Two CFTR mutations within codon 970 differently impact on the chloride channel functionality

Pharmacological rescue of mutant cystic fibrosis transmembrane conductance regulator (CFTR) in cystic fibrosis (CF) depends on the specific defect caused by different mutation classes. We asked whether a patient with the rare p.Gly970Asp (c.2909G>A) mutation could benefit from CFTR pharmacotherapy since a similar missense mutant p.Gly970Arg (c.2908G>C) was previously found to be sensitive to potentiators in vitro but not in vivo. By complementary DNA transfection, we found that both mutations are associated with defective CFTR function amenable to pharmacological treatment. However, analysis of messenger RNA (mRNA) from patient's cells revealed that c.2908G>C impairs RNA splicing whereas c.2909G>A does not perturb splicing and leads to the expected p.Gly970Asp mutation. In agreement with these results, nasal epithelial cells from the p.Gly970Asp patient showed significant improvement of CFTR function upon pharmacological treatment. Our results underline the importance of controlling the effect of CF mutation at the mRNA level to determine if the pharmacotherapy of CFTR basic defect is appropriate.     

Identification of a Novel Mutation (S13F) in the CFTR Gene in a CF Patient of Sardinian Origin

In this paper, we describe a novel CF mutation consisting in a C→T substitution at nucleotide 170 in exon 1 of CFTR gene, converting a serine residue into phenylalanine at position 13 (S13F) of the CFTR protein. This mutation was detected in a single patient of Sardinian descent in compound heterozygosity with T338I, who presented at 9 years of age with hyponatremic dehydration associated with hypochloremia, hypokaliemia and metabolic alkalosis. Sweat chloride values were 120mmol/l. Now the patient is 11 years old and has not shown so far any pancreatic or lung involvement. The serine to phenylalanine substitution is a non-conservative change, replacing a non polar for a polar aminoacid residue and therefore is most likely a disease-causing mutation.     

Cis variants identified in F508del complex alleles modulate CFTR channel rescue by small molecules

Molecules correcting the trafficking (correctors) and gating defects (potentiators) of the cystic fibrosis causing mutation c.1521_1523delCTT (p.Phe508del) begin to be a useful treatment for CF patients bearing p.Phe508del. This mutation has been identified in different genetic contexts, alone or in combination with variants in cis. Until now, 21 exonic variants in cis of p.Phe508del have been identified, albeit at a low frequency. The aim of this study was to evaluate their impact on the efficacy of CFTR‐directed corrector/potentiator therapy (Orkambi). The analysis by minigene showed that two out of 15 cis variants tested increased exon skipping (c.609C > T and c.2770G > A). Four cis variants were studied functionally in the absence of p.Phe508del, one of which was found to be deleterious for protein maturation c.1399C > T (p.Leu467Phe). In the presence of p.Phe508del, this variant was the only to prevent the response to Orkambi treatment. This study showed that some patients carrying p.Phe508del complex alleles are predicted to poorly respond to corrector/potentiator treatments. Our results underline the importance to validate treatment efficacy in the context of complex alleles.     

Carrier frequency of CFTR variants in the non-Caucasian populations by genome aggregation database (gnomAD)-based analysis

The complexity in the molecular diagnosis of Cystic Fibrosis (CF) also depends on the variable prevalence/incidence of the disease associated with the wide CFTR allelic heterogeneity among different populations. In fact, CF incidence in Asian and African countries is underestimated and the few patients reported so far have rare or unique CFTR pathogenic variants. To obtain insights into CF variants profile and frequency, we used the large population sequencing data in the Genome Aggregation Database (gnomAD). We selected 207 CF-causing/varying clinical consequence variants from CFTR2 database and additional 15 variants submitted to the ClinVar database. Only 14 of these variants were found in the East-Asian population, while for South-Asian and African populations we identified 43 and 52 variants, respectively, confirming the peculiarity of the CFTR allelic spectrum with only few population-specific variants. These data could be used to optimize CFTR carrier screening in non-Caucasian subjects, choosing between the full gene sequencing and cost and time-effective targeted panels.     

