1
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Couloigner L, Planes M, Ka C, Audebert-Bellanger S, Redon S, Benech C, Rouault K, Küry S, Peudenier S, Autret S, Gourlaouen I, Bonneau D, Odent S, Bézieau S, Gilbert-Dussardier B, Toutain A, Boland A, Deleuze JF, Le Marechal C, Le Gac G, Ferec C, Uguen K. A new case of Kaufman Oculocerebrofacial syndrome caused by two splicing variants in UBE3B and review of the literature. Clin Genet 2023; 103:377-379. [PMID: 36444497 DOI: 10.1111/cge.14270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Loïc Couloigner
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
| | - Marc Planes
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
| | - Chandran Ka
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Séverine Audebert-Bellanger
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
| | - Sylvia Redon
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | - Karen Rouault
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Sebastien Küry
- Service de Génétique Médicale, Nantes Université, CHU Nantes, Nantes, France
- INSERM, l'institut du thorax, Nantes Université, CHU Nantes, CNRS, Nantes, France
| | - Sylviane Peudenier
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
| | - Sandrine Autret
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | | | - Sylvie Odent
- Service de Génétique Clinique, CHU de Rennes, UMR6290 CNRS, Université Rennes, Rennes, France
| | - Stéphane Bézieau
- Service de Génétique Médicale, Nantes Université, CHU Nantes, Nantes, France
- INSERM, l'institut du thorax, Nantes Université, CHU Nantes, CNRS, Nantes, France
| | | | - Annick Toutain
- Service de Génétique, CHU de Tours, UMR1253 iBrain INSERM, Université de Tours, Tours, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, CEA, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, CEA, Evry, France
| | - Cédric Le Marechal
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Gérald Le Gac
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Claude Ferec
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Kevin Uguen
- Service de Génétique Médicale, CHU de Brest, Brest, France
- Centre de Référence Déficiences Intellectuelles, Service de Pédiatrie, CHU de Brest, Brest, France
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
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2
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Leman R, Parfait B, Vidaud D, Girodon E, Pacot L, Le Gac G, Ka C, Ferec C, Fichou Y, Quesnelle C, Aucouturier C, Muller E, Vaur D, Castera L, Boulouard F, Ricou A, Tubeuf H, Soukarieh O, Gaildrat P, Riant F, Guillaud‐Bataille M, Caputo SM, Caux‐Moncoutier V, Boutry‐Kryza N, Bonnet‐Dorion F, Schultz I, Rossing M, Quenez O, Goldenberg L, Harter V, Parsons MT, Spurdle AB, Frébourg T, Martins A, Houdayer C, Krieger S. SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing. Hum Mutat 2022; 43:2308-2323. [PMID: 36273432 PMCID: PMC10946553 DOI: 10.1002/humu.24491] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/06/2022] [Accepted: 10/18/2022] [Indexed: 01/25/2023]
Abstract
Modeling splicing is essential for tackling the challenge of variant interpretation as each nucleotide variation can be pathogenic by affecting pre-mRNA splicing via disruption/creation of splicing motifs such as 5'/3' splice sites, branch sites, or splicing regulatory elements. Unfortunately, most in silico tools focus on a specific type of splicing motif, which is why we developed the Splicing Prediction Pipeline (SPiP) to perform, in one single bioinformatic analysis based on a machine learning approach, a comprehensive assessment of the variant effect on different splicing motifs. We gathered a curated set of 4616 variants scattered all along the sequence of 227 genes, with their corresponding splicing studies. The Bayesian analysis provided us with the number of control variants, that is, variants without impact on splicing, to mimic the deluge of variants from high-throughput sequencing data. Results show that SPiP can deal with the diversity of splicing alterations, with 83.13% sensitivity and 99% specificity to detect spliceogenic variants. Overall performance as measured by area under the receiving operator curve was 0.986, better than SpliceAI and SQUIRLS (0.965 and 0.766) for the same data set. SPiP lends itself to a unique suite for comprehensive prediction of spliceogenicity in the genomic medicine era. SPiP is available at: https://sourceforge.net/projects/splicing-prediction-pipeline/.
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- UNICAENNormandie UniversitéCaenFrance
| | - Béatrice Parfait
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Dominique Vidaud
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Emmanuelle Girodon
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Laurence Pacot
- Service de Génétique et Biologie Moléculaires, APHP, HUPCHôpital CochinParisFrance
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Claude Ferec
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and BiotechnologyUniversité de Bretagne OccidentaleBrestFrance
| | - Céline Quesnelle
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
| | - Camille Aucouturier
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Etienne Muller
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
| | - Dominique Vaur
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Laurent Castera
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Flavie Boulouard
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Agathe Ricou
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Hélène Tubeuf
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Integrative BiosoftwareRouenFrance
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | | | - Florence Riant
- Laboratoire de Génétique, AP‐HPGH Saint‐Louis‐Lariboisière‐Fernand WidalParisFrance
| | | | - Sandrine M. Caputo
- Department of Genetics, Institut CurieParis Sciences Lettres Research UniversityParisFrance
| | | | - Nadia Boutry‐Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers FréquentsHospices Civils de LyonLyonFrance
| | - Françoise Bonnet‐Dorion
- Departement de Biopathologie Unité de Génétique ConstitutionnelleInstitut Bergonie—INSERM U1218BordeauxFrance
| | - Ines Schultz
- Laboratoire d'OncogénétiqueCentre Paul StraussStrasbourgFrance
| | - Maria Rossing
- Centre for Genomic Medicine, RigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | - Olivier Quenez
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Louis Goldenberg
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Valentin Harter
- Department of BiostatisticsBaclesse Unicancer CenterCaenFrance
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteHerstonQueenslandAustralia
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteHerstonQueenslandAustralia
| | - Thierry Frébourg
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Department of geneticsRouen University HospitalRouenFrance
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- Department of geneticsRouen University HospitalRouenFrance
| | - Sophie Krieger
- Laboratoire de Biologie et Génétique du CancerCentre François BaclesseCaenFrance
- Inserm U1245, UNIROUEN, FHU‐G4 génomiqueNormandie UniversitéRouenFrance
- UNICAENNormandie UniversitéCaenFrance
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Le Gac G, Scotet V, Gourlaouen I, L'Hostis C, Merour MC, Karim Z, Deugnier Y, Bardou-Jacquet E, Lefebvre T, Assari S, Ferec C. Prevalence of HFE-related haemochromatosis and secondary causes of hyperferritinaemia and their association with iron overload in 1059 French patients treated by venesection. Aliment Pharmacol Ther 2022; 55:1016-1027. [PMID: 35122291 DOI: 10.1111/apt.16775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Venesection is the key therapy in haemochromatosis, but it remains controversial in hyperferritinaemia with moderate iron accumulation. There is substantial evidence that the results of HFE genotyping are routinely misinterpreted, while elevated serum ferritin has become more frequent in recent years in white adult populations following the increase of obesity and metabolic traits. AIMS To examine the reasons for prescribing venesection in 1,059 French patients during the period 2012-2015, determine the true prevalence of HFE-related haemochromatosis, and compare iron overload profiles between haemochromatosis and non-haemochromatosis patients. RESULTS Only 258 of the 488 patients referred for haemochromatosis had the p.[Cys282Tyr];[Cys282Tyr] disease causative genotype (adjusted prevalence: 24.4%). Of the 801 remaining patients, 112 (14.0%) had the debated p.[Cys282Tyr];[His63Asp] compound heterozygote genotype, 643 (80.3%) had central obesity, 475 (59.3%) had metabolic syndrome (MetS) and 93 (11.6%) were heavy drinkers. The non-haemochromatosis patients started therapeutic venesection 9 years later than haemochromatosis patients (P < 0.001). Despite similar serum ferritin values, they had lower transferrin saturation (41.1% vs 74.3%; P < 0.001), lower amounts of iron removed by venesection (1.7 vs 3.2 g; P < 0.001) and lower hepatic iron concentrations (107 vs 237 µmol/g; P < 0.001). CONCLUSIONS Haemochromatosis is over-diagnosed and is no longer the main reason for therapeutic venesection in France. Obesity and other metabolic abnormalities are frequently associated with mild elevation of serum ferritin, the MetS is confirmed in ~50% of treated patients. There is a minimal relationship between serum ferritin and iron overload in non-p.Cys282Tyr homozygotes. Our observations raise questions about venesection indications in non-haemochromatosis patients.
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Raud L, Le Tertre M, Vigneron L, Ka C, Richard G, Callebaut I, Chen JM, Férec C, Le Gac G, Fichou Y. Missense RHD single nucleotide variants induce weakened D antigen expression by altering splicing and/or protein expression. Transfusion 2021; 61:2468-2476. [PMID: 34110623 DOI: 10.1111/trf.16538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/09/2021] [Accepted: 04/28/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Although D variant phenotype is known to be due to genetic defects, including rare missense single nucleotide variants (SNVs), within the RHD gene, few studies have addressed the molecular and cellular mechanisms driving this altered expression. We and others showed previously that splicing is commonly disrupted by SNVs in constitutive splice sites and their vicinity. We thus sought to investigate whether rare missense SNVs located in "deep" exonic regions could also impair this mechanism. STUDY DESIGN AND METHODS Forty-six missense SNVs reported within exons 6 and 7 were first selected from the Human RhesusBase. Their respective effect on splicing was assessed by using an in vitro assay. An RhD-negative cell model was further generated by using the CRISPR-Cas9 approach. RhD-mutated proteins were overexpressed in the newly created model, and cell membrane expression of the D antigen was measured by flow cytometry. RESULTS Minigene splicing assay showed that 14 of 46 (30.4%) missense SNVs alter splicing. Very interestingly, further investigation of two missense SNVs, which both affect codon 338 and confer a weak D phenotype, showed various mechanisms: c.1012C>G (p.Leu338Val) disrupts splicing only, while c.1013T>C (p.Leu338Pro) alters only the protein structure, in agreement with in silico prediction tools and 3D protein structure visualization. CONCLUSION Our functional data set suggests that missense SNVs damage quantitatively D antigen expression by, at least, two different mechanisms (splicing alteration and protein destabilization) that may act independently. These data thereby contribute to extend the current knowledge of the molecular mechanisms governing weakened D expression.
