Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice

Cystic Fibrosis Diagnostic Challenges over 4 Decades: Historical Perspectives and Lessons Learned

OBJECTIVE

Because cystic fibrosis (CF) can be difficult to diagnose, and because information about the genetic complexities and pathologic basis of the disease has grown so rapidly over the decades, several consensus conferences have been held by the US CF Foundation, and a variety of other efforts to improve diagnostic practices have been organized by the European CF Society. Despite these efforts, the application of diagnostic criteria has been variable and caused confusion.

STUDY DESIGN

To improve diagnosis and achieve standardization in terms and definitions worldwide, the CF Foundation in 2015 convened a committee of 32 experts in the diagnosis of CF from 9 countries. As part of the process, all previous consensus-seeking exercises sponsored by the CF Foundation, along with the important efforts of the European CF Society, were comprehensively and critically reviewed. The goal was to better understand why consensus conferences and their publications have not led to the desired results.

RESULTS

Lessons learned from previous diagnosis consensus processes and products were identified. It was decided that participation in developing a consensus was generally not inclusive enough for global impact. It was also found that many efforts to address sweat test issues were valuable but did not always improve clinical practices as CF diagnostic testing evolved. It also became clear from this review that premature applications of potential diagnostic tests such as nasal potential difference and intestinal current measurement should be avoided until validation and standardization occur. Finally, we have learned that due to the significant and growing number of cases that are challenging to diagnose, an associated continuing medical education program is both desirable and necessary.

CONCLUSIONS

It is necessary but not sufficient to organize and publish CF diagnosis consensus processes. Follow-up implementation efforts and monitoring practices seem essential.

Applying Cystic Fibrosis Transmembrane Conductance Regulator Genetics and CFTR2 Data to Facilitate Diagnoses

OBJECTIVE

As a Mendelian disease, genetics plays an integral role in the diagnosis of cystic fibrosis (CF). The identification of 2 disease-causing mutations in the CF transmembrane conductance regulator (CFTR) in an individual with a phenotype provides evidence that the disease is CF. However, not all variations in CFTR always result in CF. Therefore, for CFTR genotype to provide the same level of evidence of CFTR dysfunction as shown by direct tests such as sweat chloride or nasal potential difference, the mutations identified must be known to always result in CF. The use of CFTR genetics in CF diagnosis, therefore, relies heavily on mutation interpretation.

STUDY DESIGN

Progress that has been made on mutation interpretation and annotation was reviewed at the recent CF Foundation Diagnosis Consensus Conference. A modified Delphi method was used to identify consensus statements on the use of genetic analysis in CF diagnosis.

RESULTS

The largest recent advance in CF genetics has come through the Clinical and Functional Translation of CFTR (CFTR2) project. This undertaking seeks to characterize CFTR mutations from patients with CF around the world. The project also established guidelines for the clinical, functional, and population/penetrance criteria that can be used to interpret mutations not yet included in CFTR2's review.

CONCLUSIONS

The use of CFTR genetics to aid in diagnosis of CF requires that the mutations identified have a known disease liability. The demonstration of 2 in trans mutations known to always result in CF is satisfactory evidence of CFTR dysfunction. However, if the identified mutations are known to be associated with variable outcomes, or have unknown consequence, that genotype may not result in a CF phenotype. In these cases, other tests of CFTR function may help.

Achromobacter xylosoxidans infection in cystic fibrosis siblings with different outcomes: Case reports

Introduction

The clinical relevance of Achromobacter xylosoxidans infection in cystic fibrosis (CF) remains controversial. This emerging agent in CF has been associated with increased lung inflammation, more frequent exacerbations and more severe lung disease. We describe a pair of CF siblings chronically colonized by the same multilocus genotype of A. xylosoxidans with different clinical courses, and assess whether this species may have developed any virulence traits and antimicrobial resistance that could have contributed to their singular outcomes.

Case presentation

Two siblings were positive for the F508del and Y1092X mutations, and were chronically colonized by Pseudomonas aeruginosa and Staphylococcus aureus. The female patient had a more severe CF phenotype and faster clinical deterioration than her brother. Her pulmonary function and computed tomography scan lesions were worse than those of her brother, and both parameters progressively declined. She died at 14 years of age, when he was 18. All isolates of A. xylosoxidans were biofilm producers. Achromobacter xylosoxidans showed less swarming motility in the female patient.

Conclusions

Biofilm production and diminution of motility allow persistence. Only swarming motility differed between the isolates recovered from the two siblings, but this finding is not sufficient to explain the different clinical outcomes despite their similar genotypes. Modifier genes, unknown environmental factors and female gender can partially explain differences between these siblings. We were unable to correlate any microbiological findings with their clinical courses, and more translational studies are necessary to decrease the gap of knowledge between laboratory and clinical data to promote better clinical interventions.

Thirty Years of Sweat Chloride Testing at One Referral Center

OBJECTIVE

To conduct a descriptive analysis of the sweat test (ST), associating ST results with epidemiological data, CFTR (cystic fibrosis transmembrane conductance regulator) mutations and reasons to indicate the ST, as well as correlating sweat sodium and sweat chloride concentrations in subjects.

METHODS

Retrospective survey and descriptive analysis of 5,721 ST at a university referral center.

RESULTS

The inclusion of the subjects was based on clinical data related with cystic fibrosis (CF) phenotype. The samples were grouped by (i) sweat chloride concentrations (mEq/L): <30: 3,249/5,277 (61.6%); ≥30 to <60: 1,326/5,277 (25.1%); ≥60: 702/5,277 (13.3%) and (ii) age: (Group A--GA) 0 to <6 months; (Group B--GB) ≥6 months to <18 years; (Group C--GC) ≥18 years. Digestive symptoms showed higher prevalence ratio for the CF diagnosis as well as association between younger age and higher values of sweat chloride, sweat sodium, and chloride/sodium ratio. The indication of ST due to respiratory symptoms was higher in GB and associated with greater age, lower values of sweat chloride, sweat sodium, and chloride/sodium ratio. There was higher prevalence of ST with sweat chloride levels <30 mEq/L in GB, ≥60 mEq/L in GC, and with borderline level in GB. There was positive correlation between sweat sodium and sweat chloride. Sweat chloride/sweat sodium and sweat sodium-sweat chloride indexes showed association with sex, reason for ST indication, and CFTR mutations. Sex alters some values presented in the ST. The number of ST/year performed before and after the newborn screening implementation was the same; however, we observed a higher number of borderlines values. A wide spectrum of CFTR mutation was found. Severe CFTR mutations and F508del/F508del genotype were associated with highest probability of ST chloride levels ≥60 mEq/L, and the absence of CFTR mutations identified was associated with borderline ST and respiratory symptoms.

CONCLUSIONS

ST data showed wide variability dependent on age, sex, reason for examination indication, CFTR mutations, and weight of the collected sweat sample. Sweat sodium concentration is directly correlated with sweat chloride levels and it could be used as a quality parameter.

