75 3 Responses of alveolar-like macrophages to lysine deacetylase inhibition Class I KDAC inhibitors do not affect the levels of metabolic enzymes Our untargeted proteomic analysis identified different metabolic pathways as processes that may be affected by treatment with KDAC1/2/3 inhibitors. This is interesting because metabolic reprogramming has been shown to be important in determining pro-and anti-inflammatory responses in different types of macrophages (45,46). We, therefore, investigated the metabolism of alveolar-like macrophages after KDAC inhibition in more detail. We first measured protein levels of enzymes that are part of the major metabolic pathways depicted in Figure 5. To obtain absolute values for these proteins, we used a targeted proteomic approach that used internal standards of concatenated signature peptides encoded by QconCAT proteins (47). None of the 59 proteins that we quantified (see Supplementary Table 3 and Supplementary Figure 3, supplementary material) was expressed at significantly different levels in any of our comparisons. These results suggest that even though a first exploratory proteome analysis suggested that alveolar-like macrophages may have changes in metabolism induced by LPS and/or KDAC inhibition, they did not seem to change their primary metabolism in response to these treatments. Figure 5: Proteins and metabolites measured in the context of macrophage metabolism. Macrophages can rely on different metabolic pathways depending on their activation state. Here the glycolytic, pentose phosphate, fatty acid oxidation, tricarboxylic acid, and electron transport chain pathways are depicted. Metabolites and proteins that were measured in this study are indicated in bold. Figure created with Biorender.com.
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