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Pina-Perez M, Martinet D, Palacios-Gorba C, Ellert C, Beyrer M. Low-energy short-term cold atmospheric plasma: Controlling the inactivation efficacy of bacterial spores in powders. Food Res Int 2020; 130:108921. [DOI: 10.1016/j.foodres.2019.108921] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/10/2019] [Accepted: 12/15/2019] [Indexed: 02/07/2023]
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El Chehadeh S, Touraine R, Prieur F, Reardon W, Bienvenu T, Chantot-Bastaraud S, Doco-Fenzy M, Landais E, Philippe C, Marle N, Callier P, Mosca-Boidron AL, Mugneret F, Le Meur N, Goldenberg A, Guerrot AM, Chambon P, Satre V, Coutton C, Jouk PS, Devillard F, Dieterich K, Afenjar A, Burglen L, Moutard ML, Addor MC, Lebon S, Martinet D, Alessandri JL, Doray B, Miguet M, Devys D, Saugier-Veber P, Drunat S, Aral B, Kremer V, Rondeau S, Tabet AC, Thevenon J, Thauvin-Robinet C, Perreton N, Des Portes V, Faivre L. Xq28 duplication includingMECP2in six unreported affected females: what can we learn for diagnosis and genetic counselling? Clin Genet 2017; 91:576-588. [DOI: 10.1111/cge.12898] [Citation(s) in RCA: 14] [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: 08/01/2016] [Revised: 10/14/2016] [Accepted: 10/17/2016] [Indexed: 11/27/2022]
Affiliation(s)
- S. El Chehadeh
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Centre de Génétique, CHU de Dijon; Dijon France
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre; Strasbourg France
| | - R. Touraine
- Service de Génétique Clinique Chromosomique et Moléculaire; CHU de Saint-Etienne; Saint-Étienne France
| | - F. Prieur
- Service de Génétique Clinique Chromosomique et Moléculaire; CHU de Saint-Etienne; Saint-Étienne France
| | - W. Reardon
- Clinical Genetics, Division National Centre for Medical Genetics; Our Lady's Children's Hospital; Dublin Ireland
| | - T. Bienvenu
- AP-HP, Laboratoire de Génétique et Biologie Moléculaires, HU Paris Centre, Site Cochin, France; Université Paris Descartes; Institut Cochin, INSERM U1016; Paris France
| | - S. Chantot-Bastaraud
- Service de Génétique et Embryologie Médicales; CHU Paris Est - Hôpital d'Enfants Armand-Trousseau; Paris France
| | - M. Doco-Fenzy
- Service de Génétique, EA3801; SFR-CAP Santé, CHU de Reims; Reims France
| | - E. Landais
- PRBI, Pôle de Biologie Médicale; CHU de Reims; Reims France
| | - C. Philippe
- Laboratoire de Génétique Médicale; Hôpitaux de Brabois CHRU; Vandoeuvre les Nancy France
| | - N. Marle
- Service de Cytogénétique; CHU de Dijon; Dijon France
| | - P. Callier
- Service de Cytogénétique; CHU de Dijon; Dijon France
| | | | - F. Mugneret
- Service de Cytogénétique; CHU de Dijon; Dijon France
| | - N. Le Meur
- Etablissement Français du Sang; CHU de Rouen; Rouen France
| | - A. Goldenberg
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen; Inserm et Université de Rouen; Rouen France
| | - A.-M. Guerrot
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen; Inserm et Université de Rouen; Rouen France
| | - P. Chambon
- Laboratoire D'histologie, Cytogénétique et Biologie de la Reproduction; CHU de Rouen; Rouen France
| | - V. Satre
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - C. Coutton
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - P.-S. Jouk
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - F. Devillard
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - K. Dieterich
- Département de Génétique et Procréation, CHU Grenoble Alpes; Université Grenoble Alpes; Grenoble France
| | - A. Afenjar
- Service de Génétique; CHU Paris Est - Hôpital d'Enfants Armand-Trousseau; Paris France
| | - L. Burglen
- Service de Génétique; CHU Paris Est - Hôpital d'Enfants Armand-Trousseau; Paris France
| | - M.-L. Moutard
- Unité de neuropédiatrie et pathologie du développement; CHU Paris Est - Hôpital d'Enfants Armand-Trousseau; Paris France
| | - M.-C. Addor
- Service de Génétique Médicale; Centre Hospitalier Universitaire Vaudois CHUV; Lausanne Switzerland
| | - S. Lebon
- Unité de Neuropédiatrie; Centre Hospitalier Universitaire Vaudois CHUV; Lausanne Switzerland
| | - D. Martinet
- Laboratoire de Cytogénétique Constitutionnelle et Prénatale; Centre Hospitalier Universitaire Vaudois CHUV; Lausanne Switzerland
| | - J.-L. Alessandri
- Pôle Enfants; CHU de la Réunion - Hôpital Félix Guyon; Saint-Denis France
| | - B. Doray
- Service de Génétique; CHU de la Réunion - Hôpital Félix Guyon; Saint-Denis France
| | - M. Miguet
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre; Strasbourg France
| | - D. Devys
- Laboratoire de Diagnostic Génétique; CHU de Strasbourg - Hôpital Civil; Strasbourg France
| | - P. Saugier-Veber
- Laboratoire de Génétique Moléculaire; Faculté de Médecine et de Pharmacie; Rouen France
| | - S. Drunat
- Laboratoire de Biologie Moléculaire; Hôpital Robert Debré; Paris France
| | - B. Aral
- Service de Biologie Moléculaire; CHU de Dijon; Dijon France
| | - V. Kremer
- Laboratoire de Cytogénétique, Hôpitaux Universitaires de Strasbourg; Hôpital de Hautepierre; Strasbourg France
| | - S. Rondeau
- Service de Pédiatrie Néonatale et Réanimation; CHU de Rouen; Rouen France
| | - A.-C. Tabet
- Laboratoire de Cytogénétique; Hôpital Robert Debré; Paris France
| | - J. Thevenon
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Centre de Génétique, CHU de Dijon; Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | - C. Thauvin-Robinet
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Centre de Génétique, CHU de Dijon; Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
| | - N. Perreton
- EPICIME-CIC 1407 de Lyon, Inserm; Service de Pharmacologie Clinique, CHU-Lyon; Bron France
| | - V. Des Portes
- Service de Neurologie Pédiatrique; CHU de Lyon-GH Est; Bron France
| | - L. Faivre
- FHU TRANSLAD, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs» de l'Est; Centre de Génétique, CHU de Dijon; Dijon France
- GAD, EA4271, Génétique et Anomalies du Développement; Université de Bourgogne; Dijon France
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Droz-Georget Lathion S, Rochat A, Knott G, Recchia A, Martinet D, Benmohammed S, Grasset N, Zaffalon A, Besuchet Schmutz N, Savioz-Dayer E, Beckmann JS, Rougemont J, Mavilio F, Barrandon Y. A single epidermal stem cell strategy for safe ex vivo gene therapy. EMBO Mol Med 2015; 7:380-93. [PMID: 25724200 PMCID: PMC4403041 DOI: 10.15252/emmm.201404353] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [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] [Indexed: 01/13/2023] Open
Abstract
There is a widespread agreement from patient and professional organisations alike that the safety of stem cell therapeutics is of paramount importance, particularly for ex vivo autologous gene therapy. Yet current technology makes it difficult to thoroughly evaluate the behaviour of genetically corrected stem cells before they are transplanted. To address this, we have developed a strategy that permits transplantation of a clonal population of genetically corrected autologous stem cells that meet stringent selection criteria and the principle of precaution. As a proof of concept, we have stably transduced epidermal stem cells (holoclones) obtained from a patient suffering from recessive dystrophic epidermolysis bullosa. Holoclones were infected with self-inactivating retroviruses bearing a COL7A1 cDNA and cloned before the progeny of individual stem cells were characterised using a number of criteria. Clonal analysis revealed a great deal of heterogeneity among transduced stem cells in their capacity to produce functional type VII collagen (COLVII). Selected transduced stem cells transplanted onto immunodeficient mice regenerated a non-blistering epidermis for months and produced a functional COLVII. Safety was assessed by determining the sites of proviral integration, rearrangements and hit genes and by whole-genome sequencing. The progeny of the selected stem cells also had a diploid karyotype, was not tumorigenic and did not disseminate after long-term transplantation onto immunodeficient mice. In conclusion, a clonal strategy is a powerful and efficient means of by-passing the heterogeneity of a transduced stem cell population. It guarantees a safe and homogenous medicinal product, fulfilling the principle of precaution and the requirements of regulatory affairs. Furthermore, a clonal strategy makes it possible to envision exciting gene-editing technologies like zinc finger nucleases, TALENs and homologous recombination for next-generation gene therapy.
