The transcriptional signal of laser capture microdissection fibroblkastic foci from idiopathic pulmonary fibrosis (IPF) patients. Homo sapiens

Contractile and highly synthetic myofibroblasts are the key effector cells involved in excessive extracellular matrix (ECM) deposition in multiple fibrotic conditions, including idiopathic pulmonary fibrosis (IPF). In order to define the key drivers of the fibrotic response, we used laser capture microdissection to isolate RNA from myofibroblasts within fibroblastic foci and performed microarray analysis in combination with a novel eigengene approach to identify functional clusters of genes which associate with collagen gene expression. Overall design: Using laser capture microdissection (LCM) the myofibroblast core was isolated from multiple fibroblastic foci in each of 13 patient samples taken either as lung biopsies (3 samples) or at the time of lung transplant (10 samples). Care was taken to avoid capturing the overlying epithelium and parallel staining of sections for α-smooth muscle actin (αSMA) indicated the captured cells represented an almost pure population of myofibroblasts. Each sample was independently processed and hybridised on microarrays before computational pooling of all detected genes in patients where gene expression was noted in at least two of the foci captured.