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Affiliation(s)
- Loann Raud
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Marlène Le Tertre
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | | | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | - Gaëlle Richard
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | - Gérald Le Gac
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
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Le Tertre M, Ka C, Raud L, Berlivet I, Gourlaouen I, Richard G, Uguen K, Chen JM, Férec C, Fichou Y, Le Gac G. Splicing analysis of SLC40A1 missense variations and contribution to hemochromatosis type 4 phenotypes. Blood Cells Mol Dis 2020; 87:102527. [PMID: 33341511 DOI: 10.1016/j.bcmd.2020.102527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/24/2020] [Accepted: 11/24/2020] [Indexed: 02/09/2023]
Abstract
Hemochromatosis type 4, or ferroportin disease, is considered as the second leading cause of primary iron overload after HFE-related hemochromatosis. The disease, which is predominantly associated with missense variations in the SLC40A1 gene, is characterized by wide clinical heterogeneity. We tested the possibility that some of the reported missense mutations, despite their positions within exons, cause splicing defects. Fifty-eight genetic variants were selected from the literature based on two criteria: a precise description of the nucleotide change and individual evidence of iron overload. The selected variants were investigated by different in silico prediction tools and prioritized for midigene splicing assays. Of the 15 variations tested in vitro, only two were associated with splicing changes. We confirm that the c.1402G>A transition (p.Gly468Ser) disrupts the exon 7 donor site, leading to the use of an exonic cryptic splicing site and the generation of a truncated reading frame. We observed, for the first time, that the p.Gly468Ser substitution has no effect on the ferroportin iron export function. We demonstrate alternative splicing of exon 5 in different cell lines and show that the c.430A>G (p.Asn144Asp) variant promotes exon 5 inclusion. This could be part of a gain-of-function mechanism. We conclude that splicing mutations rarely contribute to hemochromatosis type 4 phenotypes. An in-depth investigation of exon 5 auxiliary splicing sequences may help to elucidate the mechanism by which splicing regulatory proteins regulate the production of the full length SLC40A1 transcript and to clarify its physiological importance.
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Affiliation(s)
- Marlène Le Tertre
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France
| | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | - Loann Raud
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Association Gaétan Saleün, F-29200, France
| | | | - Isabelle Gourlaouen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | | | - Kévin Uguen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Association Gaétan Saleün, F-29200, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France
| | - Gérald Le Gac
- Univ Brest, Inserm, EFS, UMR1078, GGB, F-29200, France; CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, F-29200, France; Laboratory of Excellence GR-Ex, F-75015, France.
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6
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Rodríguez-Palmero A, Schlüter A, Verdura E, Ruiz M, Martínez JJ, Gourlaouen I, Ka C, Lobato R, Casasnovas C, Le Gac G, Fourcade S, Pujol A. A novel hypomorphic splice variant in EIF2B5 gene is associated with mild ovarioleukodystrophy. Ann Clin Transl Neurol 2020; 7:1574-1579. [PMID: 33245593 PMCID: PMC7480926 DOI: 10.1002/acn3.51131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 06/27/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE To identify the genetic cause in an adult ovarioleukodystrophy patient resistant to diagnosis. METHODS We applied whole-exome sequencing (WES) to a vanishing white matter disease patient associated with premature ovarian failure at 26 years of age. We functionally tested an intronic variant by RT-PCR on patient's peripheral blood mononuclear cells (PBMC) and by minigene splicing assay. RESULTS WES analysis identified two novel variants in the EIF2B5 gene: c.725A > G (p.Tyr242Cys) and an intronic noncanonical mutation (c.1156 + 13G>A). This intronic mutation resulted into generation of various isoforms both in patient's PBMC and in the minigene splicing assay, showing that ~20% residual wild-type isoform is still expressed by the intronic-mutated allele alone, concordant with an hypomorphic effect of this variant. CONCLUSION We report two novel variants in EIF2B5, one of them a noncanonical intronic splice variant, located at a +13 intronic position. This position is mutated only in 0.05% of ClinVar intronic mutations described so far. Furthermore, we illustrate how minigene splicing assay may be advantageous when validating splice-altering variants, in this case highlighting the coexistence of wild-type and mutated forms, probably explaining this patient's milder, late-onset phenotype.
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Affiliation(s)
- Agustí Rodríguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Spain.,Pediatrics Department, University Hospital Germans Trias i Pujol, Badalona, 08916, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Edgard Verdura
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Juan José Martínez
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Chandran Ka
- INSERM U1078, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Laboratoire de Génétique Moleculaire et Histocompatibilité, CHRU de Brest, Hôpital Morvan, Brest, France
| | - Ricardo Lobato
- Neurology Department, Hospital Universitario Infanta Sofía, San Sebastián de los Reyes, 28703, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Neuromuscular Unit, Neurology Department, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, 08908, Spain
| | - Gérald Le Gac
- INSERM U1078, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Laboratoire de Génétique Moleculaire et Histocompatibilité, CHRU de Brest, Hôpital Morvan, Brest, France.,Université Bretagne Loire, Université de Bretagne Occidentale, IBSAM, Brest, France
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
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7
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Leman R, Tubeuf H, Raad S, Tournier I, Derambure C, Lanos R, Gaildrat P, Castelain G, Hauchard J, Killian A, Baert-Desurmont S, Legros A, Goardon N, Quesnelle C, Ricou A, Castera L, Vaur D, Le Gac G, Ka C, Fichou Y, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Boutry-Kryza N, Schultz I, Caux-Moncoutier V, Rossing M, Walker LC, Spurdle AB, Houdayer C, Martins A, Krieger S. Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants. BMC Genomics 2020; 21:86. [PMID: 31992191 PMCID: PMC6988378 DOI: 10.1186/s12864-020-6484-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 01/10/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Branch points (BPs) map within short motifs upstream of acceptor splice sites (3'ss) and are essential for splicing of pre-mature mRNA. Several BP-dedicated bioinformatics tools, including HSF, SVM-BPfinder, BPP, Branchpointer, LaBranchoR and RNABPS were developed during the last decade. Here, we evaluated their capability to detect the position of BPs, and also to predict the impact on splicing of variants occurring upstream of 3'ss. RESULTS We used a large set of constitutive and alternative human 3'ss collected from Ensembl (n = 264,787 3'ss) and from in-house RNAseq experiments (n = 51,986 3'ss). We also gathered an unprecedented collection of functional splicing data for 120 variants (62 unpublished) occurring in BP areas of disease-causing genes. Branchpointer showed the best performance to detect the relevant BPs upstream of constitutive and alternative 3'ss (99.48 and 65.84% accuracies, respectively). For variants occurring in a BP area, BPP emerged as having the best performance to predict effects on mRNA splicing, with an accuracy of 89.17%. CONCLUSIONS Our investigations revealed that Branchpointer was optimal to detect BPs upstream of 3'ss, and that BPP was most relevant to predict splicing alteration due to variants in the BP area.
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France. .,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France. .,Université Caen-Normandie, Caen, France.
| | - Hélène Tubeuf
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France.,Interactive Biosoftware, Rouen, France
| | - Sabine Raad
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Isabelle Tournier
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Céline Derambure
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Raphaël Lanos
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Pascaline Gaildrat
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Gaia Castelain
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Julie Hauchard
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Audrey Killian
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Stéphanie Baert-Desurmont
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Angelina Legros
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France
| | - Nicolas Goardon
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Céline Quesnelle
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France
| | - Agathe Ricou
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Laurent Castera
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Dominique Vaur
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France.,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, Brest, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, Bordeaux, France
| | | | - Nadia Boutry-Kryza
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, Lyon, France
| | - Inès Schultz
- Laboratoire d'Oncogénétique, Centre Paul Strauss, Strasbourg, France
| | | | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Claude Houdayer
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Alexandra Martins
- Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, Caen, France. .,Inserm U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, UNIROUEN, Normandy University, Caen, France. .,Université Caen-Normandie, Caen, France. .,Present address: Laboratoire de biologie et génétique des cancers, Centre François Baclesse, Caen, France.
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8
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Leman R, Gaildrat P, Le Gac G, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Bressac-de Paillerets B, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2019; 48:1600-1601. [PMID: 31863589 PMCID: PMC7026662 DOI: 10.1093/nar/gkz1212] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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9
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Guellec J, Elbahnsi A, Le Tertre M, Uguen K, Gourlaouen I, Férec C, Ka C, Callebaut I, Le Gac G. Molecular model of the ferroportin intracellular gate and implications for the human iron transport cycle and hemochromatosis type 4A. FASEB J 2019; 33:14625-14635. [PMID: 31690120 DOI: 10.1096/fj.201901857r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ferroportin 1 (FPN1) is a major facilitator superfamily transporter that is essential for proper maintenance of human iron homeostasis at the systemic and cellular level. FPN1 dysfunction leads to the progressive accumulation of iron in reticuloendothelial cells, causing hemochromatosis type 4A (or ferroportin disease), an autosomal dominant disorder that displays large phenotypic heterogeneity. Although crystal structures have unveiled the outward- and inward-facing conformations of the bacterial homolog Bdellovibrio bacteriovorus Fpn (or Bd2019) and calcium has recently been identified as an essential cofactor, our molecular understanding of the iron transport mechanism remains incomplete. Here, we used a combination of molecular modeling, molecular dynamics simulations, and Ala site-directed mutagenesis, followed by complementary in vitro functional analyses, to explore the structural architecture of the human FPN1 intracellular gate. We reveal an interdomain network that involves 5 key amino acids and is likely very important for stability of the iron exporter facing the extracellular milieu. We also identify inter- and intradomain interactions that rely on the 2 Asp84 and Asn174 critical residues and do not exist in the bacterial homolog. These interactions are thought to play an important role in the modulation of conformational changes during the transport cycle. We interpret these results in the context of hemochromatosis type 4A, reinforcing the idea that different categories of loss-of-function mutations exist. Our findings provide an unprecedented view of the human FPN1 outward-facing structure and the particular function of the so-called "gating residues" in the mechanism of iron export.-Guellec, J., Elbahnsi, A., Le Tertre, M., Uguen, K., Gourlaouen, I., Férec, C., Ka, C., Callebaut, I., Le Gac, G. Molecular model of the ferroportin intracellular gate and implications for the human iron transport cycle and hemochromatosis type 4A.