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Affiliation(s)
- Stéphanie Droz-Georget Lathion
- Department of Experimental Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland Laboratory of Stem Cell Dynamics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ariane Rochat
- Department of Experimental Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland Laboratory of Stem Cell Dynamics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Graham Knott
- Interdisciplinary Center for Electron Microscopy, Faculty of Life Sciences EPFL, Lausanne, Switzerland
| | - Alessandra Recchia
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Danielle Martinet
- Service de Génétique Médicale, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sara Benmohammed
- Department of Medical Genetics, Université de Lausanne, Lausanne, Switzerland
| | - Nicolas Grasset
- Department of Experimental Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland Laboratory of Stem Cell Dynamics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Andrea Zaffalon
- Department of Experimental Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland Laboratory of Stem Cell Dynamics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Emmanuelle Savioz-Dayer
- Department of Experimental Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland Laboratory of Stem Cell Dynamics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jacques Samuel Beckmann
- Service de Génétique Médicale, Lausanne University Hospital (CHUV), Lausanne, Switzerland Department of Medical Genetics, Université de Lausanne, Lausanne, Switzerland
| | - Jacques Rougemont
- Bioinformatics and Biostatistics Core Facility, Faculty of Life Sciences EPFL, Lausanne, Switzerland
| | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy Genethon, Evry, France
| | - Yann Barrandon
- Department of Experimental Surgery, Lausanne University Hospital (CHUV), Lausanne, Switzerland Laboratory of Stem Cell Dynamics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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Capobianco S, Lava SA, Bianchetti MG, Martinet D, Belfiore M, Ramelli GP, Ferrarini A. Chromosomal microarray among children with intellectual disability: a useful diagnostic tool for the clinical geneticist. Dev Med Child Neurol 2014; 56:290. [PMID: 24266756 DOI: 10.1111/dmcn.12341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 11/28/2022]
Affiliation(s)
- Stephanie Capobianco
- Integrated Department of Pediatrics, Ente Ospedaliero Cantonale Ticinese, Bellinzona, Switzerland
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Kannu P, Campos-Xavier A, Hull D, Martinet D, Ballhausen D, Bonafé L. Corrigendum to “Post-axial polydactyly type A2, overgrowth and autistic traits associated with a chromosome 13q31.3 microduplication encompassing miR-17-92 and GPC5” [Eur J Med Genet 56 (8) (2013) 452–457]. Eur J Med Genet 2014. [DOI: 10.1016/j.ejmg.2014.01.001] [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: 11/28/2022]
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Ferrarini A, Gaillard M, Guerry F, Ramelli G, Heidi F, Keddache CV, Wieland I, Beckmann JS, Jaquemont S, Martinet D. Potocki-Shaffer deletion encompassing ALX4 in a patient with frontonasal dysplasia phenotype. Am J Med Genet A 2013; 164A:346-52. [PMID: 24376213 DOI: 10.1002/ajmg.a.36140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 05/24/2013] [Accepted: 06/21/2013] [Indexed: 12/14/2022]
Abstract
Frontonasal dysplasia (FND) is a genetically heterogeneous malformation spectrum with marked hypertelorism, broad nasal tip and bifid nose. Only a small number of genes have been associated with FND phenotypes until now, the first gene being EFNB1, related to craniofrontonasal syndrome (CFNS) with craniosynostosis in addition, and more recently the aristaless-like homeobox genes ALX3, ALX4, and ALX1, which have been related with distinct phenotypes named FND1, FND2, and FND3 respectively. We here report on a female patient presenting with severe FND features along with partial alopecia, hypogonadism and intellectual disability. While molecular investigations did not reveal mutations in any of the known genes, ALX4, ALX3, ALX1 and EFNB1, comparative genomic hybridization (array CGH) techniques showed a large heterozygous de novo deletion at 11p11.12p12, encompassing the ALX4 gene. Deletions in this region have been described in patients with Potocki-Shaffer syndrome (PSS), characterized by biparietal foramina, multiple exostoses, and intellectual disability. Although the patient reported herein manifests some overlapping features of FND and PPS, it is likely that the observed phenotype maybe due to a second unidentified mutation in the ALX4 gene. The phenotype will be discussed in view of the deleted region encompassing the ALX4 gene.
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Dauber A, Golzio C, Guenot C, Jodelka FM, Kibaek M, Kjaergaard S, Leheup B, Martinet D, Nowaczyk MJM, Rosenfeld JA, Zeesman S, Zunich J, Beckmann JS, Hirschhorn JN, Hastings ML, Jacquemont S, Katsanis N. SCRIB and PUF60 are primary drivers of the multisystemic phenotypes of the 8q24.3 copy-number variant. Am J Hum Genet 2013; 93:798-811. [PMID: 24140112 DOI: 10.1016/j.ajhg.2013.09.010] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/10/2013] [Accepted: 09/16/2013] [Indexed: 11/19/2022] Open
Abstract
Copy-number variants (CNVs) represent a significant interpretative challenge, given that each CNV typically affects the dosage of multiple genes. Here we report on five individuals with coloboma, microcephaly, developmental delay, short stature, and craniofacial, cardiac, and renal defects who harbor overlapping microdeletions on 8q24.3. Fine mapping localized a commonly deleted 78 kb region that contains three genes: SCRIB, NRBP2, and PUF60. In vivo dissection of the CNV showed discrete contributions of the planar cell polarity effector SCRIB and the splicing factor PUF60 to the syndromic phenotype, and the combinatorial suppression of both genes exacerbated some, but not all, phenotypic components. Consistent with these findings, we identified an individual with microcephaly, short stature, intellectual disability, and heart defects with a de novo c.505C>T variant leading to a p.His169Tyr change in PUF60. Functional testing of this allele in vivo and in vitro showed that the mutation perturbs the relative dosage of two PUF60 isoforms and, subsequently, the splicing efficiency of downstream PUF60 targets. These data inform the functions of two genes not associated previously with human genetic disease and demonstrate how CNVs can exhibit complex genetic architecture, with the phenotype being the amalgam of both discrete dosage dysfunction of single transcripts and also of binary genetic interactions.
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Affiliation(s)
- Andrew Dauber
- Division of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02115, USA
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Dauber A, Golzio C, Guenot C, Jodelka F, Kibaek M, Kjaergaard S, Leheup B, Martinet D, Nowaczyk M, Rosenfeld J, Zeesman S, Zunich J, Beckmann J, Hirschhorn J, Hastings M, Jacquemont S, Katsanis N. SCRIB and PUF60 Are Primary Drivers of the Multisystemic Phenotypes of the 8q24.3 Copy-Number Variant. Am J Hum Genet 2013. [DOI: 10.1016/j.ajhg.2013.10.018] [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: 10/26/2022] Open
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Kannu P, Campos-Xavier AB, Hull D, Martinet D, Ballhausen D, Bonafé L. Post-axial polydactyly type A2, overgrowth and autistic traits associated with a chromosome 13q31.3 microduplication encompassing miR-17-92 and GPC5. Eur J Med Genet 2013; 56:452-7. [PMID: 23792790 DOI: 10.1016/j.ejmg.2013.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 08/03/2011] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
Abstract
Genomic rearrangements at chromosome 13q31.3q32.1 have been associated with digital anomalies, dysmorphic features, and variable degree of mental disability. Microdeletions leading to haploinsufficiency of miR17∼92, a cluster of micro RNA genes closely linked to GPC5 in both mouse and human genomes, has recently been associated with digital anomalies in the Feingold like syndrome. Here, we report on a boy with familial dominant post-axial polydactyly (PAP) type A, overgrowth, significant facial dysmorphisms and autistic traits who carries the smallest germline microduplication known so far in that region. The microduplication encompasses the whole miR17∼92 cluster and the first 5 exons of GPC5. This report supports the newly recognized role of miR17∼92 gene dosage in digital developmental anomalies, and suggests a possible role of GPC5 in growth regulation and in cognitive development.
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Affiliation(s)
- P Kannu
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, Ontario Canada.
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Marle N, Martinet D, Aboura A, Joly-Helas G, Andrieux J, Flori E, Puechberty J, Vialard F, Sanlaville D, Fert Ferrer S, Bourrouillou G, Tabet AC, Quilichini B, Simon-Bouy B, Bazin A, Becker M, Stora H, Amblard S, Doco-Fenzy M, Molina Gomes D, Girard-Lemaire F, Cordier MP, Satre V, Schneider A, Lemeur N, Chambon P, Jacquemont S, Fellmann F, Vigouroux-Castera A, Molignier R, Delaye A, Pipiras E, Liquier A, Rousseau T, Mosca AL, Kremer V, Payet M, Rangon C, Mugneret F, Aho S, Faivre L, Callier P. Molecular characterization of 39 de novo sSMC: contribution to prognosis and genetic counselling, a prospective study. Clin Genet 2013; 85:233-44. [PMID: 23489061 DOI: 10.1111/cge.12138] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 11/27/2012] [Revised: 03/05/2012] [Accepted: 03/05/2012] [Indexed: 11/27/2022]
Abstract
Small supernumerary marker chromosomes (sSMCs) are structurally abnormal chromosomes that cannot be characterized by karyotype. In many prenatal cases of de novo sSMC, the outcome of pregnancy is difficult to predict because the euchromatin content is unclear. This study aimed to determine the presence or absence of euchromatin material of 39 de novo prenatally ascertained sSMC by array-comparative genomic hybridization (array-CGH) or single nucleotide polymorphism (SNP) array. Cases were prospectively ascertained from the study of 65,000 prenatal samples [0.060%; 95% confidence interval (CI), 0.042-0.082]. Array-CGH showed that 22 markers were derived from non-acrocentric markers (56.4%) and 7 from acrocentic markers (18%). The 10 additional cases remained unidentified (25.6%), but 7 of 10 could be further identified using fluorescence in situ hybridization; 69% of de novo sSMC contained euchromatin material, 95.4% of which for non-acrocentric markers. Some sSMC containing euchromatin had a normal phenotype (31% for non-acrocentric and 75% for acrocentric markers). Statistical differences between normal and abnormal phenotypes were shown for the size of the euchromatin material (more or less than 1 Mb, p = 0.0006) and number of genes (more or less than 10, p = 0.0009). This study is the largest to date and shows the utility of array-CGH or SNP array in the detection and characterization of de novo sSMC in a prenatal context.
