145 5 General Discussion respiration. This is consistent with the current literature on immunometabolism indicating that alveolar macrophages rely on oxidative phosphorylation for cytokine production [21,24] and more generally with what has been shown to occur in macrophages having an anti-inflammatory phenotype [25]. However, no changes were observed when the cells were pre-treated with MS275, which may be because this KDACi has a weaker anti-inflammatory effect. In fact, when cells were treated with this compound, only differences at the level of gene expression were observed. It is possible that differences were observed at the gene expression level but not in metabolism because the measurements were taken at a specific time point, and transcription and translation still had to occur before the effects of changes in gene expression are fully expressed in metabolism. In fact, after a gene is transcribed, the resulting mRNA molecule must be processed and transported to the cytoplasm, where it is translated into a protein. The rate of protein synthesis is influenced by several factors, including amino acids availability, translation efficiency, and mRNA molecule stability. Therefore, if differences in gene expression are observed but not in metabolism, it may be because the effects of changes in gene expression have not yet been fully translated into changes in the levels of metabolic enzymes or metabolites. In addition to the time required for transcription and translation, other regulatory mechanisms can influence the correlation between gene expression and metabolism. For example, posttranscriptional and post-translational modifications can affect the stability and activity of metabolic enzymes, even if their gene expression levels remain unchanged. After investigating how alveolar-like macrophages shift their metabolism in response to different pro- and anti-inflammatory stimuli, we investigated how the metabolic pathways would change depending on the morphological and mechanical characteristics of the tissue. In Chapter 4 alveolar-like macrophages were seeded on plastic, plastic coated with fibrous collagen, or plastic coated with globular collagen. Fibrous collagen is obtained at a neutral pH, while an acidic pH results in globular collagen. From a previous study, it was already known that culturing macrophages on either type of collagen coating led to a higher expression of surface markers associated with M2-like polarization (CD206) compared to control macrophages seeded on an uncoated surface [26], and this expression was higher in macrophages seeded on globular collagen compared to fibrous. In macrophages seeded on fibrous collagen, instead, higher levels of the surface marker YM1, a marker of anti-inflammatory, pro-repair, macrophages, were demonstrated compared to macrophages seeded on globular collagen. Accompanying these differences in marker expression changes
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