Gene:

CFTR

cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)

Introduction

The cystic fibrosis transmembrane conductance regulator (CFTR, ATP-binding cassette sub-family C, member 7, ABCC7) protein is 1480 amino acids in length. It is encoded by a single large gene with 27 exons spanning around 250kbp on chromosome 7q31.2, which was identified in the search to find the gene underlying cystic fibrosis (CF) disease [Articles:22698459, 1710598, 2772657, 1375392]. The protein structure is made up of two units, each with six transmembrane helices and an intracellular nucleotide-binding domain (NBD) that can interact with adenosine triphosphate (ATP). A regulatory "R" domain connects the two units and contains sites for protein kinase phosphorylation [Article:22698459]. The structure creates a channel in the plasma membrane through which anions can flow, and the gate is thought to be opened and closed by ATP binding and hydrolysis (NBDs) and phosphorylation mechanisms (R domain) which alter the protein's conformation [Articles:22698459, 8910473, 24727426].

CFTR is expressed predominantly in epithelial tissues, but is also found in other cell types such as smooth muscle, cardiac myocytes, macrophages, and erythrocytes [Article:22698459]. CFTR is multi-functional. It is an anion channel that transports chloride (Cl-) and bicarbonate. It is also involved in the regulation of a range of transporters including the epithelial sodium channel (ENaC encoded by SCNN1A, SCNN1B, SCNN1D and SCNN1G) and outwardly rectifying chloride channels (ORCC) [Articles:22698459, 24004658, 7683773, 7515570, 23895508]. In addition, CFTR has been proposed to be a hub for signaling pathways and may regulate a variety of other physiological processes including exocytosis and endocytosis, ATP export, proinflammatory cytokine expression and intracellular pH [Articles:22698459, 23895508]. Defective CFTR therefore results in widespread cellular homeostasis dysfunction [Article:23895508].

CF is an autosomal recessive disease resulting from a defect-causing variant on each CFTR allele. More than 1800 variants in the CFTR gene have been reported (CF mutation database). Despite a large collection of variants, there is a gap in our knowledge regarding which cause CF disease. To address this, the Clinical and Functional Translation of CFTR project was established to collect information regarding the functional consequences and resulting phenotypes associated with CFTR variants [Article:23974870]. Data for 39,696 subjects from 25 CF patient registries or specialty clinics were collected for the CFTR2 database, and an initial set of 159 CFTR variants (those with a frequency of =0.01% in the CFTR2 database) was evaluated for whether they cause CF disease by both clinical phenotype and functional analysis. A variant was defined clinically as causing CF if mean sweat chloride concentration was =60mM for at least three individuals with the variant or >90mM if only 2 individuals with the variant were available; 140 variants met the clinical criteria to be CF-causing. The variants were sorted by their predicted functional effect, and 77 were investigated further using in vitro assays appropriate to the genetic variant (<10% of wild-type CFTR function was considered disease-causing); 133 variants were deemed CF-causing by functional criteria. In total, 127 variants met both the clinical and functional criteria, and were defined as CF-causing. Penetrance analysis in fathers with CF children was carried out on the variants that did not meet both/either criteria and 12 variants were deemed non-CF causing, with the remaining 20 variants indeterminate [Article:23974870].

CF is a disease that predominantly affects the lungs but has a diverse array of phenotypes due to the expression of CFTR in different tissues, its wide-ranging physiological role, and its involvement in many signaling pathways [Articles:22698459, 24004658, 23895508]. Progressive lung disease, pancreatic dysfunction, infertility in males and elevated sweat electrolytes characterize a "classical" CF diagnosis (WHO report, 2004). CF is also associated with a reduced life expectancy (early adulthood) and an increased risk of cancer [Articles:22698459, 23895508]. There is however wide variability in clinical presentation, severity and the rate of disease progression between patients, which can be influenced by the underlying CFTR genotype as well as other genetic modifiers and environmental factors [Articles:22698459, 24004658, 2233932, 24057835, 21602797, 23895508] (WHO report, 2004). The incidence of CF is thought to be around 70,000 cases worldwide (CFF.org), though it may be largely under-diagnosed in parts of Asia, Africa and Latin America (WHO report, 2004)[Article:24736905]. Genetic testing is now a routine part of CF diagnosis in many countries. A recommended panel for genetic screening for determining prenatal and preconception carrier status of CF in the US includes 23 CFTR variants, designed to cover variants with a frequency of at least 0.1% in CF patients that are associated with classical CF disease, for a pan-ethnic US population [Articles:21422883, 15371902, 24014130]. The WHO recommends sequencing of the complete CFTR gene in CF patients from populations where CF is likely under-diagnosed in order to establish panels of population-specific variants known to cause disease (WHO report, 2004).

