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Wu H, Lin JH, Tang XY, Marenne G, Zou WB, Schutz S, Masson E, Génin E, Fichou Y, Le Gac G, Férec C, Liao Z, Chen JM. Combining full-length gene assay and SpliceAI to interpret the splicing impact of all possible SPINK1 coding variants. Hum Genomics 2024; 18:21. [PMID: 38414044 PMCID: PMC10898081 DOI: 10.1186/s40246-024-00586-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/13/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Single-nucleotide variants (SNVs) within gene coding sequences can significantly impact pre-mRNA splicing, bearing profound implications for pathogenic mechanisms and precision medicine. In this study, we aim to harness the well-established full-length gene splicing assay (FLGSA) in conjunction with SpliceAI to prospectively interpret the splicing effects of all potential coding SNVs within the four-exon SPINK1 gene, a gene associated with chronic pancreatitis. RESULTS Our study began with a retrospective analysis of 27 SPINK1 coding SNVs previously assessed using FLGSA, proceeded with a prospective analysis of 35 new FLGSA-tested SPINK1 coding SNVs, followed by data extrapolation, and ended with further validation. In total, we analyzed 67 SPINK1 coding SNVs, which account for 9.3% of the 720 possible coding SNVs. Among these 67 FLGSA-analyzed SNVs, 12 were found to impact splicing. Through detailed comparison of FLGSA results and SpliceAI predictions, we inferred that the remaining 653 untested coding SNVs in the SPINK1 gene are unlikely to significantly affect splicing. Of the 12 splice-altering events, nine produced both normally spliced and aberrantly spliced transcripts, while the remaining three only generated aberrantly spliced transcripts. These splice-impacting SNVs were found solely in exons 1 and 2, notably at the first and/or last coding nucleotides of these exons. Among the 12 splice-altering events, 11 were missense variants (2.17% of 506 potential missense variants), and one was synonymous (0.61% of 164 potential synonymous variants). Notably, adjusting the SpliceAI cut-off to 0.30 instead of the conventional 0.20 would improve specificity without reducing sensitivity. CONCLUSIONS By integrating FLGSA with SpliceAI, we have determined that less than 2% (1.67%) of all possible coding SNVs in SPINK1 significantly influence splicing outcomes. Our findings emphasize the critical importance of conducting splicing analysis within the broader genomic sequence context of the study gene and highlight the inherent uncertainties associated with intermediate SpliceAI scores (0.20 to 0.80). This study contributes to the field by being the first to prospectively interpret all potential coding SNVs in a disease-associated gene with a high degree of accuracy, representing a meaningful attempt at shifting from retrospective to prospective variant analysis in the era of exome and genome sequencing.
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Affiliation(s)
- Hao Wu
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jin-Huan Lin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Xin-Ying Tang
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
- Department of Prevention and Health Care, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Gaëlle Marenne
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Sacha Schutz
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Service de Génétique Médicale et de Biologie de La Reproduction, CHRU Brest, Brest, France
| | - Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Service de Génétique Médicale et de Biologie de La Reproduction, CHRU Brest, Brest, France
| | | | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- Service de Génétique Médicale et de Biologie de La Reproduction, CHRU Brest, Brest, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, 168 Changhai Road, Shanghai, 200433, China.
- Shanghai Institute of Pancreatic Diseases, Shanghai, China.
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France.
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2
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Masson E, Berthet S, Le Gac G, Le Rhun M, Ka C, Autret S, Gourlaouen I, Cooper DN, Férec C, Rebours V, Chen JM. Identification of protease-sensitive but not misfolding PNLIP variants in familial and hereditary pancreatitis. Pancreatology 2023; 23:507-511. [PMID: 37270400 DOI: 10.1016/j.pan.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/05/2023]
Abstract
Mutations in the PNLIP gene have recently been implicated in chronic pancreatitis. Several PNLIP missense variants have been reported to cause protein misfolding and endoplasmic reticulum stress although genetic evidence supporting their association with chronic pancreatitis is currently lacking. Protease-sensitive PNLIP missense variants have also been associated with early-onset chronic pancreatitis although the underlying pathological mechanism remains enigmatic. Herein, we provide new evidence to support the association of protease-sensitive PNLIP variants (but not misfolding PNLIP variants) with pancreatitis. Specifically, we identified protease-sensitive PNLIP variants in 5 of 373 probands (1.3%) with a positive family history of pancreatitis. The protease-sensitive variants, p.F300L and p.I265R, were found to segregate with the disease in three families, including one exhibiting a classical autosomal dominant inheritance pattern. Consistent with previous findings, protease-sensitive variant-positive patients were often characterized by early-onset disease and invariably experienced recurrent acute pancreatitis, although none has so far developed chronic pancreatitis.
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Affiliation(s)
- Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France; Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Stéphanie Berthet
- Service de Pédiatrie, Hépato-Gastro-Entérologie et Nutrition Pédiatrique, Hôpitaux Pédiatriques de Nice CHU Lenval, Nice, France
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France; Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Marc Le Rhun
- Service d'Hépato-Gastroentérologie et Assistance Nutritionnelle, Institut des Maladies de l'Appareil Digestif (IMAD), Centre Hospitalo-Universitaire (CHU), Nantes, France
| | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France; Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Sandrine Autret
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France; Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | | | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France
| | - Vinciane Rebours
- Pancreatology and Digestive Oncology Department, Beaujon Hospital, APHP - Clichy, Université Paris Cité, Paris, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200, Brest, France.
