The transcriptome of IPF fibrotic foci identifies the fatty acid metabolism as a critical pathway in fibrogenesis

Background: Fibroblastic foci represent the key pathogenic lesion in idiopathic pulmonary fibrosis (IPF) and comprise activated myofibroblasts, the key effector cells responsible for dysregulated extracellular matrix deposition in IPF and multiple fibrotic conditions. Aim: To define the major transcriptional programmes involved in fibrogenesis in IPF by profiling non-manipulated myofibroblasts captured in situ by laser capture microdissection. Results: The challenges associated with deriving gene calls from low amounts of RNA and the recognized absence of a meaningful comparator group were overcome by adopting an eigengene-based approach to identify transcriptional signatures which correlate with pathogenic collagen expression. Collagen eigengene analysis revealed that TGF-b1, RhoA kinase and the fatty acid axis formed major signalling clusters associated with collagen gene expression. Fatty acid oxidation generates more ATP than glucose oxidation and therefore represents the preferred energy source for highly metabolic cells. Functional studies showed that 1uM ND-630, an inhibitor of the acetylCoA carboxylases, the rate limiting enzymes of fatty acid metabolism, was able to inhibit 65% of TGF-b1-induced collagen synthesis in primary human lung fibroblasts, which demonstrated a key role for the fatty acid metabolism in regulating TGF-b1-induced collagen synthesis in mesenchymal cells reflecting IPF disease. Conclusion: These data provide strong support for this human tissue-based and bioinformatics approach to identify critical transcriptional nodes associated with the key pathogenic cell responsible for fibrogenesis in situ and further identifies the fatty acid metabolism as a novel target for interfering with excessive matrix deposition in the context of fibrotic conditions.