Genotype-Phenotype Interactions in Familial Interstitial Pneumonia

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PROJECT SUMMARY Ascertainment of kindreds with familial interstitial pneumonia (FIP) has proven to be a valuable resource for studying genetic susceptibility and underlying mechanisms that promote interstitial lung disease. Studies of FIP kindreds during the current funding period have led to several important findings, including the observation that rare variants (RVs) in a variety of genes can predispose to FIP. Based on whole exome sequencing (WES) from FIP patients during the current funding cycle, we have identified novel RVs in several genes that we believe are causative in FIP, including the telomerase pathway genes DKC1 and RTEL1, a G protein- coupled receptor GPR87, a centromere gene CENPN, and a gene of unknown function SYDE1. Preliminary studies to examine the functional importance of RVs in these genes have linked RTEL1 and GPR87 to the p53 pathway, suggesting that this pathway may integrate at least a portion of our genetic findings. To identify additional gene candidates, we used an unbiased approach to uncover pathways that were over-represented in the set of candidate RV-containing genes implicated by WES. Using this approach, two interrelated pathways containing microtubule/cilia genes and centrosome genes were found to be markedly over- represented. Together, our preliminary data point to a defined set of interacting pathways that show promise for containing RVs that predispose to FIP. The primary goal of this project during the current funding period was to identify, enroll, and phenotype members of families at risk for developing FIP. To date, we have enrolled 372 asymptomatic first-degree relatives of FIP patients in this ongoing cohort study and obtained blood samples and high resolution CT (HRCT) scans, as well as 100 bronchoscopies. In addition, through our ongoing collaboration with Dr. Schwartz (PI of Project 3), we have recently enrolled another 503 individuals at risk for FIP in this ongoing cohort study. Together, this cohort of 875 asymptomatic individuals provides a powerful resource to identify the earliest manifestations of FIP, better define the natural history of FIP, and determine endophenotypes based on genetic predisposition. In this competitive renewal, we hypothesize that damaging rare genetic variants in several inter-related pathways (including telomere genes, microtubule/cilia/centrosome genes, and p53-related genes) predispose to FIP through a common mechanism related to altered cell survival/proliferation. Specific aims are designed to: 1) evaluate genes with candidate rare genetic variants identified in FIP families and prioritize them for functional studies, 2) perform functional analysis of candidate rare genetic variants in targeted pathways, and 3) characterize genotype-phenotype relationships in individuals at risk for FIP. By validating and testing the function of new disease-associated alleles and using this information to determine genotype-phenotype relationships in individuals enrolled in our ongoing cohort study, these proposed studies provide an unprecedented opportunity to define the impact of genetic predisposition on key aspects of interstitial lung disease pathogenesis.