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3
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Ganapathi M, Friocourt G, Gueguen N, Friederich MW, Le Gac G, Okur V, Loaëc N, Ludwig T, Ka C, Tanji K, Marcorelles P, Theodorou E, Lignelli-Dipple A, Voisset C, Walker MA, Briere LC, Bourhis A, Blondel M, LeDuc C, Hagen J, Cooper C, Muraresku C, Ferec C, Garenne A, Lelez-Soquet S, Rogers CA, Shen Y, Strode DK, Bizargity P, Iglesias A, Goldstein A, High FA, Network UD, Sweetser DA, Ganetzky R, Van Hove JLK, Procaccio V, Le Marechal C, Chung WK. A homozygous splice variant in ATP5PO, disrupts mitochondrial complex V function and causes Leigh syndrome in two unrelated families. J Inherit Metab Dis 2022; 45:996-1012. [PMID: 35621276 PMCID: PMC9474623 DOI: 10.1002/jimd.12526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 11/10/2022]
Abstract
Mitochondrial complex V plays an important role in oxidative phosphorylation by catalyzing the generation of ATP. Most complex V subunits are nuclear encoded and not yet associated with recognized Mendelian disorders. Using exome sequencing, we identified a rare homozygous splice variant (c.87+3A>G) in ATP5PO, the complex V subunit which encodes the oligomycin sensitivity conferring protein, in three individuals from two unrelated families, with clinical suspicion of a mitochondrial disorder. These individuals had a similar, severe infantile and often lethal multi-systemic disorder that included hypotonia, developmental delay, hypertrophic cardiomyopathy, progressive epileptic encephalopathy, progressive cerebral atrophy, and white matter abnormalities on brain MRI consistent with Leigh syndrome. cDNA studies showed a predominant shortened transcript with skipping of exon 2 and low levels of the normal full-length transcript. Fibroblasts from the affected individuals demonstrated decreased ATP5PO protein, defective assembly of complex V with markedly reduced amounts of peripheral stalk proteins, and complex V hydrolytic activity. Further, expression of human ATP5PO cDNA without exon 2 (hATP5PO-∆ex2) in yeast cells deleted for yATP5 (ATP5PO homolog) was unable to rescue growth on media which requires oxidative phosphorylation when compared to the wild type construct (hATP5PO-WT), indicating that exon 2 deletion leads to a non-functional protein. Collectively, our findings support the pathogenicity of the ATP5PO c.87+3A>G variant, which significantly reduces but does not eliminate complex V activity. These data along with the recent report of an affected individual with ATP5PO variants, add to the evidence that rare biallelic variants in ATP5PO result in defective complex V assembly, function and are associated with Leigh syndrome.
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Affiliation(s)
- Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Naig Gueguen
- MitoLab, UMR CNRS 6015 - INSERM U1083, MitoVasc Institute, Angers University Hospital, Angers, France
| | - Marisa W Friederich
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Volkan Okur
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Thomas Ludwig
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Kurenai Tanji
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Pascale Marcorelles
- CHRU de Brest, Service d'anatomie cytologie pathologie, CHU et centre de référence des maladies neuromusculaires, Brest, France
| | - Evangelos Theodorou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Angela Lignelli-Dipple
- Department of Radiology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Melissa A Walker
- Division of Neurogenetics, Child Neurology, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Lauren C Briere
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Amélie Bourhis
- CHRU de Brest, Service d'anatomie cytologie pathologie, CHU et centre de référence des maladies neuromusculaires, Brest, France
| | | | - Charles LeDuc
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Jacob Hagen
- Department of Biomedical Sciences, Columbia University Irving Medical Center, New York, New York, USA
| | - Cathleen Cooper
- Department of Radiology, Columbia University Irving Medical Center, New York, New York, USA
| | - Colleen Muraresku
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Cassandra A Rogers
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yufeng Shen
- Department of Biomedical Sciences, Columbia University Irving Medical Center, New York, New York, USA
| | - Dana K Strode
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
| | - Peyman Bizargity
- Division of Medical Genetics, Cohen Children's Medical Center, New York, New York, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, New York, USA
| | - Alejandro Iglesias
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | - Amy Goldstein
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frances A High
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - David A Sweetser
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Division of Medical Genetics & Metabolism, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rebecca Ganetzky
- Department of Pediatrics, Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Johan L K Van Hove
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado, USA
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015 - INSERM U1083, MitoVasc Institute, Angers University Hospital, Angers, France
| | - Cedric Le Marechal
- Univ Brest, Inserm, EFS, UMR1078, France
- CHRU de Brest, Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, France
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
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4