Cystic Fibrosis is Associated with Adverse Neonatal Outcomes in Washington State, 1996-2013

OBJECTIVE

To determine whether cystic fibrosis (CF) is associated with adverse neonatal outcomes in a recent birth cohort in the US.

STUDY DESIGN

A retrospective matched cohort study of infants born in Washington State from 1996 to 2013 was identified through birth certificate data and linked to statewide hospital discharge data. Infants with CF were identified by hospitalization (through age 5 years) in which a CF-specific International Classification of Diseases, Ninth Revision code was recorded. "Unexposed" infants lacked CF-related International Classification of Diseases, Ninth Revision codes and were randomly selected among births, frequency-matched to "exposed" infants on birth year. Associations of CF with adverse neonatal outcomes (low birth weight [LBW], small for gestational age [SGA], preterm birth, and infant mortality) were estimated through Poisson regression. We performed extreme value imputation to address possible ascertainment bias.

RESULTS

We identified 170 infants with CF and 3400 unexposed infants. CF was associated with increased relative risk (95% CI) of 3.5 (2.5-4.9), 1.6 (1.1-2.4), 3.0 (2.2-4.0), and 6.8 (1.7-26.5) for LBW, SGA, preterm birth, and infant death, respectively. The estimated relative risks were similar among infants born from 2006 to 2013, except SGA was no longer associated with CF diagnosis. Results were robust to extreme value imputation and exclusion of infants with meconium ileus.

CONCLUSIONS

Observed associations of CF with LBW, preterm birth, and infant death are unlikely to be due to ascertainment bias. Further work is needed to determine how to prevent these adverse neonatal outcomes.

Survival of Patients with Cystic Fibrosis Depending on Mutation Type and Nutritional Status

The purpose of the study was to evaluate the influence of nutrition and of the severity of mutation type on survival rate in cystic fibrosis (CF) patients. Data were longitudinally collected from 60 hospitalized adult CF patients, aged 18-50. The variables consisted of body mass index (BMI) ratio, Cole's BMI cut-off points, severity of mutation type, and survival rate of CF patients. We found that the mean BMI was strongly associated with the severity of mutation type and was significantly lower in patients with severe mutations of grade I and II. The mutation type significantly affected the patients' survival rate; survival was greater in patients with mild and undefined mutation types. The BMI and Cole's cut-off points also had a significant influence on survival rate. CF patients, who suffered from malnutrition and emaciation, had a shorter survival rate than those with proper nutritional status. In conclusion, the study findings confirmed a significant effect of nutritional status and of mutation type on survival rate of CF patients.

New horizons for cystic fibrosis treatment

Cystic fibrosis is an inherited multi-system disease associated with chronic lung infection, malabsorption, salt loss syndromes, male infertility and leading to numerous comorbidities. The landscape in cystic fibrosis care has changed markedly with currently more adult patients than children in many countries. Over 2000 different mutations in the CFTR gene have been reported and the majority are extremely rare. Understanding how CFTR mutations translate to disturbed synthesis or function of the CFTR protein has opened the way to 'personalized' treatments to correct the basic defect. The first 2 drugs have reached the clinic: a CFTR potentiator to augment CFTR channel function, and the combination of this potentiator with a corrector to increase CFTR expression at the cell membrane. To obtain robust correction of CFTR expression at the cell membrane, combinations of correctors with additive efficacy are under investigation. Other mutation type-specific treatments under clinical investigation are premature stop codon-read through drugs and antisense oligonucleotides that correct the basic defect at the mRNA level. Restoring the defective gene by gene editing can already be achieved ex vivo. Mutation agnostic treatments are explored as well: stabilizing CFTR expression at the cell membrane, circumventing the CFTR channel by blocking or activating other ion channels, and gene therapy. Combinations of these therapies can be anticipated. The pipeline of corrective strategies under clinical investigation is increasing continuously and a rising number of pharmaceutical companies are entering the field.

Assessment of serology and spirometry and the combination of both to complement microbiological isolation for earlier detection of Pseudomonas aeruginosa infection in children with cystic fibrosis

Background

The aim of this study was to assess whether serology and spirometry and the combination of both can complement culture-based detection for earlier recognition of Pseudomonas aeruginosa infection in children with cystic fibrosis.

Methods

A 4 year longitudinal prospective study that included 67 Slovenian children with cystic fibrosis with a mean age of 10.5 years was conducted. Serology, spirometry and a scoring system combining serology and spirometry were assessed and compared. Infection was confirmed with isolation of Pseudomonas aeruginosa from respiratory samples.

Results

There was a significantly positive correlation between serology and the combination of serology and spirometry and Pseudomonas aeruginosa isolation (P < 0.01 for both) and a significantly negative correlation between spirometry and Pseudomonas aeruginosa isolation (P < 0.05). An increase in serology for 1 ELISA unit increased the possibility of Pseudomonas aeruginosa isolation 1.6 times. A fall in FEV1% predicted for 10% increased the possibility of Pseudomonas aeruginosa isolation 9.8 times. Binary logistic regression analysis was used to determine the odds ratios and 95% confidence intervals for all three approaches. Serology had the highest specificity (0.80) and the combination of serology and spirometry the highest sensitivity (0.90). Both had a high negative predictive value (0.93 and 0.79 respectively).

Conclusion

Using serology and the combination of serology and lung function measurement can be beneficial for earlier detection of infection with Pseudomonas aeruginosa in children with cystic fibrosis when done simultaneously with standard culture-based detection from respiratory samples.

Can Cystic Fibrosis Patients Finally Catch a Breath With Lumacaftor/Ivacaftor?

Cystic fibrosis (CF) is a life-limiting disease caused by defective or deficient cystic fibrosis transmembrane conductance regulator (CFTR) activity. The recent US Food and Drug Administration (FDA) approval of lumacaftor combined with ivacaftor (Orkambi) targets patients with the F508del-CFTR. The question remains: Is this breakthrough combination therapy the "magic-bullet" cure for the vast majority of patients with CF? This review covers the contemporary clinical and scientific knowledge-base for lumacaftor/ivacaftor and highlights the emerging issues from recent conflicting literature reports.

