SPECTRUM OF CFTR MUTATIONS IN CYSTIC FIBROSIS AND IN CYSTIC FIBROSIS RELATED DISORDERS

A large spectrum of more than 2,000 CFTR mutations have been reported, associated with a very diverse clinical phenotype of Cystic Fibrosis (CF). In this work we analyzed the spectrum of CFTR mutations in CF and in CF-related disorders. The project specifically aims at investigating the following points:1) Validation of a new diagnostic screening method xTAG (Luminex; panel of 71 mutations), for routine analysis compared to the INNO-LiPA® (Innogenetics; panel of 36 mutations), used as a reference. Reproducible and concording results were obtained on the Luminex platform from DNA Innogenetics positive samples, using DNA extracted from different biological matrices, including blood samples, blood spots from Guthrie cards, chorionic villi and amniotic fluid. The new panel significantly increases the detection rate for patients of southern European origin.2) Study of frequencies of CFTR mutations in central Argentina in the Santa Fe province, which has never been characterized. A cohort of 83 patients out of an initial local selection of 121 was analysed. The results were combined with those of a previous study of the neighboring Cordoba province, leading to the proposal of a unique panel of 21 CFTR mutations for a first line molecular diagnosis in central Argentina.3) Analysis of the effects of mutations in the PRSS1, CFTR or SPINK1 genes on the severity of sporadic idiopathic pancreatitis. A retrospective cohort of 68 patients carrying mutations in the genes was compared to a paired cohort of age- and sex-matched patients with idiopathic pancreatitis and negative genetic testing. Clinical and morphological characteristics of patients were taken into account in the analysis. Clinical parameters were similar in the two cohorts, except for the age of pancreatic disease onset. A significantly higher occurrence of pancreas cancer was observed in the case group, particularly in patients carrying mutations in the CFTR gene. We therefore suggest that CFTR variants present a risk factor for pancreatic cancer.4) Updating the molecular analysis of the CFTR gene in a cohort of patients with allergic bronchopulmonary aspergillosis syndrome (ABPA). Samples from 18 patients previously analysed using a panel of 13 mutations and reported in a paper published in 2001 were re-analysed in 2010 using complete exon sequencing. Compared to the first analysis, 8 cases were found carrying one CFTR mutation and 4 with two mutations. The study considerably extends previous findings by demonstrating a strong link between ABPA in adults and CFTR mutations. Altogether, these studies contribute to shed new light on the molecular diagnosis of the CFTR gene in CF and in CF-related disorders.--------------------------------------------------------------------------------Un large spectre de plus de 2000 mutations CFTR ont été associées à un phénotype clinique très variable de la mucoviscidose. Dans ce travail, nous avons analysé le spectre des mutations du gène CFTR chez des patients atteints de mucoviscidose et dans les troubles associés à la mucoviscidose. Le projet vise spécifiquement à étudier les points suivants:1) Validation d'une nouvelle méthode de dépistage xTAG (Luminex, panel de 71 mutations), pour l'analyse de routine par rapport à l'INNO-LiPA® (Innogenetics, panel de 36 mutations), utilisé comme référence. Des résultats reproductibles et concordants ont été obtenus sur la plate-forme Luminex à partir d'échantillons ADN Innogenetics positifs utilisant de l'ADN extrait de différentes matrices biologiques, y compris des échantillons de sang, des taches de sang de cartes Guthrie, des villosités chorioniques et du liquide amniotique. Le nouveau panel augmente significativement le taux de détection pour les patients d'origine sud-européenne.2) Etude des fréquences des mutations du CFTR dans le centre de l'Argentine, dans la province de Santa Fe, qui n'a jamais été caractérisée. Une cohorte de 83 patients sur une sélection locale initiale de 121 a été analysée. Les résultats ont été combinés avec ceux d'une étude précédente de la province voisine de Cordoba, aboutissant à la proposition d'un panel unique de 21 mutations du CFTR pour un diagnostic moléculaire de première ligne au centre de l’Argentine.3) Analyse des effets des mutations dans les gènes PRSS1, CFTR ou SPINK1 sur la gravité de la pancréatite idiopathique sporadique. Une cohorte rétrospective de 68 patients porteurs de mutations dans ces gènes a été comparée à une cohorte, pairée pour l'âge et le sexe, de patients atteints de pancréatite idiopathique avec des tests génétiques négatifs. Les caractéristiques cliniques et morphologiques des patients ont été prises en compte dans l'analyse. Les paramètres cliniques étaient similaires dans les deux cohortes, à l'exception de l'âge d'apparition de la maladie pancréatique. Une augmentation significative du cancer du pancréas a été observée dans le groupe des patients porteurs de mutations, en particulier dans le gène CFTR. Nous suggérons donc que les variants de CFTR présentent un facteur de risque pour le cancer du pancréas.4) Mise à jour de l'analyse moléculaire du gène CFTR dans une cohorte de patients porteurs d'un syndrome d'aspergillose bronchopulmonaire allergique (ABPA). Les échantillons de 18 patients précédemment analysés à l'aide d'un panel de 13 mutations et rapportés dans un article publié en 2001 ont été ré-analysés en 2010 en utilisant le séquençage complet des exons. Comparativement à la première analyse, 8 cas ont été trouvés porteurs d'une mutation CFTR et 4 de deux mutations. L'étude a considérablement étendu les résultats précédents en démontrant une forte relation entre ABPA chez les adultes et mutations du CFTR.Au total, ces études contribuent à jeter un éclairage nouveau sur le diagnostic moléculaire du gène CFTR dans les cas de patients atteints de mucoviscidose et de syndromes associés à la mucoviscidose