CFTR与囊性纤维化

囊性纤维化跨膜传导调节因子（CFTR）是一种cAMP激活的ATP门控性氯离子通道,表达于气道,消化道和生殖道上皮细胞的顶部质膜中。囊性纤维化(CF)是白人中最常见的遗传性疾病之一,由CFTR基因突变造成。对CFTR基因的破译使人们进一步了解CF的发病机制,并为该疾病的诊断提供了新的线索。     

Novel CFTR mutations in black cystic fibrosis patients

Cystic fibrosis (CF) is considered as a rare disease in black Africans. In fact, this disease is likely to be underestimated since clinical features consistent with CF diagnosis are often ascribed to environmental factors such as malnutrition. Very little is known about CFTR mutations in affected patients from Central Africa. We report here four novel mutations, i.e., IVS2 + 28 (intron 2), 459T > A (exon 4), EX17a_EX18del (exons 17-18), and IVS22 + IG > A (intron 22), in such patients. An update of CFTR mutations reported in black patients from various ethnies is included. These data might be helpful for genetic counselling regarding CF in black patients.     

Influence of salinity on the localization and expression of the CFTR chloride channel in the ionocytes of Dicentrarchus labrax during ontogeny

The expression and localization of the cystic fibrosis transmembrane conductance regulator (CFTR) were determined in four osmoregulatory tissues during the ontogeny of the sea-bass Dicentrarchus labrax acclimated to fresh water and sea water. At hatch in sea water, immunolocalization showed an apical CFTR in the digestive tract and integumental ionocytes. During the ontogeny, although CFTR was consistently detected in the digestive tract, it shifted from the integument to the gills. In fresh water, CFTR was not present in the integument and the gills, suggesting the absence of chloride secretion. In the kidney, the CFTR expression was brief from D4 to D35, prior to the larva–juvenile transition. CFTR was apical in the renal tubules, suggesting a chloride secretion at both salinities, and it was basolateral only in sea water in the collecting ducts, suggesting chloride absorption. In the posterior intestine, CFTR was located differently from D4 depending on salinity. In sea water, the basolateral CFTR may facilitate ionic absorption, perhaps in relation to water uptake. In fresh water, CFTR was apical in the gut, suggesting chloride secretion. Increased osmoregulatory ability was acquired just before metamorphosis, which is followed by the sea-lagoon migration.     

Complete screening of the CFTR gene in Argentine cystic fibrosis patients

In order to establish the nature and the distribution of mutations causing cystic fibrosis (CF) in 220 unrelated Argentine families, the present authors conducted an extensive molecular analysis of the CF transmembrane regulator (CFTR) gene. First, a direct mutation analysis of 13 common mutations was done, enabling the detection of 319 out of 440 CF alleles (72.52%). Then an exhaustive screening of the entire coding region and the adjacent sequences of the CFTR gene was performed in all patients carrying at least one unidentified CF allele using the multiplex heteroduplex analysis assay followed by direct DNA sequencing. Thirty-nine different CF mutations, including five previously undescribed mutations (i.e. L6V, Y362X, 1353insT, 2594delGT and 2686insT) and two novel polymorphisms (i.e. 1170G/C and 3315A/C) were identified. As a result, the overall detection rate increased by up to 83.45%. Besides DeltaF508, only five mutations showed frequencies higher than 1%. In addition, a total of 49% of the mutations were rare because they were found in only one CF family. This wide spectrum of CF mutations is in agreement with the heterogeneous ethnic origin of the Argentine population. The data obtained here may have important consequences for the development of adequate strategies for the molecular diagnosis of CF in Argentina.     