Cystic fibrosis

Cystic fibrosis is a common life-limiting autosomal recessive genetic disorder, with highest prevalence in Europe, North America, and Australia. The disease is caused by mutation of a gene that encodes a chloride-conducting transmembrane channel called the cystic fibrosis transmembrane conductance regulator (CFTR), which regulates anion transport and mucociliary clearance in the airways. Functional failure of CFTR results in mucus retention and chronic infection and subsequently in local airway inflammation that is harmful to the lungs. CFTR dysfunction mainly affects epithelial cells, although there is evidence of a role in immune cells. Cystic fibrosis affects several body systems, and morbidity and mortality is mostly caused by bronchiectasis, small airways obstruction, and progressive respiratory impairment. Important comorbidities caused by epithelial cell dysfunction occur in the pancreas (malabsorption), liver (biliary cirrhosis), sweat glands (heat shock), and vas deferens (infertility). The development and delivery of drugs that improve the clearance of mucus from the lungs and treat the consequent infection, in combination with correction of pancreatic insufficiency and undernutrition by multidisciplinary teams, have resulted in remarkable improvements in quality of life and clinical outcomes in patients with cystic fibrosis, with median life expectancy now older than 40 years. Innovative and transformational therapies that target the basic defect in cystic fibrosis have recently been developed and are effective in improving lung function and reducing pulmonary exacerbations. Further small molecule and gene-based therapies are being developed to restore CFTR function; these therapies promise to be disease modifying and to improve the lives of people with cystic fibrosis.

CFTR founder mutation causes protein trafficking defects in Chinese patients with cystic fibrosis

Background

Cystic fibrosis (CF) is a rare condition in Asians. Since 1985, only about 30 Chinese patients have been reported with molecular confirmation.

Method

Using our in‐house next‐generation sequencing (NGS) pipeline for childhood bronchiectasis, we identified disease‐causing CFTR mutations in CF patients in Hong Kong. After identifying p.I1023R in multiple patients, haplotype analysis was performed with genome‐wide microarray to ascertain the likelihood of this being a founder mutation. We also assessed the processing and gating activity of the mutant protein by Western hybridization and patch‐clamp test.

Results

Molecular diagnoses were confirmed in four patients, three of whom shared a missense mutation: CFTR:c.3068T>G:p.I1023R. The results suggested that p.I1023R is a founder mutation in southern Han Chinese. In addition, the processing and gating activity of the mutant protein was assessed by gel electrophoresis and a patch‐clamp test. The mutant protein exhibited trafficking defects, suggesting that the dysfunction is caused by reduced cell surface expression of the fully glycosylated proteins.

Conclusion

Together with other previously reported mutations, the specific founder mutation presented herein suggests a unique CFTR mutation spectrum in the southern Chinese populations, and this finding has vital implications for improving molecular testing and mutation‐specific treatments for Chinese patients with CF.

Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota

Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10–22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H₂-consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes.

Comparison of Nasal Potential Difference and Intestinal Current Measurements as Surrogate Markers for CFTR Function

OBJECTIVES

Nasal potential difference (NPD) measurement is part of the diagnostic criteria for cystic fibrosis (CF) and now used routinely as an endpoint in clinical trials of correcting the basic defect in CF. Intestinal current measurement (ICM), measured ex vivo on a rectal biopsy, has been used to study cystic fibrosis transmembrane conductance regulator (CFTR) function but has not been compared to NPD in the same subject in adults and children. The aim of the study is to evaluate the potential usefulness of ICM as a marker of CFTR function for treatment studies compared NPD in patients with CF and in healthy control subjects.

METHODS

ICM and NPD were performed on healthy controls and patients with CF. The healthy adults were individuals undergoing routine screening colonoscopy at the Beth Israel Deaconess Medical Center. The healthy children were undergoing colonoscopy for suspicion of inflammation in Hadassah Hebrew University Medical Center. The CF adults were recruited from Boston Children's Hospital CF Center and CF Center Worcester Mass, the children with CF from Hadassah CF Center.

RESULTS

ICM measurements in healthy control subjects (n = 16) demonstrated a mean (±SE) carbachol response of 16.0 (2.2) μA/cm, histamine response of 13.2 (2.1) μA/cm and a forskolin response of 6.3 (2.0) μA/cm. Basal NPD of -15.9 (1.9) and response to Cl free + isoproterenol of -13.8 (2.0). These responses were inverted in CF subjects (n = 12) for ICM parameters with carbachol response of -3.0 (0.5) μA/cm, histamine -1.0 (0.8) μA/cm and a forskolin response of 0.5 (0.3) and also for NPD parameters; basal NPD of -42.2 (4.3) and response to Cl free + isoproterenol of 4.3 (0.7). Pearson correlation test showed the comparability of ICM and NPD in assessing CFTR function.

CONCLUSIONS

ICM is equivalent to NPD in the ability to distinguish patients with CF from controls and could be used as surrogate markers of CFTR activity in treatment protocols.

Gender Differences in Clinical Presentations of Cystic Fibrosis Patients in Azeri Turkish Population

BACKGROUND

Cystic fibrosis (CF) is an autosomal recessive disorder with several clinical presentations. This study was undertaken in the Azeri Turkish population in Iran, to investigate gender differences in the age at onset and diagnosis, age of death, and duration of illness of CF.

METHODS

The data of 331 CF patients from 2001 to 2015 was surveyed. Parameters including age, sex, ΔF508 mutation, age at onset, age at diagnosis, age of death and clinical presentations were evaluated for both sexes, using descriptive analysis. The association of gender with these variables was studied using logistic regression, chi-square test and Mann-Whitney U test by SPSS version 18. Odds ratio with a confidence interval of 95% and p≤0.05 was considered statistically significant.

RESULTS

The study included 191 males (57.7%) and 140 females (42.3%), all showing statistically significant difference (p<0.001). Age duration differed between genders. Male and female patients were further under 9 and 4 years, respectively. The occurrence of ΔF508 mutation was 0.51 times more in females than in males. Age, diagnosis and sex were closely associated: males were diagnosed at a significantly later age than females (p=0.05). While this compression performed based on clinical presentations, males with respiratory disease had a later median age at diagnosis than females at lifespan (p=0.001). The risk of infertility in males was approximately two times greater than in females (p=0.02).

CONCLUSION

These findings indicate gender differences in CF patients. Future studies are needed to establish other differences and evaluate the causes for the gender variations.

The role for neutrophil extracellular traps in cystic fibrosis autoimmunity

While respiratory failure in cystic fibrosis (CF) frequently associates with chronic infection by Pseudomonas aeruginosa, no single factor predicts the extent of lung damage in CF. To elucidate other causes, we studied the autoantibody profile in CF and rheumatoid arthritis (RA) patients, given the similar association of airway inflammation and autoimmunity in RA. Even though we observed that bactericidal permeability-increasing protein (BPI), carbamylated proteins, and citrullinated proteins all localized to the neutrophil extracellular traps (NETs), which are implicated in the development of autoimmunity, our study demonstrates striking autoantibody specificity in CF. Particularly, CF patients developed anti-BPI autoantibodies but hardly any anti-citrullinated protein autoantibodies (ACPA). In contrast, ACPA-positive RA patients exhibited no reactivity with BPI. Interestingly, anti-carbamylated protein autoantibodies (ACarPA) were found in both cohorts but did not cross-react with BPI. Contrary to ACPA and ACarPA, anti-BPI autoantibodies recognized the BPI C-terminus in the absence of posttranslational modifications. In fact, we discovered that P. aeruginosa-mediated NET formation results in BPI cleavage by P. aeruginosa elastase, which suggests a novel mechanism in the development of autoimmunity to BPI. In accordance with this model, autoantibodies associated with presence of P. aeruginosa on sputum culture. Finally, our results provide a role for autoimmunity in CF disease severity, as autoantibody levels associate with diminished lung function.

