Cystic Fibrosis Gene Research Articles

XV-2c and KM: 19 haplotype analysis in Chilean patients with cystic fibrosis and unknown CFTR gene mutations

Cystic fibrosis (CF) is caused by mutations in the CFTR gene. More than 1600 mutations have been described, with frequencies that differ worldwide according to the ethnic origin of patients. A small group of mutations are recurrent on several populations. It has been shown that they each tend occur on specific chromosome 7 haplotypes, supporting the notion of a single origin for them. Less than 50% of mutations in Chilean patients have been identified to date. To indirectly assess the possible presence of a predominant founder mutation in the remaining unknown alleles, we evaluated 2 polymorphic markers, XV-2c and KM.19, tightly linked to the CFTR locus. The study was done in Chilean CF patients with unknown or deltaF508 (DeltaF508) CFTR mutations and their haplotypes were compared to affected family-based controls. DeltaF508 showed marked linkage disequilibrium with XV-2c/KM.19 haplotype B, with 90% of alleles on that haplotype. There was no difference in haplotype distribution between unknown mutations and normal controls. These results support a European origin for DeltaF508 alleles in Chilean patients, and make unlikely the presence of a predominant founder mutation in the so-far unknown alleles.

Cystic Fibrosis Transmembrane Regulator Protein Mutations

Cystic fibrosis (CF) is the most common autosomal, recessive, life-span shortening disease in Caucasians. Since discovery of the gene for CF (cystic fibrosis transmembrane conductance regulator [CFTR]) in 1989, knowledge of the molecular function of this gene and its interactions has offered new therapeutic targets. New therapeutics aimed at improving mutant CFTR protein function, also known as 'protein repair therapy,' have been proposed but are yet to be successful in clinical trials. Some of the most exciting efforts involve a new field known as small molecule discovery, which entails the identification, evaluation, and optimization of small organic compounds that can alter the function of a selected gene target or cell phenotype. More than 1300 CFTR mutations have been identified. Many of the more common mutations have been organized into five broad classes based on the fate of the mutant CFTR protein. In each of these mutation classes, interventions have been able to restore some level of CFTR function in vitro. While these 'repairs' have yet to be demonstrated clinically, some early clinical trials are underway. Questions regarding the amount of CFTR correction needed, delivery methods, and optimal therapeutic combinations, however, remain outstanding.

Cystic Fibrosis Gene Variability in Two Southern Brazilian Amerindian Populations: Analysis of the ΔF508 Mutation and the KM19 and XV2C Haplotypes

The frequencies of the deltaF508 deletion, the most common cystic fibrosis mutation in Europeans and European-derived populations, and the XV2C and KM19 restriction fragment length polymorphisms that are tightly linked to the CFTR locus vary among populations. To determine the distribution of these extragenic markers and of the deltaF508 mutation, we analyzed 326 chromosomes of individuals from two South American Indian populations, the Guarani and the Kaingang. The allele and haplotype frequencies differed greatly between the two populations as well as among Amerindians and normal European Brazilians and European Brazilian cystic fibrosis patients. The absence of the deltaF508 mutation and the B haplotype are in agreement with the hypothesis that the deltaF508 mutation occurred after the divergence of these two populations. This finding is useful for populations containing a large Amerindian component and helps us to understand the origins of the deltaF508 deletion, the most common cystic fibrosis mutation in Europeans and European-derived populations, as well as the different incidences of cystic fibrosis in continental groups.

CFTR Mutations in Congenital Absence of Vas Deferens

A qualitative diagnosis of infertility requires attention to female and male physical abnormalities, endocrine anomalies and genetic conditions that interfere with reproduction. Many genes are likely to be involved in the complex process of reproduction. Cystic fibrosis (CF) incidence varies in different White people populations (a higher incidence of CF is observed in northern–western European populations than in southern European populations), and therefore the incidence of congenital bilateral absence of the vas deferens (CBAVD) may also vary in different White people populations. As CF is mainly observed in White people, hardly any data are available of CBAVD in non-White people, but frequent polymorphisms such as 5T are observed in most populations. The spectrum and distribution of cystic fibrosis transmembrane conductance regulator gene (CFTR) mutations differs between CBAVD and CF patients, and even compared with control individuals. Combinations of particular alleles at several polymorphic loci yield insufficient functional CFTR. The combination of the 5T allele in one copy of the CFTR gene with a cystic fibrosis mutation in the other copy is the most common cause of CBAVD in Iran. Because of techniques such as intracytoplasmic sperm injection (ICSI), CBAVD patients are now able to father children, however such couples have an increased risk of having a child with cystic fibrosis, and therefore genetic testing and counseling should be provided. Around 10% of obstructive azoospermia is congenital and is due to mutations the CF gene. This paper reviews the relationship of mutations in the CFTR gene with CBAVD.