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Affiliation(s)
- Julie Guellec
- INSERM Unité Mixte de Recherche (UMR) 1078, Etablissement Français du Sang-Bretagne, Institut Brestois Santé-Agro-Matière, Université Bretagne Loire-Université de Brest, Brest, France.,Association Gaetan Saleun, Brest, France
| | - Ahmad Elbahnsi
- Muséum National d'Histoire Naturelle, UMR Centre National de la Recherche Scientifique (CNRS) 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, Paris, France
| | - Marlène Le Tertre
- INSERM Unité Mixte de Recherche (UMR) 1078, Etablissement Français du Sang-Bretagne, Institut Brestois Santé-Agro-Matière, Université Bretagne Loire-Université de Brest, Brest, France.,Service de Génétique Médicale, Centre Hospitalier Régional et Universitaire (CHRU) de Brest, Hôpital Morvan, Brest, France; and
| | - Kévin Uguen
- INSERM Unité Mixte de Recherche (UMR) 1078, Etablissement Français du Sang-Bretagne, Institut Brestois Santé-Agro-Matière, Université Bretagne Loire-Université de Brest, Brest, France.,Service de Génétique Médicale, Centre Hospitalier Régional et Universitaire (CHRU) de Brest, Hôpital Morvan, Brest, France; and
| | - Isabelle Gourlaouen
- INSERM Unité Mixte de Recherche (UMR) 1078, Etablissement Français du Sang-Bretagne, Institut Brestois Santé-Agro-Matière, Université Bretagne Loire-Université de Brest, Brest, France
| | - Claude Férec
- INSERM Unité Mixte de Recherche (UMR) 1078, Etablissement Français du Sang-Bretagne, Institut Brestois Santé-Agro-Matière, Université Bretagne Loire-Université de Brest, Brest, France.,Association Gaetan Saleun, Brest, France.,Service de Génétique Médicale, Centre Hospitalier Régional et Universitaire (CHRU) de Brest, Hôpital Morvan, Brest, France; and
| | - Chandran Ka
- INSERM Unité Mixte de Recherche (UMR) 1078, Etablissement Français du Sang-Bretagne, Institut Brestois Santé-Agro-Matière, Université Bretagne Loire-Université de Brest, Brest, France.,Service de Génétique Médicale, Centre Hospitalier Régional et Universitaire (CHRU) de Brest, Hôpital Morvan, Brest, France; and.,Laboratory of Excellence Laboratory of Excellence (GR-Ex), Paris, France
| | - Isabelle Callebaut
- Muséum National d'Histoire Naturelle, UMR Centre National de la Recherche Scientifique (CNRS) 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, Paris, France
| | - Gérald Le Gac
- INSERM Unité Mixte de Recherche (UMR) 1078, Etablissement Français du Sang-Bretagne, Institut Brestois Santé-Agro-Matière, Université Bretagne Loire-Université de Brest, Brest, France.,Service de Génétique Médicale, Centre Hospitalier Régional et Universitaire (CHRU) de Brest, Hôpital Morvan, Brest, France; and.,Laboratory of Excellence Laboratory of Excellence (GR-Ex), Paris, France
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10
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Leman R, Gaildrat P, Le Gac G, Ka C, Fichou Y, Audrezet MP, Caux-Moncoutier V, Caputo SM, Boutry-Kryza N, Léone M, Mazoyer S, Bonnet-Dorion F, Sevenet N, Guillaud-Bataille M, Rouleau E, Bressac-de Paillerets B, Wappenschmidt B, Rossing M, Muller D, Bourdon V, Revillon F, Parsons MT, Rousselin A, Davy G, Castelain G, Castéra L, Sokolowska J, Coulet F, Delnatte C, Férec C, Spurdle AB, Martins A, Krieger S, Houdayer C. Novel diagnostic tool for prediction of variant spliceogenicity derived from a set of 395 combined in silico/in vitro studies: an international collaborative effort. Nucleic Acids Res 2019; 46:7913-7923. [PMID: 29750258 PMCID: PMC6125621 DOI: 10.1093/nar/gky372] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/27/2018] [Indexed: 12/17/2022] Open
Abstract
Variant interpretation is the key issue in molecular diagnosis. Spliceogenic variants exemplify this issue as each nucleotide variant can be deleterious via disruption or creation of splice site consensus sequences. Consequently, reliable in silico prediction of variant spliceogenicity would be a major improvement. Thanks to an international effort, a set of 395 variants studied at the mRNA level and occurring in 5′ and 3′ consensus regions (defined as the 11 and 14 bases surrounding the exon/intron junction, respectively) was collected for 11 different genes, including BRCA1, BRCA2, CFTR and RHD, and used to train and validate a new prediction protocol named Splicing Prediction in Consensus Elements (SPiCE). SPiCE combines in silico predictions from SpliceSiteFinder-like and MaxEntScan and uses logistic regression to define optimal decision thresholds. It revealed an unprecedented sensitivity and specificity of 99.5 and 95.2%, respectively, and the impact on splicing was correctly predicted for 98.8% of variants. We therefore propose SPiCE as the new tool for predicting variant spliceogenicity. It could be easily implemented in any diagnostic laboratory as a routine decision making tool to help geneticists to face the deluge of variants in the next-generation sequencing era. SPiCE is accessible at (https://sourceforge.net/projects/spicev2-1/).
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Affiliation(s)
- Raphaël Leman
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Pascaline Gaildrat
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gérald Le Gac
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Chandran Ka
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Yann Fichou
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Marie-Pierre Audrezet
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Virginie Caux-Moncoutier
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
| | | | - Nadia Boutry-Kryza
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Mélanie Léone
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon, 69000 Lyon, France
| | - Sylvie Mazoyer
- Lyon Neuroscience Research Center-CRNL, Inserm U1028, CNRS UMR 5292, University of Lyon, 69008 Lyon, France
| | - Françoise Bonnet-Dorion
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | - Nicolas Sevenet
- Inserm U916, Département de Pathologie, Laboratoire de Génétique Constitutionnelle, Institut Bergonié, 33000 Bordeaux, France
| | | | - Etienne Rouleau
- Gustave Roussy, Université Paris-Saclay, Département de Biopathologie, 94805 Villejuif, France
| | | | - Barbara Wappenschmidt
- Division of Molecular Gynaeco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, 1017 Copenhagen, Denmark
| | - Danielle Muller
- Laboratoire d'Oncogénétique, Centre Paul Strauss, 67000 Strasbourg, France
| | - Violaine Bourdon
- Laboratoire d'Oncogénétique Moléculaire, Institut Paoli-Calmettes, 13009 Marseille, France
| | - Françoise Revillon
- Laboratoire d'Oncogénétique Moléculaire Humaine, Centre Oscar Lambret, 59000 Lille, France
| | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Antoine Rousselin
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Grégoire Davy
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Gaia Castelain
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Laurent Castéra
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | | | - Florence Coulet
- Service de génétique, Hôpital Pitié Salpétrière, AP-HP, 75013 Paris, France
| | - Capucine Delnatte
- Laboratoire de génétique moléculaire, CHU Nantes, 44000 Nantes, France
| | - Claude Férec
- Inserm UMR1078, Genetics, Functional Genomics and Biotechnology, Université de Bretagne Occidentale, 29200 Brest, France
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, 4006 Herston, Queensland, Australia
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France
| | - Sophie Krieger
- Laboratoire de Biologie Clinique et Oncologique, Centre François Baclesse, 14000 Caen, France.,Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, Normandie Univ, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine, 76031 Rouen, France.,Normandie Univ, UNICAEN, 14000 Caen, France
| | - Claude Houdayer
- Inserm U830, Institut Curie Centre de Recherches, 75005 Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, 75005 Paris, France.,Service de Génétique, Institut Curie, 75005 Paris, France
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11
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Ramsay L, Quillé ML, Orset C, de la Grange P, Rousselet E, Férec C, Le Gac G, Génin E, Timsit S. Blood transcriptomic biomarker as a surrogate of ischemic brain gene expression. Ann Clin Transl Neurol 2019; 6:1681-1695. [PMID: 31400065 PMCID: PMC6764628 DOI: 10.1002/acn3.50861] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 01/18/2023] Open
Abstract
Objectives Blood biomarkers for cerebral tissue ischemia are lacking. The goal was to identify a blood transcriptomic signature jointly identified in the ischemic brain. Methods A nonhuman primate model with middle cerebral artery (MCA) territory infarction was used to study gene expression by microarray during acute ischemic cerebral stroke in the brain and the blood. Brain samples were collected in the infarcted and contralateral non‐infarcted cortex as well as blood samples before and after occlusion. Gene expression was compared between the two brain locations to find differentially expressed genes. The expressions of these genes were then compared in the blood pre‐ and post‐occlusion. Results Hierarchical clustering of brain expression data revealed strong independent clustering of ischemic and nonischemic brain samples. The top five enriched, up‐regulated gene sets in the brain were TNF α signaling, apoptosis, P53 pathway, hypoxia, and UV response up. A comparison of differentially expressed genes in the brain and blood revealed a significant overlap of gene expression patterns. Stringent analysis of blood expression data from pre‐ and post‐occlusion samples in each monkey identified nine genes highly differentially expressed in both the brain and the blood. Many of these up‐regulated genes belong to pathways involved in cell death and DNA damage repair. Interpretation Common gene expression profile can be identified in the brain and blood and clearly differentiates ischemic from nonischemic conditions. Therefore, specific blood transcriptomic signature may represent a surrogate for brain ischemic gene expression.
