Cystic Fibrosis Mutations Research Articles

Ivacaftor in cystic fibrosis with residual function: Lung function results from an N-of-1 study

BackgroundIvacaftor shows benefit in patients with cystic fibrosis (CF) and CFTR mutations associated with residual CF transmembrane conductance regulator (CFTR) function. Here we further assess the effect of ivacaftor in such patients using an N-of-1 study design. MethodsPatients aged ≥12 years with CF with clinical or molecular evidence of residual CFTR function were randomized to 1 of 4 treatment sequences for two 4-week, double-blind crossover cycles (each divided into 2 weeks of ivacaftor treatment and placebo) followed by 8 weeks of open-label ivacaftor treatment. The primary endpoint was absolute change from cycle baseline of percent predicted forced expiratory volume in 1 s (ppFEV1) after 2 weeks of treatment with ivacaftor relative to placebo. ResultsAbsolute change (SD) from study baseline in ppFEV1 favored ivacaftor by 2.3 (1.0) percentage points (95% credible interval, 0.4–4.1) after 2 weeks of treatment. Absolute mean change (SD) from open-label baseline (defined as day 1 of the open-label ivacaftor treatment period) in ppFEV1 after 8 weeks of treatment was 4.7 (4.2) percentage points (P<.0001). Safety of ivacaftor was consistent with that observed in prior studies. ConclusionsIvacaftor improved lung function during the double-blind and open-label treatment periods in patients with CF and CFTR mutations associated with residual CFTR function (ClinicalTrials.gov, NCT01685801).

CFTR: New insights into structure and function and implications for modulation by small molecules

Structural biology and functional studies are a powerful combination to elucidate fundamental knowledge about the cystic fibrosis transmembrane conductance regulator (CFTR). Here, we discuss the latest findings, including how clinically-approved drugs restore function to mutant CFTR, leading to better clinical outcomes for people with cystic fibrosis (CF). Despite the prospect of regulatory approval of a CFTR-targeting therapy for most CF mutations, strenuous efforts are still needed to fully comprehend CFTR structure-and-function for the development of better drugs to enable people with CF to live full and active lives.

Biological Characterization of F508delCFTR Protein Processing by the CFTR Corrector ABBV-2222/GLPG2222.

Cystic fibrosis (CF) is the most common monogenic autosomal recessive disease in Caucasians caused by pathogenic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene (CFTR). Significant small molecule therapeutic advances over the past two decades have been made to target the defective CFTR protein and enhance its function. To address the most prevalent defect of the defective CFTR protein (i.e., F508del mutation) in CF, two biomolecular activities are required, namely, correctors to increase the amount of properly folded F508delCFTR levels at the cell surface and potentiators to allow the effective opening, i.e., function of the F508delCFTR channel. Combined, these activities enhance chloride ion transport yielding improved hydration of the lung surface and subsequent restoration of mucociliary clearance. To enhance clinical benefits to CF patients, a complementary triple combination therapy consisting of two corrector molecules, type 1 (C1) and type 2, with additive mechanisms along with a potentiator are being investigated in the clinic for maximum restoration of mutated CFTR function. We report the identification and in vitro biologic characterization of ABBV-2222/GLPG2222 (4-[(2R,4R)-4-({[1-(2,2-difluoro-1,3-benzodioxol-5-yl)cyclopropyl]carbonyl}amino)-7-(difluoromethoxy)-3,4-dihydro-2H-chromen-2-yl]benzoic acid),-a novel, potent, and orally bioavailable C1 corrector developed by AbbVie-Galapagos and currently in clinical trials-which exhibits substantial improvements over the existing C1 correctors. This includes improvements in potency and drug-drug interaction (DDI) compared with 3-(6-(1-(2,2-difluorobenzo[d][1,3]dioxol-5-yl)cyclopropanecarboxamido)-3-methylpyridin-2-yl)benzoic acid (VX-809, Lumacaftor) and improvements in potency and efficacy compared with 1-(2,2-difluoro-1,3-benzodioxol-5-yl)-N-[1-[(2R)-2,3-dihydroxypropyl]-6-fluoro-2-(1-hydroxy-2-methylpropan-2-yl)indol-5-yl]cyclopropane-1-carboxamide (VX-661, Tezacaftor). ABBV-2222/GLPG2222 exhibits potent in vitro functional activity in primary patient cells harboring F508del/F508del CFTR with an EC50 value <10 nM. SIGNIFICANCE STATEMENT: To address the most prevalent defect of the defective CFTR protein (i.e., F508del mutation) in cystic fibrosis, AbbVie-Galapagos has developed ABBV-2222/GLPG2222, a novel, potent, and orally bioavailable C1 corrector of this protein. ABBV-2222/GLPG2222, which is currently in clinical trials, exhibits potent in vitro functional activity in primary patient cells harboring F508del/F508del CFTR and substantial improvements over the existing C1 correctors.

