COMMD1-Mediated Ubiquitination Regulates CFTR Trafficking

The CFTR (cystic fibrosis transmembrane conductance regulator) protein is a large polytopic protein whose biogenesis is inefficient. To better understand the regulation of CFTR processing and trafficking, we conducted a genetic screen that identified COMMD1 as a new CFTR partner. COMMD1 is a protein associated with multiple cellular pathways, including the regulation of hepatic copper excretion, sodium uptake through interaction with ENaC (epithelial sodium channel) and NF-kappaB signaling. In this study, we show that COMMD1 interacts with CFTR in cells expressing both proteins endogenously. This interaction promotes CFTR cell surface expression as assessed by biotinylation experiments in heterologously expressing cells through regulation of CFTR ubiquitination. In summary, our data demonstrate that CFTR is protected from ubiquitination by COMMD1, which sustains CFTR expression at the plasma membrane. Thus, increasing COMMD1 expression may provide an approach to simultaneously inhibit ENaC absorption and enhance CFTR trafficking, two major issues in cystic fibrosis

Deciphering an isolated lung phenotype of NKX2-1 frameshift pathogenic variant

Backgroundto perform a functional analysis of a new NK2 homeobox 1 (NKX2-1) variant (c.85_86del denominated NKX2-1DEL) identified in a family presenting with isolated respiratory disease, in comparison to another frameshift variant (c.254dup denominated NKX2-1DUP) identified in a subject with classical brain-lung-thyroid syndrome.Methodspathogenic variants were introduced into the pcDNA3-1(+)-wt-TTF1 plasmid. The proteins obtained were analyzed by western blot assay. Subcellular localization was assessed by confocal microscopy in A549 and Nthy cells. Transactivation of SFTPA, SFTPB, SFTPC, and ABCA3 promoters was assessed in A549 cells. Thyroglobulin promoter activity was measured with the paired box gene 8 (PAX8) cofactor in Nthy cells.ResultsThe two sequence variants were predicted to produce aberrant proteins identical from the 86th amino acid, with deletion of their functional homeodomain, including the nuclear localization signal. However, 3D conformation prediction of the conformation prediction of the mutant protein assumed the presence of a nuclear localization signal, a bipartite sequence, confirmed by confocal microscopy showing both mutant proteins localized in the nucleus and cytoplasm. Transcriptional activity with SFTPA, SFTPB, SFTPC, ABCA3 and thyroglobulin promoters was significantly decreased with both variants. However, with NKX2-1DEL, thyroglobulin transcriptional activity was maintained with the addition of PAX8.ConclusionThese results provide novel insights into understanding the molecular mechanism of phenotypes associated with NKX2-1 pathogenic variants

Combined Computational-Experimental Analyses of CFTR Exon Strength Uncover Predictability of Exon-Skipping Level.

International audienceWith the increased number of identified nucleotide sequence variations in genes, the current challenge is to classify them as disease causing or neutral. These variants of unknown clinical significance can alter multiple processes, from gene transcription to RNA splicing or protein function. Using an approach combining several in silico tools, we identified some exons presenting weaker splicing motifs than other exons in the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) gene. These exons exhibit higher rates of basal skipping than exons harboring no identifiable weak splicing signals using minigene assays. We then screened 19 described mutations in three different exons, and identified exon-skipping substitutions. These substitutions induced higher skipping levels in exons having one or more weak splicing motifs. Indeed, this level remained under 2% for exons with strong splicing motifs and could reach 40% for exons having at least one weak motif. Further analysis revealed a functional exon splicing enhancer within exon 3 that was associated with the SR protein SF2/ASF and whose disruption induced exon skipping. Exon skipping was confirmed in vivo in two nasal epithelial cell brushing samples. Our approach, which point out exons with some splicing signals weaknesses, will help spot splicing mutations of clinical relevance

COMMD1-Mediated Ubiquitination Regulates CFTR Trafficking

The CFTR (cystic fibrosis transmembrane conductance regulator) protein is a large polytopic protein whose biogenesis is inefficient. To better understand the regulation of CFTR processing and trafficking, we conducted a genetic screen that identified COMMD1 as a new CFTR partner. COMMD1 is a protein associated with multiple cellular pathways, including the regulation of hepatic copper excretion, sodium uptake through interaction with ENaC (epithelial sodium channel) and NF-kappaB signaling. In this study, we show that COMMD1 interacts with CFTR in cells expressing both proteins endogenously. This interaction promotes CFTR cell surface expression as assessed by biotinylation experiments in heterologously expressing cells through regulation of CFTR ubiquitination. In summary, our data demonstrate that CFTR is protected from ubiquitination by COMMD1, which sustains CFTR expression at the plasma membrane. Thus, increasing COMMD1 expression may provide an approach to simultaneously inhibit ENaC absorption and enhance CFTR trafficking, two major issues in cystic fibrosis