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Affiliation(s)
- LeeAnn Ramsay
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Marie-Lise Quillé
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Cyrille Orset
- Department of Physiopathology and Imaging of Neurological Disorders, INSERM U1237, University Caen Normandie, GIP Cyceron, Caen, France
| | | | - Estelle Rousselet
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Claude Férec
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Gérald Le Gac
- Inserm U1078, Université Bretagne Loire Université de Bretagne Occidentale, IBSAM, Laboratoire de Genetique Moleculaire et Histocompatibilité, CHRU de Brest, Hopital Morvan, Brest, France
| | - Emmanuelle Génin
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France
| | - Serge Timsit
- UMR 1078 Genetics, Functional Genomics and Biotechnology, Inserm, Université de Brest, EFS, CHU de Brest, Brest, France.,Neurology and Stroke Department, Centre Hospitalier Régional Universitaire (CHRU), Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
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12
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Raud L, Ka C, Gourlaouen I, Callebaut I, Férec C, Le Gac G, Fichou Y. Functional analysis of novelRHDvariants: splicing disruption is likely to be a common mechanism of variant D phenotype. Transfusion 2019; 59:1367-1375. [DOI: 10.1111/trf.15210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/22/2018] [Accepted: 12/06/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Loann Raud
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies"; INSERM, EFS, Université de Brest, IBSAM, CHU de Brest; Brest France
- Laboratory of Excellence GR-Ex; Paris France
| | - Chandran Ka
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies"; INSERM, EFS, Université de Brest, IBSAM, CHU de Brest; Brest France
- Laboratory of Excellence GR-Ex; Paris France
| | - Isabelle Gourlaouen
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies"; INSERM, EFS, Université de Brest, IBSAM, CHU de Brest; Brest France
- Laboratory of Excellence GR-Ex; Paris France
| | - Isabelle Callebaut
- IMPMC, Sorbonne Universités - UMR CNRS 7590, UPMC Univ Paris 06, Muséum d'Histoire Naturelle, IRD UMR 206; Paris France
| | - Claude Férec
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies"; INSERM, EFS, Université de Brest, IBSAM, CHU de Brest; Brest France
- Laboratory of Excellence GR-Ex; Paris France
| | - Gérald Le Gac
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies"; INSERM, EFS, Université de Brest, IBSAM, CHU de Brest; Brest France
- Laboratory of Excellence GR-Ex; Paris France
| | - Yann Fichou
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies"; INSERM, EFS, Université de Brest, IBSAM, CHU de Brest; Brest France
- Laboratory of Excellence GR-Ex; Paris France
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13
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Ka C, Guellec J, Pepermans X, Kannengiesser C, Ged C, Wuyts W, Cassiman D, de Ledinghen V, Varet B, de Kerguenec C, Oudin C, Gourlaouen I, Lefebvre T, Férec C, Callebaut I, Le Gac G. The SLC40A1 R178Q mutation is a recurrent cause of hemochromatosis and is associated with a novel pathogenic mechanism. Haematologica 2018; 103:1796-1805. [PMID: 30002125 PMCID: PMC6278975 DOI: 10.3324/haematol.2018.189845] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/06/2018] [Indexed: 12/29/2022] Open
Abstract
Hemochromatosis type 4 is one of the most common causes of primary iron overload, after HFE-related hemochromatosis. It is an autosomal dominant disorder, primarily due to missense mutations in SLC40A1. This gene encodes ferroportin 1 (FPN1), which is the sole iron export protein reported in mammals. Not all heterozygous missense mutations in SLC40A1 are disease-causing. Due to phenocopies and an increased demand for genetic testing, rare SLC40A1 variations are fortuitously observed in patients with a secondary cause of hyperferritinemia. Structure/function analysis is the most effective way of establishing causality when clinical and segregation data are lacking. It can also provide important insights into the mechanism of iron egress and FPN1 regulation by hepcidin. The present study aimed to determine the pathogenicity of the previously reported p.Arg178Gln variant. We present the biological, clinical, histological and radiological findings of 22 patients from six independent families of French, Belgian or Iraqi decent. Despite phenotypic variability, all patients with p.Arg178Gln had elevated serum ferritin concentrations and normal to low transferrin saturation levels. In vitro experiments demonstrated that the p.Arg178Gln mutant reduces the ability of FPN1 to export iron without causing protein mislocalization. Based on a comparative model of the 3D structure of human FPN1 in an outward facing conformation, we argue that p.Arg178 is part of an interaction network modulating the conformational changes required for iron transport. We conclude that p.Arg178Gln represents a new category of loss-of-function mutations and that the study of “gating residues” is necessary in order to fully understand the action mechanism of FPN1.
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Affiliation(s)
- Chandran Ka
- UMR1078, INSERM, Université Bretagne Loire - Université de Bretagne Occidentale, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France.,Laboratoire de Génétique Moléculaire et Histocompatibilité, CHRU de Brest, Hôpital Morvan, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Julie Guellec
- UMR1078, INSERM, Université Bretagne Loire - Université de Bretagne Occidentale, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Association Gaetan Saleun, Brest, France
| | - Xavier Pepermans
- Center for Human Genetics, University Hospital of St-Luc, Brussels, Belgium
| | - Caroline Kannengiesser
- Laboratory of Excellence GR-Ex, Paris, France.,UMR1149, INSERM, Centre de Recherche sur l'Inflammation, Université Paris Diderot, AP-HP, Hôpital Bichat, Département de Génétique, France.,On behalf of the French National Network for the Molecular Diagnosis of Inherited Iron Overload Disorders (J. Rochette, E. Cadet, C. Kannengiesser, H. Puy, C. Ged, H. de Verneuil, G. Le Gac, C. Férec, S. Pissard, V. Gérolami), Brest, France
| | - Cécile Ged
- On behalf of the French National Network for the Molecular Diagnosis of Inherited Iron Overload Disorders (J. Rochette, E. Cadet, C. Kannengiesser, H. Puy, C. Ged, H. de Verneuil, G. Le Gac, C. Férec, S. Pissard, V. Gérolami), Brest, France.,INSERM U1035, BMGIC, CHU de Bordeaux, Laboratoire de Biochimie et Biologie Moléculaire, France
| | - Wim Wuyts
- Department of Medical Genetics, University and University Hospital of Antwerp, Edegem, Belgium
| | - David Cassiman
- Department of Gastroenterology-Hepatology and Metabolic Center, University Hospital of Leuven, Belgium
| | - Victor de Ledinghen
- Department of Gastroenterology and Digestive Oncology, University Hospital of Bordeaux, France
| | - Bruno Varet
- Université Paris Descartes et AP-HP, Hôpital Necker, Service d'Hématologie, France
| | | | - Claire Oudin
- UMR1149, INSERM, Centre de Recherche sur l'Inflammation, Université Paris Diderot, AP-HP, Hôpital Bichat, Département de Génétique, France
| | - Isabelle Gourlaouen
- UMR1078, INSERM, Université Bretagne Loire - Université de Bretagne Occidentale, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Thibaud Lefebvre
- UMR1149, INSERM, Centre de Recherche sur l'Inflammation, Université Paris Diderot, AP-HP, Hôpital Bichat, Département de Génétique, France
| | - Claude Férec
- UMR1078, INSERM, Université Bretagne Loire - Université de Bretagne Occidentale, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France.,Laboratoire de Génétique Moléculaire et Histocompatibilité, CHRU de Brest, Hôpital Morvan, France.,On behalf of the French National Network for the Molecular Diagnosis of Inherited Iron Overload Disorders (J. Rochette, E. Cadet, C. Kannengiesser, H. Puy, C. Ged, H. de Verneuil, G. Le Gac, C. Férec, S. Pissard, V. Gérolami), Brest, France
| | - Isabelle Callebaut
- UMR7590, CNRS, Sorbonne Universités, Université Pierre et Marie Curie-Paris, France
| | - Gérald Le Gac
- UMR1078, INSERM, Université Bretagne Loire - Université de Bretagne Occidentale, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France .,Laboratoire de Génétique Moléculaire et Histocompatibilité, CHRU de Brest, Hôpital Morvan, France.,Laboratory of Excellence GR-Ex, Paris, France.,On behalf of the French National Network for the Molecular Diagnosis of Inherited Iron Overload Disorders (J. Rochette, E. Cadet, C. Kannengiesser, H. Puy, C. Ged, H. de Verneuil, G. Le Gac, C. Férec, S. Pissard, V. Gérolami), Brest, France
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14
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Le Gac G, Scotet V, Gourlaouen I, L’Hostis C, Merour MC, Assari S, Ferec C. Importance du diagnostic différentiel de l’hyperferritinémie chez les patients traités par phlébotomies à l’établissement français du sang (EFS) : résultats de l’étude EMSAI (étude multicentrique sur les patients admis dans un protocole de saignées itératives). Transfus Clin Biol 2017. [DOI: 10.1016/j.tracli.2017.06.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Tchernitchko D, Scotet V, Lefebvre T, L'Hostis C, Gourlaouen I, Merour MC, Rebah K, Peoc'h K, Assari S, Ferec C, Puy H, Le Gac G. GNPAT polymorphism rs11558492 is not associated with increased severity in a large cohort of HFE p.Cys282Tyr homozygous patients. Hepatology 2017; 65:1069-1071. [PMID: 27474861 DOI: 10.1002/hep.28742] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
- Dimitri Tchernitchko
