The multi-faceted nature of 15 CFTR exonic variations: Impact on their functional classification and perspectives for therapy.

BACKGROUND: The majority of variants of unknown clinical significance (VUCS) in the CFTR gene are missense variants. While change on the CFTR protein structure or function is often suspected, impact on splicing may be neglected. Such undetected splicing default of variants may complicate the interpretation of genetic analyses and the use of an appropriate pharmacotherapy. METHODS: We selected 15 variants suspected to impact CFTR splicing after in silico predictions on 319 missense variants (214 VUCS), reported in the CFTR-France database. Six specialized laboratories assessed the impact of nucleotide substitutions on splicing (minigenes), mRNA expression levels (quantitative PCR), synthesis and maturation (western blot), cellular localization (immunofluorescence) and channel function (patch clamp) of the CFTR protein. We also studied maturation and function of the truncated protein, consecutive to in-frame aberrant splicing, on additional plasmid constructs. RESULTS: Six of the 15 variants had a major impact on CFTR splicing by in-frame (n = 3) or out-of-frame (n = 3) exon skipping. We reclassified variants into: splicing variants; variants causing a splicing defect and the impairment of CFTR folding and/or function related to the amino acid substitution; deleterious missense variants that impair CFTR folding and/or function; and variants with no consequence on the different processes tested. CONCLUSION: The 15 variants have been reclassified by our comprehensive approach of in vitro experiments that should be used to properly interpret very rare exonic variants of the CFTR gene. Targeted therapies may thus be adapted to the molecular defects regarding the results of laboratory experiments.

Penetrance is a critical parameter for assessing the disease liability of CFTR variants.

BACKGROUND: Major issues of newborn screening (NBS) for CF are the assessment of disease liability of variants and of the penetrance of clinical CF, notably in inconclusive diagnosis. The penetrance of CF is defined as the risk of a particular genotype to lead to a CF phenotype. METHODS: We aimed to get insight into the penetrance of CF for fifteen CFTR variants: 5 frequent CF-causing and 10 classified as of varying clinical consequence (VCC) or associated with a CFTR-related disorder (CFTR-RD) in CFTR2 or CFTR-France databases. The penetrance was approached by: (1) comparison of variant allelic frequencies in CF patients (CFTR2) and in the general population; (2) estimation of the likelihood of a positive NBS test for the 14 compound heterozygous with F508del and the F508del homozygous genotypes, defined as the ratio of detected/expected number of neonates with a given genotype in the 2002-2017 period. RESULTS: A full penetrance was observed for severe CF-causing variants. Five variants were more frequently found in the general population than in CF patients: TG11T5, TG12T5, TG13T5, L997F and R117H;T7. The likelihood of a positive NBS test was 0.03% for TG11T5, 0.3% for TG12T5, 1.9% for TG13T5, 0.6% for L997F, 11.7% for D1152H, and 17.8% for R117H;T7. Penetrance varied greatly for variants with discrepant classification between CFTR2 and CFTR-France: 5.1% for R117C, 12.3% for T338I, 43.5% for D110H and 52.6% for L206W. CONCLUSION: These results illustrate the contribution of genetics population data to assess the disease liability of variants for diagnosis and genetic counselling purposes.

Genetics of cystic fibrosis: Basics.

Cystic fibrosis (CF) is an autosomal recessive genetic disorder whose responsible gene - the CFTR gene - was discovered 30 years ago by a positional cloning strategy. This gene, which encodes a chloride channel, contains more than 2,000 mutations including a major one (p.Phe508del). This discovery has led to considerable progress in the understanding of the pathophysiology of CF as well as in the management of patients and their families. It has also paved the way for the development of specific therapies for the disease. From an epidemiological point of view, the incidence of CF, which shows loco-regional variations, is now estimated at 1/4,700 live births in France. The face of CF has dramatically changed over the past decades: CF has gradually become a disease of the adult with, today, more than 50% of the patients being 18 years old or more and a median predicted survival age that exceeds 45 years. © 2020 French Society of Pediatrics. Published by Elsevier Masson SAS. All rights reserved.

Overexpression of certain transient receptor potential and Orai channels in prostate cancer is associated with decreased risk of systemic recurrence after radical prostatectomy.

