Multiple mutations in highly conserved residues are found in mildly affected cystic fibrosis patients

The Discrepancy Between External and Internal Load/Intensity during Blood Flow Restriction Exercise: Understanding Blood Flow Restriction Pressure as Modulating Factor

Physical exercise induces acute psychophysiological responses leading to chronic adaptations when the exercise stimulus is applied repeatedly, at sufficient time periods, and with appropriate magnitude. To maximize long-term training adaptations, it is crucial to control and manipulate the external load and the resulting psychophysiological strain. Therefore, scientists have developed a theoretical framework that distinguishes between the physical work performed during exercise (i.e., external load/intensity) and indicators of the body's psychophysiological response (i.e., internal load/intensity). However, the application of blood flow restriction (BFR) during exercise with low external loads/intensities (e.g., ≤ 30% of the one-repetition-maximum, ≤ 50% of maximum oxygen uptake) can induce physiological and perceptual responses, which are commonly associated with high external loads/intensities. This current opinion aimed to emphasize the mismatch between external and internal load/intensity when BFR is applied during exercise. In this regard, there is evidence that BFR can be used to manipulate both external load/intensity (by reducing total work when exercise is performed to exhaustion) and internal load/intensity (by leading to higher physiological and perceptual responses compared to exercise performed with the same external load/intensity without BFR). Furthermore, it is proposed to consider BFR as an additional exercise determinant, given that the amount of BFR pressure can determine not only the internal but also external load/intensity. Finally, terminological recommendations for the use of the proposed terms in the scientific context and for practitioners are given, which should be considered when designing, reporting, discussing, and presenting BFR studies, exercise, and/or training programs.

Rare host variants in ciliary expressed genes contribute to COVID-19 severity in Bulgarian patients

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a pneumonia with extremely heterogeneous clinical presentation, ranging from asymptomatic to severely ill patients. Previous studies have reported links between the presence of host genetic variants and the outcome of the COVID-19 infection. In our study, we used whole exome sequencing in a cohort of 444 SARS-CoV-2 patients, admitted to hospital in the period October-2020-April-2022, to search for associations between rare pathogenic/potentially pathogenic variants and COVID-19 progression. We used gene prioritization-based analysis in genes that have been reported by host genetic studies. Although we did not identify correlation between the presence of rare pathogenic variants and COVID-19 outcome, in critically ill patients we detected known mutations in a number of genes associated with severe disease related to cardiovascular disease, primary ciliary dyskinesia, cystic fibrosis, DNA damage repair response, coagulation, primary immune disorder, hemoglobin subunit β, and others. Additionally, we report 93 novel pathogenic variants found in severely infected patients who required intubation or died. A network analysis showed main component, consisting of 13 highly interconnected genes related to epithelial cilium. In conclusion, we have detected rare pathogenic host variants that may have influenced the COVID-19 outcome in Bulgarian patients.

Tweaking the catalytic efficiency of the CFTR ion channel

CFTR, unique among ABC transporters, evolved to function as an ion channel in part by optimizing the stability of the open state.

Optimization of CFTR gating through the evolution of its extracellular loops

CFTR chloride channel mutations cause the lethal and incurable disease cystic fibrosis (CF). CFTR is activated by phosphorylation, and phosphorylated channels exhibit "bursting" behavior-"bursts" of openings separated by short "flickery" closures and flanked by long "interburst" closures-driven by ATP binding/hydrolysis at two nucleotide-binding domains. The human channel (hCFTR) and the distant zebrafish ortholog (zCFTR) display differences both in their gating properties and structures. In phosphorylated ATP-bound hCFTR, the hR117 side chain, conserved across evolution, forms an H-bond that stabilizes the open state. Lack of that bond in the hR117H mutant causes CF. In the phosphorylated ATP-bound zCFTR structure that H-bond is not observable. Here, we show that the zR118H mutation does not affect the function of zCFTR. Instead, we identify an H-bond between the zS109 and zS120 side chains of phosphorylated ATP-bound, but not of unphosphorylated apo-, zCFTR. We investigate the role of that interaction using thermodynamic mutant cycles built on gating parameters determined in inside-out patch clamp recordings. We find that zS109 indeed forms an H-bond with zN120 in the flickery closed state, but not in the open or interburst closed states. Although in hCFTR an isoleucine (hI119) replaces the asparagine, mutation hS108A produces a strong hR117H-like phenotype. Since the effects of the latter two mutations are not additive, we conclude that in hCFTR these two positions interact, and the hS108-hR117 and hR117-hE1124 H-bonds cooperate to stabilize the open state. These findings highlight an example of how the gating mechanism was optimized during CFTR molecular evolution.

Molecular pathology of the R117H cystic fibrosis mutation is explained by loss of a hydrogen bond

The phosphorylation-activated anion channel cystic fibrosis transmembrane conductance regulator (CFTR) is gated by an ATP hydrolysis cycle at its two cytosolic nucleotide-binding domains, and is essential for epithelial salt-water transport. A large number of CFTR mutations cause cystic fibrosis. Since recent breakthrough in targeted pharmacotherapy, CFTR mutants with impaired gating are candidates for stimulation by potentiator drugs. Thus, understanding the molecular pathology of individual mutations has become important. The relatively common R117H mutation affects an extracellular loop, but nevertheless causes a strong gating defect. Here, we identify a hydrogen bond between the side chain of arginine 117 and the backbone carbonyl group of glutamate 1124 in the cryo-electronmicroscopic structure of phosphorylated, ATP-bound CFTR. We address the functional relevance of that interaction for CFTR gating using macroscopic and microscopic inside-out patch-clamp recordings. Employing thermodynamic double-mutant cycles, we systematically track gating-state-dependent changes in the strength of the R117-E1124 interaction. We find that the H-bond is formed only in the open state, but neither in the short-lived ‘flickery’ nor in the long-lived ‘interburst’ closed state. Loss of this H-bond explains the strong gating phenotype of the R117H mutant, including robustly shortened burst durations and strongly reduced intraburst open probability. The findings may help targeted potentiator design.

Laboratory reporting on the clinical spectrum of CFTR p.Arg117His: Still room for improvement

BACKGROUND

The clinical spectrum associated with cystic fibrosis transmembrane conductance regulator (CFTR) variant p.Arg117His is highly variable, ranging from full-blown cystic fibrosis (CF) in a small number of cases to CFTR-related disorders (CFTR-RDs) or no symptoms at all. Therefore, taking into account phenotype variability is essential for interpretation. External quality assessment (EQA) schemes can help laboratories to objectively assess the quality of genotyping and reporting by the laboratory.

METHODS

We performed a retrospective longitudinal data analysis on laboratory performance regarding the interpretation of p.Arg117His during CF EQA scheme participation. Completeness and accuracy of reporting on two mock clinical cases were each compared over time (case 1: 2005, 2007 and 2012; case 2: 2015 and 2018). These cases concerned subjects compound heterozygous for p.Phe508del and p.Arg117His in cis with 7T, but with different clinical backgrounds (family planning (case 1) versus diagnostic testing for a child (case 2)). Furthermore, we analyzed the influence of previous participations, annual test volume, accreditation status and laboratory setting on overall performance.

