ABSTRACT
Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are two devastating
chronic lung diseases associated with aging and with a common environmental risk factor, cigarette smoking,
but with differing physiology and pathology, which may be due to genetics. Our group has led two large-scale
COPD genome-wide association studies (GWASs), identifying five loci (near FAM13A, DSP, MAPT-KANSL1,
ZKSCAN1, and STN1) where the genetic variant alleles associated with an increased COPD risk are associated
with a decreased IPF risk. These opposite risk loci may reside in regulatory elements that act as “molecular
switches” in disease-relevant cell types that impact gene expression to shunt biologic processes toward
producing a COPD or IPF end-phenotype. However, GWASs do not directly implicate the functional
consequence of genetic variants or the effector genes, cell types, or gene regulatory networks through which the
genetic variants are acting. MicroRNAs, which have been implicated in the pathogenesis of both COPD and IPF,
modulate gene expression levels and may impact the gene regulatory networks at the opposite risk loci. The
goal of this project is to define COPD/IPF opposite risk loci and describe the functional mechanisms, effector
genes, and relevant lung cell types through which these opposite risk loci are acting. We hypothesize that
opposite risk genetic loci for COPD and IPF are due to shared causal variants acting as molecular switches
through regulatory elements affecting gene expression in specific lung cell types. Furthermore, we hypothesize
that these molecular switches are marked by discrete microRNA and RNA differences as well as divergent gene
regulatory networks in COPD compared to IPF lung tissue. To address these hypotheses, we propose a series
of investigations starting by refining the five known COPD/IPF opposite risk loci and identifying new opposite risk
loci using expanded COPD and IPF GWASs and TOPMed WGS data. Next, we will perform joint single nucleus
Assay for Transposase-Accessible Chromatin sequencing (snATAC-seq) and snRNA-seq in COPD and IPF lung
tissue from the Lung Tissue Research Consortium (LTRC) to predict the disease-specific and lung cell-type-
specific regulatory elements and effector genes at each of the COPD/IPF opposite risk loci. We will use CRISPR
interference genome editing in implicated cell types to functionally validated predicted relationships of regulatory
elements to effector genes. Next, we will generate microRNA sequencing data in IPF lung tissue from the LTRC
and build disease-specific gene regulatory networks integrating genetic, microRNA, and RNA data at each
opposite risk locus. We will highlight therapeutic opportunities by assessing these gene regulatory networks for
drug-related pathway enrichment. We will then examine the COPD- and IPF-related cellular phenotypes that
result from perturbations (CRISPR interference, CRISPR activation, and microRNA targeting) of the genes in
the opposite risk loci gene regulatory networks. This study will help define the pathobiology and improve our
understanding of the susceptibility for the two most deadly chronic lung diseases.