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Masson E, Zou WB, Génin E, Cooper DN, Le Gac G, Fichou Y, Pu N, Rebours V, Férec C, Liao Z, Chen JM. Expanding ACMG variant classification guidelines into a general framework. Hum Genomics 2022; 16:31. [PMID: 35974416 PMCID: PMC9380380 DOI: 10.1186/s40246-022-00407-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 06/16/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The American College of Medical Genetics and Genomics (ACMG)-recommended five variant classification categories (pathogenic, likely pathogenic, uncertain significance, likely benign, and benign) have been widely used in medical genetics. However, these guidelines are fundamentally constrained in practice owing to their focus upon Mendelian disease genes and their dichotomous classification of variants as being either causal or not. Herein, we attempt to expand the ACMG guidelines into a general variant classification framework that takes into account not only the continuum of clinical phenotypes, but also the continuum of the variants' genetic effects, and the different pathological roles of the implicated genes. MAIN BODY As a disease model, we employed chronic pancreatitis (CP), which manifests clinically as a spectrum from monogenic to multifactorial. Bearing in mind that any general conceptual proposal should be based upon sound data, we focused our analysis on the four most extensively studied CP genes, PRSS1, CFTR, SPINK1 and CTRC. Based upon several cross-gene and cross-variant comparisons, we first assigned the different genes to two distinct categories in terms of disease causation: CP-causing (PRSS1 and SPINK1) and CP-predisposing (CFTR and CTRC). We then employed two new classificatory categories, "predisposing" and "likely predisposing", to replace ACMG's "pathogenic" and "likely pathogenic" categories in the context of CP-predisposing genes, thereby classifying all pathologically relevant variants in these genes as "predisposing". In the case of CP-causing genes, the two new classificatory categories served to extend the five ACMG categories whilst two thresholds (allele frequency and functional) were introduced to discriminate "pathogenic" from "predisposing" variants. CONCLUSION Employing CP as a disease model, we expand ACMG guidelines into a five-category classification system (predisposing, likely predisposing, uncertain significance, likely benign, and benign) and a seven-category classification system (pathogenic, likely pathogenic, predisposing, likely predisposing, uncertain significance, likely benign, and benign) in the context of disease-predisposing and disease-causing genes, respectively. Taken together, the two systems constitute a general variant classification framework that, in principle, should span the entire spectrum of variants in any disease-related gene. The maximal compliance of our five-category and seven-category classification systems with the ACMG guidelines ought to facilitate their practical application.
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Affiliation(s)
- Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, The Secondary Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Génin
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, F-29200, Brest, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - Na Pu
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.,Department of Critical Care Medicine, Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Vinciane Rebours
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, Assistance Publique-Hôpitaux de Paris, Clichy, Université de Paris, Paris, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, The Secondary Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 22 Avenue Camille Desmoulins, F-29200, Brest, France.
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5
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Lin JH, Wu H, Zou WB, Masson E, Fichou Y, Le Gac G, Cooper DN, Férec C, Liao Z, Chen JM. Splicing Outcomes of 5' Splice Site GT>GC Variants That Generate Wild-Type Transcripts Differ Significantly Between Full-Length and Minigene Splicing Assays. Front Genet 2021; 12:701652. [PMID: 34422003 PMCID: PMC8375439 DOI: 10.3389/fgene.2021.701652] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 04/28/2021] [Accepted: 07/13/2021] [Indexed: 12/18/2022] Open
Abstract
Combining data derived from a meta-analysis of human disease-associated 5' splice site GT>GC (i.e., +2T>C) variants and a cell culture-based full-length gene splicing assay (FLGSA) of forward engineered +2T>C substitutions, we recently estimated that ∼15-18% of +2T>C variants can generate up to 84% wild-type transcripts relative to their wild-type counterparts. Herein, we analyzed the splicing outcomes of 20 +2T>C variants that generate some wild-type transcripts in two minigene assays. We found a high discordance rate in terms of the generation of wild-type transcripts, not only between FLGSA and the minigene assays but also between the different minigene assays. In the pET01 context, all 20 wild-type minigene constructs generated the expected wild-type transcripts; of the 20 corresponding variant minigene constructs, 14 (70%) generated wild-type transcripts. In the pSPL3 context, only 18 of the 20 wild-type minigene constructs generated the expected wild-type transcripts whereas 8 of the 18 (44%) corresponding variant minigene constructs generated wild-type transcripts. Thus, in the context of a particular type of variant, we raise awareness of the limitations of minigene splicing assays and emphasize the importance of sequence context in regulating splicing. Whether or not our findings apply to other types of splice-altering variant remains to be investigated.