Deciphering the role of protein kinase CK2 in the maturation/stability of F508del-CFTR

F508del-CFTR, the most common mutation in cystic fibrosis (CF) patients, impairs CFTR trafficking to plasma membrane leading to its premature proteasomal degradation. Several post-translational modifications have been identified on CFTR with multiple roles in stability, localization and channel function, and the possibility to control the enzymes responsible of these modifications has been long considered a potential therapeutic strategy. Protein kinase CK2 has been previously suggested as an important player in regulating CFTR functions and it has been proposed as a pharmacological target in a combinatory therapy to treat CF patients. However, the real implication of CK2 in F508del-CFTR proteostasis, and in particular the hypothesis that its inhibition could be important in CF therapies, is still elusive. Here, by using immortalized cell lines, primary human cells, and knockout cell lines deprived of CK2 subunits, we do not disclose any direct correlation between F508del-CFTR proteostasis and CK2 expression/activity. Rather, our data indicate that the CK2α′ catalytic subunit should be preserved rather than inhibited for F508del rescue by the correctors of class-1, such as VX-809, disclosing new important features in CF therapeutic approaches.

Forskolin-induced swelling of intestinal organoids correlates with disease severity in adults with cystic fibrosis and homozygous F508del mutations

BackgroundCFTR function measurements in intestinal organoids may help to better characterise individual disease expression in F508del homozygous people. Our objective was to study correlations between CFTR function as measured with forskolin-induced swelling in rectal organoids with clinical parameters in adult patients with homozygous F508del mutations. MethodsMulticentre observational study. Thirty-four adults underwent rectal biopsy, pulmonary function tests (FEV1 and FVC), chest X-ray and chest CT. Body-mass index (BMI) was assessed at study visit and exacerbation rate was determined during five years prior to study visit. Organoids were cultured and measured after stimulation with 5 µm forskolin for three hours to quantitate CFTR residual function. FindingsFIS was positively correlated with FEV1 (r = 0.36, 95% CI 0.02–0.62, p = 0.04) and BMI (r = 0.42, 95% CI 0.09–0.66, p = 0.015). FIS was negatively correlated with PRAGMA-CF CT score for% of disease (r = −0.37, 95% CI -0.62- -0.03, p = 0.049). We found no significant correlation between FIS and chest radiography score for CF (r = −0.16, 95% CI -0.48–0.20, p = 0.44). We observed a trend between higher FIS and a lower mean number of exacerbations over the last 5 years of observation, but this was not statistically significant (Poisson regression, p = 0.089). InterpretationFIS of intestinal organoids varied between subjects with homozygous F508del and correlated with pulmonary and nutritional parameters. These findings suggest that differences at low CFTR residual function may contribute to clinical heterogeneity in F508del homozygous patients and small changes in CFTR residual function might impact long-term disease expression.