A novel CFTR frame-shift mutation, 935delA, in two Hispanic cystic fibrosis patients

The currently available mutation analysis panel detects about 50-60% of CFTR mutations in Hispanic patients. In order to search for Hispanic CF mutations, we developed a temporal temperature gradient gel electrophoresis (TTGE) method to screen for unknown mutations. Using TTGE to study the CFTR gene has lead to the discovery of many novel mutations in Hispanic patients. A novel frame-shift mutation, 935delA, was found in two unrelated patients. One was heterozygous for two novel frame-shift mutations, 663delT and 935delA, and the other was heterozygous for DeltaF508 and 935delA. Both patients showed severe phenotype with meconium ileus, pancreatic insufficiency, and early pulmonary microbial colonization with Pseudomonas aeruginosa. Patient 1 died at 4 years of age. Patient 2 had an upper lobectomy. The 935delA mutation produces a truncated polypeptide with only 21% of the full-length protein. The severe course of clinical manifestation is consistent with two oppressively truncated mutant polypeptides encoded by both mutant alleles in patient 1 and the compound heterozygosity truncation and DeltaF508 mutations in patient 2.     

Cystic fibrosis: a worldwide analysis of CFTR mutations--correlation with incidence data and application to screening

Although there have been numerous reports from around the world of mutations in the gene of chromosome 7 known as CFTR (cystic fibrosis transmembrane conductance regulator), little attention has been given to integrating these mutant alleles into a global understanding of the population molecular genetics associated with cystic fibrosis (CF). We determined the distribution of CFTR mutations in as many regions throughout the world as possible in an effort designed to: 1) increase our understanding of ancestry-genotype relationships, 2) compare mutational arrays with disease incidence, and 3) gain insight for decisions regarding screening program enhancement through CFTR multi-mutational analyses. Information on all mutations that have been published since the identification and cloning of the CFTR gene's most common allele, DeltaF508 (or F508del), was reviewed and integrated into a centralized database. The data were then sorted and regional CFTR arrays were determined using mutations that appeared in a given region with a frequency of 0.5% or greater. Final analyses were based on 72,431 CF chromosomes, using data compiled from over 100 original papers, and over 80 regions from around the world, including all nations where CF has been studied using analytical molecular genetics. Initial results confirmed wide mutational heterogeneity throughout the world; however, characterization of the most common mutations across most populations was possible. We also examined CF incidence, DeltaF508 frequency, and regional mutational heterogeneity in a subset of populations. Data for these analyses were filtered for reliability and methodological strength before being incorporated into the final analysis. Statistical assessment of these variables revealed that there is a significant positive correlation between DeltaF508 frequency and the CF incidence levels of regional populations. Regional analyses were also performed to search for trends in the distribution of CFTR mutations across migrant and related populations; this led to clarification of ancestry-genotype patterns that can be used to design CFTR multi-mutation panels for CF screening programs. From comprehensive assessment of these data, we offer recommendations that multiple CFTR alleles should eventually be included to increase the sensitivity of newborn screening programs employing two-tier testing with trypsinogen and DNA analysis.     

Spectrum of CFTR mutations in Argentine cystic fibrosis patients

The identification of different mutations which cause cystic fibrosis (CF) in Argentine patients has been performed. Initially, 10 of the most commonly mutated loci in 228 independent chromosomes were analyzed. Each allele was detected by PCR amplification of DNA samples either directly on polyacrylamide gels, by restriction enzyme digestion and agarose gels electrophoresis, or by hybridization with allele specific oligonucleotides. The AF508 mutation was found in 57% of the alleles. The frequencies of the other CF mutations were as follows: G542X 3.9%, W1282X 3.1%, N1303K 1.7%, 1717 1-G→A 0.9%, R553X 0.4%, R1162X 0.4%, whereas G551D, AI507 and S549N were not found. This direct mutation analysis enabled the detection of 155/228 CF alleles (67%). Of the remaining 73 unidentified CF alleles, 22 were investigated for the 27 exons by DGGE and 9 rare mutations were identified. The incidence of the main CF mutations analyzed was similar to that of the South European population and markedly different from other Latin American countries. The mutation data presented here may be useful for designing DNA testing strategies for CF in Argentina.     