- Inserm UMR1149, Center for Inflammation Research, Paris, France; Department of Genetics, Bichat University Hospital, Paris, France; Center for Porphyria Research, Louis Mourier Hospital, Colombes, France; Laboratory of excellence, GR-Ex Paris, France
| | - Virginie Scotet
- Inserm UMR1078, French Blood Agency, Brest, France Gaëtan Saleun Fondation
| | - Thibaud Lefebvre
- Inserm UMR1149, Center for Inflammation Research, Paris, France; Department of Genetics, Bichat University Hospital, Paris, France; Center for Porphyria Research, Louis Mourier Hospital, Colombes, France; Laboratory of excellence, GR-Ex Paris, France
| | - Carine L'Hostis
- Inserm UMR1078, French Blood Agency, Brest, France Gaëtan Saleun Fondation
| | | | | | - Khadidja Rebah
- Inserm UMR1149, Center for Inflammation Research, Paris, France; Department of Genetics, Bichat University Hospital, Paris, France; Center for Porphyria Research, Louis Mourier Hospital, Colombes, France; Laboratory of excellence, GR-Ex Paris, France
| | - Katell Peoc'h
- Inserm UMR1149, Center for Inflammation Research, Paris, France; Department of Genetics, Bichat University Hospital, Paris, France; Center for Porphyria Research, Louis Mourier Hospital, Colombes, France; Laboratory of excellence, GR-Ex Paris, France
| | - Suzanne Assari
- French Blood Agency - Medical Direction, La Plaine Saint-Denis, France
| | - Claude Ferec
- Inserm UMR1078, French Blood Agency, Brest, France Gaëtan Saleun Fondation.,Department of Molecular Genetics and Histocompatibility, University Hospital of Brest, Brest, France
| | - Hervé Puy
- Inserm UMR1149, Center for Inflammation Research, Paris, France; Department of Genetics, Bichat University Hospital, Paris, France; Center for Porphyria Research, Louis Mourier Hospital, Colombes, France; Laboratory of excellence, GR-Ex Paris, France
| | - Gérald Le Gac
- Inserm UMR1078, French Blood Agency, Brest, France Gaëtan Saleun Fondation.,Department of Molecular Genetics and Histocompatibility, University Hospital of Brest, Brest, France
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16
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Le Gac G, Gourlaouen I, Ka C, Férec C. The p.Leu96Pro Missense Mutation in the BMP6 Gene Is Repeatedly Associated With Hyperferritinemia in Patients of French Origin. Gastroenterology 2016; 151:769-70. [PMID: 27590690 DOI: 10.1053/j.gastro.2016.03.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/18/2016] [Indexed: 02/08/2023]
Affiliation(s)
- Gérald Le Gac
- Inserm U1078, Université Bretagne Loire-Université de Bretagne Occidentale, IBSAM, CHRU de Brest, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Etablissement Français du Sang-Bretagne, Brest, France
| | - Isabelle Gourlaouen
- Inserm U1078, Université Bretagne Loire-Université de Bretagne Occidentale, IBSAM, CHRU de Brest, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Etablissement Français du Sang-Bretagne, Brest, France
| | - Chandran Ka
- Inserm U1078, Université Bretagne Loire-Université de Bretagne Occidentale, IBSAM, CHRU de Brest, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Etablissement Français du Sang-Bretagne, Brest, France
| | - Claude Férec
- Inserm U1078, Université Bretagne Loire-Université de Bretagne Occidentale, IBSAM, CHRU de Brest, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Etablissement Français du Sang-Bretagne, Brest, France
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17
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Quéré G, Descourt R, Robinet G, Autret S, Raguenes O, Fercot B, Alemany P, Uguen A, Férec C, Quintin-Roué I, Le Gac G. Mutational status of synchronous and metachronous tumor samples in patients with metastatic non-small-cell lung cancer. BMC Cancer 2016; 16:210. [PMID: 26968843 PMCID: PMC4788951 DOI: 10.1186/s12885-016-2249-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 03/03/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUNDS Despite reported discordance between the mutational status of primary lung cancers and their metastases, metastatic sites are rarely biopsied and targeted therapy is guided by genetic biomarkers detected in the primary tumor. This situation is mostly explained by the apparent stability of EGFR-activating mutations. Given the dramatic increase in the range of candidate drugs and high rates of drug resistance, rebiopsy or liquid biopsy may become widespread. The purpose of this study was to test genetic biomarkers used in clinical practice (EGFR, ALK) and candidate biomarkers identified by the French National Cancer Institute (KRAS, BRAF, PIK3CA, HER2) in patients with metastatic non-small-cell lung cancer for whom two tumor samples were available. METHODS A retrospective study identified 88 tumor samples collected synchronously or metachronously, from the same or two different sites, in 44 patients. Mutation analysis used SNaPshot (EGFR, KRAS, BRAF missense mutations), pyrosequencing (EGFR and PIK3CA missense mutations), sizing assays (EGFR and HER2 indels) and IHC and/or FISH (ALK rearrangements). RESULTS About half the patients (52%) harbored at least one mutation. Five patients had an activating mutation of EGFR in both the primary tumor and the metastasis. The T790M resistance mutation was detected in metastases in 3 patients with acquired resistance to EGFR tyrosine kinase inhibitors. FISH showed discordance in ALK status between a small biopsy sample and the surgical specimen. KRAS mutations were observed in 36% of samples, six patients (14%) having discordant genotypes; all discordances concerned sampling from different sites. Two patients (5%) showed PI3KCA mutations. One metastasis harbored both PI3KCA and KRAS mutations, while the synchronously sampled primary tumor was mutation free. No mutations were detected in BRAF and HER2. CONCLUSIONS This study highlighted noteworthy intra-individual discordance in KRAS mutational status, whereas EGFR status was stable. Intratumoral heterogeneity for ALK rearrangement suggests a limitation of single-biopsy analysis for therapeutic strategy with crizotinib.
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Affiliation(s)
- Gilles Quéré
- CHRU de Brest, Institut de Cancérologie et d'Hématologie, Brest, France
| | - Renaud Descourt
- CHRU de Brest, Institut de Cancérologie et d'Hématologie, Brest, France
| | - Gilles Robinet
- CHRU de Brest, Institut de Cancérologie et d'Hématologie, Brest, France
| | - Sandrine Autret
- CHRU de Brest, Hôpital Morvan, Bat 5 bis, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, 2 Avenue Foch, 29200, Brest, France.,Plateforme de Génétique Moléculaire des Cancers (INCa), Brest, France
| | - Odile Raguenes
- CHRU de Brest, Hôpital Morvan, Bat 5 bis, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, 2 Avenue Foch, 29200, Brest, France.,Plateforme de Génétique Moléculaire des Cancers (INCa), Brest, France
| | - Brigitte Fercot
- CHRU de Brest, Hôpital Morvan, Bat 5 bis, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, 2 Avenue Foch, 29200, Brest, France.,Plateforme de Génétique Moléculaire des Cancers (INCa), Brest, France
| | - Pierre Alemany
- Plateforme de Génétique Moléculaire des Cancers (INCa), Brest, France.,CHRU de Brest, Service d'Anatomopathologie, Brest, France
| | - Arnaud Uguen
- Plateforme de Génétique Moléculaire des Cancers (INCa), Brest, France.,Inserm U1078, Université de Brest, SFR SnInBioS, Brest, France.,CHRU de Brest, Service d'Anatomopathologie, Brest, France
| | - Claude Férec
- CHRU de Brest, Hôpital Morvan, Bat 5 bis, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, 2 Avenue Foch, 29200, Brest, France.,Plateforme de Génétique Moléculaire des Cancers (INCa), Brest, France.,Inserm U1078, Université de Brest, SFR SnInBioS, Brest, France
| | - Isabelle Quintin-Roué
- Plateforme de Génétique Moléculaire des Cancers (INCa), Brest, France.,CHRU de Brest, Service d'Anatomopathologie, Brest, France
| | - Gérald Le Gac
- CHRU de Brest, Hôpital Morvan, Bat 5 bis, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, 2 Avenue Foch, 29200, Brest, France. .,Plateforme de Génétique Moléculaire des Cancers (INCa), Brest, France. .,Inserm U1078, Université de Brest, SFR SnInBioS, Brest, France.
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18
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Moisan S, Berlivet S, Ka C, Le Gac G, Dostie J, Férec C. Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements. Nucleic Acids Res 2015; 44:2564-76. [PMID: 26615198 PMCID: PMC4824072 DOI: 10.1093/nar/gkv1300] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 11/07/2015] [Indexed: 12/19/2022] Open
Abstract
A mechanism by which control DNA elements regulate transcription over large linear genomic distances is by achieving close physical proximity with genes, and looping of the intervening chromatin paths. Alterations of such regulatory 'chromatin looping' systems are likely to play a critical role in human genetic disease at large. Here, we studied the spatial organization of a ≈790 kb locus encompassing the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Dysregulation of CFTR is responsible for cystic fibrosis, which is the most common lethal genetic disorder in Caucasian populations. CFTR is a relatively large gene of 189 kb with a rather complex tissue-specific and temporal expression profile. We used chromatin conformation at the CFTR locus to identify new DNA sequences that regulate its transcription. By comparing 5C chromatin interaction maps of the CFTR locus in expressing and non-expressing human primary cells, we identified several new contact points between the CFTR promoter and its surroundings, in addition to regions featuring previously described regulatory elements. We demonstrate that two of these novel interacting regions cooperatively increase CFTR expression, and suggest that the new enhancer elements located on either side of the gene are brought together through chromatin looping via CTCF.