RESULTS

Overall performance improved over time, except during the 2007 CF EQA scheme. In addition, previous participations had a beneficial effect on laboratory performance. Accreditation status, annual test volume and laboratory setting did not significantly influence total interpretation scores.

CONCLUSIONS

In general, laboratories performed well on both cases, although reporting on the variable clinical spectrum of p.Arg117His in cis with 7T and on the disease liability of individual CFTR variants can still improve. Moreover, this study underlined the educational role of CF EQA schemes.

Use of ivacaftor in late diagnosed cystic fibrosis monozygotic twins heterozygous for F508del and R117H-7T - a case report

BACKGROUND

CFTR modulator therapy with ivacaftor is a treatment option for Cystic Fibrosis (CF) patients with at least one copy of a R117H-7T mutation in the CFTR gene. Desirable effects of this therapy are improvement of lung function, decrease in exacerbation rate, normalization or reduction of sweat chloride and weight gain. Monogenetic CF-twins carry identical genetic information, so therapy response and side effects are expected to be nearly identical under this specific therapy.

CASE PRESENTATION

In monozygotic twins, at the age of 55, two pathogenic variants in the CFTR gene (F508del and R117H-7T) were detected. Both patients presented with a borderline sweat test (30-59 mmol/L) and despite the same genetic information and similar life circumstances the disease proceeds completely different. While one patient has severe pulmonary involvement with chronic P. aeruginosa infection, her twin sister is almost unimpaired. Liver or pancreatic involvement was not seen in either patient. Due to the presence of one copy of a R117H-7T mutation, CFTR modulator therapy with ivacaftor was initiated in both. Response and side effects were significantly different. In the less affected patient, we observed an improvement in lung function and a normalization of sweat chloride. In the severely affected patient, no functional response to treatment was seen, but stabilization of the disease state with a decrease in exacerbation and hospitalization rate and weight gain as well as a normalization of sweat chloride. There was an increase in liver enzymes in the less affected patient, which normalized after halving the dose of ivacaftor, while the therapeutic effect was maintained.

CONCLUSIONS

Despite nearly identical genetic information, as in monogenetic twins, therapy response and onset of side effects of CFTR modulating therapy are very different. In patients with late diagnosis and severe pulmonary involvement, ivacaftor does not seem to improve lung function, whereas in patients with late diagnosis and low disease severity a relevant therapy response was obtained. In addition to lung function, additional clinical parameters such as reduction of exacerbation and hospitalization rate and weight gain should be used to assess therapy response, especially in severely affected patients.

Lung function decline is delayed but not decreased in patients with cystic fibrosis and the R117H gene mutation

BACKGROUND

Patients with cystic fibrosis (CF) experience variable lung disease phenotypes. The R117H mutation is often associated with preserved lung function. Our objective was to compare the rate of lung function decline in patients with the R117H mutation and patients homozygous for the F508del mutation.

METHODS

Rate of decline in percentage-of-predicted FEV₁ (ppFEV₁) was analyzed using the 2006-2010 US CF Foundation Patient Registry.

RESULTS

4-year rate of decline was slower in 156 R117H patients compared with 6251 F508del patients (-0.61 vs -2.03 ppFEV₁/year, P<0.001). Rates of decline in children were slower in R117H vs F508del patients (6-12-year-olds: +0.73 vs -1.91 ppFEV₁/year, P<0.001 and 13-17-year-olds: -1.55 vs -2.66 ppFEV₁/year, P=0.046), whereas rates in adults were not significantly different (18-24-year-olds: -1.52 vs -2.12, P=0.26 and ≥25-year-olds: -1.17 vs -1.40, P=0.33).

CONCLUSIONS

These findings are consistent with a delayed onset, but ultimately similar progression, of lung disease in R117H compared with homozygous F508del patients.

Ulceration of the Small and Large Bowel Mucosain Resection Specimens of Cystic Fibrosis Patients with Fibrosing Colonopathy

Fibrosing colonopathy (FC), observed in cystic fibrosis patients taking high-strength pancreatic enzyme preparations, is characterized by progressive obstruction of the ascending colon, with long-segment fusiform stenosis due to the deposition of submucosal fibrous tissue. The pathogenesis is uncertain, although direct toxic damage to the colonic mucosa by a constituent of such preparations has been proposed as an explanation. Mucosal defects and rectal bleeding have been observed by colonoscopy in cystic fibrosis patients at risk for and with evident FC. In a quantitative, observational study, mucosal defects were studied in six ileo-cecal resection specimens with FC confirmed by three independent pathologists' review. Representative areas (2.5-cm-long segments) were taken of terminal ileum, cecal colon, and ascending colon both at the site of most severe stenosis and at the most distal ascending colon site available; after processing with paraffin, the areas were serially sectioned at 500-μm intervals for the preparation of 5-μm sections for microscopical assessment. Marking in each section the area affected by (repairing) ulceration, and using three-dimensional reconstructions of the bowel lining, individual mucosal lesions were reconstructed. Using the reconstructed bowels, point scoring analysis of the area fraction affected by ulceration as well as the area of individual lesions was carried out. Lesions of variable age were found in the terminal

A rapid molecular approach for chromosomal phasing

Determining the chromosomal phase of pairs of sequence variants - the arrangement of specific alleles as haplotypes - is a routine challenge in molecular genetics. Here we describe Drop-Phase, a molecular method for quickly ascertaining the phase of pairs of DNA sequence variants (separated by 1-200 kb) without cloning or manual single-molecule dilution. In each Drop-Phase reaction, genomic DNA segments are isolated in tens of thousands of nanoliter-sized droplets together with allele-specific fluorescence probes, in a single reaction well. Physically linked alleles partition into the same droplets, revealing their chromosomal phase in the co-distribution of fluorophores across droplets. We demonstrated the accuracy of this method by phasing members of trios (revealing 100% concordance with inheritance information), and demonstrate a common clinical application by phasing CFTR alleles at genomic distances of 11-116 kb in the genomes of cystic fibrosis patients. Drop-Phase is rapid (requiring less than 4 hours), scalable (to hundreds of samples), and effective at long genomic distances (200 kb).

Development of allele-specific multiplex PCR to determine the length of poly-T in intron 8 of CFTR

Cystic fibrosis transmembrane conductance regulator (CFTR) gene mutation analysis has been implemented for Cystic Fibrosis (CF) carrier screening, and molecular diagnosis of CF and congenital bilateral absence of the vas deferens (CBAVD). Although poly-T allele analysis in intron 8 of CFTR is required when a patient is positive for R117H, it is not recommended for routine carrier screening. Therefore, commercial kits for CFTR mutation analysis were designed either to mask the poly-T allele results, unless a patient is R117H positive, or to have the poly-T analysis as a standalone reflex test using the same commercial platform. There are other standalone assays developed to detect poly-T alleles, such as heteroduplex analysis, High Resolution Melting (HRM) curve analysis, allele-specific PCR (AS-PCR) and Sanger sequencing. In this report, we developed a simple and easy-to-implement multiplex AS-PCR assay using unlabeled standard length primers, which can be used as a reflex or standalone test for CFTR poly-T track analysis. Out of 115 human gDNA samples tested, results from our new AS-PCR matched to the previous known poly-T results or results from Sanger sequencing.