BACKGROUND: Several studies had suggested the potential role of calcium signaling in prostate cancer (PCa) prognosis and agressiveness. We aimed to investigate selected proteins contributing to calcium (Ca2+ ) signaling, (Orai, stromal interaction molecule (STIM), and transient receptor potential (TRP) channels) and involved in cancer hallmarks, as independent predictors of systemic recurrence after radical prostatectomy (RP). METHODS: A case-control study including 112 patients with clinically localized PCa treated by RP between 2002 and 2009 and with at least 6-years' follow-up. Patients were divided into two groups according to the absence or presence of systemic recurrence. Expression levels of 10 proteins involved in Ca2+ signaling (TRPC1, TRPC4, TRPV5, TRPV6, TRPM8, STIM1, STIM2, Orai1, Orai2, and Orai3), were assessed by immunohistochemistry using tissue microarrays (TMAs) constructed from paraffin-embedded PCa specimens. The level of expression of the various transcripts in PCa was assessed using quantitative polymerase chain reaction (qPCR) analysis. RNA samples for qPCR were obtained from fresh frozen tissue samples of PCa after laser capture microdissection on RP specimens. Relative gene expression was analyzed using the 2-▵▵Ct method. RESULTS: Multivariate analysis showed that increased expression of TRPC1, TRPC4, TRPV5, TRPV6, TRPM8, and Orai2 was significantly associated with a lower risk of systemic recurrence after RP, independently of the prostate-specific antigen (PSA) level, percentage of positive biopsies, and surgical margin (SM) status (P = .007, P = .01, P < .001, P = .0065, P = .007, and P = .01, respectively). For TRPC4, TRPV5, and TRPV6, this association was also independent of Gleason score and pT stage. Moreover, overexpression of TRPV6 and Orai2 was significantly associated with longer time to recurrence after RP (P = .048 and .023, respectively). Overexpression of TRPC4, TRPV5, TRPV6, and Orai2 transcripts was observed in group R- (3.71-, 5.7-, 1.14-, and 2.65-fold increase, respectively). CONCLUSIONS: This is the first study to suggest the independent prognostic value of certain proteins involved in Ca2+ influx in systemic recurrence after RP: overexpression of TRPC1, TRPC4, TRPV5, TRPV6, TRPM8, and Orai2 is associated with a lower risk of systemic recurrence. TRPC4, TRPV5, and TRPV6 appear to be particularly interesting, as they are independent of the five commonly used predictive factors, that is, PSA, percentage of positive biopsies, SM status, Gleason score, and pT stage.

Functional characterization and phenotypic spectrum of three recurrent disease-causing deep intronic variants of the CFTR gene.

BACKGROUND: The CFTR genotype remains incomplete in 1% of Cystic Fibrosis (CF) cases, because only one or no disease-causing variants is detected after extended analysis. This fraction is probably higher in CFTR-Related Disorders (CFTR-RD). Deep-intronic CFTR variants are putative candidates to fill this gap. However, the recurrence, phenotypic spectrum and full molecular characterization of newly reported variants are unknown. METHODS: Minigenes and analysis of CFTR transcripts in nasal epithelial cells were used to determine the impact on CFTR splicing of intronic variants that we previously identified by next generation sequencing of the whole CFTR locus. Phenotypic data were collected in 19 patients with CF and CFTR-RD, in whom one of the deep intronic variants has been detected. RESULTS: Three deep-intronic variants promoted the inclusion of pseudo-exons (PE) in the CFTR transcript, hindering the synthesis of a functional protein. The c.2989-313A > T variant, detected in four patients with CF or CFTR-RD from three different families, led to the inclusion of a 118 bp PE. The c.3469-1304C > G variant promoted the inclusion of a 214 bp-PE and was identified in five patients with CF from four families. Haplotype analysis confirmed that this variant was associated with one CF chromosome of African origin. The most represented variant in our cohort was the c.3874-4522A > G, detected in 10 patients with various phenotypes, from male infertility to CF with pancreatic insufficiency. CONCLUSION: These three deep intronic CFTR variants are associated with a large phenotypic spectrum, including typical CF. They should be included in CF diagnostic testing and carrier screening strategies.