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Affiliation(s)
- Jin-Huan Lin
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Hao Wu
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, Brest, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Gerald Le Gac
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France.,Service de Génétique Médicale et de Biologie de la Reproduction, CHRU Brest, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
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6
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Martinez G, Beurois J, Dacheux D, Cazin C, Bidart M, Kherraf ZE, Robinson DR, Satre V, Le Gac G, Ka C, Gourlaouen I, Fichou Y, Petre G, Dulioust E, Zouari R, Thierry-Mieg N, Touré A, Arnoult C, Bonhivers M, Ray P, Coutton C. Biallelic variants in MAATS1 encoding CFAP91, a calmodulin-associated and spoke-associated complex protein, cause severe astheno-teratozoospermia and male infertility. J Med Genet 2020; 57:708-716. [PMID: 32161152 DOI: 10.1136/jmedgenet-2019-106775] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 12/13/2019] [Revised: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Multiple morphological abnormalities of the flagella (MMAF) consistently lead to male infertility due to a reduced or absent sperm motility defined as asthenozoospermia. Despite numerous genes recently described to be recurrently associated with MMAF, more than half of the cases analysed remain unresolved, suggesting that many yet uncharacterised gene defects account for this phenotype METHODS: Exome sequencing was performed on 167 infertile men with an MMAF phenotype. Immunostaining and transmission electron microscopy (TEM) in sperm cells from affected individuals were performed to characterise the ultrastructural sperm defects. Gene inactivation using RNA interference (RNAi) was subsequently performed in Trypanosoma. RESULTS We identified six unrelated affected patients carrying a homozygous deleterious variants in MAATS1, a gene encoding CFAP91, a calmodulin-associated and spoke-associated complex (CSC) protein. TEM and immunostaining experiments in sperm cells showed severe central pair complex (CPC) and radial spokes defects. Moreover, we confirmed that the WDR66 protein is a physical and functional partner of CFAP91 into the CSC. Study of Trypanosoma MAATS1's orthologue (TbCFAP91) highlighted high sequence and structural analogies with the human protein and confirmed the axonemal localisation of the protein. Knockdown of TbCFAP91 using RNAi impaired flagellar movement led to CPC defects in Trypanosoma as observed in humans. CONCLUSIONS We showed that CFAP91 is essential for normal sperm flagellum structure and function in human and Trypanosoma and that biallelic variants in this gene lead to severe flagellum malformations resulting in astheno-teratozoospermia and primary male infertility.
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Affiliation(s)
- Guillaume Martinez
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM de Génétique Chromosomique, Grenoble, France
| | - Julie Beurois
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France
| | - Denis Dacheux
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Bordeaux, France.,Institut Polytechnique de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Bordeaux, France
| | - Caroline Cazin
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France
| | - Marie Bidart
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, Unité Médicale de Génétique Moléculaire : Maladies Héréditaires et Oncologie, Pôle Biologie, Institut de Biologie et de Pathologie, Grenoble, France
| | - Zine-Eddine Kherraf
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | - Derrick R Robinson
- Institut Polytechnique de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Bordeaux, France
| | - Véronique Satre
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM de Génétique Chromosomique, Grenoble, France
| | - Gerald Le Gac
- INSERM UMR1078, Université Bretagne Loire - Université de Brest, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France.,Service de Génétique Médicale et Biologie de la Reproduction, Laboratoire de Génétique Moléculaire et Histocompatibilité, CHRU de Brest, Hôpital Morvan, Brest, France
| | - Chandran Ka
- INSERM UMR1078, Université Bretagne Loire - Université de Brest, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France
| | - Isabelle Gourlaouen
- INSERM UMR1078, Université Bretagne Loire - Université de Brest, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France
| | - Yann Fichou
- INSERM UMR1078, Université Bretagne Loire - Université de Brest, Etablissement Français du Sang - Bretagne, Institut Brestois Santé-Agro-Matière, Brest, France
| | - Graciane Petre
- INSERM U1205, UFR Chimie Biologie, Univ. Grenoble Alpes, Grenoble, France
| | - Emmanuel Dulioust
- Laboratoire d'Histologie Embryologie - Biologie de la Reproduction, GH Cochin Broca Hôtel Dieu, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
| | - Raoudha Zouari
- Polyclinique les Jasmins, Centre d'Aide Médicale à la Procréation, Centre Urbain Nord, Tunis, Tunisia
| | | | - Aminata Touré
- Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France.,INSERM U1016, Institut Cochin, Paris, France.,Centre National de la Recherche Scientifique UMR8104, Paris, France
| | - Christophe Arnoult
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France
| | - Mélanie Bonhivers
- Université de Bordeaux, Microbiologie Fondamentale et Pathogénicité, CNRS UMR 5234, Bordeaux, France
| | - Pierre Ray
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France.,CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | - Charles Coutton
- Univ. Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France .,CHU Grenoble Alpes, UM de Génétique Chromosomique, Grenoble, France
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7
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Lin JH, Tang XY, Boulling A, Zou WB, Masson E, Fichou Y, Raud L, Le Tertre M, Deng SJ, Berlivet I, Ka C, Mort M, Hayden M, Leman R, Houdayer C, Le Gac G, Cooper DN, Li ZS, Férec C, Liao Z, Chen JM. First estimate of the scale of canonical 5' splice site GT>GC variants capable of generating wild-type transcripts. Hum Mutat 2019; 40:1856-1873. [PMID: 31131953 DOI: 10.1002/humu.23821] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/10/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022]
Abstract
It has long been known that canonical 5' splice site (5'SS) GT>GC variants may be compatible with normal splicing. However, to date, the actual scale of canonical 5'SSs capable of generating wild-type transcripts in the case of GT>GC substitutions remains unknown. Herein, combining data derived from a meta-analysis of 45 human disease-causing 5'SS GT>GC variants and a cell culture-based full-length gene splicing assay of 103 5'SS GT>GC substitutions, we estimate that ~15-18% of canonical GT 5'SSs retain their capacity to generate between 1% and 84% normal transcripts when GT is substituted by GC. We further demonstrate that the canonical 5'SSs in which substitution of GT by GC-generated normal transcripts exhibit stronger complementarity to the 5' end of U1 snRNA than those sites whose substitutions of GT by GC did not lead to the generation of normal transcripts. We also observed a correlation between the generation of wild-type transcripts and a milder than expected clinical phenotype but found that none of the available splicing prediction tools were capable of reliably distinguishing 5'SS GT>GC variants that generated wild-type transcripts from those that did not. Our findings imply that 5'SS GT>GC variants in human disease genes may not invariably be pathogenic.