Genes, environments, development and asthma: a reappraisal

Significant advances have been made in our understanding of the role of genetic variation in determining complex human phenotypes such as asthma. It is now well established that there is no single "gene for asthma", in the way that the cystic fibrosis transmembrane receptor is the "gene for cystic fibrosis". It is also clear that among all genetic variants eventually found to be associated with asthma, only a few will be replicated, and in the same direction, in the majority of well-performed studies. Current evidence suggests that most asthma-related polymorphisms determine risk for the disease in a context-dependent manner, i.e. they interact with environmental factors, with polymorphisms in other genes and with the specific developmental phase of the disease in which the association is tested. Elucidating these complex interactions will allow us to understand better the heterogeneity of the disease and thus to develop therapeutic tools tailored to the specific form of the disease in each patient.

Report on evaluation of the azoospermic male

Report on evaluation of the azoospermic male

Electrochemical genosensors for biomedical applications based on gold nanoparticles

Two gold nanoparticles-based genomagnetic sensors designs for detection of DNA hybridization are described. Both assays are based on a magnetically induced direct electrochemical detection of gold tags on magnetic graphite-epoxy composite electrodes. The first design is a two strands assay format that consists of the hybridization between a capture DNA strand which is linked with paramagnetic beads and another DNA strand related to BRCA1 breast cancer gene used as a target which is coupled with streptavidin-gold nanoparticles. The second genomagnetic sensor design is a sandwich assay format with more application possibilities. A cystic fibrosis related DNA strand is used as a target and sandwiched between two complementary DNA probes: the first one linked with paramagnetic beads and a second one modified with gold nanoparticles via biotin–streptavidin complexation reactions. The electrochemical detection of gold nanoparticles by differential pulse voltammetry was performed in both cases. The developed genomagnetic sensors provide a reliable discrimination against noncomplementary DNA as well against one and three-base mismatches. Optimization parameters affecting the hybridization and analytical performance of the developed genosensors are shown for genomagnetic assays of DNA sequences related with the breast cancer and cystic fibrosis genes.

Comprehensive genetic analysis of the cystic fibrosis transmembrane conductance regulator from dried blood specimens – Implications for newborn screening

PurposeIn the United States, approximately 1/3,700 babies is born with cystic fibrosis each year. The >1,300 documented sequence variants pose a challenge for detection of cystic fibrosis through genetic screening. To investigate whether comprehensive characterization of the cystic fibrosis gene is feasible using dried newborn blood specimens, we modified the whole blood Ambry Test™: CF and determined its sensitivity by testing DNA from individuals with cystic fibrosis who still had unknown mutations after commercial mutation panel testing. MethodsDNA from 42 archived newborn dried blood specimens of affected Hispanic, African-American and Caucasian individuals in California was analyzed by temporal temperature gradient electrophoresis screening and targeted sequencing, and by gross deletion analysis. ResultsExcluding two specimens that could not be analyzed due to poor DNA quality, we report a 100% sensitivity and clinical detection rate in the remaining 40 patients. Eighty-three mutations representing 40 different variants were detected, including 8 novel mutations. ConclusionsThis study demonstrates the feasibility of temporal temperature gradient electrophoresis-based full sequence analysis and targeted sequencing from DNA in newborn blood specimens. The Ambry Test™: CF, as an additional step in cystic fibrosis newborn screening models, can be used to dramatically reduce the number of cystic fibrosis carrier sweat test referrals.

O-141: Preimplantation genetic diagnosis for new cases of single gene mutations - using “reverse linkage” for colnfirming the mutation status of embryos

Linkage analysis, first described in tracking Cystic Fibrosis gene mutations 20 years ago, can also be applied to track single gene defects from parents to their embryos. Genetic PGD cases usually combine mutation detection and linkage analysis in a family where primary relatives with the mutation are used to identify a linked polymorphism pattern. This information is required before offering PGD. Combining linkage confirmation with direct mutation testing gives confidence in the accuracy of the analysis, given the problems of allele dropout and differential amplification often associated with the amplification of extremely low amounts of target DNA.

