Gene Set Enrichment Analysis of Bronchial Alveolar Lavage Fluid Identifies Key Innate Immune Pathways in Primary Graft Dysfunction after Lung Transplantation

Abstract

Purpose Primary graft dysfunction (PGD) is a complex phenotype. We hypothesized that alterations in gene expression could identify important pathways involved in transplant lung injury. Methods and Materials Bronchoalveolar lavage fluid was sampled from donors prior to procurement and in recipients within an hour of reperfusion as part of the NIAID Clinical Trials in Organ Transplantation (CTOT-03) Study. Total RNA was analyzed using the Affymetrix Human Gene 1.0 ST array. Using a nested case control design, 23 patients with Grade 3 PGD were frequency matched with controls based on donor age and recipient diagnosis. Normalized candidate gene expression was log transformed and differences between donor and post-reperfusion mRNA expression were ranked. The resulting ranked gene list was tested for over-representation of networks of gene interactions using Gene Set Enrichment Analysis. Results From 106 subjects enrolled, 23 PGD cases were matched with 23 controls. 362 gene sets were upregulated following implantation, and 8 met significance with a family-wise error rate corrected p-value Conclusions Gene set enrichment analyses implicate inflammasome mediated and innate immune signaling pathways as key mediators of the development of PGD in lung transplant patients.