Deciphering the molecular basis of ferroportin resistance to hepcidin: Structure/function analysis of rare SLC40A1 missense mutations found in suspected hemochromatosis type 4 patients.

Genetic medicine applied to the study of hemochromatosis has identified the systemic loop controlling iron homeostasis, centered on hepcidin-ferroportin interaction. Current challenges are to dissect the molecular pathways underlying liver hepcidin synthesis in response to circulatory iron, HFE, TFR2, HJV, TMPRSS6 and BMP6 functions, and to define the major structural elements of hepcidin-ferroportin interaction. We built a first 3D model of human ferroportin structure, using the crystal structure of EmrD, a bacterial drug efflux transporter of the Major Facilitator Superfamily, as template. The model enabled study of disease-associated mutations, and guided mutagenesis experiments to determine the role of conserved residues in protein stability and iron transport. Results revealed novel amino acids that are critical for the iron export function and the hepcidin-mediated inhibition mechanism: for example, tryptophan 42, localized in the extracellular end of the ferroportin pore and involved in both biological functions. Here, we propose a strategy that is not limited to structure analysis, but integrates information from different sources, including human disease-associated mutations and functional in vitro assays. The first major hypothesis of this PhD thesis is that ferroportin resistance to hepcidin relies on different molecular mechanisms that are critical for ferroportin endocytosis, and include at least three fundamental steps: (i) hepcidin binding to ferroportin, (ii) structural reorganization of the N- and C-ter ferroportin lobes, and (iii) ferroportin ubiquitination.

From genetic variability to phenotypic expression of blood group systems.

More than 300 red blood cell (RBC) antigens belonging to 36 blood group systems have been officially reported in humans by the International Society of Blood Transfusion (ISBT). Phenotypic variability is directly linked to the expression of the 41 blood group genes. The Rh blood group system, which is composed of 54 antigens, is the most complex and polymorphic system. Many rare genetic variants within the RH (RHD and RHCE) genes, involving various mutational mechanisms (single-nucleotide substitutions, short insertions/deletions, rearrangements, large deletions), have been reported in the literature and reference databases. Expression of the variants induces variable clinical outcomes depending on their nature and impact on antigen structure. Their respective molecular and cellular effects remain however poorly studied. Biological resources to conduct this research are also barely available. We have paid a specific attention to three different classes of single-nucleotide substitutions: 1/ splice site variants in the Rh, Kell, Kidd, Junior and Langereis systems by the minigene splicing assay developed locally; 2/ missense variants in the RhD protein and their effect on intermolecular interaction with its protein partner RhAG, intracellular trafficking and plasma membrane integration; and 3/ synonymous variants in the RHD gene. Overall not only this project has fundamental objectives by analyzing the functional effect of variants in order to make genotype-phenotype correlation, but the aim is also to develop/engineer molecular tools and cell models to carry out those studies.

NGS and blood group systems: State of the art and perspectives.

Molecular analysis, or genotyping, of genes involved in the expression of blood group antigens has been a standard strategy used in immunohaematology laboratories routinely. For the past ten years, next-generation sequencing (NGS), or second-generation sequencing, has become the reference method in genetics. Extensive study of distinct targets, large genomic regions, and even whole genome is henceforth possible by this approach at minimal cost. Blood group genotyping has thus taken advantage of this technological advent. A few preliminary studies have open the way to NGS in this field by studying one or several genes, in a wide range of samples (donors and patients) by using several different platforms. These works have helped in the identification of both the benefits and limitations of the technology. Other recently published studies have benefited from these preliminary data to improve the methodology, specificity and accuracy of output data. In parallel novel strategies, i.e. third-generation sequencing, which can sequence long DNA regions at the single-molecule level, have emerged and shown promise for the potential resolution of complex rearrangements involving genes of the Rh and MNS blood group systems respectively. As technological and methodological hurdles have been overcome, these approaches may be used in a clinical situation in a near future.

Evaluation of quantitative PCR for early diagnosis of Pseudomonas aeruginosa infection in cystic fibrosis: a prospective cohort study.