Genotype-phenotype correlation and functional studies in patients with cystic fibrosis bearing CFTR complex alleles

BACKGROUND

The effect of complex alleles in cystic fibrosis (CF) is poorly defined for the lack of functional studies.

OBJECTIVES

To describe the genotype-phenotype correlation and the results of either in vitro and ex vivo studies performed on nasal epithelial cells (NEC) in a cohort of patients with CF carrying cystic fibrosis transmembrane conductance regulator (CFTR) complex alleles.

METHODS

We studied 70 homozygous, compound heterozygous or heterozygous for CFTR mutations: p.[Arg74Trp;Val201Met;Asp1270Asn], n=8; p.[Ile148Thr;Ile1023_Val1024del], n=5; p.[Arg117Leu;Leu997Phe], n=6; c.[1210-34TG[12];1210-12T[5];2930C>T], n=3; p.[Arg74Trp;Asp1270Asn], n=4; p.Asp1270Asn, n=2; p.Ile148Thr, n=6; p.Leu997Phe, n=36. In 39 patients, we analysed the CFTR gating activity on NEC in comparison with patients with CF (n=8) and carriers (n=4). Finally, we analysed in vitro the p.[Arg74Trp;Val201Met;Asp1270Asn] complex allele.

RESULTS

The p.[Ile148Thr;Ile1023_Val1024del] caused severe CF in five compound heterozygous with a class I-II mutation. Their CFTR activity on NEC was comparable with patients with two class I-II mutations (mean 7.3% vs 6.9%). The p.[Arg74Trp;Asp1270Asn] and the p.Asp1270Asn have scarce functional effects, while p.[Arg74Trp;Val201Met;Asp1270Asn] caused mild CF in four of five subjects carrying a class I-II mutation in trans, or CFTR-related disorders (CFTR-RD) in three having in trans a class IV-V mutation. The p.[Arg74Trp;Val201Met;Asp1270Asn] causes significantly (p<0.001) higher CFTR activity compared with compound heterozygous for class I-II mutations. Furthermore, five of six compounds heterozygous with the p.[Arg117Leu;Leu997Phe] had mild CF, whereas the p.Leu997Phe, in trans with a class I-II CFTR mutation, caused CFTR-RD or a healthy status (CFTR activity: 21.3-36.9%). Finally, compounds heterozygous for the c.[1210-34TG[12];1210-12T[5];2930C>T] and a class I-II mutation had mild CF or CFTR-RD (gating activity: 18.5-19.0%).

CONCLUSIONS

The effect of complex alleles partially depends on the mutation in trans. Although larger studies are necessary, the CFTR activity on NEC is a rapid contributory tool to classify patients with CFTR dysfunction.

Novel CFTR Mutations in Two Iranian Families with Severe Cystic Fibrosis

BACKGROUND

Cystic fibrosis (CF) is a common autosomal recessive disorder that affects many body systems and is produced by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CF is also the most frequently inherited disorder in the West. The aim of this study was to detect the mutations in the CFTR gene in two Iranian families with CF.

METHODS

After DNA extraction using the salting out method, a mutation panel consisting of 35 common mutations was tested by PCR, followed by reverse hybridization Strip Assay. To confirm the mutations, we have also performed Sanger sequencing for all 27 exons, intronic flanking regions, and 5' and 3' UTRs of the CFTR gene.

RESULTS

Carrier testing in a spouse revealed a novel nonsense mutation in the CFTR gene (c.2777 T>A (p.L926X)) in exon 17 for husband and a previously described heterozygous splice site pathogenic mutation (c.1393-1G>A) in his wife. The other novel compound heterozygous missense mutation (c.3119 T>A (p.L1040H)), which was previously reported as nonsense c.3484C>T (p.R1162X) mutation, was found in exon 19 in patient screening.

CONCLUSION

Two novel CFTR mutations in exons 17 and 19 are responsible for CF with severe phenotypes in two Iranian families. These two mutations supplement the mutation spectrum of CFTR and may contribute to a better understanding of CFTR protein function.

Pharmacogenetics of cystic fibrosis treatment

Cystic fibrosis (CF) is genetic autosomal recessive disease caused by reduced or absent function of CFTR protein. Treatments for patients with CF have primarily focused on the downstream end-organ consequences of defective CFTR. Since the discovery of the CFTR gene that causes CF in 1989 there have been tremendous advances in our understanding of the genetics and pathophysiology of CF. This has recently led to the development of new CFTR mutation-specific targeted therapies for select patients with CF. This review will discuss the characteristics of the CFTR gene, the CFTR mutations that cause CF and the new mutation specific pharmacological treatments including gene therapy that are contributing to the dawning of a new era in cystic fibrosis care.

β2-Adrenergic receptor agonists activate CFTR in intestinal organoids and subjects with cystic fibrosis

We hypothesized that people with cystic fibrosis (CF) who express CFTR (cystic fibrosis transmembrane conductance regulator) gene mutations associated with residual function may benefit from G-protein coupled receptor (GPCR)-targeting drugs that can activate and enhance CFTR function.We used intestinal organoids to screen a GPCR-modulating compound library and identified β2-adrenergic receptor agonists as the most potent inducers of CFTR function.β2-Agonist-induced organoid swelling correlated with the CFTR genotype, and could be induced in homozygous CFTR-F508del organoids and highly differentiated primary CF airway epithelial cells after rescue of CFTR trafficking by small molecules. The in vivo response to treatment with an oral or inhaled β2-agonist (salbutamol) in CF patients with residual CFTR function was evaluated in a pilot study. 10 subjects with a R117H or A455E mutation were included and showed changes in the nasal potential difference measurement after treatment with oral salbutamol, including a significant improvement of the baseline potential difference of the nasal mucosa (+6.35 mV, p<0.05), suggesting that this treatment might be effective in vivo Furthermore, plasma that was collected after oral salbutamol treatment induced CFTR activation when administered ex vivo to organoids.This proof-of-concept study suggests that organoids can be used to identify drugs that activate CFTR function in vivo and to select route of administration.

Mutation spectrum of Egyptian children with cystic fibrosis

Objective

To know the common CFTR mutations in the Egyptian patients with cystic fibrosis as it was previously thought to be uncommon disease in Egypt.

Methods

This is a cross sectional study of 60 patients diagnosed as cystic fibrosis by sweat chloride testing. They were enrolled from the Allergy and Pulmonology Unit Children’s Hospital Cairo University. They were screened for the presence of the frequent 36 mutations in Caucasians by reverse hybridization line probe technique, using INNO-LiPACFTR19 and CFTR17 + Tn kits.