Molecular diagnosis of ATP-binding cassette transporter-related diseases

ATP-binding cassette (ABC) transporters are involved in a variety of physiologic processes such as xenobiotic defense, lipid metabolism, ion homeostasis and immune functions. A large number of ABC proteins have been causatively linked to rare and common human genetic diseases including familial high-density lipoprotein deficiency, retinopathies, cystic fibrosis, diabetes and cardiomyopathies. Furthermore, genetic variations in ABC transporter genes and dysregulated expression patterns of these molecules significantly contribute to drug resistance in human cancer cells and alter the pharmacokinetic properties of a variety of drugs. In order to analyze DNA sequence alterations or define disease-associated mRNA expression patterns of the complete ABC transporter superfamily, novel high-throughput molecular methods such as quantitative real-time PCR and DNA microarray analysis are emerging. The aim of this review is to provide an overview and to present some examples of human ABC transporters involved in monogenic diseases, cancer and pharmacogenetics. Methodologic aspects of molecular diagnostics applied to analyze genetic variations, mRNA and protein expression levels and functional characteristics of ABC transporters are discussed.

Whole exome sequencing identifies a mutation for a novel form of corneal intraepithelial dyskeratosis

BACKGROUND

Corneal intraepithelial dyskeratosis is an extremely rare condition. The classical form, affecting Native American Haliwa-Saponi tribe members, is called hereditary benign intraepithelial dyskeratosis (HBID). Herein, we present a new form of corneal intraepithelial dyskeratosis for which we identified the causative gene by using deep sequencing technology.

METHODS AND RESULTS

A seven member Caucasian French family with two corneal intraepithelial dyskeratosis affected individuals (6-year-old proband and his mother) was ascertained. The proband presented with bilateral complete corneal opacification and dyskeratosis. Palmoplantar hyperkeratosis and laryngeal dyskeratosis were associated with the phenotype. Histopathology studies of cornea and vocal cord biopsies showed dyskeratotic keratinisation. Quantitative PCR ruled out 4q35 duplication, classically described in HBID cases. Next generation sequencing with mean coverage of 50× using the Illumina Hi Seq and whole exome capture processing was performed. Sequence reads were aligned, and screened for single nucleotide variants and insertion/deletion calls. In-house pipeline filtering analyses and comparisons with available databases were performed. A novel missense mutation M77T was discovered for the gene NLRP1 which maps to chromosome 17p13.2. This was a de novo mutation in the proband's mother, following segregation in the family, and not found in 738 control DNA samples. NLRP1 expression was determined in adult corneal epithelium. The amino acid change was found to destabilise significantly the protein structure.

CONCLUSIONS

We describe a new corneal intraepithelial dyskeratosis and how we identified its causative gene. The NLRP1 gene product is implicated in inflammation, autoimmune disorders, and caspase mediated apoptosis. NLRP1 polymorphisms are associated with various diseases.

Allelic discrimination of cis-trans relationships by digital polymerase chain reaction: GJB2 (p.V27I/p.E114G) and CFTR (p.R117H/5T)

PURPOSE

: To distinguish the cis-trans relationship of two sequence changes and to arrive at an accurate molecular diagnosis for autosomal recessive disorders, methods such as Sanger sequencing cannot differentiate whether sequence changes are in cis or trans. In addition, most techniques theoretically appropriate for allelic discrimination depend on the specific identified sequence changes for assay design, need extensive optimization, or may not be suitable. We developed a method that does not fully depend on the specific nucleotide changes. It enables efficient assay design and practical implementation of allelic discrimination.

METHODS

: Digital polymerase chain reaction (PCR) was used to separate and amplify alleles. Sanger sequencing was subsequently used to identify sequence changes.

RESULTS

: We developed a cost-effective digital PCR method for allelic discrimination of short amplicons and demonstrated it with p.Val27Ile and p.Glu114Gly in GJB2 as an example. We also successfully developed a long-range digital PCR approach to determine the cis-trans relationship of p.Arg117His and 5T in the CFTR gene.

CONCLUSION

: Digital PCR for allelic discrimination can be clinically implemented to determine the allelic configuration of relatively common sequence changes which frequently appear together and have clinical ramifications, such as the combination of p.Val27Ile and p.Glu114Gly in the GJB2 gene and p.Arg117His and 5T in CFTR.

Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides

The human ATP-binding cassette (ABC) transporter ABCB6 is involved in haem-precursor transport across the mitochondrial membrane. The crystal structure of its nucleotide-binding domain (NBD) has been determined in the apo form and in complexes with ADP, with ADP and Mg(2+) and with ATP at high resolution. The overall structure is L-shaped and consists of two lobes, consistent with other reported NBD structures. Nucleotide binding is mediated by the highly conserved Tyr599 and the Walker A motif, and induces notable structural changes. Structural comparison with other structurally characterized NBDs and full-length ABC transporters gives the first insight into the possible catalytic mechanism of ABCB6 and the role of the N-terminal helix alpha(1) in full-length ABCB6.

Genetic variation in the ABCA1 gene, HDL cholesterol, and risk of ischemic heart disease in the general population

Epidemiological studies consistently demonstrate a strong inverse association between low levels of high-density lipoprotein (HDL) cholesterol and increased risk of ischemic heart disease (IHD). This review focuses on whether both rare and common genetic variation in ABCA1 contributes to plasma levels of HDL cholesterol and to risk of IHD in the general population, and further seeks to understand whether low levels of HDL cholesterol per se are causally related to IHD. Studies of the ABCA1 gene demonstrate a general strategy for detecting functional genetic variants, and show that both common and rare ABCA1 variants contribute to levels of HDL cholesterol and risk of IHD in the general population. The association between ABCA1 variants and risk of IHD appears, however, to be independent of plasma levels of HDL cholesterol. With the recent identification of the largest number of individuals heterozygous for loss-of-function mutations in ABCA1 worldwide, population studies suggests that genetically low HDL cholesterol per se does not predict an increased risk of IHD, and thus questions the causality of isolated low levels of HDL cholesterol for the development of IHD.

Genetic analysis of Rwandan patients with cystic fibrosis-like symptoms: identification of novel cystic fibrosis transmembrane conductance regulator and epithelial sodium channel gene variants

BACKGROUND

The defect in chloride and sodium transport in cystic fibrosis (CF) patients is a consequence of CF transmembrane conductance regulator (CFTR) loss of function and an abnormal interaction between CFTR and the epithelial sodium channel (ENaC). A few patients were described with CF-like symptoms, a single CFTR mutation, and an ENaC mutation.