Cost-effectiveness of 4 Neonatal Screening Strategies for Cystic Fibrosis

The purpose of this work was to assess the costs of 4 neonatal screening strategies for cystic fibrosis in relation to health effects. In each strategy, the first test was the measurement of serum concentration of immunoreactive trypsin. The second step consisted of either a second immunoreactive trypsin test (strategy 1) or a multiple mutation analysis (strategy 2). In strategies 3 and 4, a third step was added to strategy 2: a second immunoreactive trypsin test (strategy 3) or an extended mutation analysis of the cystic fibrosis gene, that is, a denaturing gradient gel electrophoresis analysis (strategy 4). We conducted an economic-modeling exercise in the Netherlands based on published data and expert opinions. Subjects were a hypothetical cohort of 200 000 neonates, the approximate number of children born annually in the Netherlands, and we assessed the costs and number of life-years gained as a result of neonatal screening for cystic fibrosis. The costs and effects of changes in reproductive decisions because of neonatal screening were also assessed. Immunoreactive trypsin + immunoreactive trypsin had the most favorable cost-effectiveness ratio of 24,800 euro per life-year gained. Immunoreactive trypsin + DNA + denaturing gradient gel electrophoresis achieved more health effects than immunoreactive trypsin + DNA + immunoreactive trypsin at lower cost. The incremental costs per life-year gained of the immunoreactive trypsin + DNA + denaturing gradient gel electrophoresis strategy compared with the immunoreactive trypsin + immunoreactive trypsin strategy were 130,700 euro, whereas the incremental costs of the immunoreactive trypsin + DNA strategy compared with the immunoreactive trypsin + DNA + denaturing gradient gel electrophoresis strategy were 2,154,300 euro. When changes in reproductive decisions as a result of neonatal screening are also taken into account, neonatal screening for cystic fibrosis may lead to financial savings of approximately 1.8 million euro annually, depending on the screening strategy used. Cystic fibrosis screening for neonates is a good economic option, and positive health effects can also be expected. Immunoreactive trypsin + immunoreactive trypsin and immunoreactive trypsin + DNA + denaturing gradient gel electrophoresis are the most cost-effective strategies.

De Novo Biosynthetic Profiling of High Abundance Proteins in Cystic Fibrosis Lung Epithelial Cells

In previous studies with cystic fibrosis (CF) IB3-1 lung epithelial cells in culture, we identified 194 unique high abundance proteins by conventional two-dimensional gel electrophoresis and mass spectrometry (Pollard, H. B., Ji, X.-D., Jozwik, C. J., and Jacobowitz, D. M. (2005) High abundance protein profiling of cystic fibrosis lung epithelial cells. Proteomics 5, 2210-2226). In the present work we compared the IB3-1 cells with IB3-1/S9 daughter cells repaired by gene transfer with AAV-(wild type)CFTR. We report that gene transfer resulted in significant changes in silver stain intensity of only 20 of the 194 proteins. However, simultaneous measurement of de novo biosynthetic rates with [(35)S]methionine of all 194 proteins in both cell types resulted in the identification of an additional 31 CF-specific proteins. Of the 51 proteins identified by this hybrid approach, only six proteins changed similarly in both the mass and kinetics categories. This kinetic portion of the high abundance CF proteome, hidden from direct analysis of abundance, included proteins from transcription and signaling pathways such as NFkappaB, chaperones such as HSC70, cytoskeletal proteins, and others. Connectivity analysis indicated that approximately 30% of the 51-member hybrid high abundance CF proteome interacts with the NFkappaB signaling pathway. In conclusion, measurement of biosynthetic rates on a global scale can be used to identify disease-specific differences within the high abundance cystic fibrosis proteome. Most of these kinetically defined proteins are unaffected in expression level when using conventional silver stain analysis. We anticipate that this novel hybrid approach to discovery of the high abundance CF proteome will find general application to other proteomic problems in biology and medicine.

