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Nasal Lavage Exosome Analysis Specifies Therapeutic Targets for Precision Treatment in Cystic Fibrosis

Cystic Fibrosis (CF) is the most common lethal genetic disorder in Caucasians in the United States, caused by mutations in CFTR, with the leading cause of illness and death being lung disease. Healthcare providers, researchers, and people with CF have long noted that across people with the same mutations in CFTR, for example amongst siblings (or even twins), there is a very broad range of lung disease severity. Heritability studies, or studies to define contributing genetic factors, show "modifier genes" aside from CFTR itself are responsible for most of that variability in CF lung disease. In 134 CF patients with genomic data, we have performed transcriptome-wide investigation of respiratory (nasal) epithelial transcriptomic mRNA to determine modifier genes correlated with long-term lung disease severity. This study identified differences in gene expression in pathways important to the pathophysiology of CF lung disease, particularly highlighting that dysregulated inflammation is adverse in CF. Yet, the mechanism for most of these newly identified candidate modifier genes remains incompletely understood in CF.

miRNAs are small non-coding RNAs that control the expression of multiple genes. miRNA regulation is one undefined mechanism of effect for modifier genes on CF lung disease, and our partnership with the KIPM COBRE cores has enabled us to isolate miRNAs from small extracellular vesicles in the nasal lavage and plasma of people with CF. Building on our previous transcriptomic studies, we are testing the hypothesis that extracellular vesicle miRNAs modify inflammatory signaling and contribute to the severity and progression of CF lung disease. We are performing miRNASeq on nasal lavage from 134 CF patients, and identifying miRNAs associated with CF lung disease severity. We are further studying the effects of the identified miRNAs on gene regulation using our existing nasal RNAseq data and validating candidate miRNAs in a new and independent CF cohort. As one example, in our transcriptomic studies, we found that increased expression of genes in the methionine salvage pathway is associated with worse CF lung disease. We observed that the key substrate of this pathway, methylthioadenosine (MTA), reduces levels of one of our top-ranked candidate modifers, miRNA-21 (identified by our predictive analyses) extracellular vesicles secreted from a macrophage cell line. Importantly, miRNA-21 is known to stimulate inflammatory signaling. We are testing the hypothesis that MTA treatment decreases secreted EV miRNA-21 levels and results in reduced inflammatory cytokine production directly in macrophages, which are critical to CF inflammation. We will further test the effect of these secreted EVs, and the direct effects of reduced miRNA-21, on lowering the inflammation in human CF airway epithelial cells. Our proposed studies will identify candidate miRNAs and begin to define mechanisms by which they exert influence in CF airways.


  1. Polineni D, Dang H, Gallins PJ, et al. Airway Mucosal Host Defense Is Key to Genomic Regulation of Cystic Fibrosis Lung Disease Severity. Am J Respir Crit Care Med. 2018;197(1):79-93. doi:10.1164/rccm.201701-0134OC
  2. Gong J, Wang F, Xiao B, et al. Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci. PLoS Genet. 2019;15(2):e1008007. Published 2019 Feb 26. doi:10.1371/journal.pgen.1008007
  3. Middleton PG, Mall MA, Dřevínek P, et al. Elexacaftor-Tezacaftor-Ivacaftor for Cystic Fibrosis with a Single Phe508del Allele. N Engl J Med. 2019;381(19):1809-1819. doi:10.1056/NEJMoa1908639

Deepika Polineni
Deepika Polineni, M.D., MPH
Assistant Professor of Internal Medicine, Division of Pulmonary Critical Care and Sleep Medicine, University of Kansas School of Medicine
Junior Faculty, Kansas Institute for Precision Medicine COBRE

Last modified: Sep 14, 2020