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Affiliation(s)
- N Marle
- Département de Génétique, Hôpital Le Bocage, Université de Bourgogne, Dijon, France
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Zufferey F, Sherr EH, Beckmann ND, Hanson E, Maillard AM, Hippolyte L, Macé A, Ferrari C, Kutalik Z, Andrieux J, Aylward E, Barker M, Bernier R, Bouquillon S, Conus P, Delobel B, Faucett WA, Goin-Kochel RP, Grant E, Harewood L, Hunter JV, Lebon S, Ledbetter DH, Martin CL, Männik K, Martinet D, Mukherjee P, Ramocki MB, Spence SJ, Steinman KJ, Tjernagel J, Spiro JE, Reymond A, Beckmann JS, Chung WK, Jacquemont S. A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders. J Med Genet 2013; 49:660-8. [PMID: 23054248 PMCID: PMC3494011 DOI: 10.1136/jmedgenet-2012-101203] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [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] [Indexed: 12/29/2022]
Abstract
Background The recurrent ∼600 kb 16p11.2 BP4-BP5 deletion is among the most frequent known genetic aetiologies of autism spectrum disorder (ASD) and related neurodevelopmental disorders. Objective To define the medical, neuropsychological, and behavioural phenotypes in carriers of this deletion. Methods We collected clinical data on 285 deletion carriers and performed detailed evaluations on 72 carriers and 68 intrafamilial non-carrier controls. Results When compared to intrafamilial controls, full scale intelligence quotient (FSIQ) is two standard deviations lower in carriers, and there is no difference between carriers referred for neurodevelopmental disorders and carriers identified through cascade family testing. Verbal IQ (mean 74) is lower than non-verbal IQ (mean 83) and a majority of carriers require speech therapy. Over 80% of individuals exhibit psychiatric disorders including ASD, which is present in 15% of the paediatric carriers. Increase in head circumference (HC) during infancy is similar to the HC and brain growth patterns observed in idiopathic ASD. Obesity, a major comorbidity present in 50% of the carriers by the age of 7 years, does not correlate with FSIQ or any behavioural trait. Seizures are present in 24% of carriers and occur independently of other symptoms. Malformations are infrequently found, confirming only a few of the previously reported associations. Conclusions The 16p11.2 deletion impacts in a quantitative and independent manner FSIQ, behaviour and body mass index, possibly through direct influences on neural circuitry. Although non-specific, these features are clinically significant and reproducible. Lastly, this study demonstrates the necessity of studying large patient cohorts ascertained through multiple methods to characterise the clinical consequences of rare variants involved in common diseases.
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Affiliation(s)
- Flore Zufferey
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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Walters RG, Coin LJM, Ruokonen A, de Smith AJ, El-Sayed Moustafa JS, Jacquemont S, Elliott P, Esko T, Hartikainen AL, Laitinen J, Männik K, Martinet D, Meyre D, Nauck M, Schurmann C, Sladek R, Thorleifsson G, Thorsteinsdóttir U, Valsesia A, Waeber G, Zufferey F, Balkau B, Pattou F, Metspalu A, Völzke H, Vollenweider P, Stefansson K, Järvelin MR, Beckmann JS, Froguel P, Blakemore AIF. Rare genomic structural variants in complex disease: lessons from the replication of associations with obesity. PLoS One 2013; 8:e58048. [PMID: 23554873 PMCID: PMC3595275 DOI: 10.1371/journal.pone.0058048] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 01/30/2013] [Indexed: 01/19/2023] Open
Abstract
The limited ability of common variants to account for the genetic contribution to complex disease has prompted searches for rare variants of large effect, to partly explain the ‘missing heritability’. Analyses of genome-wide genotyping data have identified genomic structural variants (GSVs) as a source of such rare causal variants. Recent studies have reported multiple GSV loci associated with risk of obesity. We attempted to replicate these associations by similar analysis of two familial-obesity case-control cohorts and a population cohort, and detected GSVs at 11 out of 18 loci, at frequencies similar to those previously reported. Based on their reported frequencies and effect sizes (OR≥25), we had sufficient statistical power to detect the large majority (80%) of genuine associations at these loci. However, only one obesity association was replicated. Deletion of a 220 kb region on chromosome 16p11.2 has a carrier population frequency of 2×10−4 (95% confidence interval [9.6×10−5–3.1×10−4]); accounts overall for 0.5% [0.19%–0.82%] of severe childhood obesity cases (P = 3.8×10−10; odds ratio = 25.0 [9.9–60.6]); and results in a mean body mass index (BMI) increase of 5.8 kg.m−2 [1.8–10.3] in adults from the general population. We also attempted replication using BMI as a quantitative trait in our population cohort; associations with BMI at or near nominal significance were detected at two further loci near KIF2B and within FOXP2, but these did not survive correction for multiple testing. These findings emphasise several issues of importance when conducting rare GSV association, including the need for careful cohort selection and replication strategy, accurate GSV identification, and appropriate correction for multiple testing and/or control of false discovery rate. Moreover, they highlight the potential difficulty in replicating rare CNV associations across different populations. Nevertheless, we show that such studies are potentially valuable for the identification of variants making an appreciable contribution to complex disease.
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Affiliation(s)
- Robin G. Walters
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Clinical Trial Service Unit and Epidemiological Studies Unit, University of Oxford, Oxford, United Kingdom
| | - Lachlan J. M. Coin
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Aimo Ruokonen
- Institute of Diagnostics, Clinical Chemistry, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Adam J. de Smith
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | | | - Sebastien Jacquemont
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Tõnu Esko
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Anna-Liisa Hartikainen
- Institute of Clinical Sciences/Obstetrics and Gynecology, University of Oulu, Oulu, Finland
| | | | - Katrin Männik
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- The Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Danielle Martinet
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - David Meyre
- CNRS 8199-Institute of Biology, Pasteur Institute, Lille, France
- Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada
| | - Matthias Nauck
- Institute of Clinical Chemistry and Laboratory Medicine, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Rob Sladek
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
- Department of Medicine and Human Genetics, McGill University, Montreal, Canada
| | | | - Unnur Thorsteinsdóttir
- deCODE Genetics, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Armand Valsesia
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Gerard Waeber
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Flore Zufferey
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Beverley Balkau
- INSERM, CESP Centre for Research in Epidemiology and Population Health, U1018, Villejuif, France
- University Paris Sud 11, UMRS 1018, Villejuif, France
| | - François Pattou
- INSERM U859, Lille, France
- Université Lille Nord de France, Centre Hospitalier Universitaire Lille, Lille, France
| | - Andres Metspalu
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Henry Völzke
- Institute for Community Medicine, Ernst-Moritz-Arndt-University, Greifswald, Germany
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Kári Stefansson
- deCODE Genetics, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, Imperial College London, London, United Kingdom
- MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London, London, United Kingdom
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Lifecourse and Services, National Institute for Health and Welfare, Oulu, Finland
| | - Jacques S. Beckmann
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Philippe Froguel
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- CNRS 8199-Institute of Biology, Pasteur Institute, Lille, France
- * E-mail: (AIFB); (PF)
| | - Alexandra I. F. Blakemore
- Department of Genomics of Common Disease, Imperial College London, London, United Kingdom
- Section of Investigative Medicine, Imperial College London, London, United Kingdom
- * E-mail: (AIFB); (PF)
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DeScipio C, Conlin L, Rosenfeld J, Tepperberg J, Pasion R, Patel A, McDonald MT, Aradhya S, Ho D, Goldstein J, McGuire M, Mulchandani S, Medne L, Rupps R, Serrano AH, Thorland EC, Tsai ACH, Hilhorst-Hofstee Y, Ruivenkamp CAL, Van Esch H, Addor MC, Martinet D, Mason TBA, Clark D, Spinner NB, Krantz ID. Subtelomeric deletion of chromosome 10p15.3: clinical findings and molecular cytogenetic characterization. Am J Med Genet A 2012; 158A:2152-61. [PMID: 22847950 DOI: 10.1002/ajmg.a.35574] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 06/28/2012] [Indexed: 11/06/2022]
Abstract
We describe 19 unrelated individuals with submicroscopic deletions involving 10p15.3 characterized by chromosomal microarray (CMA). Interestingly, to our knowledge, only two individuals with isolated, submicroscopic 10p15.3 deletion have been reported to date; however, only limited clinical information is available for these probands and the deleted region has not been molecularly mapped. Comprehensive clinical history was obtained for 12 of the 19 individuals described in this study. Common features among these 12 individuals include: cognitive/behavioral/developmental differences (11/11), speech delay/language disorder (10/10), motor delay (10/10), craniofacial dysmorphism (9/12), hypotonia (7/11), brain anomalies (4/6) and seizures (3/7). Parental studies were performed for nine of the 19 individuals; the 10p15.3 deletion was de novo in seven of the probands, not maternally inherited in one proband and inherited from an apparently affected mother in one proband. Molecular mapping of the 19 individuals reported in this study has identified two genes, ZMYND11 (OMIM 608668) and DIP2C (OMIM 611380; UCSC Genome Browser), mapping within 10p15.3 which are most commonly deleted. Although no single gene has been identified which is deleted in all 19 individuals studied, the deleted region in all but one individual includes ZMYND11 and the deleted region in all but one other individual includes DIP2C. There is not a clearly identifiable phenotypic difference between these two individuals and the size of the deleted region does not generally predict clinical features. Little is currently known about these genes complicating a direct genotype/phenotype correlation at this time. These data however, suggest that ZMYND11 and/or DIP2C haploinsufficiency contributes to the clinical features associated with 10p15 deletions in probands described in this study.
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Affiliation(s)
- Cheryl DeScipio
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA.
