116 Chapter 4 Higher expression of hexokinase 2 and phosphoglycerate mutase family member 5 by macrophages cultured on fibrous collagen as compared to globular collagen. Culturing macrophages on collagen type I clearly affected the expression of proteins. Next, we investigated if the morphology type of collagen would influence protein expression by comparing macrophages grown on fibrous collagen to macrophages cultured on globular collagen. Fibrous collagen led to a more than two-fold higher expression of 23 proteins compared to globular collagen (Table 2), with the most pronounced fold-change observed for pigment epithelium-derived factor (Serpinf1). The expression of four proteins was found to be at least two-fold lower in macrophages grown on fibrous collagen. These proteins are pyridoxal kinase (Pdxk), thioredoxin reductase 1, cytoplasmic (Txnrd1), nuclear cap-binding protein subunit 1 (Ncbp1) and translocating chain-associated membrane protein 1 (Tram1). Biological process and pathway analysis of the proteins with a >1.25-fold change different expression (Supplementary Table 2) did not yield any significantly enriched pathways. However, as we found the glycolysis pathway significantly enriched in cells grown on any type of collagen, we specifically investigated important metabolic enzymes in the list of significant proteins (Supplementary Table 2) and found hexokinase 2 (Hk2) and phosphoglycerate mutase family member 5 (Pgam5) to be differentially expressed (Figure 3b). Therefore, glycolysis may again be one of the biological processes affected by the culture conditions of macrophages (Figure 3b). In addition, four proteins in the list are part of the mitochondrial respiratory chain (Cytochrome b-c1, part of the ubiquinol-cytochrome c complex, elongation factorlike GTPase 1, NADH dehydrogenase (ubiquinone), and V-type proton ATPase), possibly pointing at changes in oxidative phosphorylation.
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