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Affiliation(s)
- Stéphanie Moisan
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France
| | - Soizik Berlivet
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Chandran Ka
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France
| | - Gérald Le Gac
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France
| | - Josée Dostie
- Department of Biochemistry and Goodman Cancer Research Center, McGill University, Montréal, Québec, H3G 1Y6, Canada
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR ScInBioS, CHRU de Brest, Établissement Français du Sang - Bretagne, Brest, France
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19
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Chauveau A, Luque Paz D, Lecucq L, Le Gac G, Le Maréchal C, Gueguen P, Berthou C, Ugo V. A new point mutation in EPOR inducing a short deletion in congenital erythrocytosis. Br J Haematol 2015; 172:475-7. [PMID: 26010769 DOI: 10.1111/bjh.13511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Aurélie Chauveau
- CHU Brest, Laboratoire d'Hématologie, Brest, France.,Université de Brest, UFR Médecine, Brest, France.,INSERM U1078, Brest, France
| | - Damien Luque Paz
- CHU Brest, Laboratoire d'Hématologie, Brest, France.,INSERM U1078, Brest, France
| | - Lydie Lecucq
- CHU Brest, Laboratoire d'Hématologie, Brest, France.,Plateforme INCa de Génétique Hospitalière des Cancers de Brest, Brest, France
| | - Gérald Le Gac
- Université de Brest, UFR Médecine, Brest, France.,INSERM U1078, Brest, France.,CHU Brest, Laboratoire de Génétique, Brest, France
| | - Cédric Le Maréchal
- Université de Brest, UFR Médecine, Brest, France.,INSERM U1078, Brest, France.,CHU Brest, Laboratoire de Génétique, Brest, France
| | - Paul Gueguen
- Université de Brest, UFR Médecine, Brest, France.,INSERM U1078, Brest, France.,CHU Brest, Laboratoire de Génétique, Brest, France
| | - Christian Berthou
- Université de Brest, UFR Médecine, Brest, France.,CHU Brest, Service d'Hématologie, Institut de Cancérologie et d'Hématologie, Brest, France
| | - Valérie Ugo
- CHU Brest, Laboratoire d'Hématologie, Brest, France. .,Université de Brest, UFR Médecine, Brest, France. .,INSERM U1078, Brest, France.
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20
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Fichou Y, Gehannin P, Corre M, Le Guern A, Le Maréchal C, Le Gac G, Férec C. Extensive functional analyses ofRHDsplice site variants: Insights into the potential role of splicing in the physiology of Rh. Transfusion 2015; 55:1432-43. [DOI: 10.1111/trf.13083] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 01/08/2015] [Accepted: 02/10/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Yann Fichou
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078
- Etablissement Français du Sang (EFS)-Région Bretagne
| | - Pierre Gehannin
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078
- Etablissement Français du Sang (EFS)-Région Bretagne
| | - Manon Corre
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078
- Etablissement Français du Sang (EFS)-Région Bretagne
| | - Alice Le Guern
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078
- Etablissement Français du Sang (EFS)-Région Bretagne
| | - Cédric Le Maréchal
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078
- Etablissement Français du Sang (EFS)-Région Bretagne
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire (CHRU), Hôpital Morvan
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale; Brest France
| | - Gérald Le Gac
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078
- Etablissement Français du Sang (EFS)-Région Bretagne
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire (CHRU), Hôpital Morvan
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale; Brest France
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale (Inserm), UMR1078
- Etablissement Français du Sang (EFS)-Région Bretagne
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Régional Universitaire (CHRU), Hôpital Morvan
- Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale; Brest France
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21
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Saliou P, Le Gac G, Mérour MC, Tripogney C, Chanu B, Gourlaouen I, Nousbaum JB, Férec C, Scotet V. HFE hemochromatosis: influence of dietary iron intake on the iron overload of C282Y homozygous patients. Ann Hematol 2015; 94:1225-7. [DOI: 10.1007/s00277-015-2343-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/16/2015] [Indexed: 12/13/2022]
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22
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Ka C, Chen JM, Gourlaouen I, Quemener S, Ronsin C, Massonnet S, Thérond JP, Férec C, Le Gac G. Characterization of the second HFE gross deletion highlights the potential importance of Alu-mediated recombination in haemochromatosis. Br J Haematol 2014; 168:759-62. [PMID: 25284364 DOI: 10.1111/bjh.13145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chandran Ka
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Etablissement Français du Sang - Bretagne, Inserm U1078, Université de Brest, SFR SnInBioS, CHRU de Brest, Brest, France
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23
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Callebaut I, Joubrel R, Pissard S, Kannengiesser C, Gérolami V, Ged C, Cadet E, Cartault F, Ka C, Gourlaouen I, Gourhant L, Oudin C, Goossens M, Grandchamp B, De Verneuil H, Rochette J, Férec C, Le Gac G. Comprehensive functional annotation of 18 missense mutations found in suspected hemochromatosis type 4 patients. Hum Mol Genet 2014; 23:4479-90. [PMID: 24714983 DOI: 10.1093/hmg/ddu160] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Hemochromatosis type 4 is a rare form of primary iron overload transmitted as an autosomal dominant trait caused by mutations in the gene encoding the iron transport protein ferroportin 1 (SLC40A1). SLC40A1 mutations fall into two functional categories (loss- versus gain-of-function) underlying two distinct clinical entities (hemochromatosis type 4A versus type 4B). However, the vast majority of SLC40A1 mutations are rare missense variations, with only a few showing strong evidence of causality. The present study reports the results of an integrated approach collecting genetic and phenotypic data from 44 suspected hemochromatosis type 4 patients, with comprehensive structural and functional annotations. Causality was demonstrated for 10 missense variants, showing a clear dichotomy between the two hemochromatosis type 4 subtypes. Two subgroups of loss-of-function mutations were distinguished: one impairing cell-surface expression and one altering only iron egress. Additionally, a new gain-of-function mutation was identified, and the degradation of ferroportin on hepcidin binding was shown to probably depend on the integrity of a large extracellular loop outside of the hepcidin-binding domain. Eight further missense variations, on the other hand, were shown to have no discernible effects at either protein or RNA level; these were found in apparently isolated patients and were associated with a less severe phenotype. The present findings illustrate the importance of combining in silico and biochemical approaches to fully distinguish pathogenic SLC40A1 mutations from benign variants. This has profound implications for patient management.
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Affiliation(s)
- Isabelle Callebaut
- IMPMC, Sorbonne Universités - UMR CNRS 7590, UPMC Univ Paris 06, Muséum d'Histoire Naturelle, IRD UMR 206, Paris, France
| | - Rozenn Joubrel
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR SnInBioS, CHRU de Brest, Etablissement Français du Sang - Bretagne, Brest, France
| | - Serge Pissard
- Laboratoire de Génétique, UPEC (Université Paris Est Creteil), GHU Henri Mondor, Créteil, France
| | - Caroline Kannengiesser
- Hôpital Bichat, Département de Génétique, Inserm U1149 - Center for Research on Inflammation, Université Paris Diderot, AP-HP, Paris, France
| | | | - Cécile Ged
- Inserm U1035, Biothérapies des Maladies Génétiques et Cancers, Université de Bordeaux, CHU de Bordeaux, Pôle de Biologie et Pathologie, Bordeaux, France
| | - Estelle Cadet
- Laboratoire de Génétique Moléculaire, UPJV EA4666, CHU d'Amiens, Amiens, France
| | | | - Chandran Ka
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR SnInBioS, CHRU de Brest, Etablissement Français du Sang - Bretagne, Brest, France
| | - Isabelle Gourlaouen
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR SnInBioS, CHRU de Brest, Etablissement Français du Sang - Bretagne, Brest, France
| | | | - Claire Oudin
- Hôpital Bichat, Département de Génétique, Inserm U1149 - Center for Research on Inflammation, Université Paris Diderot, AP-HP, Paris, France
| | - Michel Goossens
- Laboratoire de Génétique, UPEC (Université Paris Est Creteil), GHU Henri Mondor, Créteil, France
| | - Bernard Grandchamp
- Hôpital Bichat, Département de Génétique, Inserm U1149 - Center for Research on Inflammation, Université Paris Diderot, AP-HP, Paris, France
| | - Hubert De Verneuil
- Inserm U1035, Biothérapies des Maladies Génétiques et Cancers, Université de Bordeaux, CHU de Bordeaux, Pôle de Biologie et Pathologie, Bordeaux, France
| | - Jacques Rochette
- Laboratoire de Génétique Moléculaire, UPJV EA4666, CHU d'Amiens, Amiens, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR SnInBioS, CHRU de Brest, Etablissement Français du Sang - Bretagne, Brest, France
| | - Gérald Le Gac
- Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Inserm U1078, Université de Brest, SFR SnInBioS, CHRU de Brest, Etablissement Français du Sang - Bretagne, Brest, France CHRU de Brest, Inserm CIC0502, Brest, France
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Le Gac G, Ka C, Joubrel R, Gourlaouen I, Lehn P, Mornon JP, Férec C, Callebaut I. Structure-function analysis of the human ferroportin iron exporter (SLC40A1): effect of hemochromatosis type 4 disease mutations and identification of critical residues. Hum Mutat 2013; 34:1371-80. [PMID: 23784628 DOI: 10.1002/humu.22369] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 06/06/2013] [Indexed: 11/06/2022]
Abstract
Ferroportin (SLC40A1) is the only known iron exporter in mammals and is considered a key coordinator of the iron balance between intracellular and systemic iron homeostasis. However, the structural organization of ferroportin in the lipid bilayer remains controversial and very little is known about the mechanism underlying iron egress. In the present study, we have developed an approach based on comparative modeling, which has led to the construction of a model of the three-dimensional (3D) structure of ferroportin by homology to the crystal structure of a Major Facilitator Superfamily member (EmrD). This model predicts atomic details for the organization of ferroportin transmembrane helices and is in agreement with our current understanding of the ferroportin function and its interaction with hepcidin. Using in vitro experiments, we demonstrate that this model can be used to identify novel critical amino acids. In particular, we show that the tryptophan residue 42 (p.Trp42), which is localized within the extracellular end of the ferroportin pore, is likely involved in both the iron export function and in the mechanism of inhibition by hepcidin. Thus, our 3D model provides a new perspective for understanding the molecular basis of ferroportin functions and dysfunctions.