METHODS

To study African patients with CF-like symptoms and to relate the disease to gene mutations of both CFTR and ENaC genes, we collected clinical data and DNA samples from 60 African patients with a CF phenotype. The CFTR gene was first analyzed in all patients by denaturing high-performance liquid chromatography followed by direct sequencing; whereas, the sodium channel non-voltage-gated 1 alpha (SCNN1A), sodium channel non-voltage-gated 1 beta (SCNN1B), and sodium channel non-voltage-gated 1 gamma (SCNN1G) subunits of the ENaC gene were analyzed by sequencing in the five patients who carried only one CF mutation. The frequency of all identified ENaC variants was established in a control group of 200 healthy individuals and in the 55 CF-like patients without any CFTR mutation.

RESULTS

Three CFTR mutants, including one previously undescribed missense mutation (p.A204T), and a 5T/7T variant were identified in five patients. ENaC gene sequencing in these five patients detected the following eight ENaC variants: c.72T>C and p.V573I in SCNN1A; p.V348M, p.G442V, c.1473 + 28C>T, and p.T577T in SCNN1B; and p.S212S and c.1176 + 30G>C in SCNN1G. In the 55 CF-like patients without any CFTR mutation, we identified five of these eight ENaC variants, including the frequent p.G442V polymorphism, but we did not detect the presence of the p.V348M, p.T577T, and c.1176 + 30G>C ENaC variants. Moreover, these last three ENaC variants, p.V348M, p.T577T, and c.1176 + 30G>C, were not found in the control group.

CONCLUSION

Our data suggest that CF-like syndrome in Africa could be associated with CFTR and ENaC mutations.

Implication of the cystic fibrosis transmembrane conductance regulator gene in infertile family members of Indian CF patients

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. Among males with CF, 95% are infertile due to congenital absence of the vas deferens. We investigated the role of family history of infertility among CF subjects and characterized mutations in them. Among 50 CF subjects, four had a family history of infertility. A homozygous c.1521_1523delCTT mutation was detected in one, two had a compound heterozygous genotype (c.1521_1523delCTT/c.3717 + 10 kbC>T), and c.1521_1523delCTT mutation was identified on one allele of fourth CF subject. Genetic analysis of each infertile family members of CF subjects revealed the c.1521_1523delCTT mutation on one allele; however, no mutation could be identified on other allele. Haplotype analysis of the infertile family members showed that at least one of the alleles shared the same haplotype as that of the index case. It is suggested that the CFTR gene is implicated in the infertile members of the CF families. Failure to detect mutations on the other allele by SSCP analysis demands direct gene sequencing to detect mutations in the intronic or promoter region.

Identification and characterization of CFTR gene mutations in Indian CF patients

Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. This study was performed on Indian CF patients (n = 50) to investigate the spectrum of mutations in the CFTR gene and their association with intragenic and extragenic marker haplotypes. We report identification of 14 previously known and eight novel mutations, namely 3986-3987delC, 876-6del4, 1792InsA, L69H, S158N, Q493L, I530L and E1329Q. The frequency of delta F508 was found to be 27%. Absolute linkage between delta F508 and the KM.19-GATT-TUB9-M470V-T854T haplotype (2-2-1-1-1) predicts a relatively recent appearance of delta F508 in Indian CF patients. Low frequency of delta F508 mutation and detection of eight novel and thirteen rare mutations reflect a heterogeneous spectrum of mutations in Indian CF patients. Failure to detect mutations in 34% of alleles indicates the possible presence of gross deletions involving one or more exons or may indicate the location of the molecular defects in either the noncoding parts of the gene or in the promoter region, which warrants analysis of those regions.

Infertility and abnormal cervical mucus in two sisters who are compound heterozygotes for the cystic fibrosis (CF) DeltaF508 and R117H/7T mutations

OBJECTIVE

To describe two cases of infertile sisters who are compound heterozygote carriers of the cystic fibrosis (CF) DeltaF508 and R117H/7T mutations and who were found to have significantly abnormal cervical mucus.

DESIGN

Case reports and review of literature.

SETTING

Infertility practice based in an academic medical center.

PATIENT(S)

Two sisters (ages 34 and 42), compound heterozygote carriers of CF mutations, who presented with involuntary infertility.

INTERVENTION(S)

The partners of both patients tested negative for CF. The evaluation of both sisters did not indicate other causes of infertility aside from advanced maternal age in the 42-year-old patient. Both sisters underwent natural-cycle intrauterine insemination.

MAIN OUTCOME MEASURE(S)

Pregnancy conception.

RESULT(S)

The 34-year-old patient has subsequently conceived twice through natural-cycle inseminations.

CONCLUSION(S)

This is the first reported case of infertility due to a cervical mucus factor in a patient who is a compound heterozygote of the DeltaF508 and R117H/7T mutations. This case is important not only because of the distinct phenotypic abnormality seen with specific CF mutations but also because of the associated genotype.

PCR-SSCP: a method for the molecular analysis of genetic diseases

Single strand conformation polymorphism (SSCP) is a reproducible, rapid and quite simple method for the detection of deletions/insertions/rearrangements in polymerase chain reaction amplified DNA. All the details for the use of PCR-SSCP are presented in the direction of genetic diseases (beta-thalassaemia, cystic fibrosis), optimum gel conditions, sensitivity and the latest modifications of the method, which are applied in most laboratories. This non-radioactive PCR-SSCP method can be reliably used to identify mutations in patients (beta-globin, CFTR), provided suitable controls are available. Moreover, it is widely used for mutation identification in carriers (beta-thalassaemia, cystic fibrosis), making it particularly useful in population screening.

The importance of company: Na+ and Cl- influence substrate interaction with SLC6 transporters and other proteins

SLC6 transporters, which include transporters for gamma-aminobutyric acid (GABA), norepinephrine, dopamine, serotonin, glycine, taurine, L-proline, creatine, betaine, and neutral cationic amino acids, require Na+ and Cl- for their function, and this review covers the interaction between transporters of this family with Na+ and Cl- from a structure-function standpoint. Because detailed structure-function information regarding ion interactions with SLC6 transporters is limited, we cover other proteins cotransporting Na+ or Cl- with substrate (SLClA2, PutP, SLC5A1, melB), or ion binding to proteins in general (rhodanese, ATPase, LacY, thermolysine, angiotensin-converting enzyme, halorhodopsin, CFTR). Residues can be involved in directly binding Na+ or Cl-, in coupling ion binding to conformational changes in transporter, in coupling Na+ or Cl- movement to transport, or in conferring ion selectivity. Coordination of ions can involve a number of residues, and portions of the substrate and coupling ion binding sites can be distal in space in the tertiary structure of the transporter, with other portions that are close in space thought to be crucial for the coupling process. The reactivity with methanethiosulfonate reagents of cysteines placed in strategic positions in the transporter provides a readout for conformational changes upon ion or substrate binding. More work is needed to establish the relationships between ion interactions and oligomerization of SLC6 transporters.