CFTR‐France,a national relational patient database for sharing genetic and phenotypic data associated with rare CFTR variants

Most of the 2,000 variants identified in the CFTR (cystic fibrosis transmembrane regulator) gene are rare or private. Their interpretation is hampered by the lack of available data and resources, making patient care and genetic counseling challenging. We developed a patient‐based database dedicated to the annotations of rare CFTR variants in the context of their cis‐ and trans‐allelic combinations. Based on almost 30 years of experience of CFTR testing, CFTR‐France ( https://cftr.iurc.montp.inserm.fr/cftr ) currently compiles 16,819 variant records from 4,615 individuals with cystic fibrosis (CF) or CFTR‐RD (related disorders), fetuses with ultrasound bowel anomalies, newborns awaiting clinical diagnosis, and asymptomatic compound heterozygotes. For each of the 736 different variants reported in the database, patient characteristics and genetic information (other variations in cis or in trans) have been thoroughly checked by a dedicated curator. Combining updated clinical, epidemiological, in silico, or in vitro functional data helps to the interpretation of unclassified and the reassessment of misclassified variants. This comprehensive CFTR database is now an invaluable tool for diagnostic laboratories gathering information on rare variants, especially in the context of genetic counseling, prenatal and preimplantation genetic diagnosis. CFTR‐France is thus highly complementary to the international database CFTR2 focused so far on the most common CF‐causing alleles.     

Geographic distribution and regional origin of 272 cystic fibrosis mutations in European populations

The geographic distribution of 272 cystic fibrosis (CF) mutations has been studied by assessing the origin of 27,177 CF chromosomes from 29 European countries and three countries from the North of Africa. The 5 most common mutations are ΔF308 (66.8%), G542X (2.6%), N1303K (1.6%), G551D (1.5%) and W1282X (1.0%). The ΔF508 mutation has the highest relative frequency in Denmark (87.2%) and the lowest in Algeria (26.3%). Mutation G542X is common in the Mediterranean countries, with a mean frequency of 6.1%. N1303K is found in most of the western and Mediterranean countries and has the highest frequency in Tunisia (17.2%). The wide distribution of these mutations suggests an ancient origin. G551D is common in north-west and central Europe, but is uncommon in other parts of Europe. W1282X has the highest frequency in Israel (36.2%), being also common in most Mediterranean countries and north Africa. Seventeen mutations have frequencies between 0.1 and 0.9%, 1717-1G→A (0.83%), R553X (0.75%), R1162X (0.51%), 621+1G→T (0.54%) and 2183AA→G (0.36%), being the most common ones. Some mutations reach relatively high frequencies in some extended geographic regions, such as mutation 394delTT in northern Europe (1.1-28.8%), R117H in northwestern Europe (1.3-3.0%), R553X in central Europe (1.1-24.4%), 1717-1G→A in Belgium and France (1.1-5.3%), and 2183AA→G in Italy and Greece (3.2%). Other mutations are only common in small regions: T338I (Sardinia), 711+1G→T (Tunisia), R1162X (Algeria and north of Italy), 1609delCA (east of Spain), 1811+1.6kbA→G (southeastern Spain), R1066C (Portugal), S549R (Algeria), R334W (Crete), 621+1G→T (Central Greece), 3849+10kbC→T (Israel), 2789+5G→A (south of Greece), 451+1G→A (Israel), R347P (south of Bulgaria), 1677delTA (south of Bulgaria and Turkey), G85E (south of Greece), R347H (Turkey), 3905insT (Switzerland), 1078delT (Brittany), 1898+1G→A (Wales), A455E (The Netherlands), ΔI507 (Brittany), 3659delC (Sweden) and R560T (northern Ireland). Most of these mutations must have an origin and diffusion in the specific European population subgroup. Overall 55 mutations are common in one or several countries or regions of Europe and 217 mutations are rare with relative frequencies of lower than 1% in any of these regions and countries. This information might facilitate mutation analysis of CF in the different regions of Europe. Hum Mutat 10:135–154, 1997. © 1997 Wiley-Liss, Inc.     