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14
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Hegi ME, Janzer RC, Lambiv WL, Gorlia T, Kouwenhoven MCM, Hartmann C, von Deimling A, Martinet D, Besuchet Schmutz N, Diserens AC, Hamou MF, Bady P, Weller M, van den Bent MJ, Mason WP, Mirimanoff RO, Stupp R, Mokhtari K, Wesseling P. Presence of an oligodendroglioma-like component in newly diagnosed glioblastoma identifies a pathogenetically heterogeneous subgroup and lacks prognostic value: central pathology review of the EORTC_26981/NCIC_CE.3 trial. Acta Neuropathol 2012; 123:841-52. [PMID: 22249618 DOI: 10.1007/s00401-011-0938-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 12/29/2011] [Accepted: 12/30/2011] [Indexed: 10/14/2022]
Abstract
Glioblastoma (GBM) is a morphologically heterogeneous tumor type with a median survival of only 15 months in clinical trial populations. However, survival varies greatly among patients. As part of a central pathology review, we addressed the question if patients with GBM displaying distinct morphologic features respond differently to combined chemo-radiotherapy with temozolomide. Morphologic features were systematically recorded for 360 cases with particular focus on the presence of an oligodendroglioma-like component and respective correlations with outcome and relevant molecular markers. GBM with an oligodendroglioma-like component (GBM-O) represented 15% of all confirmed GBM (52/339) and was not associated with a more favorable outcome. GBM-O encompassed a pathogenetically heterogeneous group, significantly enriched for IDH1 mutations (19 vs. 3%, p = 0.003) and EGFR amplifications (71 vs. 48%, p = 0.04) compared with other GBM, while co-deletion of 1p/19q was found in only one case and the MGMT methylation frequency was alike (47 vs. 46%). Expression profiles classified most of the GBM-O into two subtypes, 36% (5/14 evaluable) as proneural and 43% as classical GBM. The detection of pseudo-palisading necrosis (PPN) was associated with benefit from chemotherapy (p = 0.0002), while no such effect was present in the absence of PPN (p = 0.86). In the adjusted interaction model including clinical prognostic factors and MGMT status, PPN was borderline nonsignificant (p = 0.063). Taken together, recognition of an oligodendroglioma-like component in an otherwise classic GBM identifies a pathogenetically mixed group without prognostic significance. However, the presence of PPN may indicate biological features of clinical relevance for further improvement of therapy.
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Stankiewicz P, Kulkarni S, Dharmadhikari AV, Sampath S, Bhatt SS, Shaikh TH, Xia Z, Pursley AN, Cooper ML, Shinawi M, Paciorkowski AR, Grange DK, Noetzel MJ, Saunders S, Simons P, Summar M, Lee B, Scaglia F, Fellmann F, Martinet D, Beckmann JS, Asamoah A, Platky K, Sparks S, Martin AS, Madan-Khetarpal S, Hoover J, Medne L, Bonnemann CG, Moeschler JB, Vallee SE, Parikh S, Irwin P, Dalzell VP, Smith WE, Banks VC, Flannery DB, Lovell CM, Bellus GA, Golden-Grant K, Gorski JL, Kussmann JL, McGregor TL, Hamid R, Pfotenhauer J, Ballif BC, Shaw CA, Kang SHL, Bacino CA, Patel A, Rosenfeld JA, Cheung SW, Shaffer LG. Recurrent deletions and reciprocal duplications of 10q11.21q11.23 including CHAT and SLC18A3 are likely mediated by complex low-copy repeats. Hum Mutat 2011; 33:165-79. [PMID: 21948486 DOI: 10.1002/humu.21614] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 09/06/2011] [Indexed: 11/11/2022]
Abstract
We report 24 unrelated individuals with deletions and 17 additional cases with duplications at 10q11.21q21.1 identified by chromosomal microarray analysis. The rearrangements range in size from 0.3 to 12 Mb. Nineteen of the deletions and eight duplications are flanked by large, directly oriented segmental duplications of >98% sequence identity, suggesting that nonallelic homologous recombination (NAHR) caused these genomic rearrangements. Nine individuals with deletions and five with duplications have additional copy number changes. Detailed clinical evaluation of 20 patients with deletions revealed variable clinical features, with developmental delay (DD) and/or intellectual disability (ID) as the only features common to a majority of individuals. We suggest that some of the other features present in more than one patient with deletion, including hypotonia, sleep apnea, chronic constipation, gastroesophageal and vesicoureteral refluxes, epilepsy, ataxia, dysphagia, nystagmus, and ptosis may result from deletion of the CHAT gene, encoding choline acetyltransferase, and the SLC18A3 gene, mapping in the first intron of CHAT and encoding vesicular acetylcholine transporter. The phenotypic diversity and presence of the deletion in apparently normal carrier parents suggest that subjects carrying 10q11.21q11.23 deletions may exhibit variable phenotypic expressivity and incomplete penetrance influenced by additional genetic and nongenetic modifiers.
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Affiliation(s)
- Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
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16
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Grandjean M, Girod PA, Calabrese D, Kostyrko K, Wicht M, Yerly F, Mazza C, Beckmann JS, Martinet D, Mermod N. High-level transgene expression by homologous recombination-mediated gene transfer. Nucleic Acids Res 2011; 39:e104. [PMID: 21652640 PMCID: PMC3159483 DOI: 10.1093/nar/gkr436] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [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] [Indexed: 02/01/2023] Open
Abstract
Gene transfer and expression in eukaryotes is often limited by a number of stably maintained gene copies and by epigenetic silencing effects. Silencing may be limited by the use of epigenetic regulatory sequences such as matrix attachment regions (MAR). Here, we show that successive transfections of MAR-containing vectors allow a synergistic increase of transgene expression. This finding is partly explained by an increased entry into the cell nuclei and genomic integration of the DNA, an effect that requires both the MAR element and iterative transfections. Fluorescence in situ hybridization analysis often showed single integration events, indicating that DNAs introduced in successive transfections could recombine. High expression was also linked to the cell division cycle, so that nuclear transport of the DNA occurs when homologous recombination is most active. Use of cells deficient in either non-homologous end-joining or homologous recombination suggested that efficient integration and expression may require homologous recombination-based genomic integration of MAR-containing plasmids and the lack of epigenetic silencing events associated with tandem gene copies. We conclude that MAR elements may promote homologous recombination, and that cells and vectors can be engineered to take advantage of this property to mediate highly efficient gene transfer and expression.
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Affiliation(s)
- Mélanie Grandjean
- Laboratory of Molecular Biotechnology, Center for Biotechnology UNIL-EPFL, University of Lausanne, Lausanne, Switzerland
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Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, Quadroni M, Waridel P, Gaillard M, Pidoux M, Rapin B, Rivolta C, Xenarios I, Simpson AJG, Antonarakis SE, Beckmann JS, Jongeneel CV, Iseli C, Stevenson BJ. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 2011; 6:e18369. [PMID: 21494657 PMCID: PMC3072964 DOI: 10.1371/journal.pone.0018369] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [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: 12/14/2010] [Accepted: 02/28/2011] [Indexed: 12/21/2022] Open
Abstract
Cancer genomes frequently contain somatic copy number alterations (SCNA) that can significantly perturb the expression level of affected genes and thus disrupt pathways controlling normal growth. In melanoma, many studies have focussed on the copy number and gene expression levels of the BRAF, PTEN and MITF genes, but little has been done to identify new genes using these parameters at the genome-wide scale. Using karyotyping, SNP and CGH arrays, and RNA-seq, we have identified SCNA affecting gene expression ('SCNA-genes') in seven human metastatic melanoma cell lines. We showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. Since few of these alterations were recurrent across our samples, we used a protein network-guided approach to determine whether any pathways were enriched in SCNA-genes in one or more samples. From this unbiased genome-wide analysis, we identified 28 significantly enriched pathway modules. Comparison with two large, independent melanoma SCNA datasets showed less than 10% overlap at the individual gene level, but network-guided analysis revealed 66% shared pathways, including all but three of the pathways identified in our data. Frequently altered pathways included WNT, cadherin signalling, angiogenesis and melanogenesis. Additionally, our results emphasize the potential of the EPHA3 and FRS2 gene products, involved in angiogenesis and migration, as possible therapeutic targets in melanoma. Our study demonstrates the utility of network-guided approaches, for both large and small datasets, to identify pathways recurrently perturbed in cancer.
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Affiliation(s)
- Armand Valsesia
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Donata Rimoldi
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Danielle Martinet
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Mark Ibberson
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paola Benaglio
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, Lausanne, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, Center for Integrative Genomics, Lausanne, Switzerland
| | - Muriel Gaillard
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Mireille Pidoux
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Blandine Rapin
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | | | - Andrew J. G. Simpson
- Ludwig Institute for Cancer Research, New York, New York, United States of America
| | | | - Jacques S. Beckmann
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - C. Victor Jongeneel
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute for Genomic Biology and National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Christian Iseli
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail: (CI); (BJS)
| | - Brian J. Stevenson
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail: (CI); (BJS)
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van Bon BWM, Balciuniene J, Fruhman G, Nagamani SCS, Broome DL, Cameron E, Martinet D, Roulet E, Jacquemont S, Beckmann JS, Irons M, Potocki L, Lee B, Cheung SW, Patel A, Bellini M, Selicorni A, Ciccone R, Silengo M, Vetro A, Knoers NV, de Leeuw N, Pfundt R, Wolf B, Jira P, Aradhya S, Stankiewicz P, Brunner HG, Zuffardi O, Selleck SB, Lupski JR, de Vries BBA. The phenotype of recurrent 10q22q23 deletions and duplications. Eur J Hum Genet 2011; 19:400-8. [PMID: 21248748 DOI: 10.1038/ejhg.2010.211] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The genomic architecture of the 10q22q23 region is characterised by two low-copy repeats (LCRs3 and 4), and deletions in this region appear to be rare. We report the clinical and molecular characterisation of eight novel deletions and six duplications within the 10q22.3q23.3 region. Five deletions and three duplications occur between LCRs3 and 4, whereas three deletions and three duplications have unique breakpoints. Most of the individuals with the LCR3-4 deletion had developmental delay, mainly affecting speech. In addition, macrocephaly, mild facial dysmorphisms, cerebellar anomalies, cardiac defects and congenital breast aplasia were observed. For congenital breast aplasia, the NRG3 gene, known to be involved in early mammary gland development in mice, is a putative candidate gene. For cardiac defects, BMPR1A and GRID1 are putative candidate genes because of their association with cardiac structure and function. Duplications between LCRs3 and 4 are associated with variable phenotypic penetrance. Probands had speech and/or motor delays and dysmorphisms including a broad forehead, deep-set eyes, upslanting palpebral fissures, a smooth philtrum and a thin upper lip. In conclusion, duplications between LCRs3 and 4 on 10q22.3q23.2 may lead to a distinct facial appearance and delays in speech and motor development. However, the phenotypic spectrum is broad, and duplications have also been found in healthy family members of a proband. Reciprocal deletions lead to speech and language delay, mild facial dysmorphisms and, in some individuals, to cerebellar, breast developmental and cardiac defects.