OBJECTIVES: Early detection of Pseudomonas aeruginosa lung positivity is a key element in cystic fibrosis (CF) management. PCR has increased the accuracy of detection of many microorganisms. Clinical relevance of P. aeruginosa quantitative PCR (qPCR) in this context is unclear. Our aim was to determine P. aeruginosa qPCR sensitivity and specificity, and to assess the possible time saved by qPCR in comparison with standard practice (culture). METHODS: A multicentre cohort study was conducted over a 3-year period in 96 patients with CF without chronic P. aeruginosa colonization. Sputum samples were collected at each visit. Conventional culture and two-step qPCR (oprL qPCR and gyrB/ecfX qPCR) were performed for 707 samples. The positivity criteria were based on the qPCR results, defined in a previous study as follow: oprL qPCR positivity alone if bacterial density was <730 CFU/mL or oprL qPCR combined with gyrB/ecfX qPCR if bacterial density was ≥730 CFU/mL. RESULTS: During follow up, 36 of the 96 patients with CF were diagnosed on culture as colonized with P. aeruginosa. This two-step qPCR displayed a sensitivity of 94.3% (95% CI 79.7%-98.6%), and a specificity of 86.3% (95% CI 83.4%-88.7%). It enabled P. aeruginosa acquisition to be diagnosed earlier in 20 patients, providing a median detection time gain of 8 months (interquartile range 3.7-17.6) for them. CONCLUSIONS: Implementing oprL and gyrB/ecfX qPCR in the management of patients with CF allowed earlier detection of first P. aeruginosa lung positivity than culture alone.

The experience of extended blood group genotyping by next-generation sequencing (NGS): investigation of patients with sickle-cell disease.

BACKGROUND: Patients suffering from haemoglobinopathies may be treated by red blood cell (RBC) transfusion on a regular basis and then exposed to multiple antigens with a recurrent, potential risk of alloimmunization routinely prevented by extended RBC antigen cross-matching. While time-consuming and labour-intensive serological analyses are the gold standard for RBC typing, genotyping by current high-throughput molecular tools, including next-generation sequencing (NGS), appears to offer a potent alternative. STUDY DESIGN AND METHODS: The potential of extended blood group genotyping (EBGG) by NGS of 17 genes involved in 14 blood group systems was evaluated in a cohort of 48 patients with sickle-cell disease. Sample preparation and sequencing were simplified and automated for future routine implementation. RESULTS: Sequencing data were obtained for all DNA samples with two different sequencing machines. Prediction of phenotypes could be made in 12 blood group systems and partially in two other blood group systems (Rh and MNS). Importantly, predicted phenotypes in the MNS (S/s), Duffy, Kidd and Kell systems matched well with serological data (98·9%), when available. Unreferenced alleles in the ACHE and ART4 genes, respectively, involved in the Yt and Dombrock blood groups, were identified, then contributing to extend the current knowledge of blood group molecular genetics. CONCLUSIONS: Overall, we consider that our strategy for NGS-based EBGG, assisted by a simple method for genotyping exons 1 and 2 of the pairs of homologous genes (i.e. RHD/RHCE and GYPA/GYPB), as well as the future support of potent bioinformatics tools, may be implemented for routine diagnosis in specific populations.

Function and regulation of TRPM7, as well as intracellular magnesium content, are altered in cells expressing ΔF508-CFTR and G551D-CFTR.

Cystic fibrosis (CF), one of the most common fatal hereditary disorders, is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The CFTR gene product is a multidomain adenosine triphosphate-binding cassette (ABC) protein that functions as a chloride (Cl(-)) channel that is regulated by intracellular magnesium [Mg(2+)]i. The most common mutations in CFTR are a deletion of a phenylalanine residue at position 508 (ΔF508-CFTR, 70-80 % of CF phenotypes) and a Gly551Asp substitution (G551D-CFTR, 4-5 % of alleles), which lead to decreased or almost abolished Cl(-) channel function, respectively. Magnesium ions have to be finely regulated within cells for optimal expression and function of CFTR. Therefore, the melastatin-like transient receptor potential cation channel, subfamily M, member 7 (TRPM7), which is responsible for Mg(2+) entry, was studies and [Mg(2+)]i measured in cells stably expressing wildtype CFTR, and two mutant proteins (ΔF508-CFTR and G551D-CFTR). This study shows for the first time that [Mg(2+)]i is decreased in cells expressing ΔF508-CFTR and G551D-CFTR mutated proteins. It was also observed that the expression of the TRPM7 protein is increased; however, membrane localization was altered for both ΔF508del-CFTR and G551D-CFTR. Furthermore, both the function and regulation of the TRPM7 channel regarding Mg(2+) is decreased in the cells expressing the mutated CFTR. Ca(2+) influx via TRPM7 were also modified in cells expressing a mutated CFTR. Therefore, there appears to be a direct involvement of TRPM7 in CF physiopathology. Finally, we propose that the TRPM7 activator Naltriben is a new potentiator for G551D-CFTR as the function of this mutant increases upon activation of TRPM7 by Naltriben.