A New Insertion/Deletion of the Cystic Fibrosis Transmembrane Conductance Regulator Gene Accounts for 3.4% of Cystic Fibrosis Mutations in Sardinia: Implications for Population Screening

Previous studies performed on Sardinian patients affected by cystic fibrosis (CF) have led to the identification of molecular defects in 87 of 88 patients. Two mutations, the F508del and T338I, were quite prevalent and accounted for 50% and 20% of the molecular defects, respectively. T338I has been detected rarely in other populations, most likely because of the genetic isolation of Sardinians. In the present study, we have performed a molecular analysis of the CF gene in eight Sardinian patients in whom only a single mutation has been defined. Using DNA analyses (Southern blot, single nucleotide polymorphisms, microsatellite analyses, and Extra-Long polymerase chain reaction) selected to detect gross gene rearrangement and by using mRNA studies, we detected a novel mutation c.54-5811_164 + 2186del8108ins182 in six of the eight patients investigated. This mutation consists of a gross deletion of 8108 bp spanning exon 2 with an insertion of 182 bp at the deletion junction, between nucleotide 54-5811 of intron 1 (IVS1 nt16864) and nucleotide 164 + 2186 of intron 2 (IVS2 nt 2186). By including the novel mutation in our mutation panel we are now able to reach a 95% detection rate, thereby improving the process of carrier detection and genetic counseling in Sardinia.

Airway Epithelium Directed Gene Therapy for Cystic Fibrosis

Gene therapy is a promising therapeutic modality for the treatment of cystic fibrosis (CF). Despite a better understanding of the molecular organization of the cystic fibrosis transmembrane conductance regulator (CFTR) gene and mutations resulting in pathophysiological and phenotypic alterations, several forms of treatments including gene therapy have failed to yield clinical success. Major limitations for the delivery of drugs and gene therapy vectors from reaching target cells in CF patients lie in physical and immunological barriers of airway epithelium. Over the last decade, non-viral and viral gene therapy approaches have been tested in preclinical studies and human clinical trials of CF. Outcomes of these studies have helped to identify hurdles that need to be overcome before such approaches can be routinely applied to patients. In addition to the physiological and immunological barriers of airway epithelium, vector transduction is also impaired by the absence or low-abundance of cellular receptors and co-receptors for viral binding and internalization. Thus, the initial enthusiasm for gene replacement therapy for CF following cloning of the CFTR gene dampened, as more limitations were recognized. Research directed towards improving the efficiency of gene transfer technology in CF, is focused on testing of compounds to enhance vector permeability and trafficking, identification and development of vectors which can transduce through alternate pathways, identification of airway epithelium-specific targeting ligands, and the identification of stem cells for combining cell therapy and gene therapy by ex vivo methods. Details provided in this article will give a comprehensive analysis of the prospects and limitations in CF gene therapy using viral and non-viral vectors.

Gene therapy progress and prospects: cystic fibrosis

Our first review on progress and prospects in cystic fibrosis (CF) gene therapy was published in this series in October 2002. We now summarize the progress made since then and comment on the prospects for CF gene therapy over the next couple of years. Three clinical trials have been carried out, further supporting the proof-of-principle that gene transfer to the airway epithelium is feasible. Developments in viral and non-viral vectors, as well as recent alternative strategies such as gene repair, trans-splicing and stem cell therapy will be reviewed.

Regulation of Chemokine Expression by NaCl Occurs Independently of Cystic Fibrosis Transmembrane Conductance Regulator in Macrophages

Chronic pulmonary inflammation and infection are the leading causes of morbidity and mortality in cystic fibrosis (CF). While the effect of mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) on airways remains controversial, some groups have demonstrated increases in Na(+) and Cl(-) in CF airway surface liquid compared to normal airways. We investigated the consequences of NaCl on pro-inflammatory chemokine and cytokine production by macrophages. Stimulation of mouse macrophages with increasing amounts of NaCl induced macrophage inflammatory protein-2 (MIP-2) and tumor necrosis factor-alpha (TNF-alpha) production. Further, co-incubation of macrophages with NaCl in the presence of either lipopolysaccharide (LPS) or TNF-alpha synergistically increased MIP-2 production. Both the NaCl and NaCl plus LPS responses were partially dependent on endogenous production and autocrine signaling by TNF-alpha. To investigate the role of CFTR in MIP-2 production, we compared the responses of wild-type and DeltaF508 CF mouse macrophages to NaCl and LPS. The responses of macrophages from both strains were indistinguishable. In addition, CFTR mRNA was not expressed in macrophages. Taken together, these findings suggest that NaCl stimulates MIP-2 production by macrophages through a mechanism that is partially dependent on TNF-alpha but independent of macrophage CFTR expression.