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Affiliation(s)
- Bregje W M van Bon
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
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Jacquemont S, Curie A, des Portes V, Torrioli MG, Berry-Kravis E, Hagerman RJ, Ramos FJ, Cornish K, He Y, Paulding C, Neri G, Chen F, Hadjikhani N, Martinet D, Meyer J, Beckmann JS, Delange K, Brun A, Bussy G, Gasparini F, Hilse T, Floesser A, Branson J, Bilbe G, Johns D, Gomez-Mancilla B. Epigenetic Modification of the FMR1 Gene in Fragile X Syndrome Is Associated with Differential Response to the mGluR5 Antagonist AFQ056. Sci Transl Med 2011; 3:64ra1. [DOI: 10.1126/scitranslmed.3001708] [Citation(s) in RCA: 294] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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20
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Sciuscio D, Diserens AC, van Dommelen K, Martinet D, Jones G, Janzer RC, Pollo C, Hamou MF, Kaina B, Stupp R, Levivier M, Hegi ME. Extent and patterns of MGMT promoter methylation in glioblastoma- and respective glioblastoma-derived spheres. Clin Cancer Res 2010; 17:255-66. [PMID: 21097691 DOI: 10.1158/1078-0432.ccr-10-1931] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [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
PURPOSE Quantitative methylation-specific tests suggest that not all cells in a glioblastoma with detectable promoter methylation of the O6-methylguanine DNA methyltransferase (MGMT) gene carry a methylated MGMT allele. This observation may indicate cell subpopulations with distinct MGMT status, raising the question of the clinically relevant cutoff of MGMT methylation therapy. Epigenetic silencing of the MGMT gene by promoter methylation blunts repair of O6-methyl guanine and has been shown to be a predictive factor for benefit from alkylating agent therapy in glioblastoma. EXPERIMENTAL DESIGN Ten paired samples of glioblastoma and respective glioblastoma-derived spheres (GS), cultured under stem cell conditions, were analyzed for the degree and pattern of MGMT promoter methylation by methylation-specific clone sequencing, MGMT gene dosage, chromatin status, and respective effects on MGMT expression and MGMT activity. RESULTS In glioblastoma, MGMT-methylated alleles ranged from 10% to 90%. In contrast, methylated alleles were highly enriched (100% of clones) in respective GS, even when 2 MGMT alleles were present, with 1 exception (<50%). The CpG methylation patterns were characteristic for each glioblastoma exhibiting 25% to 90% methylated CpGs of 28 sites interrogated. Furthermore, MGMT promoter methylation was associated with a nonpermissive chromatin status in accordance with very low MGMT transcript levels and undetectable MGMT activity. CONCLUSIONS In MGMT-methylated glioblastoma, MGMT promoter methylation is highly enriched in GS that supposedly comprise glioma-initiating cells. Thus, even a low percentage of MGMT methylation measured in a glioblastoma sample may be relevant and predict benefit from an alkylating agent therapy.
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Affiliation(s)
- Davide Sciuscio
- Laboratory of Brain Tumor Biology, Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
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21
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Sciuscio D, Diserens AC, Martinet D, Vlassenbroeck I, Hamou MF, Janzer RC, Pollo C, Stupp R, Levivier M, Hegi ME. Abstract 4927: MGMT promoter methylation is enriched in glioblastoma derived spheres as compared to respective original tumor tissue and is associated with loss of expression. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic silencing of the O6-methylaguanine DNA methyl transferase (MGMT) gene by promoter hypermethylation blunts repair of O6-methyl guanine and has been shown to be a predictive factor for benefit from alkylating agent therapy in glioblastoma. Quantitative methylation specific PCR (Q-MSP) suggests that not all cells in a glioblastoma exhibiting MGMT methylation carry a methylated MGMT allele, even after adjustment for tumor cell content. This raises the question of the clinically relevant methylation threshold for predicting response to therapy for treatment stratification. There are several potential reasons: heterogeneity of glioblastoma; contaminating normal tissue; a heterogenous methylation pattern not correctly detectable by the assay, or presence of MGMT methylation in distinct subpopulations of cells, namely tumor initiating cells. In order to address the question we investigated the degree and pattern of MGMT promoter methylation in 10 paired samples of glioblastoma and spheres derived thereof using Q-MSP and methylation specific clone sequencing. We observed that in MGMT methylated glioblastoma, the percentage of methylated alleles ranged from 10 to 90%. In contrast, in most of the respective glioblastoma derived spheres, cultured under stem cell conditions, methylated alleles were highly enriched (10/10 clones), even if both MGMT-alleles were retained. The methylation pattern was conserved in the spheres, even when passing them in nude mice. Most importantly, this hypermethylation was associated with complete loss of MGMT expression. For one case we observed only 50% methylated clones in the sphere fraction, associated with low expression of MGMT.
Taken together, our data suggest that in MGMT methylated glioblastoma, cells with MGMT promoter hypermethylation are enriched in the sphere fraction which supposedly comprises cancer initiating cells. Thus, even a low percentage of MGMT methylation in a glioblastoma could be predictive marker for a benefit from alkylating agent therapy.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4927.
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Affiliation(s)
| | | | | | | | | | | | - Claudio Pollo
- 1Ctr. Hospitalier Univ. Vaudois, Lausanne, Switzerland
| | - Roger Stupp
- 1Ctr. Hospitalier Univ. Vaudois, Lausanne, Switzerland
| | - Marc Levivier
- 1Ctr. Hospitalier Univ. Vaudois, Lausanne, Switzerland
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Ferrarini A, Jacquemont S, Popovic MB, Bonafé L, Martinet D. [Array CGH: why and to whom]. Rev Med Suisse 2010; 6:390-396. [PMID: 20383968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Structural genomic abnormalities play a key role in the pathogenesis of human disorders and represent one of the first causes of mental impairment, complex syndromes and tumors. In order to detect these chromosomal abnormalities, many methodologies have been developed with limits. The new ARRAY based Comparative Genomic Hybridization (ARRAY CGH) is a revolutionary approach which allows to characterize very small genetic abnormalities undetectable by the standard approaches and in the absence of any associated clinical information. The aim of this article is to describe why the application of a new array CGH methodology is necessary in the etiological search for genetic diseases, what the limits of the standard approaches are and to whom arrayCGH analyses can be applied in a pediatric environment. Examples of our practice will be presented.
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Affiliation(s)
- Alessandra Ferrarini
- Service de génétique médicale et Département médico-chirurgical de pédiatrie, CHUV, 1011 Lausanne.
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23
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Walters RG, Jacquemont S, Valsesia A, de Smith AJ, Martinet D, Andersson J, Falchi M, Chen F, Andrieux J, Lobbens S, Delobel B, Stutzmann F, Moustafa JSES, Chèvre JC, Lecoeur C, Vatin V, Bouquillon S, Buxton JL, Boute O, Holder-Espinasse M, Cuisset JM, Lemaitre MP, Ambresin AE, Brioshi A, Gaillard M, Giusti V, Fellmann F, Ferrarini A, Hadjikhani N, Campion D, Guilmatre A, Goldenberg A, Calmels N, Mandel JL, Le Caignec C, David A, Isidor B, Cordier MP, Dupuis-Girod S, Labalme A, Sanlaville D, Béri-Deixheimer M, Jonveaux P, Leheup B, Õunap K, Bochukova EG, Henning E, Keogh J, Ellis RJ, MacDermot KD, Vincent-Delorme C, Plessis G, Touraine R, Philippe A, Malan V, Mathieu-Dramard M, Chiesa J, Blaumeiser B, Kooy RF, Caiazzo R, Pigeyre M, Balkau B, Sladek R, Bergmann S, Mooser V, Waterworth D, Reymond A, Vollenweider P, Waeber G, Kurg A, Palta P, Esko T, Metspalu A, Nelis M, Elliott P, Hartikainen AL, McCarthy MI, Peltonen L, Carlsson L, Jacobson P, Sjöström L, Huang N, Hurles ME, O’Rahilly S, Farooqi IS, Männik K, Jarvelin MR, Pattou F, Meyre D, Walley AJ, Coin LJM, Blakemore AIF, Froguel P, Beckmann JS. A new highly penetrant form of obesity due to deletions on chromosome 16p11.2. Nature 2010; 463:671-5. [PMID: 20130649 PMCID: PMC2880448 DOI: 10.1038/nature08727] [Citation(s) in RCA: 345] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Accepted: 12/01/2009] [Indexed: 01/04/2023]
Abstract
Obesity has become a major worldwide challenge to public health, owing to an interaction between the Western 'obesogenic' environment and a strong genetic contribution. Recent extensive genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms associated with obesity, but these loci together account for only a small fraction of the known heritable component. Thus, the 'common disease, common variant' hypothesis is increasingly coming under challenge. Here we report a highly penetrant form of obesity, initially observed in 31 subjects who were heterozygous for deletions of at least 593 kilobases at 16p11.2 and whose ascertainment included cognitive deficits. Nineteen similar deletions were identified from GWAS data in 16,053 individuals from eight European cohorts. These deletions were absent from healthy non-obese controls and accounted for 0.7% of our morbid obesity cases (body mass index (BMI) >or= 40 kg m(-2) or BMI standard deviation score >or= 4; P = 6.4 x 10(-8), odds ratio 43.0), demonstrating the potential importance in common disease of rare variants with strong effects. This highlights a promising strategy for identifying missing heritability in obesity and other complex traits: cohorts with extreme phenotypes are likely to be enriched for rare variants, thereby improving power for their discovery. Subsequent analysis of the loci so identified may well reveal additional rare variants that further contribute to the missing heritability, as recently reported for SIM1 (ref. 3). The most productive approach may therefore be to combine the 'power of the extreme' in small, well-phenotyped cohorts, with targeted follow-up in case-control and population cohorts.