Inhibition of CFTR Cl- channel function caused by enzymatic hydrolysis of sphingomyelin

Numerous mutations in the cystic fibrosis (CF) transmembrane conductance regulator (CFTR, a Cl(-) channel) disrupt salt and fluid transport and lead to the formation of thick mucus in patients' airways. Obstruction by mucus predisposes CF patients to chronic infections and inflammation, which become gradually harder to control and eventually fatal. Aggressive antibiotic therapy and supportive measures have dramatically lengthened CF patients' lives. Here, we report that sphingomyelinases (SMase) from human respiratory pathogens strongly inhibit CFTR function. The hydrolysis of sphingomyelin by SMase makes it more difficult to activate CFTR by phosphorylation of its regulatory domain. By inhibiting CFTR currents, SMase-producing respiratory tract bacteria may not only aggravate pulmonary infection in some CF patients but may also elicit a condition, analogous to CFTR deficiency, in non-CF patients suffering from bacterial lung infection.

Transcriptional and functional analyses of SLC12A3 mutations: new clues for the pathogenesis of Gitelman syndrome

Gitelman syndrome (GS) is a recessive salt-losing tubulopathy that is caused by mutations in the SLC12A3 gene that encodes the sodium-chloride co-transporter (NCC). GS is characterized by significant inter- and intrafamilial phenotype variability, with early onset and/or severe clinical manifestations in some patients. No correlations between the disease variability and the position/nature of SLC12A3 mutations have been investigated thus far. In this study, extensive mutational analyses of SLC12A3 were performed in 27 patients with GS, including genomic DNA sequencing, multiplex ligation-dependent probe amplification, cDNA analysis, and quantification of allele-specific transcripts, in parallel with functional analyses in Xenopus laevis oocytes and detailed phenotyping. Twenty-six SLC12A3 mutations were identified in 25 patients with GS, including eight novel (detection rate 80%). Transcript analysis demonstrated that splicing mutations of SLC12A3 lead to frameshifted mRNA subject to degradation by nonsense-mediated decay. Heterologous expression documented a novel class of NCC mutants with defective intrinsic transport activity. A subgroup of patients presented with early onset, growth retardation, and/or detrimental manifestations, confirming the potential severity of GS. The mutations that were associated with a severe presentation were the combination at least for one allele of a missplicing resulting in a truncated transcript that was downregulated by nonsense-mediated decay or a nonfunctional, cell surface-absent mutant. The most recurrent mutation on the second allele was a newly described NCC mutant that affected the functional properties of the co-transporter. These data suggest that the nature/position of SLC12A3 mutation, combined with male gender, is a determinant factor in the severity of GS and provide new insights in the underlying pathogenic mechanisms of the disease.

Mutation in ABCA1 predicted risk of ischemic heart disease in the Copenhagen City Heart Study Population

OBJECTIVES

We tested whether heterozygosity for the K776N mutation (frequency: 0.4%) in ATP-binding cassette transporter A1 (ABCA1) predicted ischemic heart disease (IHD) in the Copenhagen City Heart Study population.

BACKGROUND

In a complex trait like IHD, genetic variation is considered to be conferred by common DNA polymorphisms, although rare mutations may have a larger impact. Tangier disease, a rare high-density lipoprotein cholesterol (HDL-C) deficiency syndrome with IHD, is caused by homozygous ABCA1 mutations.

METHODS

We analyzed blood samples from a large cohort study of 9,076 Danish individuals followed for 24 years (167,287 person-years), during which 1,033 incident IHD events occurred. The hypothesis was retested in an independent case-control study comparing 562 IHD patients with 3,103 controls.

RESULTS

The cumulative incidence of IHD as a function of age was increased in K776N heterozygotes compared with non-carriers (log-rank test: p = 0.005). At the age of 80 years, 48% of heterozygotes and 23% of non-carriers had IHD. Incidence rates in non-carriers and K776N heterozygotes were 61 and 157 per 10,000 person-years. The age-adjusted hazard ratio for IHD in K776N heterozygotes versus non-carriers was 2.4 (95% confidence interval 1.3 to 4.5). Adjusting for HDL-C, or for smoking, diabetes, and hypertension did not change the result, suggesting that genotype predicted risk of IHD beyond that offered by HDL-C, and by other conventional risk factors. Similar trends were obtained in an independent case-control study.

CONCLUSIONS

Heterozygosity for an ABCA1 mutation (K776N) conferred two- to three-fold risk of IHD in 37 participants in the Copenhagen City Heart study.

Rational approach to genetic testing of cystic fibrosis (CF) in infertile men

Male infertility as a result of isolated congenital bilateral absence of the vas deferens (CBAVD) is one primary genital form of cystic fibrosis (CF) and occurs in 1-2% of infertile men. Assisted fertilization in patients with CBAVD increases the risk of transmitting mutations in the CF gene. We developed a rational approach to genetic CF testing in infertile men. A total of 282 infertile male patients were screened for the most common CF mutations (DeltaF508, R117H, IVS8-5T). Clinical data including medical history, examination, semen analysis, sweat tests, karyotypes and hormonal values were analysed. We identified 23 patients carrying mutations in the CF gene (DeltaF508: 10 patients; R117H: six patients; IVS8-5T: 11 patients). Two patients were compound heterozygote for DeltaF508/R117H, two others for DeltaF508/IVS8-5T. Correlating these molecular analyses with the clinical data pertaining to serum follicle-stimulating hormone concentration, semen pH, sperm count and total testicular volume, we were able to develop a score with a high specificity (98.4) for the presence of a cystic fibrosis transmembrane conductance regulator (CFTR) mutation, but only with a low sensitivity (positive post-test likelihood: 62.5%; negative post-test likelihood: 6.3%). With regard to the low sensitivity and the high number of CFTR mutations found in this heterogeneous group of infertile men, we still recommend genetic CF testing before assisted fertilization.

De novo interstitial direct duplication of Xq21.1q25 associated with skewed X-inactivation pattern

Genotype-phenotype correlation in women with an abnormal phenotype associated with a duplication of the long arm of the X chromosome remains unclear. We report on prenatal diagnosis and follow-up of a girl with an Xq duplication and dysmorphic features. The abnormal phenotype included growth retardation, hypotonia, and nystagmus. In order to improve the resolution of the cytogenetic analysis, we used both conventional and array-based comparative genomic hybridization to perform a global molecular cytogenetic analysis of the genome. These molecular cytogenetic analyses showed a direct duplication Xq21.1 --> q25 without other chromosomal abnormalities. This duplication was originating from the paternal X chromosome. Moreover, a skewed X-inactivation pattern was observed leading to a partial functional disomy of the chromosomal region Xq21.1q25. This report and review of the literature suggest that functional disomy for chromosome X could explain the abnormal phenotype. In prenatal diagnosis, this can have implication for patient management and genetic counseling.

Genotype-phenotype correlation and frequency of the 3199del6 cystic fibrosis mutation among I148T carriers: results from a collaborative study

PURPOSE

We expect that the mutation panel currently recommended for preconception/prenatal CF carrier screening will be modified as new information is learned regarding the phenotype associated with specific mutations and allele frequencies in various populations. One such example is the I148T mutation, originally described as a severe CF mutation. After implementation of CF population-based carrier screening, we learned that I148T exists as a complex allele with 3199del6 in patients with clinical CF, whereas asymptomatic compound heterozygotes for I148T and a second severe CF mutation were negative for 3199del6.

METHODS

We performed reflex testing for 3199del6 on 663 unrelated specimens, including I148T heterozygotes, compound heterozygotes, and a homozygous individual.