Alternative Splicing at a NAGNAG Acceptor Site as a Novel Phenotype Modifier

Approximately 30% of alleles causing genetic disorders generate premature termination codons (PTCs), which are usually associated with severe phenotypes. However, bypassing the deleterious stop codon can lead to a mild disease outcome. Splicing at NAGNAG tandem splice sites has been reported to result in insertion or deletion (indel) of three nucleotides. We identified such a mechanism as the origin of the mild to asymptomatic phenotype observed in cystic fibrosis patients homozygous for the E831X mutation (2623G>T) in the CFTR gene. Analyses performed on nasal epithelial cell mRNA detected three distinct isoforms, a considerably more complex situation than expected for a single nucleotide substitution. Structure-function studies and in silico analyses provided the first experimental evidence of an indel of a stop codon by alternative splicing at a NAGNAG acceptor site. In addition to contributing to proteome plasticity, alternative splicing at a NAGNAG tandem site can thus remove a disease-causing UAG stop codon. This molecular study reveals a naturally occurring mechanism where the effect of either modifier genes or epigenetic factors could be suspected. This finding is of importance for genetic counseling as well as for deciding appropriate therapeutic strategies

Contribution à l’amélioration des connaissances sur la relation génotype-phénotype dans la mucoviscidose et caractérisation phénotypique de l’inflammation pulmonaire

Cystic fibrosis (CF) is the most common severe autosomal recessive disorder in the Caucasian population. Apart from classical CF, there is a broad range of phenotypes associated with a huge genotypic variability concerning the mutations in the CFTR gene. In order to develop a mutation specific therapeutic approach, a better understanding of the phenotype]genotype correlation and its underlying mechanism is primordial. In the first part of our work, we focused on genotype‐phenotype correlation. With a retrospective study on 694 cases of prenatal diagnosis of CF for fetal bowel anomalies, we report on the most evocative digestive abnormal patterns and propose to revise current strategies for the CFTR gene analysis. The second part concerns the CFTR promoter functional analysis. Mutations which conserve a residual CFTR channel function, such as mutations affecting the gene regulation, can be involved in atypical phenotypes. However, knowledge about the CFTR promoter reminds poor and the clinical significance of new variants identified in this region is difficult to evaluate. Our implementation of functional analysis tools will improve the appreciation of such new variants in the CFTR promoter and open new insights for the gene regulation study. In the third part, we contributed to study the inappropriate pulmonary inflammation which characterizes CF, the respiratory affection being the major factor of morbidity and mortality in the disease. COMMD1 is a pleiotropic protein involved in CFTR trafficking, ionic exchanges in the airways surface liquid and inflammation inhibition. In our study, we show the anti]inflammatory role of COMMD1 in the context of cystic fibrosis. Modulation of the exaggerated inflammation belongs to currently therapeutic challenges, and we show the ability of COMMD1, a protein partner of CFTR, to buffer the NF-kB pathway activationLa mucoviscidose est la maladie autosomique récessive grave la plus fréquente dans la population d'origine caucasienne. Elle est due a des anomalies du gène CFTR, dont les multiples mutations décrites rendent compte en partie de la grande variabilité phénotypique. A l'heure du développement de thérapies ciblées selon les mutations portées par les patients, mieux comprendre les mécanismes sous-jacents des relations génotype-phénotype semble de première importance. La première partie de ce travail est focalisée sur la relation génotype-phénotype. Par une étude rétrospective de 694 demandes de diagnostic prénatal de la mucoviscidose sur signes d'appel échographique, nous définissons les profils d'anomalies digestives les plus discriminants, et proposons en conséquence une révision de la stratégie d'analyse moléculaire du gène CFTR. La deuxième partie concerne la mise en place d’outils nécessaires à l’exploration fonctionnelle du promoteur CFTR. En effet, dans les formes atypiques de la maladie, la fonction résiduelle de CFTR peut expliquer le phénotype. Des anomalies de régulation de la transcription peuvent parfois être à l’origine de telles formes modérées. La mise en place des outils d’analyse des variants du promoteur permettra de mieux interpréter leur pathogénicité et d’ouvrir de nouvelles pistes pour la compréhension de la régulation de ce gène. La troisième partie s'intéresse a l'inflammation pulmonaire anormalement régulée qui est une caractéristique phénotypique et le premier facteur de morbidité et de mortalité de la mucoviscidose. La protéine COMMD1 est une protéine pleiotrope participant a de nombreux processus cellulaires, principalement par un mécanisme de stabilisation d'interactions protéiques. Elle est impliquée dans les trois voies thérapeutiques : modulation de CFTR, restauration du liquide de surface des voies aériennes et inhibition de l'inflammation. Notre étude a permis d'observer l'activité anti-inflammatoire de COMMD1 dans le contexte d'inflammation exacerbée décrite chez les patients atteints de mucoviscidose. La réduction de cette réaction exacerbée fait partie des enjeux thérapeutiques actuels et nous montrons ici que la protéine COMMD1 est un bon candidat comme modérateur de l'inflammation mediee par NF-kB dans cette pathologie

Contribution to the appreciation of the genotype‐phenotype correlation in cystic fibrosis and phenotypic characterization of lung inflammation