Results

Most of patients presented with classic manifestations of CF such as variable pulmonary disease and pancreatic insufficiency, and hepatomegaly with or without ascites. The mutations detected were F508 del (58 %), 2183AA/G (10 %), N1303K (6 %), I148T (4 %), W1282X (4 %), G155D (2 %), CFTRdel2-3 (21 KB) (2 %), 3199del6 (2 %), R347P (2 %). Unique to the Egyptian population are these mutations R1162X and A544E (6, 4 %) respectively they were found in our cohort study and were not reported elsewhere in the Arab population till now. There was no association between the initial clinical presentation of CF and the genotypes detected.

Conclusion

The F508 del is still the most commonly encountered mutation (58 %), however other rare mutations were identified where each ranged from (2 to 10 %).

CFTR and/or pancreatitis susceptibility genes mutations as risk factors of pancreatitis in cystic fibrosis patients?

BACKGROUND/OBJECTIVES

Currently, factors that promote the occurrence of pancreatitis episodes in patients affected with cystic fibrosis (CF) and pancreatic sufficiency (PS) are largely unknown.

METHODS

Six genes involved in pancreatitis or in ion transport into the pancreatic duct were investigated by next generation sequencing in 59 adult CF-PS patients with two identified CF mutations. Data on predisposing environmental factors were also recorded.

RESULTS

19 experienced at least one episode of acute pancreatitis (AP) (AP+) and 40 patients did not (AP-). No influence of environmental factor was evidenced. No specific CFTR genotype was found predictive of pancreatitis. Patients sharing the same CFTR genotype may or may not experience AP episodes. Frequent and rare missense variants were found in 78.9% patients in group AP+ and 67.5% in group AP- but a few of them were pathogenic.

CONCLUSIONS

AP or recurrent AP (RAP) is a frequent complication in our series of adult CF-PS patients. The majority of mild CFTR mutations found in group AP+ were located in the first transmembrane region. No clear other genetic factor could be found predictive of AP/RAP. Further experiments in large homogenous cohorts of CF-PS patients, including whole genome sequencing, may identify genetic predisposing factors to pancreatitis.

CT-abnormalities, bacteriology and symptoms of sinonasal disease in children with Cystic Fibrosis

BACKGROUND

Sinonasal pathology in adults with Cystic Fibrosis (CF) is common but the extent of CT-abnormalities and symptoms of sinonasal disease in children with CF and the age of onset are less frequently studied.

METHODS

In this observational, cross-sectional study 58 children with CF from two CF centres were included. All subjects completed a questionnaire regarding sinonasal symptoms, underwent a CT scan of the paranasal sinuses, and in each subject a culture of the upper airways was performed. Subjects were divided in 6 age cohorts (0-2, 3-5, 6-8, 9-11, 12-14 and 15-17years) and were divided into severe and mild CF based on their CFTR mutation. Opacification of the sinonasal system of the subjects was compared with opacification on MRI-scans of an age-matched control group without CF.

RESULTS

Most frequently reported symptoms were nasal obstruction and posterior/anterior nasal discharge. Opacification was abundant in every age cohort of the study group and was significantly more compared to the control group. In patients with severe CF the opacification was higher than subjects with mild CF. Upper airway cultures showed predominantly Staphylococcus aureus, Haemophilus influenzae and Pseudomonas aeruginosa.

CONCLUSION

CT-abnormalities indicating sinonasal disease and symptoms are present from shortly after birth which may argue for a thorough examination of the upper airways in children with CF.

New and emerging targeted therapies for cystic fibrosis

Cystic fibrosis (CF) is a monogenic autosomal recessive disorder that affects about 70,000 people worldwide. The clinical manifestations of the disease are caused by defects in the cystic fibrosis transmembrane conductance regulator (CFTR) protein. The discovery of the CFTR gene in 1989 has led to a sophisticated understanding of how thousands of mutations in the CFTR gene affect the structure and function of the CFTR protein. Much progress has been made over the past decade with the development of orally bioavailable small molecule drugs that target defective CFTR proteins caused by specific mutations. Furthermore, there is considerable optimism about the prospect of gene replacement or editing therapies to correct all mutations in cystic fibrosis. The recent approvals of ivacaftor and lumacaftor represent the genesis of a new era of precision medicine in the treatment of this condition. These drugs are having a positive impact on the lives of people with cystic fibrosis and are potentially disease modifying. This review provides an update on advances in our understanding of the structure and function of the CFTR, with a focus on state of the art targeted drugs that are in development.

Applicability and Efficiency of NGS in Routine Diagnosis: In-Depth Performance Analysis of a Complete Workflow for CFTR Mutation Analysis

BACKGROUND

Actually, about 2000 sequence variations have been documented in the CFTR gene requiring extensive and multi-step genetic testing in the diagnosis of cystic fibrosis and CFTR-related disorders. We present a two phases study, with validation and performance monitoring, of a single experiment methodology based on multiplex PCR and high throughput sequencing that allows detection of all variants, including large rearrangements, affecting the coding regions plus three deep intronic loci.

METHODS

A total of 340 samples, including 257 patients and 83 previously characterized control samples, were sequenced in 17 MiSeq runs and analyzed with two bioinformatic pipelines in routine diagnostic conditions. We obtained 100% coverage for all the target regions in every tested sample.

RESULTS

We correctly identified all the 87 known variants in the control samples and successfully confirmed the 62 variants identified among the patients without observing false positive results. Large rearrangements were identified in 18/18 control samples. Only 17 patient samples showed false positive signals (6.6%), 12 of which showed a borderline result for a single amplicon. We also demonstrated the ability of the assay to detect allele specific dropout of amplicons when a sequence variation occurs at a primer binding site thus limiting the risk for false negative results.

CONCLUSIONS

We described here the first NGS workflow for CFTR routine analysis that demonstrated equivalent diagnostic performances compared to Sanger sequencing and multiplex ligation-dependent probe amplification. This study illustrates the advantages of NGS in term of scalability, workload reduction and cost-effectiveness in combination with an improvement of the overall data quality due to the simultaneous detection of SNVs and large rearrangements.

[Therapeutic advances in cystic fibrosis in 2014]

Twenty-five years after the cystic fibrosis (CF) gene identification, this discovery actually begins to benefit to patients. Increasing our knowledge on CFTR biology, as well as technical progress made in order to screen for new drugs have made therapeutic strategies move an important step forward. It is likely that in the forthcoming years, the panel of molecules available for CF patients will be larger, with new activators and potentiators. The disease by itself may consequently change in its natural history. CF is an example of the so-called personalized medicine, aiming to fit treatment according to patient's genetic background. Ongoing clinical trials may enlarge the actually limited eligible number of CF patients for new drugs such as ivacaftor. Beyond this exciting and promising new therapeutic approach, one may not push symptomatic treatments on the side. Improvements have been made for inhaled antibiotics administration, aiming to simplify patient's life; clinical trials using new molecules able to liquefy mucus or with anti-inflammatory properties are actually underway. One important next step in the care for CF will be to design and conduct early intervention trials in CF infants. Newborn screening program have been widely implanted around the word, and cohorts studies have shown that both functional and structural abnormalities occurred very early, making the therapeutic window of opportunity tight.