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Affiliation(s)
- Gérald Le Gac
- Inserm UMR1078, Université de Brest, SFR SnInBioS, Centre Hospitalier Régional Universitaire - Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Etablissement Français du Sang - Bretagne, Brest, France
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Cézard C, Rabbind Singh A, Le Gac G, Gourlaouen I, Ferec C, Rochette J. Phenotypic expression of a novel C282Y/R226G compound heterozygous state in HFE hemochromatosis: molecular dynamics and biochemical studies. Blood Cells Mol Dis 2013; 52:27-34. [PMID: 23953397 DOI: 10.1016/j.bcmd.2013.07.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/28/2013] [Accepted: 07/05/2013] [Indexed: 11/15/2022]
Abstract
Most adults affected with hereditary hemochromatosis are homozygous for a single point mutation of HFE (p.Cys282Tyr). Apart from the compound heterozygous state for the p.Cys282Tyr mutant and the widespread p.His63Asp variant allele, other rare HFE mutations can be found in trans and may have clinical impact. In the present report we describe the structural and functional consequences of a new mutation, namely the p.Arg226Gly which was inherited in trans with the p.Cys282Tyr allele in a patient affected with a mild iron overload. Because the R226G substitution is located in the vicinity of the normal Cys225S-S282Cys disulfide bond we initially investigated the structure of the variant by molecular dynamics techniques in order to estimate the effect of the mutation on the global structure of HFE domain α3. We found that the solvation free energy, hydrophobicity and formation of salt bridges are slightly modified with the global secondary structure of the α3 domain being conserved. In a previous paper, we demonstrated that the Q283P substitution leads to the loss of the normal Cys225S-S282Cys disulfide bridge. Similar to the Q283P substitution, the R226G substitution does not substitute a residue directly involved in the formation of the disulfide bridge. However, unlike the p.Gln283Pro variant which destroyed the normal disulfide bridge, the R226G mutation does not affect the normal Cys225S-S282Cys bridge. Furthermore based on cell line studies we clearly show that the mutation does not prevent cell surface localization, β2-microglobulin association and binding to transferrin receptor 1. This new compound heterozygous phenotype is very close to those of the C282Y/H63D compound heterozygous patients who display the biochemical hemochromatosis phenotype but with lower body iron stores than C282Y homozygotes. Our results do not exclude unknown genetic and/or metabolic factors that may act synergistically to increase the ferritin level.
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Affiliation(s)
- Christine Cézard
- Laboratoire des Glucides, CNRS FRE 3517, Université de Picardie Jules Verne, Amiens 80037 Cedex 1, France
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Fichou Y, Le Maréchal C, Jamet D, Bryckaert L, Ka C, Audrézet MP, Le Gac G, Dupont I, Chen JM, Férec C. Establishment of a medium-throughput approach for the genotyping ofRHDvariants and report of nine novel rare alleles. Transfusion 2012; 53:1821-8. [DOI: 10.1111/trf.12009] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 09/24/2012] [Accepted: 10/01/2012] [Indexed: 01/22/2023]
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Boulling A, Le Gac G, Dujardin G, Chen JM, Férec C. The c.1275A>G putative chronic pancreatitis-associated synonymous polymorphism in the glycoprotein 2 (GP2) gene decreases exon 9 inclusion. Mol Genet Metab 2010; 99:319-24. [PMID: 19919903 DOI: 10.1016/j.ymgme.2009.10.176] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 10/20/2009] [Accepted: 10/20/2009] [Indexed: 01/14/2023]
Abstract
We have recently found that a common synonymous single nucleotide polymorphism (SNP), c.1275A>G, in exon 9 of the glycoprotein 2 (GP2) gene was significantly underrepresented in French idiopathic chronic pancreatitis patients 20years old or younger at disease onset than in the control population. To further investigate to this preliminary genetic finding, we characterized the functionality of c.1275A>G in the context of a minigene system. Bioinformatics analysis predicted that c.1275A>G could lead to disruption/generation of exonic splicing enhancer hexamers within exon 9 of the GP2 gene. Minigene analysis revealed that both the wild-type and mutant sequences expressed a full-length transcript and a short transcript lacking exon 9. Quantitation of the relative amount of the two transcripts indicated that the fraction of the full-length transcript derived from c.1275A>G is much lower than that derived from the wild-type (51.9% vs 77.4%). Extinction of two splicing factors (SF2/ASF and SC35) by RNA interference also affected c.1275A>G more seriously than the wild-type in terms of exon 9 skipping. Exon 9 skipping was presumed to cause a loss of GP2 function. This study represents the first detailed analysis of any variation in the GP2 gene and gives some support to the putative association of c.1275A>G with disease protection.
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Affiliation(s)
- Arnaud Boulling
- Institut National de la Santé et de la Recherche Médicale, U613, Brest, France
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Milet J, Le Gac G, Scotet V, Gourlaouen I, Thèze C, Mosser J, Bourgain C, Deugnier Y, Férec C. A common SNP near BMP2 is associated with severity of the iron burden in HFE p.C282Y homozygous patients: A follow-up study. Blood Cells Mol Dis 2010; 44:34-7. [DOI: 10.1016/j.bcmd.2009.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 09/23/2009] [Indexed: 12/29/2022]
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Le Gac G, Congiu R, Gourlaouen I, Cau M, Férec C, Melis MA. Homozygous deletion of HFE is the common cause of hemochromatosis in Sardinia. Haematologica 2009; 95:685-7. [PMID: 20007136 DOI: 10.3324/haematol.2009.016816] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Létocart E, Le Gac G, Majore S, Ka C, Radio FC, Gourlaouen I, De Bernardo C, Férec C, Grammatico P. A novel missense mutation in SLC40A1 results in resistance to hepcidin and confirms the existence of two ferroportin-associated iron overload diseases. Br J Haematol 2009; 147:379-85. [PMID: 19709084 DOI: 10.1111/j.1365-2141.2009.07834.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Ferroportin-related iron overload disease differs from haemochromatosis in that it has a dominant mode of inheritance and is usually associated with macrophage iron sequestration. However, it is thought that mutations with opposite effects on protein functions, i.e. loss-of-function versus gain-of-function mutations, are responsible for variable phenotype presentations. The present study investigated the functional relevance of a novel ferroportin variant: the c.1502 A>G transition, which changes amino acid 501 from tyrosine to cysteine (p.Y501C). This novel variant was identified in a pedigree originating from Central Italy and, although an intra-familial phenotype heterogeneity was observed, it co-segregated with an iron overload picture similar to that of the HFE-related typical haemochromatosis. In cultured cells, the p.Y501C mutant protein reached the plasma membrane and retained a full iron export ability. By contrast, it was resistant to inhibition by hepcidin. These findings confirm that certain ferroportin mutations compromise the activity of hepcidin in iron homeostasis, mimicking hepcidin deficiency as described in all types of hemochromatosis.
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Affiliation(s)
- Emilie Létocart
- Inserm U613, Etablissement Français du Sang - Bretagne, Université de Bretagne Occidentale, Brest, France
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Ka C, Le Gac G, Letocart E, Gourlaouen I, Martin B, Férec C. Phenotypic and functional data confirm causality of the recently identified hemojuvelin p.r176c missense mutation. Haematologica 2008; 92:1262-3. [PMID: 17768121 DOI: 10.3324/haematol.11247] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In the present study, we correlate homozygosity for the very recently identified HJV p.R176C substitution with a juvenile hemochromatosis phenotype. We also show that the p.R176C variant fails to up-regulate the hepcidin promoter activity. Altogether, our results definitively show the R176C amino-acid change to be a novel hemojuvelin loss-of-function mutation.
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Abstract
The molecular basis of haemochromatosis has proved more complex than expected. After the 1996 identification of the main causative gene HFE and confirmation that most patients were homozygous for the founder C282Y mutation, it became clear that some families were linked to rarer conditions, first named 'non-HFE haemochromatosis'. The genetics of these less common forms was intensively studied between 2000 and 2004, leading to the recognition of haemojuvelin (HJV), hepcidin (HAMP), transferrin receptor 2 (TFR2) and ferroportin-related haemochromatosis, and opening the way for novel hypotheses such as those related to digenic modes of inheritance or the involvement of modifier genes. Molecular studies of rare haemochromatosis disorders have contributed to our understanding of iron homeostasis. In turn, recent findings from studies of knockout mice and functional studies have confirmed that HAMP plays a central role in mobilization of iron, shown that HFE, TFR2 and HJV modulate HAMP production according to the body's iron status, and demonstrated that HAMP negatively regulates cellular iron efflux by affecting the ferroportin cell surface availability. These data shed new light on the pathophysiology of all types of haemochromatosis, and offer novel opportunities to comment on phenotypic differences and distinguish mutations.
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Ka C, Le Gac G, Dupradeau FY, Rochette J, Férec C. The Q283P amino-acid change in HFE leads to structural and functional consequences similar to those described for the mutated 282Y HFE protein. Hum Genet 2005; 117:467-75. [PMID: 15965644 DOI: 10.1007/s00439-005-1307-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Accepted: 03/12/2005] [Indexed: 12/23/2022]
Abstract
In Caucasians, 4-35% of hemochromatosis patients carry at least one chromosome without a common HFE mutation (i.e. C282Y, H63D and S65C). Several studies have now shown that iron overload phenotypes in such patients can be associated with uncommon HFE mutations. We previously supported implication of the C282Y/Q283P compound heterozygous genotype in hemochromatosis phenotypes and, based on molecular dynamics simulations, proposed that the Q283P substitution prevents normal folding of the HFE alpha3-domain. In the current work, we have used HeLa cells carrying wild-type or Q283P-mutant HFE cDNA under the control of a tetracycline-sensitive promoter to functionally characterise the Q283P mutation. Experiments using cells over-expressing wild-type HFE confirm the existence of beta2microglobulin(beta2m)/HFE and HFE/transferrin receptor 1 (TfR1) interactions, as well as the capacity of HFE to reduce transferrin-mediated iron uptake. In contrast, neither beta2m/HFE nor HFE/TfR1 complex formation was detected in cells over-expressing the mutated form of HFE. Moreover, the 283P HFE protein was found to have a very limited effect on the major cellular iron uptake pathway. Combined, our results indicate that the Q283P mutation leads to structural and functional consequences similar to those described for the main hereditary hemochromatosis mutation. As a consequence, our study has implications for the screening of hemochromatosis patients that have one or two copies of HFE which lack the main mutations. It also highlights that protein structure prediction methods could be more generally used to better interpret relationships between rare genotypes and molecular diagnosis of a human inherited disorder.