Mutation-specific dual potentiators maximize rescue of CFTR gating mutants

BackgroundThe potentiator ivacaftor (VX-770) has been approved for therapy of 38 cystic fibrosis (CF) mutations (∼10% of the patient population) associated with a gating defect of the CF transmembrane conductance regulator (CFTR). Despite the success of VX-770 treatment of patients carrying at least one allele of the most common gating mutation G551D-CFTR, some lung function decline and P. aeruginosa colonization persist. This study aims at identifying potentiator combinations that can considerably enhance the limited channel activity of a panel of CFTR gating mutants over monotherapy. MethodsThe functional response of 13 CFTR mutants to single potentiators or systematic potentiator combinations was determined in the human bronchial epithelial cell line CFBE41o- and a subset of them was confirmed in primary human nasal epithelia (HNE). ResultsIn six out of thirteen CFTR missense mutants the fractional plasma membrane (PM) activity, a surrogate measure of CFTR channel gating, reached only ∼10–50% of WT channel activity upon VX-770 treatment, indicating incomplete gating correction. Combinatorial potentiator profiling and cluster analysis of mutant responses to 24 diverse investigational potentiators identified several compound pairs that improved the gating activity of R352Q-, S549R-, S549N-, G551D-, and G1244E-CFTR to ∼70–120% of the WT. Similarly, the potentiator combinations were able to confer WT-like function to G551D-CFTR in patient-derived human nasal epithelia. ConclusionThis study suggests that half of CF patients with missense mutations approved for VX-770 administration, could benefit from the development of dual potentiator therapy.

CFTR processing, trafficking and interactions

Mutations associated with cystic fibrosis (CF) have complex effects on the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The most common CF mutation, F508del, disrupts the processing to and stability at the plasma membrane and function as a Cl- channel. CFTR is surrounded by a dynamic network of interacting components, referred to as the CFTR Functional Landscape, that impact its synthesis, folding, stability, trafficking and function. CFTR interacting proteins can be manipulated by functional genomic approaches to rescue the trafficking and functional defects characteristic of CF. Here we review recent efforts to elucidate the impact of genetic variation on the ability of the nascent CFTR polypeptide to interact with the proteostatic environment. We also provide an overview of how specific components of this protein network can be modulated to rescue the trafficking and functional defects associated with the F508del variant of CFTR. The identification of novel proteins playing key roles in the processing of CFTR could pave the way for their use as novel therapeutic targets to provide synergistic correction of mutant CFTR for the greater benefit of individuals with CF.

37 Depot Medroxyprogesterone Acetate in the Management of Recurrent Acute Pancreatitis in Patients With Cystic Fibrosis Gene Mutations

INTRODUCTION: In patients presenting with recurrent acute pancreatitis, cystic fibrosis (CF) gene variants are found at an increased frequency. Pancreatitis also occurs in patients being followed with CF mutations, generally occurring in patients with less severe mutations or in the setting of CF-related sorder (CFRD). There are no established treatment options for CF mutation-related pancreatitis. Some evidence has suggested that lung function fluctuates during the menstrual cycle, and in CF, that estradiol may inhibit chloride secretion. It has been hypothesized that hormonal contraceptives could play a role in modulating the disease process in women with CF. This study examined the impact of depot medroxyprogesterone acetate on the course of recurrent pancreatitis in female patients with established CF gene mutations. METHODS: In this single center retrospective study, medical records of all adult female patients with CF and acute recurrent pancreatitis between 2008–2018 were reviewed. Patients were included if they had experienced at least two episodes of acute pancreatitis, had been started on depot medroxyprogesterone, and had at least one CF gene mutation. Patients were excluded if they had developed pancreatitis from gallstones or heavy alcohol use. Total hospitalizations, episodes of pancreatitis, and average lipase values were examined and compared before and after the initiation of the depot medroxyprogesterone. RESULTS: A total of 13 patients met the study screening criteria and were recommended to start depot medroxyprogesterone. All patients were Caucasian females with a mean age of 45 years. The average time of treatment from which the endpoints were collected was 5.6 months. After the initiation of the depot medroxyprogesterone, there were no episodes of acute pancreatitis and one hospitalization unrelated to pancreatitis. The average lipase values were significantly decreased (261 units/L vs 41 units/L, P = 0.039) after the patients had been started on depot medroxyprogesterone. CONCLUSION: In this cohort, there were no further episodes of recurrent acute pancreatitis following the initiation of depot medroxyprogesterone in female patients with CF mutations. This data will be combined with other institutions shortly to examine the outcomes in a larger retrospective sample. A multicenter prospective study is being developed to study the outcomes being seen clinically and reported here in this sample.

