Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci

Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in 15%. Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10(-10)); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p<2.2x10(-16), 2.81x10(-11), respectively); and replicated a suggestive locus on chromosome 7 near PRSS1 (min p = 2.55x10(-7)). PRSS1 is exclusively expressed in the exocrine pancreas and was previously associated with non-CF pancreatitis with functional characterization demonstrating impact on PRSS1 gene expression. We thus asked whether the other meconium ileus modifier loci impact gene expression and in which organ. We developed and applied a colocalization framework called the Simple Sum (SS) that integrates regulatory and genetic association information, and also contrasts colocalization evidence across tissues or genes. The associated modifier loci colocalized with expression quantitative trait loci (eQTLs) for ATP12A (p = 3.35x10(-8)), SLC6A14 (p = 1.12x10(-10)) and SLC26A9 (p = 4.48x10(-5)) in the pancreas, even though meconium ileus manifests in the intestine. The meconium ileus susceptibility locus on chromosome X appeared shifted in location from a previously identified locus for CF lung disease severity. Using the SS we integrated the lung disease association locus with eQTLs from nasal epithelia of 63 CF participants and demonstrated evidence of colocalization with airway-specific regulation of SLC6A14 (p = 2.3x10(-4)). Cystic Fibrosis is realizing the promise of personalized medicine, and identification of the contributing organ and understanding of tissue specificity for a gene modifier is essential for the next phase of personalizing therapeutic strategies. Author summary Cystic Fibrosis (CF) impacts the normal functioning of several organs including the pancreas, intestines and lungs. CF is caused by mutations in the CF transmembrane conductance regulator, but individuals with the same mutations have different disease severity. For example, only 15% of individuals with CF are born with intestinal obstruction at birth (meconium ileus) while all have progressive lung disease with varying severity. Modifier genes contribute to variation across individuals with CF. In this study we identified modifiers of meconium ileus susceptibility, encompassing the previously identified SLC26A9 and SLC6A14, and two new loci ATP12A and PRSS1. To understand the mechanism by which these modifier genes impact CF severity we developed a new statistical method that assesses colocalization with regulatory information. Using this methodology we show, surprisingly, that all the meconium ileus association signals colocalize with gene expression in the pancreas rather than in intestinal tissues. A distinct and neighbouring locus near SLC6A14 also contributes to CF lung disease. Aided by transcriptomics of nasal epithelia from CF patients we found that each locus impacts variation in gene expression of SLC6A14 with tissue specificity. Understanding the contributing tissue and responsible gene are necessary to prioritize modifiers as alternative therapeutic targets.