Recent advances in developing therapeutics for cystic fibrosis

Abstract

Despite hope that a cure was imminent when the causative gene was cloned nearly 30 years ago, cystic fibrosis (CF [MIM: 219700]) remains a life-shortening disease affecting more than 70 000 individuals worldwide. However, within the last 6 years the Food and Drug Administration's approval of Ivacaftor, the first drug that corrects the defective cystic fibrosis transmembrane conductance regulator protein [CFTR (MIM: 602421)] in patients with the G551D mutation, marks a watershed in the development of novel therapeutics for this devastating disease. Here we review recent progress in diverse research areas, which all focus on curing CF at the genetic, biochemical or physiological level. In the near future it seems probable that development of mutation-specific therapies will be the focus, since it is unlikely that any one approach will be efficient in correcting the more than 2000 disease-associated variants. We discuss the new drugs and combinations of drugs that either enhance delivery of misfolded CFTR protein to the cell membrane, where it functions as an ion channel, or that activate channel opening. Next we consider approaches to correct the causative genetic lesion at the DNA or RNA level, through repressing stop mutations and nonsense-mediated decay, modulating splice mutations, fixing errors by gene editing or using novel routes to gene replacement. Finally, we explore how modifier genes, loci elsewhere in the genome that modify CF disease severity, may be used to restore a normal phenotype. Progress in all of these areas has been dramatic, generating enthusiasm that CF may soon become a broadly treatable disease.

Figure 1.

Pathophysiology of CF Disease. Process by which mutations in CFTR ultimately lead to reduced lung functional capacity. Therapeutic strategies currently target all phases of this process: Gene therapy and gene editing target the gene defect; RNA and protein therapies and modulating alternative channels aim to improve ion transport; early therapeutic paradigms targeted the downstream consequences of this process with airway clearance techniques, mucolytics, antibiotics and lung transplantation.

Figure 2.

Open chromatin/DNase I hypersensitive sites (DHS) across the CFTR locus in CF-relevant cell types. DNase-seq data from Caco2 (colon carcinoma), Calu3 (lung adenocarcinoma) cell lines and HTE (primary human tracheal epithelial cells) (30,31). DHS are seen at the CFTR promoter and at several cell-type selective sites (23). Airway sites: teal dashed box (−44kb, −35 kb from the CFTR translational start site). Intestinal sites: purple boxes (introns 1, 10, 11). Ubiquitous sites; black boxes (−80.1kb, +15.6 kb, +48.9 kb 3′ to the CFTR last coding base). Each lane shows combined data from two biological replicas of the cell type. Pink arrow denotes a potential location of cDNA insertion in intron 1 of CFTR.

Figure 3.

Cell-type-specific chromatin structure at the CFTR locus. 4C-seq profiles with a CFTR promoter viewpoint. Genomic location of CFTR and adjacent genes (chr 7) (top) and known cis-regulatory elements for the CFTR locus (below). The sites are named as in Figure 2. Open chromatin mapped by DNase-seq and 4C-seq data are shown for Caco2, Calu3 and skin fibroblasts. Representative data from one replica are shown. DNase-seq peaks show our data visualized on the UCSC genome browser. 4C-seq data are presented in alignment with the DNase-seq data and have two parts. The upper panel indicates the main trend of the contact profile using a 5-kb window size. Relative interactions are normalized to the strongest point (which is set to 1) within each panel. The lower panel is a domainogram with color-coded intensity values (see main text) to show relative interactions with window sizes varying from 2 to 50 kb. Arrows denote key data features: turquoise, known intestinal cis-regulatory elements in CFTR; peaks of interaction with CFTR promoter of known (black) cis-elements; orange, airway-selective regulatory elements and their interaction with the CFTR promoter in Calu3.

Figure 4.

Hypothetical graphic of candidate therapeutic targets for CF airway disease. Figure adapted from (32,35,36). CFTR dysfunction in CF leads to decreases in chloride and bicarbonate secretion, which in turn lower ASL height due to impaired anion and fluid secretion (32). The impaired fluid secretion leads to severe mucus plugging and susceptibility to infection (37). Proteins shown in red are CF modifiers identified by Genome-Wide Association Studies (GWAS) (38–41). SLC6A14 stimulation has been shown to impact Pseudomonas aeruginosa infection (42). Stimulation of SLC26A9 and or ANO-1 (anoctamin-1; also known as TMEM16A) may restore chloride secretion into the lumen and thus fluidity. Inhibition of ENaC, either directly or indirectly by targeting proteolytic enzymes may also restore ASL hydration and height by preventing reabsorption of sodium ions. Lastly, ATP12A, a subunit of the nongastric H⁺/K⁺-ATPase, impairs the functioning of innate immune defenses, likely due to an increase in H⁺ secretion, and thus, both ATP12A and SLC9A3 (aka. NHE3) could be inhibited in the apical membrane (and or stimulated in the basolateral membrane for SLC9A3) to prevent secretion of hydrogen ions into the ASL. Inhibition of SLC9A3 at the apical membrane is also beneficial due to reduced sodium reabsorption, which improves ASL fluidity. SLC, solute carrier; CA, carbonic anhydrase; ENaC, epithelial sodium channel; ASL, airway surface liquid; Arg⁺, arginine; NHE3, Na⁺/H⁺ exchanger 3; CFTR, cystic fibrosis transmembrane conductance regulator.

Figure 5.

Genetic association of Peak Expiratory Flow (PEF) and Meconium Ileus (MI) co-localize at the SLC26A9 locus. The lines connect the lowest P-value at 3.2 kb windows across the genomic region from the GWAS of the International CF Gene Modifier Consortium for MI (green line) (40) and lung function (magenta line) (89). Dots in the figure represent the genetic association with PEF in 307 638 unrelated individuals from the UK Biobank resource [analyzed and available in the Global Biobank Engine, Stanford, CA (http://gbe.stanford.edu) accessed January 2018]. The marked SNP (purple diamond shaped) was the top SNP in the MI GWAS (40). These individuals are sampled across the United Kingdom and are aged between 40 and 69 at recruitment (98). PEF is measured in L/min and measures the maximal exhalation rate during an expiratory effort. The MI genetic association at the SLC26A9 locus mirrors the association pattern observed for PEF in the UK population, whereas there is not evidence of genetic association for lung function in patients with CF. The CF MI and lung GWAS P-values may be accessed from http://lab.research.sickkids.ca/strug/publications-software/; date last accessed June 2018.