrophage activation as in Xue et al (3).…”

“…Detailed metabolic regulation has been recently investigated in in vitro-activated macrophages and showed that M2(IL-4) macrophage profile was associated with glutamine metabolism, involved in activation of tricarboxylic acid (TCA) cycle and oxidative phosphorylation (15). Most of the genes (16/22) identified as being dependent on glutamine in Jha et al's study (15) were upregulated during the late steps of muscle regeneration (Fig. 7A), suggesting that oxidative metabolism is associated with Ly6C neg macrophage functions that are more numerous at this time.…”

Innate immunity of carp : fishing for receptors

“…Besides glycolysis and the pentose phosphate pathway, another pivotal metabolic module is the TCA cycle. In M1 macrophages the TCA cycle is 'broken' in two places: after citrate and after succinate, leading to the accumulation of these two metabolites (Jha et al, 2015), (Tannahill et al, 2013). The citrate is subsequently funnelled into fatty acid synthesis or into pathways leading to ROS, nitric oxide and prostaglandin synthesis (Infantino et al, 2011).…”

“…Furthermore, there is an up-regulation of the synthesis of UDP-GlcNAc intermediates that are necessary for the N-glycosylation of M2-associated receptors, such as the mannose receptor (Jha et al, 2015). In contrast to the situation in M1 macrophages, the pentose phosphate pathway is inhibited in M2 macrophages, mainly due to high expression levels of the enzyme CARKL that limits the flux through this pathway (Haschemi et al, 2012), another example of the opposing nature of M1 vs M2 macrophages.…”