Detection of 100% of the CFTR mutations in 63 CF families from Tyrol

We identified 100% of the CFTR gene mutations, including three novel mutations, in 126 unrelated cystic fibrosis chromosomes from Tyrol, Austria. The frequency of the major mutation ΔF508 (74.6%) was not significantly different in Tyrolian CF-patients than in patients from Bavaria (71.0%) and Middle-and Northern Germany (71.9%), but was significantly higher than in patients from Styria (58.1%) or Northern Italy (47.6%). Interestingly, the distribution of the next most frequent mutations, R1162X (8.7%) 2183AA→G, 2789 +5G→A and G542X (2.4% each), was more similar to the distribution of these mutations among CF-patients from Northern Italy than to those from Styria, Bavaria or Middle-and Northern Germany. Nine further mutations occurred once or twice. One of these, the missense mutation M1101K, is rare worldwide but very frequent in the Hutterite brethren, a small founder population which came from Southern Austria to Northern America. Three other different mutations (ΔL453, 1874insT and 4108delT) were present in single Tyrolian families and have not been described before. The identification of 100% of CFTR gene mutations in a particular CF population demonstrates the power of genetic analysis for the diagnosis and counselling of CF families in this restricted geographical area of Austria. Our study provides evidence for a closer genetic relation between CF patients from Tyrol and those from Bavaria or Middle-and Northern Germany as well as Northern Italy, than between CF patients from the two Austrian states Tyrol and Styria.     

Spectrum of Mutations in the CFTR Gene in Cystic Fibrosis Patients of Spanish Ancestry

We analyzed 1,954 Spanish cystic fibrosis (CF) alleles in order to define the molecular spectrum of mutations in the CFTR gene in Spanish CF patients. Commercial panels showed a limited detection power, leading to the identification of only 76% of alleles. Two scanning techniques, denaturing gradient gel electrophoresis (DGGE) and single strand conformation polymorphism/hetroduplex (SSCP/HD), were carried out to detect CFTR sequence changes. In addition, intragenic markers IVS8CA, IVS8-6(T)n and IVS17bTA were also analyzed. Twelve mutations showed frequencies above 1%, p.F508del being the most frequent mutation (51%). We found that eighteen mutations need to be studied to achieve a detection level of 80%. Fifty-one mutations (42%) were observed once. In total, 121 disease-causing mutations were identified, accounting for 96% (1,877 out of 1,954) of CF alleles. Specific geographic distributions for the most common mutations, p.F508del, p.G542X, c.1811 + 1.6kbA > G and c.1609delCA, were confirmed. Furthermore, two other relatively common mutations (p.V232D and c.2789 + 5G > A) showed uneven geographic distributions. This updated information on the spectrum of CF mutations in Spain will be useful for improving genetic testing, as well as to facilitate counselling in people of Spanish ancestry. In addition, this study contributes to defining the molecular spectrum of CF in Europe, and corroborates the high molecular mutation heterogeneity of Mediterranean populations.     

