60 Chapter 3 TOC SUMMARY This study explores how inhibiting lysine deacetylases (KDAC) affects macrophages, which play a key role in the immune system. KDAC inhibition resulted in reduced production of inflammatory mediators in lipopolysaccharide-treated macrophages, however, only minor changes in macrophage metabolism were observed. KDAC inhibition specifically enhanced the expression of proteins involved in ubiquitination, which may be a driver of the anti-inflammatory effects of KDAC inhibitors. A multi-omics approach provides novel insights into how macrophages interact with cues from their environment. ABSTRACT Macrophages are key immune cells that can adapt their metabolic phenotype in response to different stimuli. Lysine deacetylases (KDAC) are important enzymes regulating inflammatory gene expression and KDAC inhibitors have been shown to exert anti-inflammatory effects in models of chronic obstructive pulmonary disease (COPD). We hypothesized that these anti-inflammatory effects may be associated with metabolic changes in macrophages. To validate this hypothesis, we used an unbiased and a targeted proteomic approach to investigate metabolic enzymes as well as LC- and GC-MS to quantify metabolites in combination with the measurement of functional parameters in primary murine alveolar-like macrophages after lipopolysaccharide (LPS)-induced activation in the presence or absence of KDAC inhibition. We found that KDAC inhibition resulted in reduced production of inflammatory mediators such as TNF-α and IL-1β. However, only minor changes in macrophage metabolism were observed, as only one of the KDAC inhibitors slightly increased mitochondrial respiration while no changes in metabolite levels were seen. However, KDAC inhibition specifically enhanced expression of proteins involved in ubiquitination, which may be a driver of the antiinflammatory effects of KDAC inhibitors. Our data illustrate that a multi-omics approach provides novel insights into how macrophages interact with cues from their environment. More detailed studies investigating ubiquitination as a potential driver of KDAC inhibition will help developing novel anti-inflammatory drugs for difficult to treat diseases such as COPD. Keywords: Lung, proteasome, immunometabolism, metabolome analysis, proteome analysis, multi-omics.
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