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Affiliation(s)
- Jin-Huan Lin
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Xin-Ying Tang
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Arnaud Boulling
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France
| | - Yann Fichou
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Loann Raud
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | | | - Shun-Jiang Deng
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | | | - Chandran Ka
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Matthew Hayden
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Raphaël Leman
- Laboratoire de Biologie et Génétique du Cancer, Centre François Baclesse, Caen, France.,Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - Claude Houdayer
- Department of Genetics, F76000 and Normandy University, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - Gerald Le Gac
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France.,CHU Brest, Service de Génétique, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Claude Férec
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- EFS, Univ Brest, Inserm, UMR 1078, GGB, F-29200, Brest, France
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8
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Scotet V, Saliou P, Uguen M, L'Hostis C, Merour MC, Triponey C, Chanu B, Nousbaum JB, Le Gac G, Ferec C. Do pregnancies reduce iron overload in HFE hemochromatosis women? results from an observational prospective study. BMC Pregnancy Childbirth 2018; 18:53. [PMID: 29454332 PMCID: PMC5816504 DOI: 10.1186/s12884-018-1684-6] [Citation(s) in RCA: 2] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 02/06/2018] [Indexed: 12/17/2022] Open
Abstract
Background HFE hemochromatosis is an inborn error of iron metabolism linked to a defect in the regulation of hepcidin synthesis. This autosomal recessive disease typically manifests later in women than men. Although it is commonly stated that pregnancy is, with menses, one of the factors that offsets iron accumulation in women, no epidemiological study has yet supported this hypothesis. The aim of our study was to evaluate the influence of pregnancy on expression of the predominant HFE p.[Cys282Tyr];[Cys282Tyr] genotype. Methods One hundred and forty p.Cys282Tyr homozygous women enrolled in a phlebotomy program between 2004 and 2011 at a blood centre in western Brittany (France) were included in the study. After checking whether the disease expression was delayed in women than in men in our study, the association between pregnancy and iron overload was assessed using multivariable regression analysis. Results Our study confirms that women with HFE hemochromatosis were diagnosed later than men cared for during the same period (52.6 vs. 47.4 y., P < 0.001). Compared to no pregnancy, having at least one pregnancy was not associated with lower iron markers. In contrast, the amount of iron removed by phlebotomies appeared significantly higher in women who had at least one pregnancy (eβ = 1.50, P = 0.047). This relationship disappeared after adjustment for confounding factors (eβ = 1.35, P = 0.088). Conclusions Our study shows that pregnancy status has no impact on iron markers level, and is not in favour of pregnancy being a protective factor in progressive iron accumulation. Our results are consistent with recent experimental data suggesting that the difference in disease expression observed between men and women may be explained by other factors such as hormones.
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Affiliation(s)
- Virginie Scotet
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", Inserm, EFS, Université de Brest, ISBAM, 22 avenue Camille Desmoulins, 29200, Brest, France.
| | - Philippe Saliou
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", Inserm, EFS, Université de Brest, ISBAM, 22 avenue Camille Desmoulins, 29200, Brest, France.,Laboratoire d'Hygiene et de Sante Publique, Hopital Morvan, Brest, France
| | - Marianne Uguen
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", Inserm, EFS, Université de Brest, ISBAM, 22 avenue Camille Desmoulins, 29200, Brest, France
| | - Carine L'Hostis
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", Inserm, EFS, Université de Brest, ISBAM, 22 avenue Camille Desmoulins, 29200, Brest, France
| | | | - Céline Triponey
- Etablissement Français du Sang - Bretagne, Site de Brest, Brest, France
| | - Brigitte Chanu
- Etablissement Français du Sang - Bretagne, Site de Brest, Brest, France
| | - Jean-Baptiste Nousbaum
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", Inserm, EFS, Université de Brest, ISBAM, 22 avenue Camille Desmoulins, 29200, Brest, France.,Service d'Hepato-Gastroenterologie, Hopital La Cavale Blanche, Brest, France
| | - Gerald Le Gac
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", Inserm, EFS, Université de Brest, ISBAM, 22 avenue Camille Desmoulins, 29200, Brest, France.,Laboratoire de Genetique Moleculaire et d'Histocompatibilite, Hopital Morvan, Brest, France
| | - Claude Ferec