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Further phenotype description, genotype characterization in patients with de novo interstitial deletion on 2p23.2-24.1

Interstitial deletions of the distal part of chromosome 2p seem to be rarely identified or reported: to date, only nine distinct patients have been published. The last three patients were diagnosed with the use of more recent molecular karyotyping technology (SNP array). We report on the natural history of an 8-year-old boy with dysmorphic features, postnatal overgrowth, microcephaly, generalized hypotonia, and global developmental delay. The diagnosis was accomplished by SNP array investigation that led to the identification of a de novo 7.4 Mb deletion of 2p23.2-p24.1. The present patient also developed a nonsyndromic auditory neuropathy. Since the deletion encompassed the OTOF gene, this haploinsufficiency suggests second allele sequencing as a possible cause (DFNB9). We describe the phenotype of the patient and review reports in patients with del 2p23 subsequent to the advent of the genomic era. At the time of identification of "new" micro- deletion and -duplication syndromes, the present report adds to the description of phenotype in patients with del(2)p(23.2;24.1) and the 2p23.2 region in particular

Identification and frequencies of cystic fibrosis mutations in central Argentina.

BACKGROUND: The Argentinian population is mainly of Caucasian origin, with a small contingent of indigenous descent. The aim of this study is to test the hypothesis that a panel of mutations designed for European countries is not optimal as a first-line molecular diagnosis for routine use in this country of mixed European origin. METHODS: Phenotype analyses combined with a European screening panel of 71 mutations followed by Sanger sequencing and large rearrangement study, were used to characterize the identification and distribution of CFTR mutations in the Santa Fe province of Argentina. RESULTS: Clinical review of 121 subjects suspected of CF during childhood led to selection of 83 unrelated patients. Thirty four different mutations, including two new ones, c.2554dupT and p.Leu49Pro, were detected. The total sensitivity was 91% (n = 151/166 alleles). CONCLUSIONS: Frequencies of CFTR mutations in Argentinian populations differ from those of their European ancestry. A new first line panel of 21 CFTR mutations with a sensitivity of 84% is proposed for routine use in central Argentin

Clinical and Morphological Characteristics of Sporadic Genetically Determined Pancreatitis as Compared to Idiopathic Pancreatitis: Higher Risk of Pancreatic Cancer in CFTR Variants.

Background/Aims: Idiopathic pancreatitis is considered to be a multigenic and multifactorial disease. Genetically determined pancreatitis is associated with mutations in the PRSS1,SPINK1 and CFTR genes. This study aimed at examining the clinical and morphological characteristics of patients diagnosed with genetically determined sporadic pancreatitis. Methods: Inclusion criteria were the presence of PRSS1,CFTR or SPINK1 gene mutations in patients with idiopathic recurrent or chronic pancreatitis. Patients with hereditary pancreatitis were excluded. Age- and sex-matched patients with idiopathic pancreatitis and negative genetic testing served as controls (n = 68). Results: Genetic testing was performed in 351 probands referred to our centre since 1999. Sixty-one patients (17.4%) carried at least 1 detected mutation in 1 of the 3 tested genes (34 CFTR, 10 PRSS1 and 13 SPINK1 mutations), and 4 patients showed a combination of mutations. Follow-up has been currently extended to a median of 5 years (range 1-40). Similar clinical features were noted in the case and matched groups except for an earlier age of onset of pancreatic symptoms and a higher incidence of pancreatic cancer in the case group and in patients with CFTR mutations compared to the control group (p < 0.05). The standardized incidence ratio, the ratio of observed to expected pancreatic cancers, averaged 26.5 (95% confidence interval 8.6-61.9). All pancreatic cancer patients were smokers. Conclusion: Clinical parameters of patients with sporadic idiopathic pancreatitis and gene mutations are similar to those of age- and sex-matched patients without gene mutations, except for the age of pancreatic disease onset. A significantly higher occurrence of pancreas cancer was observed in the case group, particularly in those patients carrying CFTR mutations. We therefore suggest to include patients with CFTR variants presenting with risk factors in a screening and surveillance programme and to strongly advise them to stop smoking