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Affiliation(s)
- R. G. Walters
- Section of Genomic Medicine, Imperial College London, London, UK
- Department of Epidemiology and Public Health, Imperial College London, London, UK
| | - S. Jacquemont
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - A. Valsesia
- Departement de Génétique Médicale, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - A. J. de Smith
- Section of Genomic Medicine, Imperial College London, London, UK
| | - D. Martinet
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - J. Andersson
- Section of Genomic Medicine, Imperial College London, London, UK
| | - M. Falchi
- Section of Genomic Medicine, Imperial College London, London, UK
| | - F. Chen
- Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - J. Andrieux
- Laboratoire de Génétique Médicale, Centre Hospitalier Régional Universitaire, Lille, France
| | - S. Lobbens
- CNRS 8090-Institute of Biology, Pasteur Institute, Lille, France
| | - B. Delobel
- Centre de Génétique Chromosomique, Hôpital Saint-Vincent de Paul, GHICL, Lille, France
| | - F. Stutzmann
- CNRS 8090-Institute of Biology, Pasteur Institute, Lille, France
| | | | - J.-C. Chèvre
- CNRS 8090-Institute of Biology, Pasteur Institute, Lille, France
| | - C. Lecoeur
- CNRS 8090-Institute of Biology, Pasteur Institute, Lille, France
| | - V. Vatin
- CNRS 8090-Institute of Biology, Pasteur Institute, Lille, France
| | - S. Bouquillon
- Laboratoire de Génétique Médicale, Centre Hospitalier Régional Universitaire, Lille, France
| | - J. L. Buxton
- Section of Genomic Medicine, Imperial College London, London, UK
| | - O. Boute
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, Centre Hospitalier Universitaire de Lille, Lille, France
| | - M. Holder-Espinasse
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, Centre Hospitalier Universitaire de Lille, Lille, France
| | - J.-M. Cuisset
- Service de Neuropédiatrie, Centre Hospitalier Régional Universitaire, Lille, France
| | - M.-P. Lemaitre
- Service de Neuropédiatrie, Centre Hospitalier Régional Universitaire, Lille, France
| | - A.-E. Ambresin
- Unité Multidisciplinaire de Santé des Adolescents, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - A. Brioshi
- Service de Neuropsychologie et de Neuroréhabilitation, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - M. Gaillard
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - V. Giusti
- Service d’Endocrinologie, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - F. Fellmann
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - A. Ferrarini
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - N. Hadjikhani
- Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Athinoula A Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical School, Charlestown MA, USA
| | - D. Campion
- INSERM, U614, Faculté de Médecine, Rouen, France
| | - A. Guilmatre
- INSERM, U614, Faculté de Médecine, Rouen, France
| | - A. Goldenberg
- Service de Génétique, Centre Hospitalier Universitaire de Rouen, Rouen, France
| | - N. Calmels
- Laboratoire de Diagnostic Génétique, Nouvel hôpital civil, Strasbourg, France
| | - J.-L. Mandel
- Laboratoire de Diagnostic Génétique, Nouvel hôpital civil, Strasbourg, France
| | - C. Le Caignec
- Centre Hospitalier Universitaire Nantes, Service de Génétique Médicale, Nantes, France
- INSERM, UMR915, L’Institut du Thorax, Nantes, France
| | - A. David
- Centre Hospitalier Universitaire Nantes, Service de Génétique Médicale, Nantes, France
| | - B. Isidor
- Centre Hospitalier Universitaire Nantes, Service de Génétique Médicale, Nantes, France
| | - M.-P. Cordier
- Service de Génétique, Hospices Civils de Lyon, Hôpital de l’Hotel Dieu, Lyon, France
| | - S. Dupuis-Girod
- Service de Génétique, Hospices Civils de Lyon, Hôpital de l’Hotel Dieu, Lyon, France
| | - A. Labalme
- Service de Génétique, Hospices Civils de Lyon, Hôpital de l’Hotel Dieu, Lyon, France
| | - D. Sanlaville
- Service de Génétique, Hospices Civils de Lyon, Hôpital de l’Hotel Dieu, Lyon, France
- EA 4171, Université Claude Bernard, Lyon, France
| | - M. Béri-Deixheimer
- Laboratoire de Génétique, Centre Hospitalier Universitaire, Nancy University, Nancy, France
| | - P. Jonveaux
- Laboratoire de Génétique, Centre Hospitalier Universitaire, Nancy University, Nancy, France
| | - B. Leheup
- Laboratoire de Génétique, Centre Hospitalier Universitaire, Nancy University, Nancy, France
- EA4368 Medical School Nancy, Université Henri Poincaré, Nancy, France
| | - K. Õunap
- Department of Genetics, United Laboratories,Tartu University Children’s Hospital, Tartu, Estonia
| | - E. G. Bochukova
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - E. Henning
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - J. Keogh
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - R. J. Ellis
- North West Thames Regional Genetics Service, Northwick Park & St Marks Hospital, Harrow, UK
| | - K. D. MacDermot
- North West Thames Regional Genetics Service, Northwick Park & St Marks Hospital, Harrow, UK
| | | | - G. Plessis
- Service de Génétique Médicale, Centre Hospitalier Universitaire Clemenceau, Caen, France
| | - R. Touraine
- Centre Hospitalier Universitaire–Hôpital Nord, Service de Génétique, Saint Etienne, France
| | - A. Philippe
- Département de Génétique et INSERM U781, Université Paris Descartes, Hôpital Necker-Enfants Malades, Paris, France
| | - V. Malan
- Département de Génétique et INSERM U781, Université Paris Descartes, Hôpital Necker-Enfants Malades, Paris, France
| | - M. Mathieu-Dramard
- Service de Génétique Clinique, Centre Hospitalier Universitaire, Amiens, France
| | - J. Chiesa
- Laboratoire de Cytogénétique, Centre Hospitalier Universitaire Caremeau, Nîmes, France
| | - B. Blaumeiser
- Department of Medical Genetics, University Hospital & University of Antwerp, Antwerp, Belgium
| | - R. F. Kooy
- Department of Medical Genetics, University Hospital & University of Antwerp, Antwerp, Belgium
| | - R. Caiazzo
- INSERM U859, Biotherapies for Diabetes, Lille, France
- University Lille Nord de France, Centre Hospitalier Universitaire Lille, France
| | - M. Pigeyre
- University Lille Nord de France, Centre Hospitalier Universitaire Lille, France
| | - B. Balkau
- INSERM U780-IFR69, Villejuif, France
| | - R. Sladek
- Genome Quebec Innovation Centre, Montreal, Canada
- Department of Medicine and Human Genetics, McGill University, Montreal, Canada
| | - S. Bergmann
- Departement de Génétique Médicale, Université de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - V. Mooser
- Division of Genetics, GlaxoSmithKline, Philadelphia PA, USA
| | - D. Waterworth
- Division of Genetics, GlaxoSmithKline, Philadelphia PA, USA
| | - A. Reymond
- The Center for Integrated Genomics, University of Lausanne, Lausanne, Switzerland
| | - P. Vollenweider
- Department of Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - G. Waeber
- Department of Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - A. Kurg
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - P. Palta
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - T. Esko
- Estonian Genome Project, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - A. Metspalu
- Estonian Genome Project, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - M. Nelis
- Estonian Genome Project, University of Tartu, Tartu, Estonia
- Estonian Biocentre, Tartu, Estonia
| | - P. Elliott
- Department of Epidemiology and Public Health, Imperial College London, London, UK
| | - A.-L. Hartikainen
- Department of Obstetrics and Gynaecology, University of Oulu, Oulu, Finland
| | - M. I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L. Peltonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
- Massachusetts Institute of Technology, The Broad Institute, Cambridge MA, USA
| | - L. Carlsson
- Department of Molecular and Clinical Medicine and Center for Cardiovascular and Metabolic Research, The Sahlgrenska Academy, Göteborg, Sweden
| | - P. Jacobson
- Department of Molecular and Clinical Medicine and Center for Cardiovascular and Metabolic Research, The Sahlgrenska Academy, Göteborg, Sweden
| | - L. Sjöström
- Department of Molecular and Clinical Medicine and Center for Cardiovascular and Metabolic Research, The Sahlgrenska Academy, Göteborg, Sweden
| | - N. Huang
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - M. E. Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK
| | - S. O’Rahilly
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - I. S. Farooqi
- University of Cambridge Metabolic Research Laboratories, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, UK
| | - K. Männik
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - M.-R. Jarvelin
- Department of Epidemiology and Public Health, Imperial College London, London, UK
- Department of Child and Adolescent Health, National Public Health Institute, Oulu, Finland
- Institute of Health Sciences and Biocenter Oulu, University of Oulu, Oulu Finland
| | - F. Pattou
- INSERM U859, Biotherapies for Diabetes, Lille, France
- University Lille Nord de France, Centre Hospitalier Universitaire Lille, France
| | - D. Meyre
- CNRS 8090-Institute of Biology, Pasteur Institute, Lille, France
| | - A. J. Walley
- Section of Genomic Medicine, Imperial College London, London, UK
| | - L. J. M. Coin
- Department of Epidemiology and Public Health, Imperial College London, London, UK
| | | | - P. Froguel
- Section of Genomic Medicine, Imperial College London, London, UK
- CNRS 8090-Institute of Biology, Pasteur Institute, Lille, France
| | - J. S. Beckmann
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Departement de Génétique Médicale, Université de Lausanne, Lausanne, Switzerland
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Ferrarini A, Osterheld MC, Vial Y, de Viragh PA, Cotting J, Martinet D, Beckmann JS, Fellmann F. Familial occurrence of an association of multiple intestinal atresia and choanal atresia: a new syndrome? Am J Med Genet A 2009; 149A:2661-5. [PMID: 19938077 DOI: 10.1002/ajmg.a.33132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We report on two familial cases from a non-consanguineous marriage, presenting multiple intestinal and choanal atresia. Massive hydramnios and dilatation of the bowel were observed at 29 weeks of gestation during routine ultrasound scan of a healthy mother. The fetal karyotype was normal and cystic fibrosis screening was negative. Regular scans were performed throughout the pregnancy. The child was born at 34 weeks gestation. Choanal atresia was diagnosed at birth and abdominal investigations showed multiple atresia interesting both the small bowel and the colon. Further interventions were necessary because of recurrent obstructions. During the following pregnancy, a dilatation of the fetal intestinal tract was detected by ultrasonography at 27 weeks of gestation. Pregnancy was interrupted. Post-mortem examination of the fetus confirmed the stenosis of long segments of the small intestine associated with areas of colonic atresia. In both cases, histology and distribution were consistent with those reported in hereditary multiple intestinal atresia (HMIA). An association between multiple intestinal and choanal atresia has never been reported. We suggest it could correspond to a new autosomal recessive entity for which cytogenetic investigations and high-resolution array CGH revealed no visible anomalies.