Screening for cystic fibrosis in New York State: considerations for algorithm improvements

Newborn screening for cystic fibrosis (CF), a chronic progressive disease affecting mucus viscosity, has been beneficial in both improving life expectancy and the quality of life for individuals with CF. In New York State from 2007 to 2012 screening for CF involved measuring immunoreactive trypsinogen (IRT) levels in dried blood spots from newborns using the IMMUCHEM(™) Blood Spot Trypsin-MW ELISA kit. Any specimen in the top 5% IRT level underwent DNA analysis using the InPlex(®) CF Molecular Test. Of the 1.48 million newborns screened during the 6-year time period, 7631 babies were referred for follow-up. CF was confirmed in 251 cases, and 94 cases were diagnosed with CF transmembrane conductance regulated-related metabolic syndrome or possible CF. Nine reports of false negatives were made to the program. Variation in daily average IRT was observed depending on the season (4-6 ng/ml) and kit lot (<3 ng/ml), supporting the use of a floating cutoff. The screening method had a sensitivity of 96.5%, specificity of 99.6%, positive predictive value of 4.5%, and negative predictive value of 99.5%.

CONCLUSION

Considerations for CF screening algorithms should include IRT variations resulting from age at specimen collection, sex, race/ethnicity, season, and manufacturer kit lots.

WHAT IS KNOWN

Measuring IRT level in dried blood spots is the first-tier screen for CF. Current algorithms for CF screening lead to substantial false-positive referral rates.

WHAT IS NEW

IRT values were affected by age of infant when specimen is collected, race/ethnicity and sex of infant, and changes in seasons and manufacturer kit lots The prevalence of CF in NYS is 1 in 4200 with the highest prevalence in White infants (1 in 2600) and the lowest in Black infants (1 in 15,400).

Translating the genetics of cystic fibrosis to personalized medicine

Cystic fibrosis (CF) is the most common life-threatening recessive genetic disease in the Caucasian population. This multiorgan disease is caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein, a chloride channel recognized as regulating several apical ion channels. The gene mutations result either in the lack of the protein at the apical surface or in an improperly functioning protein. Morbidity and mortality because of the mutation of CFTR are mainly attributable to lung disease resulting from chronic infection and inflammation. Since its discovery as the causative gene in 1989, much progress has been achieved not only in clinical genetics but also in basic science studies. Recently, combinations of these efforts have been successfully translated into development and availability for patients of new therapies targeting specific CFTR mutations to correct the CFTR at the protein level. Current technologies such as next gene sequencing and novel genomic editing tools may offer new strategies to identify new CFTR variants and modifier genes, and to correct CFTR to pursue personalized medicine, which is already developed in some patient subsets. Personalized medicine or P4 medicine ("personalized," "predictive," "preventive," and "participatory") is currently booming for CF. The various current and future challenges of personalized medicine as they apply to the issues faced in CF are discussed in this review.

Refining the continuum of CFTR-associated disorders in the era of newborn screening

Clinical heterogeneity in cystic fibrosis (CF) often causes diagnostic uncertainty in infants without symptoms and in older patients with milder phenotypes. We performed a cross-sectional evaluation of a comprehensive set of clinical and laboratory descriptors in a physician-defined cohort (N = 376; Children's Hospital of Wisconsin and the American Family Children's Hospital CF centers in Milwaukee and Madison, WI, USA) to determine the robustness of categorizing CF (N = 300), cystic fibrosis transmembrane conductance regulator (CFTR)-related disorder (N = 19), and CFTR-related (CRMS) metabolic syndrome (N = 57) according to current consensus guidelines. Outcome measures included patient demographics, clinical measures, sweat chloride levels, CFTR genotype, age at diagnosis, airway microbiology, pancreatic function, infection, and nutritional status. The CF cohort had a significantly higher median sweat chloride level (105 mmol/l) than CFTR-related disorder patients (43 mmol/l) and CFTR-related metabolic syndrome patients (35 mmol/l; p ≤ 0.001). Patient groups significantly differed in pancreatic sufficiency, immunoreactive trypsinogen levels, sweat chloride values, genotype, and positive Pseudomonas aeruginosa cultures (p ≤ 0.001). An automated classification algorithm using recursive partitioning demonstrated concordance between physician diagnoses and consensus guidelines. Our analysis suggests that integrating clinical information with sweat chloride levels, CFTR genotype, and pancreatic sufficiency provides a context for continued longitudinal monitoring of patients for personalized and effective treatment.

p.G970D is the most frequent CFTR mutation in Chinese patients with cystic fibrosis

Cystic fibrosis (CF), the most common life-threatening autosomal recessive disorder in Caucasians, is caused by mutations in CF transmembrane conductance regulator gene (CFTR). We and others previously identified CFTR mutations in 20 Chinese patients with CF. In this study, eight Chinese patients with a clinical diagnosis of suspected CF were newly collected and screened for CFTR mutations using a combination of conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) analysis. The CFTR mutations observed in Chinese CF patients, both reported previously and identified in the present study, were also summarized. In the newly collected patients, we identified 10 different CFTR mutations, including p.F508del, the most common CF-causing mutation in Caucasians, and three novel mutations (p.V1212Afs*15; p.L666* and p.A969A). Most notably, the previously reported p.G970D mutation was found in six patients, making it the most frequent CFTR mutation identified in Chinese CF patients thus far. In conclusion, we detected p.F508del for the first time, identified additional novel CFTR mutations and recorded the most frequent CF-causing mutation in Chinese CF patients.

Association Between Outcomes and Demographic Factors in an Azeri Turkish Population With Cystic Fibrosis: A Cross-Sectional Study in Iran From 2001 Through 2014

Background

Outcomesforcystic fibrosis patients are improving rapidly. The demographic factors are notable variables inoutcomes, which can be evaluated and modified.

Objectives

This study was designed to investigate the association between outcome and demographic factors in patients with cystic fibrosis.

Patients and Methods

This was a cross-sectional study and data were gathered for 331 patients using the census method, from March 2001 to September 2014 in Iran. Data was analyzed using logistic regression analysis, chi-square test, and independent sample t test using SPSS 18. Odds ratio with confidence intervals of 95% and P < 0.05 were considered significant.

Results

There were 85 (25.7%) deceased patients and 246 (74.3%) living patients at the time of the study. Of the 246 living CF patients, 202 (82.2%) were less than nine years of age, and 77 (90.6%) out of the 85 deceased CF patients had died younger than four years of age. There was a significant difference between outcome and location of residence. The risk of mortality was 50% less in urban patients than in rural patients (P = 0.03). The risk of mortality was approximately two times higher in patients with a positive family history than in those with a negative family history (P = 0.02). The proportion of mortality was approximately two times, or 94%, higher for those in a consanguineous marriage than for those in a non-consanguineous marriage (P = 0.01).