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", Inserm, EFS, Université de Brest, ISBAM, 22 avenue Camille Desmoulins, 29200, Brest, France.,Etablissement Français du Sang - Bretagne, Site de Brest, Brest, France.,Laboratoire de Genetique Moleculaire et d'Histocompatibilite, Hopital Morvan, Brest, France
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9
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Uguen K, Scotet V, Ka C, Gourlaouen I, L'hostis C, Merour MC, Cuppens T, Ferec C, Le Gac G. Diagnostic value of targeted next-generation sequencing in suspected hemochromatosis patients with a single copy of the HFE p.Cys282Tyr causative allele. Am J Hematol 2017; 92:E664-E666. [PMID: 29084376 DOI: 10.1002/ajh.24912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Kevin Uguen
- Université Bretagne Loire, Université de Bretagne Occidentale, IBSAM; Brest France
| | - Virginie Scotet
- Inserm U1078; Brest France
- Etablissement Français du Sang; Brest France
| | - Chandran Ka
- Inserm U1078; Brest France
- Laboratory of Excellence GR-Ex; Paris France
- Laboratoire de Genetique Moleculaire et Histocompatibilité, CHRU de Brest, Hopital Morvan; Brest France
| | - Isabelle Gourlaouen
- Inserm U1078; Brest France
- Etablissement Français du Sang; Brest France
- Laboratoire de Genetique Moleculaire et Histocompatibilité, CHRU de Brest, Hopital Morvan; Brest France
| | - Carine L'hostis
- Inserm U1078; Brest France
- Association Gaetan Saleun; Brest France
| | | | - Tania Cuppens
- Université Bretagne Loire, Université de Bretagne Occidentale, IBSAM; Brest France
- Inserm U1078; Brest France
| | - Claude Ferec
- Université Bretagne Loire, Université de Bretagne Occidentale, IBSAM; Brest France
- Inserm U1078; Brest France
- Etablissement Français du Sang; Brest France
- Laboratoire de Genetique Moleculaire et Histocompatibilité, CHRU de Brest, Hopital Morvan; Brest France
| | - Gerald Le Gac
- Université Bretagne Loire, Université de Bretagne Occidentale, IBSAM; Brest France
- Inserm U1078; Brest France
- Etablissement Français du Sang; Brest France
- Laboratory of Excellence GR-Ex; Paris France
- Laboratoire de Genetique Moleculaire et Histocompatibilité, CHRU de Brest, Hopital Morvan; Brest France
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10
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Daher R, Kannengiesser C, Houamel D, Lefebvre T, Bardou-Jacquet E, Ducrot N, de Kerguenec C, Jouanolle AM, Robreau AM, Oudin C, Le Gac G, Moulouel B, Loustaud-Ratti V, Bedossa P, Valla D, Gouya L, Beaumont C, Brissot P, Puy H, Karim Z, Tchernitchko D. Heterozygous Mutations in BMP6 Pro-peptide Lead to Inappropriate Hepcidin Synthesis and Moderate Iron Overload in Humans. Gastroenterology 2016; 150:672-683.e4. [PMID: 26582087 DOI: 10.1053/j.gastro.2015.10.049] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 10/14/2015] [Accepted: 10/29/2015] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Hereditary hemochromatosis is a heterogeneous group of genetic disorders characterized by parenchymal iron overload. It is caused by defective expression of liver hepcidin, the main regulator of iron homeostasis. Iron stimulates the gene encoding hepcidin (HAMP) via the bone morphogenetic protein (BMP)6 signaling to SMAD. Although several genetic factors have been found to cause late-onset hemochromatosis, many patients have unexplained signs of iron overload. We investigated BMP6 function in these individuals. METHODS We sequenced the BMP6 gene in 70 consecutive patients with a moderate increase in serum ferritin and liver iron levels who did not carry genetic variants associated with hemochromatosis. We searched for BMP6 mutations in relatives of 5 probands and in 200 healthy individuals (controls), as well as in 2 other independent cohorts of hyperferritinemia patients. We measured serum levels of hepcidin by liquid chromatography-tandem mass spectrometry and analyzed BMP6 in liver biopsy specimens from patients by immunohistochemistry. The functions of mutant and normal BMP6 were assessed in transfected cells using immunofluorescence, real-time quantitative polymerase chain reaction, and immunoblot analyses. RESULTS We identified 3 heterozygous missense mutations in BMP6 (p.Pro95Ser, p.Leu96Pro, and p.Gln113Glu) in 6 unrelated patients with unexplained iron overload (9% of our cohort). These mutations were detected in less than 1% of controls. p.Leu96Pro also was found in 2 patients from the additional cohorts. Family studies indicated dominant transmission. Serum levels of hepcidin were inappropriately low in patients. A low level of BMP6, compared with controls, was found in a biopsy specimen from 1 patient. In cell lines, the mutated residues in the BMP6 propeptide resulted in defective secretion of BMP6; reduced signaling via SMAD1, SMAD5, and SMAD8; and loss of hepcidin production. CONCLUSIONS We identified 3 heterozygous missense mutations in BMP6 in patients with unexplained iron overload. These mutations lead to loss of signaling to SMAD proteins and reduced hepcidin production. These mutations might increase susceptibility to mild-to-moderate late-onset iron overload.