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Affiliation(s)
- Alessandra Ferrarini
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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25
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Chenuet S, Martinet D, Besuchet-Schmutz N, Wicht M, Jaccard N, Bon AC, Derouazi M, Hacker DL, Beckmann JS, Wurm FM. Calcium phosphate transfection generates mammalian recombinant cell lines with higher specific productivity than polyfection. Biotechnol Bioeng 2008; 101:937-45. [DOI: 10.1002/bit.21972] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Martinet D, Filges I, Besuchet Schmutz N, Morris MA, Gaide AC, Dahoun S, Bottani A, Addor MC, Antonarakis SE, Beckmann JS, Béna F. Subtelomeric 6p deletion: clinical and array-CGH characterization in two patients. Am J Med Genet A 2008; 146A:2094-102. [PMID: 18629875 DOI: 10.1002/ajmg.a.32414] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We report on two patients with de novo subtelomeric terminal deletion of chromosome 6p. Patient 1 is an 8-month-old female born with normal growth parameters, typical facial features of 6pter deletion, bilateral corectopia, and protruding tongue. She has severe developmental delay, profound bilateral neurosensory deafness, poor visual contact, and hypsarrhythmia since the age of 6 months. Patient 2 is a 5-year-old male born with normal growth parameters and unilateral hip dysplasia; he has a characteristic facial phenotype, bilateral embryotoxon, and moderate mental retardation. Further characterization of the deletion, using high-resolution array comparative genomic hybridization (array-CGH; Agilent Human Genome kit 244 K), revealed that Patient 1 has a 8.1 Mb 6pter-6p24.3 deletion associated with a contiguous 5.8 Mb 6p24.3-6p24.1 duplication and Patient 2 a 5.7 Mb 6pter-6p25.1 deletion partially overlapping with that of Patient 1. Complementary FISH and array analysis showed that the inv del dup(6) in Patient 1 originated de novo. Our results demonstrate that simple rearrangements are often more complex than defined by standard techniques. We also discuss genotype-phenotype correlations including previously reported cases of deletion 6p.
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Affiliation(s)
- Danielle Martinet
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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Girod PA, Nguyen DQ, Calabrese D, Puttini S, Grandjean M, Martinet D, Regamey A, Saugy D, Beckmann JS, Bucher P, Mermod N. Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells. Nat Methods 2007; 4:747-53. [PMID: 17676049 DOI: 10.1038/nmeth1076] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Accepted: 07/02/2007] [Indexed: 01/13/2023]
Abstract
Gene transfer in eukaryotic cells and organisms suffers from epigenetic effects that result in low or unstable transgene expression and high clonal variability. Use of epigenetic regulators such as matrix attachment regions (MARs) is a promising approach to alleviate such unwanted effects. Dissection of a known MAR allowed the identification of sequence motifs that mediate elevated transgene expression. Bioinformatics analysis implied that these motifs adopt a curved DNA structure that positions nucleosomes and binds specific transcription factors. From these observations, we computed putative MARs from the human genome. Cloning of several predicted MARs indicated that they are much more potent than the previously known element, boosting the expression of recombinant proteins from cultured cells as well as mediating high and sustained expression in mice. Thus we computationally identified potent epigenetic regulators, opening new strategies toward high and stable transgene expression for research, therapeutic production or gene-based therapies.
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Affiliation(s)
- Pierre-Alain Girod
- Institute of Biotechnology, University of Lausanne, and Center for Biotechnology of the University of Lausanne and Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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28
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Flahaut M, Mühlethaler-Mottet A, Martinet D, Fattet S, Bourloud KB, Auderset K, Meier R, Schmutz NB, Delattre O, Joseph JM, Gross N. Molecular cytogenetic characterization of doxorubicin-resistant neuroblastoma cell lines: evidence that acquired multidrug resistance results from a unique large amplification of the 7q21 region. Genes Chromosomes Cancer 2006; 45:495-508. [PMID: 16450357 DOI: 10.1002/gcc.20312] [Citation(s) in RCA: 17] [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: 12/21/2022] Open
Abstract
Neuroblastoma is a heterogeneous neural crest-derived embryonic childhood neoplasm that is the second most common solid tumor found in children. Despite recent advances in combined therapy, the overall survival of patients with high-stage disease has not improved in the last decades. Treatment failure is in part attributed to multidrug resistance. To address the mechanisms involved in the development of multidrug resistance, we have generated two doxorubicin-resistant neuroblastoma cell lines (IGRN-91R and LAN-1R). These cells were shown to overexpress the MDR1 gene coding for the P-glycoprotein and were resistant to other MDR1- and non-MDR1-substrate drugs. Indeed, the MDR1 inhibitor verapamil only partially restored sensitivity to drugs, confirming that P-glycoprotein-mediated drug efflux was not responsible for 100% resistance. High-resolution and array-based comparative genomic hybridization analyses revealed the presence of an amplicon in the 7q21 region as the unique genomic alteration common to both doxorubicin-resistant cell lines. In addition to the MDR1 locus, this large amplified region is likely to harbor additional genes potentially involved in the development of drug resistance. This study represents the first molecular cytogenetic and genomic approach to identifying genomic regions involved in the multidrug-resistant phenotype of neuroblastoma. These results could lead to the identification of relevant target genes for the development of new therapeutic modalities.
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Affiliation(s)
- Marjorie Flahaut
- Paediatric Oncology Research, Paediatric Department, University Hospital CHUV, Lausanne, Switzerland
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29
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Derouazi M, Martinet D, Besuchet Schmutz N, Flaction R, Wicht M, Bertschinger M, Hacker DL, Beckmann JS, Wurm FM. Genetic characterization of CHO production host DG44 and derivative recombinant cell lines. Biochem Biophys Res Commun 2006; 340:1069-77. [PMID: 16403443 DOI: 10.1016/j.bbrc.2005.12.111] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [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: 11/22/2005] [Accepted: 12/05/2005] [Indexed: 10/25/2022]
Abstract
The dihydrofolate reductase-deficient Chinese hamster ovary (CHO) cell line DG44 is the dominant mammalian host for recombinant protein manufacturing, in large part because of the availability of a well-characterized genetic selection and amplification system. However, this cell line has not been studied at the cytogenetic level. Here, the first detailed karyotype analysis of DG44 and several recombinant derivative cell lines is described. In contrast to the 22 chromosomes in diploid Chinese hamster cells, DG44 has 20 chromosomes, only seven of which are normal. In addition, four Z group chromosomes, seven derivative chromosomes, and 2 marker chromosomes were identified. For all but one of the 16 DG44-derived recombinant cell lines analyzed, a single integration site was detected by fluorescence in situ hybridization regardless of the gene delivery method (calcium phosphate-DNA coprecipitation or microinjection), the topology of the DNA (circular or linear), or the integrated plasmid copy number (between 1 and 51). Chromosomal aberrations, observed in more than half of the cell lines studied, were mostly unbalanced with examples of aneuploidy, deletions, and complex rearrangements. The results demonstrate that chromosomal aberrations are frequently associated with the establishment of recombinant CHO DG44 cell lines. Noteworthy, there was no direct correlation between the stability of the genome and the stability of recombinant protein expression.
