lncRNAs, Linking Genetic Susceptibility to Molecular Phenotype in IPF

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The overall goal of our proposed research is to understand how long non-protein-coding RNAs (lncRNAs) impact the effect of common idiopathic pulmonary fibrosis (IPF) risk variants on transcriptional profiles and the clinical severity of IPF. In the past 5 years, we have found that: 1) a gain-of- function MUC5B promoter variant rs35705950 is the strongest risk factor for the development of IPF (2-11); 2) epigenetic mechanisms affect the expression of MUC5B (12) and MUC5B appears to be involved in the pathogenesis of IPF (2, 13-15); and 3) IPF is a complex genetic disease with rare and common variants contributing to the development of this disease (16), including pronounced changes in DNA methylation (17) and transcriptional subtypes (18). We have recently sequenced across 10 IPF risk loci (5) in a large number of patients with IPF (N=3,642) and controls (N=4,442), and have identified 10 common variants that represent the only common independent signals in these IPF risk loci and in aggregate account for at least 40% of the risk of IPF (16). However, there is no clear explanation for the molecular/clinical heterogeneity of IPF or the low penetrance of either the MUC5B promoter variant (2) or the other common IPF risk variants (19-22) in this rare disease (23, 24). Emerging findings suggest that lncRNAs could alter the impact of common risk variants by influencing the molecular machinery that leads to IPF, and in turn account for the pathophysiologic phenotypes of IPF. In aggregate, these observations lead us to postulate that the etiology and severity of IPF will be best understood through an integrated approach that accounts for inherited factors and in turn their influence on the coding-noncoding transcriptome. Thus, we hypothesize that lncRNAs regulate the effect of common IPF risk variants on transcriptional profiles that drive the development and clinical severity of IPF. In Aim 1, we will broadly identify lncRNAs that are dysregulated in IPF lung tissue by comparing lncRNAs from the lung tissue of cases of IPF (N=450) to unaffected controls (N=300). We will use these data to identify differentially expressed lncRNAs and mRNAs, and explore networks of mRNAs regulated by lncRNAs. In Aim 2, we will determine cis- and trans-effects of IPF-associated common genetic variants on lncRNAs first in normal lung tissue and then in the IPF lung. This will enable us to hone in on candidate lncRNAs dysregulated in IPF that are driven by common IPF risk variants. In Aim 3, we will use a massively parallel reporter assay (MPRA) to identify and functionally validate regulatory variants within 10 key IPF risk loci that alter expression of coding and noncoding candidate RNAs and are associated with clinical and/or pathological subtypes of IPF. The end-result will be an enhanced understanding of the novel genes, regulatory pathways and networks, and molecular mechanisms involved in the etiology and clinical severity of IPF.