Transcriptomic Profiling of Idiopathic Pulmonary Fibrosis

Specimens were obtained from the peripheral area of the lower lobe of each lung as soon as the first recipient lung was taken out, snap frozen in liquid nitrogen, and stored at − 80 °C. RNA was extracted and hybridized to the Human Gene 1.0 set array (Affymetrix) from explanted lungs (2001–2008) in 22 patients with clinical diagnosis of sporadic IPF, entirely typical UIP HRCT pattern [16 (link)] and definite histologic UIP pattern; 10 subjects with clinical diagnosis of idiopathic NSIP and definite histologic pattern of fibrotic NSIP; and 11 normal lung samples (age 52 ± 18 years, 4 females) obtained from the region of normal tissue flanking lung cancer resections in ILD-free patients. Histopathologic diagnoses were based on whole explanted lungs. IPF cases with atypical radiographic features for UIP, and patients with other types of ILD, connective tissue disease or concomitant emphysema were excluded. A separate set of patients who underwent surgical lung biopsies at London Health Science Centre (Western University) (2005–2015) were identified and representative blocks were used for immunohistochemistry (IHC). This set included 23 cases with definite IPF/UIP and 13 with definite NSIP.
The study was approved by the Human Tissue Committees and Research Ethics Boards of the University Health Network (protocol n.11–0932) and Western University (n.105214).