Cystic fibrosis screening in assisted reproduction

The purpose of this review is to discuss the incidence of cystic fibrosis in the general population, in ethnically diverse populations and specifically in couples needing assisted reproduction caused by male factor subfertility. We review the current understanding of risks for reproductive couples and discuss ideal screening strategies. In ethnically diverse populations, a large difference in clinical sensitivity and birth prevalence exists between the broad racial/ethnic groups examined. Extensive data clearly demonstrate the cost-effectiveness of cystic fibrosis screening. Testing for cystic fibrosis gene mutations is reliable and, with a 26-mutation panel, nearly 90% of possible severe mutations can be detected. To halve the incidence of cystic fibrosis in the community, by offering genetic testing of the fetus if both partners are carrier positive, may also be possible. Recent guidelines suggest that all couples contemplating pregnancy should be informed of molecular screening for cystic fibrosis carrier status for purposes of genetic counselling. In ethnically diverse populations, ethnic-specific mutations should be included in the mutation panels.

Cystic Fibrosis Gene Therapy: Key Questions and Prospects

Cystic fibrosis is a monogenic disorder with significant morbidity and mortality, despite advances in conventional treatment. It is a good candidate for gene therapy and this field has progressed rapidly since the cystic fibrosis transmembrane conductance regulator gene was cloned. We will review the specific questions to address for successful cystic fibrosis gene therapy, such as the extra- and intracellular barriers to airway gene transfer, the target cells and the endpoints to assess efficacy. We will discuss recent advances in viral and nonviral gene transfer agents, delivery techniques and novel strategies to enhance airway gene transfer and expression.

Incest by father or by brother? A case report

In a newborn who died 5 days after birth, a rare mutation for the cystic fibrosis gene was found, allowing the clinicians to suspect that the child was a product of an incest. A forensic genetic analysis on the newborn, on the girl and her parents was very suggestive for the incest hypothesis. The girl's father was suspected, but an exclusion at two loci was found. Using the software for genetic analysis “Familias”, considering different hypothesis, the most probable situation was the existence of a girl's brother. This hypothesis allowed the Prosecutor to discover the existence of a girl's brother, who admitted the crime later.

Rescue of functional delF508-CFTR channels in cystic fibrosis epithelial cells by the α-glucosidase inhibitor miglustat

In the disease cystic fibrosis (CF), the most common mutation delF508 results in endoplasmic reticulum retention of misfolded CF gene proteins (CFTR). We show that the α-1,2-glucosidase inhibitor miglustat ( N-butyldeoxynojirimycin, NB-DNJ) prevents delF508-CFTR/calnexin interaction and restores cAMP-activated chloride current in epithelial CF cells. Moreover, miglustat rescues a mature and functional delF508-CFTR in the intestinal crypts of ileal mucosa from delF508 mice. Since miglustat is an orally active orphan drug (Zavesca ®) prescribed for the treatment of Gaucher disease, our findings provide the basis for future clinical evaluation of miglustat in CF patients.

Application of DETECTER, an evolutionary genomic tool to analyze genetic variation, to the cystic fibrosis gene family

BackgroundThe medical community requires computational tools that distinguish missense genetic differences having phenotypic impact within the vast number of sense mutations that do not. Tools that do this will become increasingly important for those seeking to use human genome sequence data to predict disease, make prognoses, and customize therapy to individual patients.ResultsAn approach, termed DETECTER, is proposed to identify sites in a protein sequence where amino acid replacements are likely to have a significant effect on phenotype, including causing genetic disease. This approach uses a model-dependent tool to estimate the normalized replacement rate at individual sites in a protein sequence, based on a history of those sites extracted from an evolutionary analysis of the corresponding protein family. This tool identifies sites that have higher-than-average, average, or lower-than-average rates of change in the lineage leading to the sequence in the population of interest. The rates are then combined with sequence data to determine the likelihoods that particular amino acids were present at individual sites in the evolutionary history of the gene family. These likelihoods are used to predict whether any specific amino acid replacements, if introduced at the site in a modern human population, would have a significant impact on fitness. The DETECTER tool is used to analyze the cystic fibrosis transmembrane conductance regulator (CFTR) gene family.ConclusionIn this system, DETECTER retrodicts amino acid replacements associated with the cystic fibrosis disease with greater accuracy than alternative approaches. While this result validates this approach for this particular family of proteins only, the approach may be applicable to the analysis of polymorphisms generally, including SNPs in a human population.