RESULTS

Less than 1% of I148T carriers were also positive for 3199del6. Excluding subjects tested because of a suspected or known CF diagnosis or positive family history, 0.6% of I148T-positive individuals were also positive for 3199del6. We identified 1 I148T homozygote and 6 unrelated compound heterozygous individuals with I148T and a second CF variant (2 of whom also carried 3199del6). In addition, one fetus with echogenic bowel and one infertile male were heterozygous for I148T (3199del6 negative).

CONCLUSIONS

Reflex testing for 3199del6 should be considered whenever I148T is identified. Reflex testing is of particular importance for any symptomatic patient or whenever one member of a couple carries a deleterious CF mutation and the other member is an I148T heterozygote. Further population data are required to determine if I148T, in the absence of 3199del6, is associated with mild or atypical CF or male infertility.

Cystic Fibrosis Transmembrane Conductance Regulator Gene Mutations in Infertile Males with Congenital Bilateral Absence of the Vas Deferens

Congenital bilateral absence of the vas deferens (CBAVD) is characterized by azoospermia and male infertility. Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene are associated with cystic fibrosis (CF), the most common autosomal recessive disorder in Caucasians. Recent publications on CBAVD raised the question whether CFTR gene mutations are responsible for CBAVD occurrence or not. This study was conducted to explore the role of CFTR gene mutations in the occurrence of CBAVD-dependent male infertility. Forty-four chromosomes of 22 CBAVD patients from Austrian ancestry were studied. For detection of the most common mutation DeltaF508, a deletion of phenylalanine at the 508th position of mature CFTR chloride channel protein, the 10th exon of the gene was screened by heteroduplex analysis. In order to identify non-DeltaF508 mutations, we also analyzed the entire coding regions, exon/intron boundaries of 27 exons and the 5'- and 3'-untranslated regions of the gene by denaturing gradient gel electrophoresis (DGGE) after polymerase chain reaction. All exons showing different banding patterns on the DGGE gels were sequenced to define existing DNA sequence variations. Among the analyzed 44 chromosomes of 22 patients, disease producing mutations were found in 31.8% (14/44). The most common mutation was DeltaF508 with a frequency of 43% (6/14), followed by R117H with 29% (4/14). Our results indicate that CFTR gene mutations are common but not the only reason for the occurrence of CBAVD-dependent male infertility. We recommend screening of the CFTR gene in these patients.

Genetic variation in ABC transporter A1 contributes to HDL cholesterol in the general population

Homozygosity for mutations in ABC transporter A1 (ABCA1) causes Tangier disease, a rare HDL-deficiency syndrome. Whether heterozygosity for genetic variation in ABCA1 also contributes to HDL cholesterol (HDL-C) levels in the general population is presently unclear. We determined whether mutations or single-nucleotide polymorphisms (SNPs) in ABCA1 were overrepresented in individuals with the lowest 1% (n=95) or highest 1% (n=95) HDL-C levels in the general population by screening the core promoter and coding region of ABCA1. For all nonsynonymous SNPs identified, we determined the effect of genotype on lipid traits in 9,259 individuals from the general population. Heterozygosity for ABCA1 mutations was identified in 10% of individuals with low HDL-C only. Three of 6 nonsynonymous SNPs (V771M, V825I, and R1587K) were associated with increases or decreases in HDL-C in women in the general population and some with consistent trends in men, determined as isolated single-site effects varying only at the relevant SNP. Finally, these results were consistent over time. In conclusion, we show that at least 10% of individuals with low HDL-C in the general population are heterozygous for mutations in ABCA1 and that both mutations and SNPs in ABCA1 contribute to HDL-C levels in the general population.

Three ATP-binding cassette transporter genes, Abca14, Abca15, and Abca16, form a cluster on mouse Chromosome 7F3

We have identified and cloned three mouse genes that belong to the ABCA subfamily of ATP-binding cassette (ABC) transporters. These three genes are arranged in a tandem head-to-tail cluster spanning about 300 kb on mouse Chromosome (Chr) 7F3. Phylogenetic analysis indicates that although the three genes are related to human and mouse ABCA3, they are not orthologs of any of the current list of 48 human ABC genes and were, therefore, named Abca14, Abca15, and Abca16. The coding region of each gene is split into 31 exons, has an open reading frame of more than 1600 amino acids, and encodes a full transporter molecule with two nucleotide-binding folds (NBF) and two transmembrane domains (TMD). All three genes are predominantly expressed in testis, which suggests that they may perform special functions in testicular development or spermatogenesis. Interestingly, the human genome contains only fragments (less than ten exons) of at least two different ABC genes in the syntenic region on Chromosome 16p12 that are scattered among other, unrelated genes and are not capable of coding functional ABC transporters.

Y chromosome assessment and its implications for the development of ICSI children

The aetiology of compromised spermatogenesis is often genetic in nature. There are only a few reports of father/son cohorts that have been evaluated to assess heritability of mutations associated with male factor infertility and the psychological well-being of the children. In the present study, multiple tissues were sampled from consenting male patients and their sons derived from intracytoplasmic sperm injection (ICSI) and underwent chromosomal and genetic analyses. Paediatric and psychological examinations were also conducted. In 87 men and 47 boys, 22 sequence tagged sites (STS) were analysed by multiplex PCR and deletion breakpoints were defined with additional loci. In one patient, the breakpoints map to the highly unstable palindrome-rich region within AZFb and proximal AZFc was investigated. A total of 86 blood, 26 semen, and 73 cheek cells samples were collected from adults, and 36 blood samples and 44 cheek cell specimens were obtained from the boys. Though all of the fathers had normal karyotypes, the incidence of chromosomal abnormalities in the somatic cells of male progeny was 8.3% (3/36). The incidence of germ line aneuploidy in these men was 0.5-2.8%. A CF mutation (Delta508) was detected in one of 87 men (1.2%) and microdeletions in Yq AZF were detected in 3.4% of 87 adults and in 2.1% of their sons (n = 47). In conclusion, screening for Y chromosome microdeletions provides crucial information in the counselling of couples seeking infertility treatment. Moreover, DNA extraction and Y deletion assessments of cheek cells provide a non-invasive approach. Inheritance of Yq deletions appears not to affect the psychological and physical development of children derived from ICSI.