Growth failure and treatment in cystic fibrosis

Poor growth has long been a characteristic feature of cystic fibrosis (CF) and is significantly linked to lung function and overall health status. Improvements in pulmonary and nutrition care for patients with cystic fibrosis (CF) have resulted in better growth outcomes; however, height gains have not paralleled the improvements in weight in children with CF, and patients with more severe CF mutations remain significantly more affected. Many factors affect the growth hormone-IGF-1 axis and the growth plate of the long bones, including the chronic inflammatory state associated with CF. There are also increasing data on the direct effects of CFTR on bone and implications for CFTR modulators in attaining optimal growth. Treatments aimed at improving growth in CF are also reviewed here.

Cystic Fibrosis Mutation Spectrum in North Macedonia: A Step Toward Personalized Therapy.

The most prevalent "rare" disease worldwide, cystic fibrosis (CF), is an autosomal recessive multisystem disease, caused by mutations in the CFTR gene. The knowledge of CFTR mutations present in certain population is important for designing a simple, fast and cost-effective genetic testing approach, also for better management of CF patients, including the administration of novel targeted therapies. Here, we present genetic results of 158 unrelated CF patients from the National CF Registry of the Republic of North Macedonia. Initially, patients were screened for the 11 most common CF mutations. Additional CF mutations and large deletions/duplications in the CFTR gene were analyzed using commercial kits. If the genotype was undetermined, all CFTR exons were analyzed using Sanger DNA sequencing or next generation sequencing (NGS) (since 2014). The most common CF mutation, c.l521_ 1523del (legacy name F508del), was found with an overall incidence of 75.9%. Additionally, 26 other pathogenic variants and three large deletions were identified in the CFTR gene as a genetic cause of CF. Two of these, c.1070 C>T (p.Ala357Val) and c.2779_2788dup CTTGCTATGG (p.Gly930AlafsTer48), were novel. According to the distribution and prevalence of the pathogenic variants detected in our patients, a fast and cost-effective method, based on a single base extension was designed as a first-line CF genetic test with a 90.0% detection rate within our population. Furthermore, the knowledge of CFTR mutation classes in our CF patients represents the first step toward personalized therapy for CF in our country.

Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. The 3272–26A>G and 3849+10kbC>T CFTR mutations alter the correct splicing of the CFTR gene, generating new acceptor and donor splice sites respectively. Here we develop a genome editing approach to permanently correct these genetic defects, using a single crRNA and the Acidaminococcus sp. BV3L6, AsCas12a. This genetic repair strategy is highly precise, showing very strong discrimination between the wild-type and mutant sequence and a complete absence of detectable off-targets. The efficacy of this gene correction strategy is verified in intestinal organoids and airway epithelial cells derived from CF patients carrying the 3272–26A>G or 3849+10kbC>T mutations, showing efficient repair and complete functional recovery of the CFTR channel. These results demonstrate that allele-specific genome editing with AsCas12a can correct aberrant CFTR splicing mutations, paving the way for a permanent splicing correction in genetic diseases.

Diagnostic prénatal et issue néonatale des calcifications intra-abdominales isolées : étude rétrospective sur 10 ans

IntroductionIntra-abdominal calcifications (iAC) detected during fetal ultrasound examinations are characterized by their isolated or associated nature, as well as their location. Our objective was to describe all cases of isolated iAC along with their etiological investigations and neonatal outcome, during a 10-year practice in a referral center. MethodsWe conducted a retrospective descriptive monocentric study on neonates diagnosed with isolated iAC after antenatal expert ultrasound scan and referred to the Multidisciplinary Center for Prenatal Diagnosis at Trousseau Hospital and born between January 1st, 2008 and June 30th, 2018. The exclusion criteria were: retroperitoneal calcifications, iAC associated with other digestive abnormalities or with congenital malformations. ResultsThe 32 isolated iAC cases accounted for 46% of all iAC. Nine cases were excluded for missing neonatal data. Among the 23 remaining isolated iAC cases, we observed 15 intra-hepatic calcifications, 5 peri-hepatic and two peritoneal calcifications. One fetus had both intra- and peri-hepatic calcifications. The majority of iAC remained stable throughout pregnancy. No cases of aneuploidy, fetal infection, or cystic fibrosis were detected. The neonatal outcome was favorable in all cases. ConclusionsIn case of isolated and stable iAC after expert ultrasound scan, after having ruled out infectious diseases of the fetus and looked for the most frequent mutations of cystic fibrosis in the parents, the prognosis is favorable. Fetal karyotyping is recommended when additional structural anomalies are present.