Cystic fibrosis in a southern Brazilian population: characteristics of 90% of the alleles

Cystic fibrosis (CF) is a genetic disease that frequently leads to death in infancy among Europeans and their descendants. The goals of the present study were to analyze the molecular aspects of CFTR gene characterizing mutations, their frequencies, and the haplotypes formed by four CFTR gene intragenic markers, IVS8-6(T)n, IVS8CA, IVS17bTA and IVS17bCA, in a southern Brazilian population of Caucasian origin. DNA samples from 56 non-related CF patients were analyzed using scanning techniques (single strand conformation polymorphism and denaturing gradient gel electrophoresis), restriction fragment length polymorphism and direct DNA sequencing to identify the mutations. Our results revealed a total of 25 different CF mutations representing nearly 90% of CF alleles, two being novel mutations. Microsatellite haplotypes were defined for CF and normal alleles. The mutational spectrum and the associated haplotypes described for the first time in this study should prove relevant for genetic counselling and CF population screening in Brazil. Moreover, our results suggest the presence of a major Mediterranean component in the contemporary Brazilian CF patient pool.     

Analysis of CA/GT microsatellite polymorphism in IVS8 of the cystic fibrosis transmembrane conductance regulator (CFTR) gene: a study of Italian CF families

Forty-six CF Italian patients and their parents were screened for a highly polymorphic microsatellite consisting of a variable number of CA/GT repeats in intron 8 of the CFTR gene. A strong degree of association was found between alleles 2 and 6 and the CF mutation delta F508. Moreover, considering the haplotypes at the closely linked locus D7S23 and the microsatellite's alleles, a strong linkage disequilibrium was again found for delta F508 and also for non-delta F508 CF chromosomes and the eight commonest haplotypes (B2, B6, C7, A6, A7, B7, D2 and D7). These data, compared with those described in the Spanish population, further support the common origin of the delta F508 mutation in Southern European populations.     

CFTR Rearrangements in Spanish Cystic Fibrosis Patients: First New Duplication (35kb) Characterised in the Mediterranean Countries

Developments in quantitative PCR technologies have greatly improved our ability to detect large genome rearrangements. In particular oligonucleotide‐based array comparative genomic hybridisation has become a useful tool for appropriate and rapid detection of breakpoints. In this work, we have analysed 80 samples (42 unknown CF alleles) applying three quantitative technologies (MLPA, qPCR and array‐CGH) to detect recurrent as well as novel large rearrangements in the Spanish CF population. Three deletions and one duplication have been identified in five alleles (12%). Interestingly, we provide the comprehensive characterisation of the first duplication in our CF cohort. The new CFTRdupProm‐3 mutation spans 35.7 kb involving the 5′‐end of the CFTR gene. Additionally, the RNA analysis has revealed a cryptic sequence with a premature termination codon leading to a disrupted protein. This duplication has been identified in five unrelated families from Spain, France and Italy with all patients showing the same associated haplotype, which is further evidence for its likely common Mediterranean origin. Overall, considering this and other previous studies, CFTR rearrangements account for 1.3% of the Spanish CF alleles.     

Identification of positive charges situated at the outer mouth of the CFTR chloride channel pore

We have used site-directed mutagenesis and functional analysis to identify positively charged amino acid residues in the cystic fibrosis transmembrane conductance regulator (CFTR) Cl⁻ channel that interact with extracellular anions. Mutation of two positively charged arginine residues in the first extracellular loop (ECL) of CFTR, R104, and R117, as well as lysine residue K335 in the sixth transmembrane region, leads to inward rectification of the current–voltage relationship and decreased single channel conductance. These effects are dependent on the charge of the substituted side chain and on the Cl⁻ concentration, suggesting that these positive charges normally act to concentrate extracellular Cl⁻ ions near the outer mouth of the pore. Side chain charge-dependent effects are mimicked by manipulating charge in situ by mutating these amino acids to cysteine followed by covalent modification with charged cysteine-reactive reagents, confirming the location of these side chains within the pore outer vestibule. State-independent modification of R104C and R117C suggests that these residues are located at the outermost part of the pore. We suggest that ECL1 contributes to the CFTR pore external vestibule and that positively charged amino acid side chains in this region act to attract Cl⁻ ions into the pore. In contrast, we find no evidence that fixed positive charges in other ECLs contribute to the permeation properties of the pore.