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Scotet V, Le Gac G, Mérour MC, Mercier AY, Chanu B, Ka C, Mura C, Nousbaum JB, Férec C. Impact of HFE genetic testing on clinical presentation of hereditary hemochromatosis: new epidemiological data. BMC Med Genet 2005; 6:24. [PMID: 15929798 PMCID: PMC1180708 DOI: 10.1186/1471-2350-6-24] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Accepted: 06/01/2005] [Indexed: 12/26/2022]
Abstract
Background Hereditary hemochromatosis (HH) is a common inherited disorder of iron metabolism in Northern European populations. The discovery of a candidate gene in 1996 (HFE), and of its main mutation (C282Y), has radically altered the way to diagnose this disease. The aim of this study was to assess the impact of the HFE gene discovery on the clinical presentation and epidemiology of HH. Methods We studied our cohort of 415 patients homozygous for the C282Y allele and included in a phlebotomy program in a blood centre in western Brittany, France. Results In this cohort, 56.9% of the patients were male and 21.9% began their phlebotomy program before the implementation of the genetic test. A significant decrease in the sex ratio was noticed following implementation of this DNA test, from 3.79 to 1.03 (p < 10-5), meaning that the proportion of diagnosed females relatives to males greatly increased. The profile of HH patients at diagnosis changed after the DNA test became available. Serum ferritin and iron values were lower and there was a reduced frequency of clinical signs displayed at diagnosis, particularly skin pigmentation (20.1 vs. 40.4%, OR = 0.37, p < 0.001) and hepatomegaly (11.0 vs. 22.7%, OR = 0.42, p = 0.006). In contrast, fatigue became a more common symptom at diagnosis (68.0 vs. 51.2%, OR = 2.03, p = 0.004). Conclusion This study highlights the importance of the HFE gene discovery, which has simplified the diagnosis of HH and modified its clinical presentation and epidemiology. This study precisely measures these changes. Enhanced diagnosis of HFE-related HH at an early stage and implementation of phlebotomy treatment are anticipated to maintain normal life expectancy for these patients.
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Affiliation(s)
- Virginie Scotet
- INSERM U 613 "Génétique moléculaire et génétique épidémiologique", Brest, France
| | - Gérald Le Gac
- Etablissement Français du Sang, Site de Brest, Brest, France
| | | | | | - Brigitte Chanu
- Etablissement Français du Sang, Site de Brest, Brest, France
| | - Chandran Ka
- Etablissement Français du Sang, Site de Brest, Brest, France
- Université de Bretagne Occidentale, Brest, France
| | | | - Jean-Baptiste Nousbaum
- Service d'Hépato-Gastroentérologie, Centre Hospitalier Universitaire La Cavale Blanche, Brest, France
| | - Claude Férec
- INSERM U 613 "Génétique moléculaire et génétique épidémiologique", Brest, France
- Etablissement Français du Sang, Site de Brest, Brest, France
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Mura C, Le Gac G, Jacolot S, Férec C. Transcriptional regulation of the human HFE gene indicates high liver expression and erythropoiesis coregulation. FASEB J 2004; 18:1922-4. [PMID: 15467009 DOI: 10.1096/fj.04-2520fje] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The human HFE gene is clearly involved in hereditary hemochromatosis, a common autosomal recessive genetic disorder of iron homeostasis. However, the precise role of the HFE protein is still undefined. Here, to obtain new insight, we analyzed the transcriptional regulation of HFE gene and defined the functional organization of the HFE promoter. Both in vitro transcription and reporter gene assay in transient transfection evidenced a high liver expression of the HFE mRNA. The 5' end analysis of mRNA showed two major initiation sites localized at -265 and -195 directed by TATA-like sequences and a window of initiation within the -120 to -10 GC-rich region upstream of the first coding nucleotide. Positive cis-regulating elements were characterized within the -1057/-8 region, and a negative one extending upstream (-1485/-1057) was identified. DNase I footprinting analysis and gel shift assay revealed several protein binding sites, and subsequent functional analysis evidenced transactivation of HFE by liver-enriched C/EBPalpha, erythropoietic-specific GATA-1, and ubiquitous Sp1 transcription factors. These data bring some evidence of a role of HFE in the liver and a coregulation with erythropoiesis as other genes involved in iron homeostasis.
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Affiliation(s)
- Catherine Mura
- INSERM U613, Génétique Moléculaire et Génétique Epidémiologique, UBO, 46 rue Félix Le Dantec, Brest 29200, France.
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Le Gac G, Scotet V, Ka C, Gourlaouen I, Bryckaert L, Jacolot S, Mura C, Férec C. The recently identified type 2A juvenile haemochromatosis gene (HJV), a second candidate modifier of the C282Y homozygous phenotype. Hum Mol Genet 2004; 13:1913-8. [PMID: 15254010 DOI: 10.1093/hmg/ddh206] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The most common form of hereditary haemochromatosis is an adult-onset condition usually associated with the HFE C282Y/C282Y genotype. The phenotypic expression of this genotype is heterogeneous and depends on a complex interplay of genetic and non-genetic factors. The aim of the present study was to determine if mutations in the recently identified HJV gene were associated with more severe iron overload phenotypes in C282Y homozygous patients. From a cohort of 310 C282Y homozygous patients, we found nine (six males and three females) with an additional HJV missense mutation in the heterozygous state (S105L, E302K, N372D, R335Q or the previously described L101P and G320V). The iron indices of eight patients appeared to be more severe than those observed in C282Y homozygous patients of identical sex and similar age ranges. The mean serum ferritin concentration of the six males with an HJV mutation was significantly higher than that of C282Y homozygous males without an additional mutation [2350.3 (sigma=1429.9) versus 1227.2 (sigma=1130.1) microg/l; P=0.0233, Student's t-test]. We have recently reported that mutations in the gene that encodes hepcidin (HAMP) could explain one part of the C282Y/C282Y-related phenotypic heterogeneity by accentuating the iron burden. Our new data reveal that mutations in the HJV gene could be associated with a similar effect. Taken together, these results emphasize that a search for modifier genes could enable us to more precisely distinguish those C282Y homozygous patients with a higher risk to develop a severe iron overload and, consequently, clinical complications.
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Scotet V, Mérour MC, Mercier AY, Chanu B, Le Faou T, Raguénes O, Le Gac G, Mura C, Nousbaum JB, Férec C. Hereditary hemochromatosis: effect of excessive alcohol consumption on disease expression in patients homozygous for the C282Y mutation. Am J Epidemiol 2003; 158:129-34. [PMID: 12851225 DOI: 10.1093/aje/kwg123] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hereditary hemochromatosis is a common inherited disorder characterized by iron overload. A single mutation (C282Y) in the HFE gene is present in 80-95% of cases in populations of northern European extraction. The disorder presents a large phenotypic heterogeneity, and its expression can be influenced by environmental factors. This 1977-2002 study aimed to identify the influence of alcohol consumption on expression of the disease. The authors retrospectively registered 378 C282Y-homozygous patients treated in a blood center of western Brittany, France. In this cohort, 33 patients reported excessive alcohol consumption (8.7%). Those subjects presented significantly increased iron parameters (serum ferritin: 1745.2 vs. 968.7 microg/liter, p< 0.0001; serum iron: 39.9 vs. 36.0 micromol/liter, p = 0.0040; transferrin saturation: 87.1 vs. 80.1%, p = 0.0071) and elevated liver enzymes (alanine aminotransferase: 66.3 vs. 41.1 IU/liter, p = 0.0003; aspartate aminotransferase: 56.2 vs. 34.9 IU/liter, p = 0.0002). Their risk of skin pigmentation was also higher (odds ratio = 3.4, p = 0.0006). Results remained unchanged after adjustment. This study provides precise quantitative data about the impact of alcohol on expression of hereditary hemochromatosis in C282Y-homozygous patients. Excessive alcohol consumption accentuates disease expression and therefore the risk of cirrhosis and cancer. Consequently, these patients should be encouraged to consume very moderate quantities of alcohol.
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Affiliation(s)
- Virginie Scotet
- INSERM EMI 01-15, Laboratoire de Génétique Moléculaire, CHU Morvan, Brest, France
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Le Gac G, Dupradeau FY, Mura C, Jacolot S, Scotet V, Esnault G, Mercier AY, Rochette J, Férec C. Phenotypic expression of the C282Y/Q283P compound heterozygosity in HFE and molecular modeling of the Q283P mutation effect. Blood Cells Mol Dis 2003; 30:231-7. [PMID: 12737937 DOI: 10.1016/s1079-9796(03)00036-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In Caucasians, from 4 to 35% of hereditary hemochromatosis (HH) patients carry a least one chromosome without a common assigned HFE mutation (i.e., C282Y, H63D, and S65C). We have undertaken a D-HPLC scanning of the HFE coding region in such patients in order to identify uncommon mutations liable to explain their high transferrin saturation level. Twenty HH patients from Brittany carrying at least one chromosome without an assigned mutation were selected on the basis of a transferrin saturation level with the following threshold: > or = 60% in men and > or = 50% in women, in the absence of other known causes of iron disorders. This strategy allowed us to detect a heterozygous sequence variant in exon 4 of the HFE gene from one individual who was also heterozygous for C282Y. Subsequent DNA sequencing analysis identified an adenine to cytosine transversion at position 848 which changes amino acid 283 from glutamine to proline (Q283P). Family study revealed a clear association between the C282Y/Q283P compound heterozygote genotype and the development of HH. Molecular modeling studies are in favor of a destabilizing effect of the Q283P mutation on the tertiary structure of the HFE protein. This is the first report of a natural protein variant describing the introduction of a proline in a central beta-strand position. Our approach may have practical implications in screening strategies for hereditary hemochromatosis, molecular diagnosis, and HFE structure-function relationships.
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Affiliation(s)
- Gérald Le Gac
- Etablissement Français du Sang-Bretagne, Brest, and INSERM EMI 0115, France
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