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Affiliation(s)
- Raed Daher
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France
| | - Caroline Kannengiesser
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France; AP-HP, Département de Génétique, Hôpital Bichat, Paris, France
| | - Dounia Houamel
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France
| | - Thibaud Lefebvre
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | | | - Nicolas Ducrot
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France
| | | | - Anne-Marie Jouanolle
- Department of Liver Disease and Molecular Genetics, CHU Rennes, Rennes, France; CHU Rennes, French Reference Center for Rare Iron Overload Diseases of Genetic Origin
| | - Anne-Marie Robreau
- AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | - Claire Oudin
- AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | - Gerald Le Gac
- INSERM U1078, Université de Brest, CHRU de Brest, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Bretagne, Brest, France
| | - Boualem Moulouel
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France
| | | | - Pierre Bedossa
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; AP-HP, Laboratoire d'Anatomo-Pathologie, Hôpital Beaujon, Clichy, France
| | - Dominique Valla
- AP-HP, Département d'Hépatologie, Hôpital Beaujon, Clichy, France
| | - Laurent Gouya
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | - Carole Beaumont
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France
| | - Pierre Brissot
- Department of Liver Disease and Molecular Genetics, CHU Rennes, Rennes, France
| | - Hervé Puy
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France; AP-HP, Centre Français des Porphyries, Hôpital Louis Mourier, Colombes, France
| | - Zoubida Karim
- INSERM UMR1149, Centre de Recherche sur l'Inflammation, Paris, France; Université Paris Diderot, Site Bichat, Sorbonne Paris Cité, Paris, France; Laboratory of Excellence, GR-Ex, Paris, France.
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11
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Jaspers A, Caers J, Le Gac G, Ferec C, Beguin Y, Fillet G. A novel mutation in the CUB sequence of matriptase-2 (TMPRSS6) is implicated in iron-resistant iron deficiency anaemia (IRIDA). Br J Haematol 2012; 160:564-5. [DOI: 10.1111/bjh.12147] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jo Caers
- Department of Haematology; CHU Liège; Liege; Belgium
| | - Gerald Le Gac
- INSERM 0115; Centre Hospitalier Universitaire; Brest; France
| | - Claude Ferec
- INSERM 0115; Centre Hospitalier Universitaire; Brest; France
| | - Yves Beguin
- Department of Haematology; CHU Liège; Liege; Belgium
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12
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Ugo V, Tondeur S, Menot ML, Bonnin N, Le Gac G, Tonetti C, Mas VMD, Lecucq L, Kiladjian JJ, Chomienne C, Dosquet C, Parquet N, Darnige L, Porneuf M, Escoffre-Barbe M, Giraudier S, Delabesse E, Cassinat B. Interlaboratory development and validation of a HRM method applied to the detection of JAK2 exon 12 mutations in polycythemia vera patients. PLoS One 2010; 5:e8893. [PMID: 20126644 PMCID: PMC2811183 DOI: 10.1371/journal.pone.0008893] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 12/28/2009] [Indexed: 11/29/2022] Open
Abstract
Background Myeloproliferative disorders are characterized by clonal expansion of normal mature blood cells. Acquired mutations giving rise to constitutive activation of the JAK2 tyrosine kinase has been shown to be present in the majority of patients. Since the demonstration that the V617F mutation in the exon 14 of the JAK2 gene is present in about 90% of patients with Polycythemia Vera (PV), the detection of this mutation has become a key tool for the diagnosis of these patients. More recently, additional mutations in the exon 12 of the JAK2 gene have been described in 5 to 10% of the patients with erythrocytosis. According to the updated WHO criteria the presence of these mutations should be looked for in PV patients with no JAK2 V617F mutation. Reliable and accurate methods dedicated to the detection of these highly variable mutations are therefore necessary. Methods/Findings For these reasons we have defined the conditions of a High Resolution DNA Melting curve analysis (HRM) method able to detect JAK2 exon 12 mutations. After having validated that the method was able to detect mutated patients, we have verified that it gave reproducible results in repeated experiments, on DNA extracted from either total blood or purified granulocytes. This HRM assay was further validated using 8 samples bearing different mutant sequences in 4 different laboratories, on 3 different instruments. Conclusion The assay we have developed is thus a valid method, adapted to routine detection of JAK2 exon 12 mutations with highly reproducible results.
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Affiliation(s)
- Valerie Ugo
- CHU BREST, Laboratoire d'Hematologie, Brest, France
- INSERM U613, Brest, France
| | - Sylvie Tondeur
- CHU Montpellier, Laboratoire d'Hématologie, Hôpital Saint-Eloi, Montpellier, France
| | | | - Nadine Bonnin
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
| | | | - Carole Tonetti
- AP-HP, Laboratoire d'Hematologie, Hopital Henri Mondor, Creteil, France
| | | | - Lydie Lecucq
- CHU BREST, Laboratoire d'Hematologie, Brest, France
| | - Jean-Jacques Kiladjian
- AP-HP, Hematology Department, Hopital Avicenne, Bobigny, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Christine Chomienne
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Christine Dosquet
- AP-HP, Unite de Thérapie Cellulaire, Hopital Saint-Louis, Paris, France
| | - Nathalie Parquet
- AP-HP, Unite de Thérapie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
| | - Luc Darnige
- AP-HP, Laboratoire d'Hematologie, Hopital Europeen G. Pompidou, Paris, France
| | - Marc Porneuf