5. NOVEL APPROACH ENABLING THE SIMULTANEOUS DETECTION OF SNV AND CNV FOR PGT-M AND PGT-A USING A SINGLE-TUBE ASSAY

Introduction Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, CFTR. An individual must inherit two defective cystic fibrosis alleles, one from each parent, to have the disease. Worldwide, over 70,000 individuals are affected by this monogenic disease. Preimplantation genetic testing (PGT) aims at selecting healthy embryos by testing for chromosome abnormalities and monogenic diseases. Often a limited number of cells or genetic material from the embryo is available to perform the detection of both aneuploidies and monogenic diseases with accuracy. To overcome this challenge, we developed a novel single tube assay enabling the simultaneous detection of both copy number variations (CNV) across the whole genome and single nucleotide variants (SNV) or small insertion/deletion (indels) located in the CFTR gene target region. Material and Methods The assay was performed using a modified SMARTer® PicoPLEX® Gold Single Cell DNA-Seq kit (Takara Bio USA, R300669). More specifically, the assay included simultaneous whole genome amplification (WGA) and targeted enrichment of selected regions of the CFTR gene. All 23 mutations of CFTR recommended to be tested by the American College of Medical Genetics (ACMG) were covered. As proof of principle, we prepared libraries from either single cells or five cells using model cell lines purchased from the Coriell Institute that contain different known CFTR variants, such as delF508, or aneuploidies of different sizes (2.5MB to 25 MB). In addition, libraries were made from trophectoderm biopsies isolated in the clinic from human blastocysts containing known CFTR mutations. The resulting libraries were sequenced on a MiSEQ to achieve 1M reads per sample (2 × 75 cycles). Results The percentage of sequencing reads allocated to both applications (CNV and SNV detections) was optimized to maximize the performance of the assay. To detect copy number variations, a shallow and even coverage of the genome is sufficient (∼0.025x). However, to detect variants, SNPs or small indels, the targeted regions of interest required a robust and deeper coverage (500x). At a sequencing depth of 1M reads, the coverage of the genome was ensured by 95% of the reads and the targeted regions of CFTR were covered by ∼5% of the reads. When using the five-cell model system, the 2.5 and 25MB chromosomal losses and the characterized heterozygous variants of CFTR were detected virtually 100% of the time (n of 18). When using single cells, we consistently detected the 25MB deletion (n of 18). Also, the expected heterozygous CFTR variants were detected over 80% of the time. Conclusion The sequencing reads allocated to both applications was optimized to maximize the performance of both CNV and SNV detection. Over 20 samples were successfully processed on a single MiSeq run. From 5 sorted cells our new approach provided representative and uniform coverage of the genome, suitable for detection of copy number variations (CNV). From the same assay, mutations contained in the CFTR gene were also accurately reported. Studies with TE biopsies with known CFTR mutations are now in progress and will be reported at the meeting.

Discovering the chloride pathway in the CFTR channel

Cystic fibrosis (CF), a lethal monogenic disease, is caused by pathogenic variants of the CFTR chloride channel. The majority of CF mutations affect protein folding and stability leading overall to diminished apical anion conductance of epithelial cells. The recently published cryo-EM structures of full-length human and zebrafish CFTR provide a good model to gain insight into structure–function relationships of CFTR variants. Although, some of the structures were determined in the phosphorylated and ATP-bound active state, none of the static structures showed an open pathway for chloride permeation. Therefore, we performed molecular dynamics simulations to generate a conformational ensemble of the protein and used channel detecting algorithms to identify conformations with an opened channel. Our simulations indicate a main intracellular entry at TM4/6, a secondary pore at TM10/12, and a bottleneck region involving numerous amino acids from TM1, TM6, and TM12 in accordance with experiments. Since chloride ions entered the pathway in our equilibrium simulations, but did not traverse the bottleneck region, we performed metadynamics simulations, which revealed two possible exits. One of the chloride ions exits includes hydrophobic lipid tails that may explain the lipid-dependency of CFTR function. In summary, our in silico study provides a detailed description of a potential chloride channel pathway based on a recent cryo-EM structure and may help to understand the gating of the CFTR chloride channel, thus contributing to novel strategies to rescue dysfunctional mutants.