Pharmacogenetics (PGx)

Traditionally, drugs used in the treatment of CF have focused on ameliorating symptoms, fighting infection, thinning mucus and dampening inflammation, rather than directly targeting the cause: variants in the CFTR gene. Gene therapy techniques aimed at replacing defective CFTR with a functional version of the gene have been extensively researched and remain a hope for curing CF after the discovery of the underlying disease cause. Unfortunately, gene therapy has encountered several barriers that have kept it from becoming a treatment option for CF [Article:24282073], though the results of an ongoing clinical trial are eagerly awaited [Article:24464978]. Drugs that are designed to correct specific defects of the CFTR protein are being developed as novel therapies for CF; these are termed "modulators" of CFTR. Repurposing of drugs for CF treatment due to their mechanism of action as a CFTR modulator is also a potential therapeutic option (see [Article:22698459]). This summary focuses on pharmacogenetics, and thus therapies that directly target defects resulting from variants in the CFTR gene. CFTR variants can be grouped into 6 classes depending on the resulting effect on the protein, and each could potentially be targeted by a treatment strategy aimed at the underlying defect: see Table 1. Modulator molecules also have the benefit of being administered orally, thus potentially targeting multiple organs and cell types affected by a defect in CFTR [Article:24561283]. Included in the spectrum of modulators are “correctors” and “potentiators”. Correctors are molecules that ‘correct’ the misfolding/trafficking of defective CFTR protein to increase expression at the cell surface, whereas potentiators enhance the channel opening of the defective protein within the cell membrane [Article:22723294].

Currently, the most commonly accepted efficacy endpoints for late phase clinical trials in CF include lung function (forced expiratory volume in one second), pulmonary exacerbation rates, growth/body mass index, and patient reported outcomes [Article:22047557]. Additional outcome measures are in development and may serve to accelerate CFTR modulator development in CF, including multiple breath washout (lung clearance index), pulmonary imaging (including CT and mucociliary clearance), cardiopulmonary exercise testing, gastrointenstinal pH, a variety of sputum biomarkers and changes in microbiome [Articles:24461666, 24927234, 25251804, 25171465]. Change in mean sweat chloride concentration is also currently used as a biomarker of CF, however there is controversy regarding sweat chloride as a predictive biomarker for improvement in lung function [Articles:23276841, 24258833, 24660233]. Guidelines recommending particular biomarkers for CF therapy trials have been published [Article:22878883]. Modulators may have different effects in different tissues/cells which should be taken into account when personalizing CF treatment for an individual patient [Article:24561283].

Table 1: CFTR variants and potential treatment strategy ^a

Ivacaftor (VX-770, kalydeco) is a potentiator and is the first FDA-approved therapeutic developed to target a specific CFTR defect. It was originally indicated in CF patients 6 years and older who have at least one G551D variant (rs75527207 genotype AA or GA) [Article:24598717]. The indication section of the FDA-approved ivacaftor drug label was amended in February 2014 to include a further eight CFTR variants (corresponds to a total of ten genetic variants listed in Table 2). All variants show defects in gating in vitro, as measured by decreased open channel probability and chloride transport, compared to wild-type CFTR [Article:22293084]. Evidence for the efficacy of ivacaftor for each variant is also provided in the table. See individual variant VIP summaries on variant pages for more detailed information.

Table 2: CFTR variants included in the indication for ivacaftor ^a

Conclusions

Cystic fibrosis (CF) is a life-shortening autosomal recessive disease, caused by variants in the CFTR gene, with considerable treatment burden and morbidity. Strategies to modify defects in CFTR are being developed in a potential new wave of CF therapies. The first to be approved by the FDA, a potentiator named ivacaftor, targets CFTR protein variants defective in gating and is indicated in patients who carry certain underlying CFTR genetic variants. Correctors and combinations of modulators are currently in clinical trials in patients with the commonly found F508del-CFTR variant. Future hopes are a panel of therapies that can be tailored for a patient's underlying genetic variants for a more effective treatment strategy to minimize symptoms and extend longevity.