La mucoviscidose est la maladie autosomique récessive grave la plus fréquente dans la population d\u81'origine caucasienne. Elle est due a des anomalies du gène CFTR, dont les multiples mutations décrites rendent compte en partie de la grande variabilité phénotypique. A l\u81'heure du développement de thérapies ciblées selon les mutations portées par les patients, mieux comprendre les mécanismes sous\u81-jacents des relations génotype\u81-phénotype semble de première importance. La première partie de ce travail est focalisée sur la relation génotype\u81-phénotype. Par une étude rétrospective de 694 demandes de diagnostic prénatal de la mucoviscidose sur signes d\u81'appel échographique, nous définissons les profils d\u81'anomalies digestives les plus discriminants, et proposons en conséquence une révision de la stratégie d\u81'analyse moléculaire du gène CFTR. La deuxième partie concerne la mise en place d’outils nécessaires à l’exploration fonctionnelle du promoteur CFTR. En effet, dans les formes atypiques de la maladie, la fonction résiduelle de CFTR peut expliquer le phénotype. Des anomalies de régulation de la transcription peuvent parfois être à l’origine de telles formes modérées. La mise en place des outils d’analyse des variants du promoteur permettra de mieux interpréter leur pathogénicité et d’ouvrir de nouvelles pistes pour la compréhension de la régulation de ce gène. La troisième partie s\u81'intéresse a l\u81'inflammation pulmonaire anormalement régulée qui est une caractéristique phénotypique et le premier facteur de morbidité et de mortalité de la mucoviscidose. La protéine COMMD1 est une protéine pleiotrope participant a de nombreux processus cellulaires, principalement par un mécanisme de stabilisation d\u81'interactions protéiques. Elle est impliquée dans les trois voies thérapeutiques : modulation de CFTR, restauration du liquide de surface des voies aériennes et inhibition de l\u81'inflammation. Notre étude a permis d\u81'observer l\u81'activité anti\u81-inflammatoire de COMMD1 dans le contexte d\u81'inflammation exacerbée décrite chez les patients atteints de mucoviscidose. La réduction de cette réaction exacerbée fait partie des enjeux thérapeutiques actuels et nous montrons ici que la protéine COMMD1 est un bon candidat comme modérateur de l\u81'inflammation mediee par NF\u81-kB dans cette pathologie.Cystic fibrosis (CF) is the most common severe autosomal recessive disorder in the Caucasian population. Apart from classical CF, there is a broad range of phenotypes associated with a huge genotypic variability concerning the mutations in the CFTR gene. In order to develop a mutation specific therapeutic approach, a better understanding of the phenotype\u81]genotype correlation and its underlying mechanism is primordial. In the first part of our work, we focused on genotype‐phenotype correlation. With a retrospective study on 694 cases of prenatal diagnosis of CF for fetal bowel anomalies, we report on the most evocative digestive abnormal patterns and propose to revise current strategies for the CFTR gene analysis. The second part concerns the CFTR promoter functional analysis. Mutations which conserve a residual CFTR channel function, such as mutations affecting the gene regulation, can be involved in atypical phenotypes. However, knowledge about the CFTR promoter reminds poor and the clinical significance of new variants identified in this region is difficult to evaluate. Our implementation of functional analysis tools will improve the appreciation of such new variants in the CFTR promoter and open new insights for the gene regulation study. In the third part, we contributed to study the inappropriate pulmonary inflammation which characterizes CF, the respiratory affection being the major factor of morbidity and mortality in the disease. COMMD1 is a pleiotropic protein involved in CFTR trafficking, ionic exchanges in the airways surface liquid and inflammation inhibition. In our study, we show the anti\u81]inflammatory role of COMMD1 in the context of cystic fibrosis. Modulation of the exaggerated inflammation belongs to currently therapeutic challenges, and we show the ability of COMMD1, a protein partner of CFTR, to buffer the NF\u81-kB pathway activatio

Structure-Based Understanding of ABCA3 Variants

International audienceABCA3 is a crucial protein of pulmonary surfactant biosynthesis, associated with recessive pulmonary disorders such as neonatal respiratory distress and interstitial lung disease. Mutations are mostly private, and accurate interpretation of variants is mandatory for genetic counseling and patient care. We used 3D structure information to complete the set of available bioinformatics tools dedicated to medical decision. Using the experimental structure of human ABCA4, we modeled at atomic resolution the human ABCA3 3D structure including transmembrane domains (TMDs), nucleotide-binding domains (NBDs), and regulatory domains (RDs) in an ATP-bound conformation. We focused and mapped known pathogenic missense variants on this model. We pinpointed amino-acids within the NBDs, the RDs and within the interfaces between the NBDs and TMDs intracellular helices (IHs), which are predicted to play key roles in the structure and/or the function of the ABCA3 transporter. This theoretical study also highlighted the possible impact of ABCA3 variants in the cytosolic part of the protein, such as the well-known p.Glu292Val and p.Arg288Lys variants

Hereditary sensory autonomic neuropathy type II: Report of two novel mutations in the FAM134B gene

International audienc

Hereditary sensory autonomic neuropathy type II: Report of two novel mutations in the FAM134B

International audienc