Gene Expression in Transformed Lymphocytes Reveals Phenotype-Modifying Pathways in Cystic Fibrosis

Heritable genetic variants modify cystic fibrosis (CF) clinical phenotypes, e.g., lung disease, age-of-onset of persistent Pseudomonas aeruginosa (P. aeruginosa), and meconium ileus (MI).  Previous genome wide association studies (GWAS) have begun to inform the genetic architecture of CF phenotypes.  Analyses of gene expression will complement GWAS, as demonstrated by analyses of gene expression in lymphoblastoid cell lines (LCLs) to identify disease-related pathophysiological processes for non-CF complex traits.  In this study, global gene expression was measured in RNA from LCLs from 754 CF patients and analyzed for association with lung disease severity, age-of-onset of persistent P. aeruginosa pulmonary infection, and MI at birth.  Each phenotype displayed distinct expression associations.  Most pathways significantly associated with lung disease were related to membranes, vesicle traffic, and Golgi/endoplasmic reticulum (ER).  Pathways containing HLA genes (Class I and II) were significantly associated with both lung and P. aeruginosa phenotypes, but they displayed qualitative differences between phenotypes.  MI associated with pathways involving oxidative phosphorylation.  The results support the concept that gene expression associated with heritable variation acts to modify phenotypes in CF. 754 samples were analyzed; 2 control samples were plated by Expression Analysis per plate and 1 pooled sample from the patient set was added to one well on each plate.