Familial concordance of phenotype and microbial variation among siblings with CF

The clinical spectrum of cystic fibrosis (CF) is influenced by the cystic fibrosis transmembrane conductance regulator (CFTR) genotype. However, variable courses of the disease were demonstrated among patients with identical genotypes. Since siblings share identical CFTR mutations and environmental factors, they can serve as a model to assess the effect of modifier genes on disease expression, and also to evaluate cross-infection. The aim of this study was to compare disease expression among siblings with CF. All sibling pairs treated at 7 CF centers in Israel were included in the study. Data were collected from patients' medical charts. Fifty families with at least 2 siblings were identified. As expected, the second-born sibling was diagnosed at an earlier age compared to the first-born. The mode of CF presentation at diagnosis showed significant familial concordance. In the families where the first sibling presented with gastrointestinal manifestations, 79% of the second siblings also presented with gastrointestinal manifestations. When gastrointestinal manifestations were absent in the first sibling, only 12% of the second siblings presented with gastrointestinal manifestations (P < 0.0001). Likewise, when the first sibling presented with respiratory symptoms, 60% of the second siblings presented with the similar symptoms. However, when the first sibling presented without respiratory symptoms, only 12% of the second siblings presented with respiratory symptoms (P < 0.001). Meconium ileus (MI) was present in 20 patients (21%). In 10 families where the first-born sibling had MI, 8 (80%) of the subsequent siblings had MI. On the other hand, in the 39 families where the first-born sibling did not have MI, only 2 (5%) subsequent siblings had MI (P < 0.001). Pancreatic insufficiency (PI) also had high familial concordance (P < 0.0001). Percentile growth for weights and heights and lung function (FVC, FEV(1), and FEF(25-75)) at ages 7 and 10 years were similar between siblings. P. aeruginosa grew from sputum in 89% of our study patients. When P. aeruginosa was isolated from the first-born patient, 91% of the second siblings were also positive for P. aeruginosa, whereas when the initial sibling was not a carrier of P. aeruginosa, only 50% of subsequent siblings were positive (P < 0.0001). This familial concordance was not observed for S. aureus. By contrast, the age of first isolation of P. aeruginosa and S. aureus was significantly earlier in the second sibling than in the first for the two bacteria: 10.3 +/- 5.1 vs. 7.3 +/- 5.2 years (P < 0.05) for P. aeruginosa, and 11.5 +/- 5.4 years vs. 6.8 +/- 5.1 years (P < 0.05) for S. aureus. CF siblings tend to share similar phenotypes that are not mutation-dependent. The lack of variability between siblings in mode of initial CF presentation, rates of MI, pulmonary function, and nutritional status supports the role of modifier genes in the determination of these factors.

Mutations of the CFTR gene in Turkish patients with congenital bilateral absence of the vas deferens

BACKGROUND

Mutations of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) can cause congenital bilateral absence of the vas deferens (CBAVD) as a primarily genital form of cystic fibrosis. The spectrum and frequency of CFTR mutations in Turkish males with CBAVD is largely unknown.

METHODS

We investigated 51 Turkish males who had been diagnosed with CBAVD at the Hacettepe University, Ankara, for the presence of CFTR gene mutations by direct sequencing of the coding region and exon/intron boundaries.

RESULTS

We identified 27 different mutations on 72.5% of the investigated alleles. Two-thirds of the patients harboured CFTR gene mutations on both chromosomes. Two predominant mutations, IVS8-5T and D1152H, accounted for more than one-third of the alleles. Five mutations are described for the first time. With one exception, all identified patients harboured at least one mutation of the missense or splicing type. Presently available mutation panels would have uncovered only 7-12% of CFTR alleles in this population cohort.

CONCLUSIONS

Although cystic fibrosis is relatively rare in Turkey, CFTR mutations are responsible for the majority of CBAVD in Turkish males. Because of a specific mutation profile, a population-specific panel should be recommended for targeted populations such as CBAVD in Turkey or elsewhere.

Approaches to identify genes for complex human diseases: lessons from Mendelian disorders

The focus of most molecular genetics research is the identification of genes involved in human disease. In the 20th century, genetics progressed from the rediscovery of Mendel's Laws to the identification of nearly every Mendelian genetic disease. At this pace, the genetic component of all complex human diseases could be identified by the end of the 21st century, and rational therapies could be developed. However, it is clear that no one approach will identify the genes for all diseases with a genetic component, because multiple mechanisms are involved in altering human phenotypes, including common alleles with small to moderate effects, rare alleles with moderate to large effects, complex gene-gene and gene-environment interactions, genomic alterations, and noninherited genetic effects. The knowledge gained from the study of Mendelian diseases may be applied to future research that combines linkage-based, association-based, and sequence-based approaches to detect most disease alleles. The technology to complete these studies is at hand and requires that modest improvements be applied on a wide scale. Improved analytical tools, phenotypic characterizations, and functional analyses will enable complete understanding of the genetic basis of complex diseases.

Mutation detection in rice waxy mutants by PCR-RF-SSCP

PCR-RF-SSCP (PRS), which combines cleaved amplified polymorphic sequence (CAPS) and single-strand conformation polymorphism (SSCP), is expected to be a useful technique for DNA polymorphism analysis. We evaluated the ability of PRS to detect single nucleotide polymorphism (SNP) using the Waxy gene, Wx, of rice, and subsequently were able to identify point mutations in wx mutant lines. The approximately 6-kb Wx gene was divided into five regions for PCR amplification. Two regions, in which most of the point mutations of the wx mutants have been identified, were amplified by PCR and cloned into a vector, and those clones containing SNPs produced as a result of the inherent inaccuracy of PCR were used for the evaluation of PRS. The efficiency of PRS in the detection of SNPs of these clones was over 70%. PRS analysis of the wx genes in 18 waxy mutants was carried out in the five regions using two different restriction endonucleases and two gel conditions, with and without glycerol. Of the 18 lines tested, 17 showed band patterns different from that of the wild type. Most of the mutations identified in this study were nucleotide changes in exons, which result in amino acid changes. One mutation generated an in-frame stop codon, and another was a frame shift mutation by one-base deletion. Two mutations found at a splice site were considered to inhibit normal splicing of mRNA. These results show that PRS is a useful technique for detecting point mutations in large plant genes.

A cystic fibrosis patient with two novel mutations in mitochondrial DNA: mild disease led to delayed diagnosis of both disorders

A 21-year-old woman who has been suspected of mitochondrial cytopathy, but negative for common mitochondrial DNA (mtDNA) point mutations and deletions, was screened for unknown mutations in the entire mitochondrial genome by temporal temperature gradient gel electrophoresis (TTGE). Her asymptomatic mother's blood DNA was also analyzed and used as a reference. Two tRNA regions showing different TTGE patterns between the proband and her mother were sequenced. Two novel mutations, G15995A in tRNA(pro) and A8326G in tRNA(lys), were revealed. These mutations are present in heteroplasmic states. They both occurred at a nucleotide position that is highly conserved throughout evolution. This patient is also a compound heterozygote for the cystic fibrosis (CF) mutations, DeltaF508 and R347P. The phenotype for R347P has been associated with mild disease. Due to the mild features of the R347P mutation in the CF transmembrane conductance regulator (CFTR) gene and the heterogeneous clinical presentation of the mtDNA disease, the patient was not definitively diagnosed until age 21. This case underscores the importance of a complete mutational analysis of the entire mitochondrial genome when a patient suspected of mitochondrial disorder is negative for common mtDNA mutations.

The I148T CFTR allele occurs on multiple haplotypes: a complex allele is associated with cystic fibrosis

PURPOSE

To determine whether intragenic changes modulate the cystic fibrosis (CF) phenotype in individuals who are positive for the I148T allele.

METHODS

The genes from individuals who carried at least one copy of the I148T allele were analyzed for additional changes that may be acting as genetic modifiers.