- CH Le Foll, Service d'Hématologie, Saint Brieuc, France
| | | | | | - Eric Delabesse
- CHU Toulouse, Laboratoire d'Hematologie, Hôpital Purpan, Toulouse, France
| | - Bruno Cassinat
- AP-HP, Unite de Biologie Cellulaire, Hopital Saint-Louis, Paris, France
- PV-Nord Group, Hopital Saint-Louis, Paris, France
- * E-mail:
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Le Gac G, Estève PO, Ferec C, Pradhan S. DNA damage-induced down-regulation of human Cdc25C and Cdc2 is mediated by cooperation between p53 and maintenance DNA (cytosine-5) methyltransferase 1. J Biol Chem 2006; 281:24161-70. [PMID: 16807237 DOI: 10.1074/jbc.m603724200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [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: 11/06/2022] Open
Abstract
The Cdc25C phosphatase mediates cellular entry into mitosis in mammalian cells. Cdc25C activates Cdc2 for entry into mitosis by dephosphorylating Thr and Tyr at the site of inhibitory phosphorylation. The Cdc25C gene contains tumor suppressor p53 binding sites and is demonstrated to contribute to the p53-dependent cell cycle arrest upon DNA damage. Here we show that both Cdc25C and Cdc2 were down-regulated in wild-type HCT116 cells but not in p53-null, DNMT1-null or DNMT1and DNMT3b-null cells, upon p53 stabilization following doxorubicin-mediated DNA damage. Furthermore, zebularine, a drug that selectively traps and depletes nuclear DNMT1 and DNMT3b, relieved p53-mediated repression of endogenous Cdc25C and Cdc2. Methylation analysis of the Cdc25C and Cdc2 promoter displayed internal CG methylation proximal to the p53 binding site upon DNA damage in a p53-dependent manner. Chromatin immunoprecipitation of doxorubicin treated wild-type HCT116 cells showed the presence of DNMT1, p53, H3K9me2, and the transcriptional repressor HDAC1 on the Cdc25C and Cdc2 promoters, suggesting their involvement as repressive complexes in Cdc25C and Cdc2 gene silencing. Thus, the general mechanism of p53-mediated gene repression may involve recruitment of other repressive factors.
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Affiliation(s)
- Gerald Le Gac
- New England Biolabs, Ipswich, Massachusetts 01938, USA
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Jacolot S, Le Gac G, Scotet V, Quere I, Mura C, Ferec C. HAMP as a modifier gene that increases the phenotypic expression of the HFE pC282Y homozygous genotype. Blood 2003; 103:2835-40. [PMID: 14670915 DOI: 10.1182/blood-2003-10-3366] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.2] [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: 02/05/2023] Open
Abstract
Hereditary hemochromatosis is a genetically heterogeneous disease of iron metabolism. The most common form of the disorder is an adult-onset form that has mainly been associated with the HFE pC282Y/pC282Y genotype. The phenotypic expression of this genotype is very heterogeneous and could be modulated by both environmental factors and modifier genes. The non-HFE hereditary hemochromatosis forms include a juvenile onset form associated with mutations in HAMP. From a cohort of 392 C282Y homozygous patients, we found 5 carriers of an additional HAMP mutation at the heterozygous state (pR59G, pG71D, or pR56X). We found that iron indices of these 5 patients were among the most elevated of the cohort. Moreover, we specified that the HAMP mutations were not detected in 300 control subjects. These results revealed that mutations in HAMP might increase the phenotypic expression of the pC282Y/pC282Y genotype. From a cohort of 31 patients with at least one chromosome lacking an HFE mutation, we further identified 4 males carrying a heterozygous HAMP mutation (pR59G or pG71D). Based on a digenic model of inheritance, these data suggest that the association of heterozygous mutations in the HFE and HAMP genes could lead, at least in some cases, to an adult-onset form of primary iron overload.
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Abstract
Abstract
Background: Between 4% and 35% of hereditary hemochromatosis (HC) probands are C282Y or H63D heterozygotes or lack both of these two common HFE mutations, and 15 novel HFE mutations have been described recently. We evaluated denaturing HPLC (DHPLC) for screening of the whole HFE coding region and further defined whether HC probands with an incomplete HFE genotype carry uncommon mutations.
Methods: Analytical conditions for each coding exon were determined by a combination of computer melting profile predictions and experimental melting curves. To test accuracy for scanning the complete HFE coding region and optimize DHPLC running conditions, each melting domain was investigated with at least one mutation or one polymorphism as reference. We tested 100 DNA samples harboring the C282Y, H63D, or S65C mutations and 17 artificially created positive controls that carried either 1 of the 14 other known HFE mutations or 3 selected polymorphisms.
Results: Investigations on each of the coding exons 1, 2, 4, 5, and 6 could be performed at one analysis temperature. Coding exon 3 displayed a more complex melting profile and required two analysis temperatures. DHPLC detected all known HFE mutations as well as the three selected polymorphisms.
Conclusions: DHPLC can be used to scan the HFE gene in HC probands in whom at least one chromosome lacks an assigned mutation.
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Affiliation(s)
- Gerald Le Gac
- Establissement Francais du Sang-Bretagne
- Laboratoire de Génétique Moléculaire, INSERM (EMI-01 15), 46 Rue Félix Le Dantec, 29200 Brest, France
| | - Catherine Mura
- Université de Bretagne Occidentale, and
- Laboratoire de Génétique Moléculaire, INSERM (EMI-01 15), 46 Rue Félix Le Dantec, 29200 Brest, France
| | - Claude Férec
- Establissement Francais du Sang-Bretagne
- Laboratoire de Génétique Moléculaire, INSERM (EMI-01 15), 46 Rue Félix Le Dantec, 29200 Brest, France
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