[Congenital bilateral absence of vas deferens: From diagnosis to assisted reproductive techniques - the experience of three centers]. / Absence bilatérale des canaux déférents : du diagnostic à l'assistance médicale à la procréation. Expérience de 3 centres.

OBJECTIVES: To review the management with assisted reproductive technologies (ART) of men with congenital bilateral absence of vas deferens (CBAVD), associated with cystic fibrosis or not, after surgical retrieval [epididymal aspiration (MESA) or testicular biopsy (TESE)]. METHODS: Multicenter retrospective study made of 2 groups: CBAVD and cystic fibrosis (CF) or CBAVD only (CF-RD). Two centers performed MESA (Brest and Nantes) and one TESE (Rennes). Sperm numeration, motility, vitality, morphology and nuclear maturity were measured in both centers performing MESA. Fertilization rate (TF) and cumulated progressive pregnancy rate by retrieved oocyte (TGC) were compared between centers following ART. RESULTS: Ninety patients underwent surgical retrieval between January 1996 and March 2013, 30 in the CF group and 60 in the CF-RD group. Semen parameters were comparable between groups and centers. Fifty-eight (22 in the CF group and 36 in the CF-RD group) patients received ART between April 1996 and October 2014. TF was 50% and 52% and TGC 26% and 32% in the CF group and CF-RD groups, respectively. The results did not differ between groups but TGC was higher in Rennes than in the other two centers. CONCLUSION: Both semen parameters and ART results are comparable and similar to those reported in the literature. As shown by the results obtained in Rennes, TESE seems to be more effective.

[Genetics and modifier genes, atypical and rare forms]. / Génétique et gènes modificateurs, formes atypiques et rares.

Cystic fibrosis (CF) is defined as the most common life shortening genetic disorder in the Caucasian populations. The cloning of the gene responsible for the disease - the CFTR (Cystic Fibrosis Transmembrane conductance Regulator) gene - twenty years ago has greatly improved our knowledge of the pathophysiology of CF. That disease is characterized by a highly phenotypic variability and the CFTR mutations cannot explain all the variability observed in the disease severity. The possible influence of the environment and modifier genes has therefore been evocated. Several genetic variants coding for genes involved in the physiopathology of the disease have been studied, like genes involve in the immunity and the inflammatory response. Some of these genes have indeed been shown to influence the disease severity. A new approach has also been developed, analyzing the whole genome. This review summarizes the genetic basis of CF in its classical and atypical forms, as well as the work performed in the field of modifier genes.

Autosomal dominant polycystic kidney disease in University Clinic of Nephrology and Haemodialysis of Cotonou: clinical and genetical findings.

Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary kidney disease, but poorly studied in Africa. Its frequency in the University Clinic of Nephrology and Hemodialysis of Cotonou during the ten last years was 7 cases per year with a hospital prevalence estimated at 18 per 1000. The mean age of patients was 47.2 years extending from 29 to 70 years. Males were predominant with a sex ratio of 1.13. Family history was found in 47% of patients. The most common manifestations were lumbar pain (62%), high blood pressure (59%) urinary tract infections (53%), hematuria (46%), and abdominal masses (43%). Hepatic cysts were the most extra renal manifestations, found in 34% of cases. Renal failure was observed in 72% of patients of our series, six of them were under dialysis. Direct sequencing of polycystin 1 gene enabled us to identify some new mutations: 4 nonsense mutations (p.Q2824X exon 23, p.Q1651X exon 15, p.W1666X exon 15, p.R966W exon 12), a duplication (c_1761.1745 dup exon 9), a deletion (c.9397 + 1_9397 + 8del intron 26) and a deletion-insertion (c.7290_7291delins CTGCA exon 18).