RESULTS

Seven of eight individuals with a known or suspected diagnosis of CF who carried I148T in combination with a severe CF mutation also carried 3199del6. Eight apparently healthy adult individuals who were compound heterozygous for I148T and a severe CF mutation or homozygous for I148T did not carry the deletion ( = 0.0014). The I148T allele occurs on at least three haplotypes: an IVS-8 9T background, a 7T background, or a 9T + 3199del6 background. The 3199del6 allele was not identified in 386 non-CF chromosomes.

CONCLUSIONS

It is concluded that I148T occurs on at least three haplotypes and the complex allele I148T + 9T + 3199del6 is associated with a classic CF phenotype.

Evolutionary analyses of ABC transporters of Dictyostelium discoideum

The ABC superfamily of genes is one of the largest in the genomes of both bacteria and eukaryotes. The proteins encoded by these genes all carry a characteristic 200- to 250-amino-acid ATP-binding cassette that gives them their family name. In bacteria they are mostly involved in nutrient import, while in eukaryotes many are involved in export. Seven different families have been defined in eukaryotes based on sequence homology, domain topology, and function. While only 6 ABC genes in Dictyostelium discoideum have been studied in detail previously, sequences from the well-advanced Dictyostelium genome project have allowed us to recognize 68 members of this superfamily. They have been classified and compared to animal, plant, and fungal orthologs in order to gain some insight into the evolution of this superfamily. It appears that many of the genes inferred to have been present in the ancestor of the crown organisms duplicated extensively in some but not all phyla, while others were lost in one lineage or the other.

Genotype-phenotype correlation in cystic fibrosis: the role of modifier genes

More than 1,000 mutations have been identified in the cystic fibrosis (CF) transmembrane regulator (CFTR) disease gene. The impact of these mutations on the protein and the wide spectrum of CF phenotypes prompted a series of Genotype-Phenotype correlation studies. The CFTR genotype is invariably correlated with pancreatic status-in about 85% of cases with pancreatic insufficiency and in about 15% of cases with pancreatic sufficiency. The correlations between the CFTR genotype and pulmonary, liver, and gastrointestinal expression are debatable. The heterogeneous phenotype in CF patients bearing the same genotype or homozygotes for nonsense mutations implicated environmental and/or genetic factors in the disease. However, the discordant phenotype observed in CF siblings argued against a major role of environmental factors and suggested that genes other than CFTR modulate the CF phenotype. A locus that modulates gastrointestinal expression was identified in mice and subsequently in humans. By analyzing nine CF patients discordant for meconium ileus we were able to show that this locus had a dominant effect. Moreover, in a collaborative study we found a higher rate of polymorphisms in beta-defensin genes 1 and 2 in CF patients and in controls. In another multicenter study mutations in alpha-1 antitrypsin (A1AT) and mannose binding lectin genes were found to be independent risk factors for liver disease in CF patients. The body of evidence available suggests that the variegated CF phenotype results from complex interactions between numerous gene products.

The pancreas in cystic fibrosis

The pancreas secretes a bicarbonate-rich fluid containing digestive enzymes via the ampulla of Vater into the duodenum. Defective secretion leads to maldigestion of fat and protein with increased faecal losses. Cystic fibrosis (CF) is the major cause of pancreatic exocrine failure in childhood, whereas pancreatic insufficiency in adults is commonly associated with chronic pancreatitis and alcohol ingestion. In cystic fibrosis, pancreatic function correlates with genotype; pancreatic-sufficient (PS) patients have a milder course of respiratory disease, improved survival and lower mean sweat chloride concentrations than those with pancreatic insufficiency. Recent observations suggest that mutant CF alleles are over-represented in patients with chronic pancreatitis. Few show evidence of sino-pulmonary disease or high sweat electrolyte concentrations.

IL-6 gene amplification and expression in human glioblastomas

The aggressiveness of human gliomas appears to be correlated with the upregulation of interleukin 6 (IL-6) gene. Using quantitative PCR methods, we detected amplification and expression of the IL-6 gene in 5 of 5 primary glioblastoma samples and in 4 of 5 glioblastoma cell lines. This finding suggests that the amplification of IL-6 gene may be a common feature in glioblastomas and may contribute to the IL-6 over-expression.

The human ATP-binding cassette (ABC) transporter superfamily

The ATP-binding cassette (ABC) transporter superfamily contains membrane proteins that translocate a variety of substrates across extra- and intra-cellular membranes. Genetic variation in these genes is the cause of or contributor to a wide variety of human disorders with Mendelian and complex inheritance, including cystic fibrosis, neurological disease, retinal degeneration, cholesterol and bile transport defects, anemia, and drug response. Conservation of the ATP-binding domains of these genes has allowed the identification of new members of the superfamily based on nucleotide and protein sequence homology. Phylogenetic analysis is used to divide all 48 known ABC transporters into seven distinct subfamilies of proteins. For each gene, the precise map location on human chromosomes, expression data, and localization within the superfamily has been determined. These data allow predictions to be made as to potential functions or disease phenotypes associated with each protein. In this paper, we review the current state of knowledge on all human ABC genes in inherited disease and drug resistance. In addition, the availability of the complete Drosophila genome sequence allows the comparison of the known human ABC genes with those in the fly genome. The combined data enable an evolutionary analysis of the superfamily. Complete characterization of all ABC from the human genome and from model organisms will lead to important insights into the physiology and the molecular basis of many human disorders.

Intron-8 polythymidine sequence in Australasian individuals with CF mutations R117H and R117C

Compound heterozygotes for a severe cystic fibrosis transmembrane conductance regulator (CFTR) mutation and the R117H or R117C mutation (R117H/C) have clinical presentations that vary from classic cystic fibrosis (CF) to an incidental genetic finding. The aim of this study was to assess the influence of the intron-8 polythvmidine sequence (IVS8) on the relationship between genotype and phenotype of individuals with R117H/C. All individuals with R117H/C known to CF clinics in Australia and New Zealand were retrospectively studied by collecting information on genotype, age, pancreatic status, sweat electrolytes, sputum microbiology and pulmonary function. Forty-one individuals (39 with R117H and two with R117C), 16 on an IVS8-5T background and 25 on an IVS8-7T background were identified. Twelve individuals presented clinically, four were siblings of known R117H/C compound heterozygotes and 25 were detected by newborn screening. Eleven of 14 of the IVS8-5T group (78%) with sweat chloride results available had sweat CI > 60 mmol x L(-1) compared to 5 (20%) of the R117H/7T group (Chi-squared=10.4, p=0.001). Two were pancreatic insufficient, both IVS8-5T. Two IVS8-5T individuals have recently died (aged 43 and 19) and of the 14 surviving IVS8-5T group, 11 (79%) are symptomatic compared to eight (32%) of the IVS8-7T individuals (Chi-squared=6.1, p=0.01). In conclusion, most individuals with R117H/C on a IVS8-5T background have an elevated sweat chloride and clinical cystic fibrosis, which in some cases is severe. Most individuals with R117H/C on an IVS8-7T background do not have clinical cystic fibrosis but should be followed for the development of clinical disease.