Integration of transcriptional and metabolic control in macrophage activation

Abstract

Macrophages react to microbial and endogenous danger signals by activating a broad panel of effector and homeostatic responses. Such responses entail rapid and stimulus-specific changes in gene expression programs accompanied by extensive rewiring of metabolism, with alterations in chromatin modifications providing one layer of integration of transcriptional and metabolic regulation. A systematic and mechanistic understanding of the mutual influences between signal-induced metabolic changes and gene expression is still lacking. Here, we discuss current evidence, controversies, knowledge gaps, and future areas of investigation on how metabolic and transcriptional changes are dynamically integrated during macrophage activation. The cross-talk between metabolism and inflammatory gene expression is in part accounted for by alterations in the production, usage, and availability of metabolic intermediates that impact the macrophage epigenome. In addition, stimulus-inducible gene expression changes alter the production of inflammatory mediators, such as nitric oxide, that in turn modulate the activity of metabolic enzymes thus determining complex regulatory loops. Critical issues remain to be understood, notably whether and how metabolic rewiring can bring about gene-specific (as opposed to global) expression changes.

Keywords: epigenetics; inflammation; macrophages; metabolism; transcription.

Figure 1. An overview of metabolic and transcriptional reprogramming in LPS‐activated macrophages

Macrophages respond to proinflammatory stimuli by extensively reprogramming their transcriptional and metabolic activity. The glycolytic flux is enhanced, and oxygen consumption is reduced, while several pathways, such as the TCA cycle, are altered and specific metabolites accumulate over time. Both glucose uptake and metabolism are rapidly upregulated, and the pyruvate produced is converted into lactate. The induction of the Nos2 gene leads to a massive burst of NO production. NO acts as an antimicrobial molecule and impairs the activity of the electron transport chain (ETC), eventually reducing cellular oxygen consumption. The TCA cycle is remodeled because of the impairment of IDH activity, leading to the accumulation of citrate which is exported to the cytoplasm via the mitochondrial citrate carrier (SLC25A1). Cleavage of cytoplasmic citrate by ACLY equilibrates the mitochondrial and the cytosolic acetyl‐CoA pool. ACOD1 induction leads to aconitate being diverted to itaconate, which functions as an immunomodulatory molecule and also affects succinate dehydrogenase (SDH), blocking its activity and thus promoting succinate accumulation. Among key transcription factors produced, HIF1α is stabilized by the accumulation of succinate and it is able to induce several key metabolic genes. Together with key transcription factors, the second wave of inflammatory mediators results from the activity of histone acetyltransferases, which rely on the acetyl‐CoA produced by the cell to support activation of gene expression.

Figure 2. IL‐4‐induced changes in metabolism and their effects on gene expression

(A) In response to IL‐4 stimulation, glycolysis is increased; the TCA cycle remains intact and both fatty acid uptake and metabolism are enhanced via regulation of metabolic genes by STAT6 and PPARγ. (B) Alpha‐ketoglutarate, an intermediate of the TCA cycle, acts as a co‐substrate of lysine demethylases such as JMJD3 to remove the repressive H3K27me3 mark, eventually activating gene transcription. (C) Glutamine and glucose are employed via the Glutamine‐UDP‐GlcNac pathway to glycosylate proteins involved in M2 macrophage function such as CD206 and MGL. (D) Arginase 1, upregulated by IL‐4, converts arginine to ornithine which is used in polyamine biosynthesis. Ornithine can be also further metabolized to spermidine which was found to be involved in the hypusination of translation factor eIF5A, which controls the production of key mitochondrial proteins involved in the TCA cycle and OXPHOS.

Figure 3. Novel aspects of metabolic remodeling and its transcriptional consequences in macrophages

(A) The glycerol phosphate shuttle plays a key role in linking increased glycolytic flux to increased oxygen consumption in the early phases of the LPS response. (B) ACLY, a key gene able to regulate global acetyl‐CoA levels in the cell, is activated via AKT in the early phase (< 3 h) after LPS exposure, and its activity is crucial for the upregulation of several proinflammatory mediators. (C) Lactate produced from pyruvate is used to generate a novel post transcriptional modification on histones, H3K18la (lactylation of K18 on histone H3), which is deposited on genes activated at late time points in the LPS response. (D) The burst of NO production inactivates PDC, ACO2, and OGDC at late time points in the LPS response by nitrosylating one of their subunits (blue circles), leading to the normalization of citrate, itaconate, and succinate levels over time.

Figure 4. Putative mechanisms linking global or local changes in metabolites concentration to changes in gene expression

Upper panel. Changes in global availability of the substrate (e.g., acetyl‐CoA) of a histone modifier (e.g., a histone acetyl transferase, HAT) differentially regulate enzymes with distinct properties. For instance, HATs such as GCN5 or P/CAF have a low Km and are thus largely insensitive to broad changes in cellular substrate concentration. Conversely, HATs such as p300/CBP have a Km which is within the range of cellular concentration of the enzyme, making them able to transduce an increase in acetyl‐CoA concentration into increased histone acetylation levels. Lower panel. Three possible mechanisms explaining the impact of metabolite concentration on gene activity. (A) A metabolite produced outside of the nucleus diffuses through the nuclear membrane and equilibrates between different compartments. Changes in its cellular concentration thus affect histone modification activity inside the nucleus. (B) Translocation of a metabolic enzyme into the nucleus increases local production of a metabolite (e.g., acetyl‐CoA), modulating the activity of histone‐modifying enzymes. (C) Direct recruitment of a metabolic enzyme onto chromatin increases the local production of substrate, enhancing the deposition of histone modifications at specific loci.