Recommendations for the classification of diseases as CFTR-related disorders.

Several diseases have been clinically or genetically related to cystic fibrosis (CF), but a consensus definition is lacking. Here, we present a proposal for consensus guidelines on cystic fibrosis transmembrane conductance regulator (CFTR)-related disorders (CFTR-RDs), reached after expert discussion and two dedicated workshops. A CFTR-RD may be defined as "a clinical entity associated with CFTR dysfunction that does not fulfil diagnostic criteria for CF". The utility of sweat testing, mutation analysis, nasal potential difference, and/or intestinal current measurement for the differential diagnosis of CF and CFTR-RD is discussed. Algorithms which use genetic and functional diagnostic tests to distinguish CF and CFTR-RDs are presented. According to present knowledge, congenital bilateral absence of vas deferens (CBAVD), acute recurrent or chronic pancreatitis and disseminated bronchiectasis, all with CFTR dysfunction, are CFTR-RDs.

Evidence of association between GDF5 polymorphisms and congenital dislocation of the hip in a Caucasian population.

OBJECTIVE: Congenital dislocation of the hip (CDH) is a multifactorial disease which involves genetic factors that are still unidentified. Recently, a functional polymorphism (rs143383) of the 5'-untranslated region of GDF5 (Growth/Differentiation Factor 5) - previously reported to be associated with osteoarthritis - has been associated with CDH in a Chinese population. The aim of our study was to determine whether GDF5, known to be involved in bone, joint and cartilage morphogenesis, is also associated with CDH in Caucasians. DESIGN: We genotyped three tagSNPs (rs224334, rs143384, rs143383) in 239 cases and 239 controls from western Brittany (France) where CDH is frequent, and tested the association using both single-locus and haplotype-based approaches. RESULTS: The most significant association was observed with rs143384. The T allele of this SNP was overrepresented in cases (65.9% vs 55.9%, P=0.002). Under a recessive model, carriers of the TT genotype had a 1.71-fold higher risk of developing CDH than carriers of the other genotypes (OR(TT vs CT+CC)=1.71, 95% CI: [1.18-2.48], P=0.005). At a nominal level, the association was also significant with rs143383 (OR(TT vs CT+CC)=1.52, 95% CI: [1.05-2.19], P=0.026). The haplotype carrying the susceptibility alleles of these SNPs was also more frequent in cases (65.9% vs 55.9%, OR=1.53, 95% CI: [1.18-1.98], P=0.002). CONCLUSION: This study reports, for the first time, the association between GDF5 polymorphisms and CDH in Caucasians, and points out another polymorphism of interest that requires further investigation. Reduction in GDF5 expression might lead to developmental deficiency of ligaments and capsule in hip joint, and therefore contribute to CDH pathogenesis.

Factors influencing disease phenotype and penetrance in HFE haemochromatosis.

Haemochromatosis is predominantly associated with the HFE p.C282Y homozygous genotype, which is present in approximately 1 in 200 people of Northern European origin. However, not all p.C282Y homozygotes develop clinical features of haemochromatosis, and not all p.C282Y homozygotes even present abnormal iron parameters justifying venesection therapy. This situation was not apparent from initial genotype/phenotype correlation studies as there was a selection bias of patients. Only those patients with a significant iron burden were included in these early studies. It is now largely accepted that the p.C282Y/p.C282Y genotype is necessary for the development of HFE haemochromatosis. However, this genotype provides few clues as to why certain symptoms are associated with the disease. Expression of iron overload in people with this genotype depends on the complex interplay of environmental factors and modifier genes. In this review, we restrict our discussion to work done in humans giving examples of animal models where this has helped clarify our understanding. We discuss penetrance, explaining that this concept normally does not apply to autosomal recessive disorders, and discuss the usefulness of different biochemical markers in ascertaining iron burden. Hepcidin, a peptide synthesized primarily by the liver, has been identified as the central regulator in iron homeostasis. Consequently, understanding its regulation is the key. We conclude that the main goal now is to identify important modifiers that have a significant and unambiguous effect on iron storage.