Dropping acid to help cystic fibrosis

Deciphering miRNA transcription factor feed-forward loops to identify drug repurposing candidates for cystic fibrosis

BACKGROUND

Cystic fibrosis (CF) is a fatal genetic disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene that primarily affects the lungs and the digestive system, and the current drug treatment is mainly able to alleviate symptoms. To improve disease management for CF, we considered the repurposing of approved drugs and hypothesized that specific microRNA (miRNA) transcription factors (TF) gene networks can be used to generate feed-forward loops (FFLs), thus providing treatment opportunities on the basis of disease specific FFLs.

METHODS

Comprehensive database searches revealed significantly enriched TFs and miRNAs in CF and CFTR gene networks. The target genes were validated using ChIPBase and by employing a consensus approach of diverse algorithms to predict miRNA gene targets. STRING analysis confirmed protein-protein interactions (PPIs) among network partners and motif searches defined composite FFLs. Using information extracted from SM2miR and Pharmaco-miR, an in silico drug repurposing pipeline was established based on the regulation of miRNA/TFs in CF/CFTR networks.

RESULTS

In human airway epithelium, a total of 15 composite FFLs were constructed based on CFTR specific miRNA/TF gene networks. Importantly, nine of them were confirmed in patient samples and CF epithelial cells lines, and STRING PPI analysis provided evidence that the targets interacted with each other. Functional analysis revealed that ubiquitin-mediated proteolysis and protein processing in the endoplasmic reticulum dominate the composite FFLs, whose major functions are folding, sorting, and degradation. Given that the mutated CFTR gene disrupts the function of the chloride channel, the constructed FFLs address mechanistic aspects of the disease and, among 48 repurposing drug candidates, 26 were confirmed with literature reports and/or existing clinical trials relevant to the treatment of CF patients.

CONCLUSION

The construction of FFLs identified promising drug repurposing candidates for CF and the developed strategy may be applied to other diseases as well.

Ceramide is increased in the lower airway epithelium of people with advanced cystic fibrosis lung disease

RATIONALE

Ceramide accumulates in the airway epithelium of mice deficient in cystic fibrosis transmembrane conductance regulator, resulting in susceptibility to Pseudomonas aeruginosa infection and inflammation.

OBJECTIVES

To investigate quantitatively ceramide levels in the lower airway of people with cystic fibrosis compared with pulmonary hypertension, emphysema, and lung donors.

METHODS

Immunohistochemistry was performed on the lower airway epithelium of explanted lungs (eight cystic fibrosis, emphysema, and pulmonary hypertension, respectively) and eight donor lungs using ceramide, neutrophil elastase, and myeloperoxidase antibodies. High-performance liquid chromatography-mass spectrometry was performed on tissue from five lungs with cystic fibrosis and five with pulmonary hypertension.

MEASUREMENTS AND MAIN RESULTS

Staining for ceramide was significantly increased in the lower airway epithelium of people with cystic fibrosis (median, 14.11%) compared with pulmonary hypertension (3.03%; P = 0.0009); unused lung donors (3.44%; P = 0.0009); and emphysema (5.06%; P = 0.01). Ceramide staining was increased in emphysematous lungs compared with pulmonary hypertension (P = 0.0135) and unused donors (P = 0.0009). The number of neutrophil elastase- and myeloperoxidase-positive cells in the airway was positively correlated with the percentage of epithelium staining for ceramide (P = 0.001). Ceramide staining was significantly increased in lungs colonized with Pseudomonas aeruginosa (10.1%) compared with those not colonized (3.14%; P = 0.0106). Significantly raised levels of ceramides C16:0, C18:0, and C20:0 were detected by mass spectrometry in lungs with cystic fibrosis compared with pulmonary hypertension. Differences in C22:0 were not significant.

CONCLUSIONS

Immunoreactive ceramide is increased in the lower airway epithelium of people with advanced cystic fibrosis. Detected by mass-spectrometry ceramide species C16:0, C18:0, and C20:0 but not C22:0 are increased.

Hepatobiliary disease in patients with cystic fibrosis

PURPOSE OF REVIEW

This review explores the recent advances in knowledge regarding hepatobiliary disease in patients with cystic fibrosis.

RECENT FINDINGS

Hepatobiliary abnormalities associated with cystic fibrosis are varied in nature and range from defects attributable to the underlying genetic defect to those related to systemic disease and malnutrition. Novel research into the underlying pathogenesis of cystic fibrosis liver disease and the primary role of cystic fibrosis transmembrane conductance regulator in biliary secretory epithelium is presented. This work has been fostered by the development of new animal models of cystic fibrosis transmembrane conductance regulator dysfunction. Of the wide range of hepatobiliary complications associated with cystic fibrosis the most clinically relevant problem is progression of focal biliary cirrhosis to multilobular cirrhosis with its attendant complications of portal hypertension and potentially end-stage liver disease. However, recent studies suggest that liver transplantation may not improve survival in patients with cystic fibrosis and significant portal hypertension.

SUMMARY

Hepatobiliary disease is a common finding in patients with cystic fibrosis; the pathogenesis is multifactorial in nature. As new therapeutic strategies emerge, life expectancy will continue to increase as will the impact of liver disease on quality of life and survival of patients with cystic fibrosis. This review will discuss novel insights into pathogenesis as well as diagnostic and management options.