Conversion of human and mouse fibroblasts into lung-like epithelial cells

Cell lineage conversion of fibroblasts to specialized cell types through transdifferentiation may provide a fast and alternative cell source for regenerative medicine. Here we show that transient transduction of fibroblasts with the four reprogramming factors (Oct4, Sox2, Klf4, and c-Myc) in addition to the early lung transcription factor Nkx2-1 (also known as Ttf1), followed by directed differentiation of the cells, can convert mouse embryonic and human adult dermal fibroblasts into induced lung-like epithelial cells (iLEC). These iLEC differentiate into multiple lung cell types in air liquid interface cultures, repopulate decellularized rat lung scaffolds, and form lung epithelia composed of Ciliated, Goblet, Basal, and Club cells after transplantation into immune-compromised mice. As proof-of-concept, differentiated human iLEC harboring the Cystic Fibrosis mutation dF508 demonstrated pharmacological rescue of CFTR function using the combination of lumacaftor and ivacaftor. Overall, this is a promising alternative approach for generation of patient-specific lung-like progenitors to study lung function, disease and future regeneration strategies.

P030 Ivacaftor responsiveness of two cystic fibrosis mutations that affect the same residue in the twelfth transmembrane segment of CFTR

P030 Ivacaftor responsiveness of two cystic fibrosis mutations that affect the same residue in the twelfth transmembrane segment of CFTR

P281 Transitory exocrine pancreatic insufficiency in children with cystic fibrosis and class IV-V CFTR mutation

P281 Transitory exocrine pancreatic insufficiency in children with cystic fibrosis and class IV-V CFTR mutation

WS13-6 Adenoviral vector gene therapy results in a wild type CFTR functional pattern in class I mutation cystic fibrosis cells

WS13-6 Adenoviral vector gene therapy results in a wild type CFTR functional pattern in class I mutation cystic fibrosis cells

Identification of a mild cystic fibrosis mutation 2789+5 G to a for the first time in Tunisian population

Identification of a mild cystic fibrosis mutation 2789+5 G to a for the first time in Tunisian population

Differential thermostability and response to cystic fibrosis transmembrane conductance regulator potentiators of human and mouse F508del-CFTR.

Cross-species comparative studies have highlighted differences between human and mouse cystic fibrosis transmembrane conductance regulator (CFTR), the epithelial Cl− channel defective in cystic fibrosis (CF). Here, we compare the impact of the most common CF mutation F508del on the function of human and mouse CFTR heterologously expressed in mammalian cells and their response to CFTR modulators using the iodide efflux and patch-clamp techniques. Once delivered to the plasma membrane, human F508del-CFTR exhibited a severe gating defect characterized by infrequent channel openings and was thermally unstable, deactivating within minutes at 37°C. By contrast, the F508del mutation was without effect on the gating pattern of mouse CFTR, and channel activity demonstrated thermostability at 37°C. Strikingly, at all concentrations tested, the clinically approved CFTR potentiator ivacaftor was without effect on the mouse F508del-CFTR Cl− channel. Moreover, eight CFTR potentiators, including ivacaftor, failed to generate CFTR-mediated iodide efflux from CHO cells expressing mouse F508del-CFTR. However, they all produced CFTR-mediated iodide efflux with human F508del-CFTR-expressing CHO cells, while fifteen CFTR correctors rescued the plasma membrane expression of both human and mouse F508del-CFTR. Interestingly, the CFTR potentiator genistein enhanced CFTR-mediated iodide efflux from CHO cells expressing either human or mouse F508del-CFTR, whereas it only potentiated human F508del-CFTR Cl− channels in cell-free membrane patches, suggesting that its action on mouse F508del-CFTR is indirect. Thus, the F508del mutation has distinct effects on human and mouse CFTR Cl− channels.