Conclusions

The results demonstrated that the mortality rate was higher in CF patients with a positive family history, a consanguineous marriage, and residence in a rural area. Therefore, demographic factors play an important role in the outcome of cystic fibrosis. Unfortunately, these parameters, which can be managed easily and with low cost, have been overlooked.

Accurate reporting of adherence to inhaled therapies in adults with cystic fibrosis: methods to calculate "normative adherence"

BACKGROUND

Preventative inhaled treatments in cystic fibrosis will only be effective in maintaining lung health if used appropriately. An accurate adherence index should therefore reflect treatment effectiveness, but the standard method of reporting adherence, that is, as a percentage of the agreed regimen between clinicians and people with cystic fibrosis, does not account for the appropriateness of the treatment regimen. We describe two different indices of inhaled therapy adherence for adults with cystic fibrosis which take into account effectiveness, that is, "simple" and "sophisticated" normative adherence.

METHODS TO CALCULATE NORMATIVE ADHERENCE

Denominator adjustment involves fixing a minimum appropriate value based on the recommended therapy given a person's characteristics. For simple normative adherence, the denominator is determined by the person's Pseudomonas status. For sophisticated normative adherence, the denominator is determined by the person's Pseudomonas status and history of pulmonary exacerbations over the previous year. Numerator adjustment involves capping the daily maximum inhaled therapy use at 100% so that medication overuse does not artificially inflate the adherence level.

THREE ILLUSTRATIVE CASES

Case A is an example of inhaled therapy under prescription based on Pseudomonas status resulting in lower simple normative adherence compared to unadjusted adherence. Case B is an example of inhaled therapy under-prescription based on previous exacerbation history resulting in lower sophisticated normative adherence compared to unadjusted adherence and simple normative adherence. Case C is an example of nebulizer overuse exaggerating the magnitude of unadjusted adherence.

CONCLUSION

Different methods of reporting adherence can result in different magnitudes of adherence. We have proposed two methods of standardizing the calculation of adherence which should better reflect treatment effectiveness. The value of these indices can be tested empirically in clinical trials in which there is careful definition of treatment regimens related to key patient characteristics, alongside accurate measurement of health outcomes.

Searching for a cure for cystic fibrosis. A 25-year quest in a nutshell

After 25 years of intensive search, there is not yet a cure for cystic fibrosis (CF). However, the quest has led to major breakthroughs in understanding the basic disease defect and defining strategies to correct it. The first cystic fibrosis transmembrane conductance regulator (CFTR) modulators have been introduced in clinic. Some show an impressive clinical benefit, like the potentiator ivacaftor for the 4% of patients with a class III defect. Others offer at present only a limited benefit, like the combination corrector lumacaftor plus potentiator ivacaftor for subjects homozygous for F508del. These findings prove that the basic defect in CF can be modified and hold the promise that one day CF will no longer be a life-shortening disease.

CONCLUSION

This review updates the clinician on recent achievements as well as on the CF research pipeline.

WHAT IS KNOWN

Cystic fibrosis (CF) is a common and life-shortening disease that currently cannot be cured. However, for each of the six CF mutation classes, disease-modifying drugs are under way.

WHAT IS NEW

This review is a concise update for the clinician on new drugs that reached the CF clinical pipeline. The research strategies in CF have become a paradigm for clinical trials in other inherited diseases.

Chronic cough with normal sweat chloride: Phenotypic descriptions of two rare cystic fibrosis genotypes

While our understanding of cystic fibrosis genetics has expanded in recent decades, the genetics and clinical manifestations of the disease remains highly heterogeneous. Diagnosis of CF in non-classical mutations remains a clinical challenge. We describe the clinical presentation of two patients with chronic cough found to have normal sweat chlorides. We discuss the subsequent evaluation that lead to the diagnosis of two rare CF mutations. We briefly discuss the use of the expanded 106-panel of CF mutations (homozygous 3849 + 10  kb C > T), and the role of whole CFTR gene sequencing (heterozygous c.2752-26 A > G/5T).

The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy

The recent focus on the cystic fibrosis (CF) complex microbiome has led to the recognition that the microbes can interact between them and with the host immune system, affecting the disease progression and treatment routes. Although the main focus remains on the interactions between traditional pathogens, growing evidence supports the contribution and the role of emergent species. Understanding the mechanisms and the biological effects involved in polymicrobial interactions may be the key to improve effective therapies and also to define new strategies for disease control. This review focuses on the interactions between microbe-microbe and host-microbe, from an ecological point of view, discussing their impact on CF disease progression. There are increasing indications that these interactions impact the success of antimicrobial therapy. Consequently, a new approach where therapy is personalized to patients by taking into account their individual CF microbiome is suggested.

Non-allergic asthma as a CFTR-related disorder

BACKGROUND

CFTR dysfunction can be involved in CBAVD, pancreatitis or bronchiectasis.

METHODS

Subjects with cystic fibrosis-like disease, equivocal sweat chloride concentrations and no or one disease-causing CFTR mutation were investigated by intestinal current and/or nasal potential difference measurements.

RESULTS

A subgroup of female patients who had been diagnosed to suffer from non-allergic asthma showed intermediary chloride concentrations in sweat test, normal chloride secretory responses in the intestine and an abnormal nasal potential difference with Sermet scores in the cystic fibrosis range.

CONCLUSION

Non-allergic asthma is a clinical entity that may be associated with CFTR dysfunction of the respiratory epithelium.

Baseline Ultrasound and Clinical Correlates in Children with Cystic Fibrosis

OBJECTIVE

To investigate the relationship between abdominal ultrasound findings and demographic, historical, and clinical features in children with cystic fibrosis (CF).

STUDY DESIGN

Children age 3-12 years with CF without known cirrhosis, were enrolled in a prospective, multicenter study of ultrasound to predict hepatic fibrosis. Consensus ultrasound patterns were assigned by 3 radiologists as normal, heterogeneous, homogeneous, or cirrhosis. Data were derived from direct collection and US or Toronto CF registries. χ(2) or ANOVA were used to compare variables among ultrasound groups and between normal and abnormal. Logistic regression was used to study risk factors for having abnormal ultrasound.

RESULTS

Findings in 719 subjects were normal (n = 590, 82.1%), heterogeneous (64, 8.9%), homogeneous (41, 5.7%), and cirrhosis (24, 3.3%). Cirrhosis (P = .0004), homogeneous (P < .0001), and heterogeneous (P = .03) were older than normal. More males were heterogeneous (P = .001). More heterogeneous (15.0%, P = .009) and cirrhosis (25.0%, P = .005) had CF-related diabetes or impaired glucose tolerance vs normal (5.4%). Early infection with Pseudomonas aeruginosa (<2 years old) was associated with a lower risk (OR 0.42, P = .0007) of abnormal. Ursodeoxycholic acid use (OR 3.69, P < .0001) and CF-related diabetes (OR 2.21, P = .019) were associated with increased risk of abnormal.

CONCLUSIONS

Unsuspected cirrhosis is seen in 3.3% of young patients with CF, heterogeneous in 8.9%. Abnormal ultrasound is associated with CF-related diabetes, and early P aeruginosa is associated with normal ultrasound. Prospective assessment of these risk factors may identify potential interventional targets.

TRIAL REGISTRATION

ClinicalTrials.gov: NCT01144507.

Nutrional status and dietary factors in cystic fibrosis patients with delta F508 mutation

Objective To examine the association between nutritional status and dietary factors in children and adolescents with cystic fibrosis that are carriers of delta F508 mutation. Methods Cross-sectional study of cystic fibrosis children and adolescents. Nutritional status (body mass index percentile) and dietary intake (3-day diet records presented as a percentage of estimated energy requirement) were assessed. Results Thirty six patients (median of 8.6; interquartile range 6.8-12.5 years; 50% male). The Poisson regression analysis showed that the carriers for delta F508 mutation had 60% lower prevalence ratio of body mass index ≥25° (PR=0.4; 95%IC=0.2-0.8) and 90% lower prevalence ratio (PR=0.1; confidence interval 95%IC=0.02-0.3) of ≥150% of estimated energy requirement when compared with non-delta F508 mutation carriers. The model was adjusted for lung function, estimated energy requirement, and body mass index. Conclusion Carriers for delta F508 mutation showed lower body mass index percentile and lower daily caloric consumption when compared with patients without this mutation.

Utility of a very high IRT/No mutation referral category in cystic fibrosis newborn screening

Newborn screening for Cystic Fibrosis (CF) began in New York in October, 2002 using immunoreactive trypsinogen (IRT)/DNA methodology. Infants with at least one CFTR mutation or very high IRT and no mutations (VHIRT) are referred for sweat testing. In a preliminary analysis, we noted a very low positive predictive value (PPV) and preponderance of Hispanic infants in the group of infants with CF referred for VHIRT, which led to a decision to revise, but not eliminate, the VHIRT category. Automatic referral for specimens with VHIRT collected on the day of birth was eliminated, and the VHIRT threshold was raised from 0.2% to 0.1%. In this report, we describe outcomes from VHIRT referrals among 2.4 million infants screened between March 2003 and February 2013. Following the algorithm change, referrals decreased by 37.8% overall (annual mean 1,485 vs. 923), and the VHIRT PPV improved (0.6-1.0%). The number of infants diagnosed has remained consistent at 1 in 4,400 births. The proportion of Black/Hispanic/Asian/Other infants with confirmed CF, CFTR-related metabolic syndrome (CRMS), or possible CF/CRMS was 21.3% in infants with 1-2 mutations, but 75.8% in the VHIRT group. In conclusion, although the PPV among VHIRT referrals remains low, had this category never been implemented, 24 infants with confirmed CF, and 9 infants with CRMS or possible CF/CRMS, most of whom were Hispanic, would have been missed over the 10 years. Information from this study may be helpful in assessing the need for the VHIRT category and algorithm changes in other screening programs.

Lumacaftor-Ivacaftor in Patients with Cystic Fibrosis Homozygous for Phe508del CFTR

BACKGROUND

Cystic fibrosis is a life-limiting disease that is caused by defective or deficient cystic fibrosis transmembrane conductance regulator (CFTR) protein activity. Phe508del is the most common CFTR mutation.

METHODS

We conducted two phase 3, randomized, double-blind, placebo-controlled studies that were designed to assess the effects of lumacaftor (VX-809), a CFTR corrector, in combination with ivacaftor (VX-770), a CFTR potentiator, in patients 12 years of age or older who had cystic fibrosis and were homozygous for the Phe508del CFTR mutation. In both studies, patients were randomly assigned to receive either lumacaftor (600 mg once daily or 400 mg every 12 hours) in combination with ivacaftor (250 mg every 12 hours) or matched placebo for 24 weeks. The primary end point was the absolute change from baseline in the percentage of predicted forced expiratory volume in 1 second (FEV1) at week 24.

RESULTS

A total of 1108 patients underwent randomization and received study drug. The mean baseline FEV1 was 61% of the predicted value. In both studies, there were significant improvements in the primary end point in both lumacaftor-ivacaftor dose groups; the difference between active treatment and placebo with respect to the mean absolute improvement in the percentage of predicted FEV1 ranged from 2.6 to 4.0 percentage points (P<0.001), which corresponded to a mean relative treatment difference of 4.3 to 6.7% (P<0.001). Pooled analyses showed that the rate of pulmonary exacerbations was 30 to 39% lower in the lumacaftor-ivacaftor groups than in the placebo group; the rate of events leading to hospitalization or the use of intravenous antibiotics was lower in the lumacaftor-ivacaftor groups as well. The incidence of adverse events was generally similar in the lumacaftor-ivacaftor and placebo groups. The rate of discontinuation due to an adverse event was 4.2% among patients who received lumacaftor-ivacaftor versus 1.6% among those who received placebo.

CONCLUSIONS

These data show that lumacaftor in combination with ivacaftor provided a benefit for patients with cystic fibrosis homozygous for the Phe508del CFTR mutation. (Funded by Vertex Pharmaceuticals and others; TRAFFIC and TRANSPORT ClinicalTrials.gov numbers, NCT01807923 and NCT01807949.).

Manifestações precoces da fibrose cística em paciente prematuro com íleo meconial complexo ao nascimento

OBJECTIVE:

CASE DESCRIPTION:

COMMENTS:

Conservation of CFTR codon frequency through primates suggests synonymous mutations could have a functional effect

Cystic fibrosis is an inherited chronic disease that affects the lungs and digestive system, with a prevalence of about 1:3000 people. Cystic fibrosis is caused by mutations in CFTR gene, which lead to a defective function of the chloride channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Up-to-date, more than 1900 mutations have been reported in CFTR. However for an important proportion of them, their functional effects and the relation to disease are still not understood. Many of these mutations are silent (or synonymous), namely they do not alter the encoded amino acid. These synonymous mutations have been considered as neutral to protein function. However, more recent evidence in bacterial and human proteins has put this concept under revision. With the aim of understanding possible functional effects of synonymous mutations in CFTR, we analyzed human and primates CFTR codon usage and divergence patterns. We report the presence of regions enriched in rare and frequent codons. This spatial pattern of codon preferences is conserved in primates, but this cannot be explained by sequence conservation alone. In sum, the results presented herein suggest a functional implication of these regions of the gene that may be maintained by purifying selection acting to preserve a particular codon usage pattern along the sequence. Overall these results support the idea that several synonymous mutations in CFTR may have functional importance, and could be involved in the disease.