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Affiliation(s)
- M Derouazi
- Laboratory of Cellular Biotechnology (LBTC), Institute of Biological Engineering and Biotechnology (IGBB), Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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Martinet D, Vial Y, Thonney F, Beckmann JS, Meagher-Villemure K, Unger S. Fetus with two identical reciprocal translocations: Description of a rare complication of consanguinity. Am J Med Genet A 2006; 140:769-74. [PMID: 16523519 DOI: 10.1002/ajmg.a.31150] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [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]
Abstract
We report on a 24-week fetus with multiple organ anomalies secondary to biparental inheritance of an apparently balanced t(17;20) reciprocal translocation. The pregnancy was terminated following the discovery by ultrasound of an abnormal heart and micrognathia. At autopsy, the following anomalies were found: Pierre-Robin sequence, hypoplasia of the right ventricle with muscular hypertrophy, and endocardial fibroelastosis, hypoplastic lungs, dysplastic left kidney, bilateral pelvicalyceal dilatation, central nervous system periventricular heterotopias and right sided club foot. Given the endocardial fibroelastosis and cleft palate, Eastman-Bixler syndrome (Facio-cardio-renal) is a possible diagnosis. The parents were first cousins and each had an identical t(17;20)(q21.1;p11.21) translocation. The fetal karyotype was 46,XX,t(17;20)(q21.1;p11.21)mat,t(17;20)(q21.1;p11.21)pat. While there are a few reports of consanguineous families where both the mother and father had the same reciprocal translocation and offspring with unbalanced karyotypes, we were unable to find any reports of a fetus/child with double identical reciprocal translocations. We propose that although the fetus had an apparently balanced karyotype, inheriting only the translocated chromosomes led to the unmasking of a recessive syndrome. It seems most likely that a gene (or genes) was disrupted by the breaks but the parents might also be heterozygous carriers of a recessive gene mutation since the fetus must be homozygous by descent for many loci on both chromosomes 17 and 20 (as well as on other chromosomal segments). It was not possible to totally exclude segmental uniparental disomy as a cause of the anomalies as no recombinations were detected for chromosome 17. However, there is no evidence to suggest that chromosome 17 is imprinted and UPD 20 was excluded thus making an imprinting error unlikely.
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Affiliation(s)
- Danielle Martinet
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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Mühlematter D, Castagné C, Beyer V, Martinet D, Parlier V, Jotterand M. [Fluorescent in situ hybridization (FISH), cytogenetic analytical complement for the diagnosis of malignant blood diseases]. Rev Med Suisse Romande 2000; 120:393-400. [PMID: 10911742] [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] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Castagné C, Mühlematter D, Martinet D, Jotterand M. Effect of conditioned medium, nutritive elements and mitotic synchronization on the accuracy of the cytogenetic analysis in patients with chronic myeloid leukemia at diagnosis and during alpha-interferon therapy. Cancer Genet Cytogenet 1999; 109:166-71. [PMID: 10087954 DOI: 10.1016/s0165-4608(98)00171-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To improve the yield of the cytogenetic analysis in patients with CML at presentation and during alpha-interferon therapy, three culture conditions for bone marrow or peripheral blood cells were tested in parallel. The effects of 5637 conditioned medium (CM), nutritive elements (NE), and methotrexate (MTX) cell synchronization were investigated in 10 Ph-positive (Ph+) CML patients at diagnosis (group 1), and in 13 Ph+ CML patients receiving treatment with alpha-interferon (group 2). In the presence of 5637 CM and NE with or without MTX, the mitotic index values were significantly improved in both groups. In group 2, the morphological index was significantly increased when using 5637 NE, and percentages of abnormal cells did not differ in 5637 NE and 5637 NE MTX compared to the control condition. Although cessation of interferon administration before sampling may improve the yield of the technique, it does not seem necessary when using 5637 CM and NE. The variability of the response of leukemic cells to different culture conditions further supports the recommendation that, in addition to the control condition, supplementations with 5637 CM and NE with or without cell synchronization be used in parallel in all CML patients. Results suggest that, when the number of cells available is not sufficient for several cultures, 5637 NE with or without MTX should replace the control condition.
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MESH Headings
- Antimetabolites, Antineoplastic/pharmacology
- Antineoplastic Agents/therapeutic use
- Bone Marrow/drug effects
- Cell Division/drug effects
- Culture Media
- Culture Media, Conditioned/pharmacology
- Cytogenetics/methods
- Humans
- Interferon-alpha/therapeutic use
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Methotrexate/pharmacology
- Mitotic Index
- Tumor Cells, Cultured/drug effects
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Affiliation(s)
- C Castagné
- Unité de cytogénétique du cancer, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
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van der Reijden BA, Dauwerse HG, Giles RH, Jagmohan-Changur S, Wijmenga C, Liu PP, Smit B, Wessels HW, Beverstock GC, Jotterand-Bellomo M, Martinet D, Mühlematter D, Lafage-Pochitaloff M, Gabert J, Reiffers J, Bilhou-Nabera C, van Ommen GJ, Hagemeijer A, Breuning MH. Genomic acute myeloid leukemia-associated inv(16)(p13q22) breakpoints are tightly clustered. Oncogene 1999; 18:543-50. [PMID: 9927211 DOI: 10.1038/sj.onc.1202321] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [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: 11/08/2022]
Abstract
The inv(16) and related t(16;16) are found in 10% of all cases with de novo acute myeloid leukemia. In these rearrangements the core binding factor beta (CBFB) gene on 16q22 is fused to the smooth muscle myosin heavy chain gene (MYH11) on 16p13. To gain insight into the mechanisms causing the inv(16) we have analysed 24 genomic CBFB-MYH11 breakpoints. All breakpoints in CBFB are located in a 15-Kb intron. More than 50% of the sequenced 6.2 Kb of this intron consists of human repetitive elements. Twenty-one of the 24 breakpoints in MYH11 are located in a 370-bp intron. The remaining three breakpoints in MYH11 are located more upstream. The localization of three breakpoints adjacent to a V(D)J recombinase signal sequence in MYH11 suggests a V(D)J recombinase-mediated rearrangement in these cases. V(D)J recombinase-associated characteristics (small nucleotide deletions and insertions of random nucleotides) were detected in six other cases. CBFB and MYH11 duplications were detected in four of six cases tested.
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Affiliation(s)
- B A van der Reijden
- Department of Human Genetics, Leiden University, Sylvius Laboratories, Leiden, The Netherlands
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Martinet D, Mühlematter D, Leeman M, Parlier V, Hess U, Gmür J, Jotterand M. Detection of 16 p deletions by FISH in patients with inv(16) or t(16;16) and acute myeloid leukemia (AML). Leukemia 1997; 11:964-70. [PMID: 9204976 DOI: 10.1038/sj.leu.2400681] [Citation(s) in RCA: 25] [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: 02/04/2023]
Abstract
Deletions of sequences centromeric to the p-arm breakpoint have been described in a subset of patients with inv(16) and acute myeloid leukemia (AML) and reported to be associated with a relatively good prognosis. We have investigated 16 p deletions in a cohort of 15 patients with AML and inv(16) or t(16;16) and compared non-deletion and deletion patients in terms of clinical course. Patients were studied by fluorescence in situ hybridization (FISH) using cosmid zit14 as a probe to detect the presence of 16 p deletions in metaphase chromosomes of leukemic cells. While seven patients (47%) revealed no evidence of a deletion, five patients (33%) presented 16 p deletions, thus bringing further support to the relatively frequent occurrence of this event in inv(16) patients. Remarkably, two patients with inv(16) and one patient with t(16;16) showed a mosaicism of deletion and non-deletion metaphases suggesting the presence of two distinct leukemic cell populations. Results let us assume that 16 p deletions are not restricted to inv(16) and may occur subsequently to inv(16) or t(16;16). The presence of a 16 p deletion in a case of inv(16) associated with CBFB-MYH11 transcript type E indicates that deletions are not limited to CBFB-MYH11 transcript type A rearrangements. Survival of deletion patients was compared with that of non-deletion and mosaic ones. No significant differences were observed. The advantage of FISH for enumerative and quantitative assessment of submicroscopic rearrangements of clinical significance is further emphasized.
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Affiliation(s)
- D Martinet
- Division Autonome de Génétique Médicale, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
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van der Reijden BA, Martinet D, Dauwerse JG, Giles RH, Wessels JW, Beverstock GC, Smit B, Mühlematter D, Jotterand Bellomo M, Gabert J, Lafage-Pochitaloff M, Reiffers J, Bilhou-Nabera C, van Ommen GJ, Hagemeijer A, Breuning MH. Simple method for detection of MYH11 DNA rearrangements in patients with inv(16)(p13q22) and acute myeloid leukemia. Leukemia 1996; 10:1459-62. [PMID: 8751463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The pericentric inversion on chromosome 16 [inv(16)(p13q22)] and related t(16;16)(p13;q22) are recurrent aberrations associated with acute myeloid leukemia (AML) M4 Eo. Both abberations result in a fusion of the core binding factor beta (CBFB) and smooth muscle myosin heavy chain gene (MYH11). A selected genomic 6.9-kb BamHl probe detects MYH11 DNA rearrangements in 18 of 19 inv(16)/t(16;16) patients tested using HindIII digested DNA. The rearranged fragments were not detectable after remission in two cases tested, while they were present after relapse in one of these two cases tested.
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Affiliation(s)
- B A van der Reijden
- Department of Human Genetics, Leiden University, Sylvius Laboratories, The Netherlands
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Martinet D, Mühlematter D, Jotterand Bellomo M. [Fluorescent in-situ hybridization technique (FISH) in the diagnosis of Philadelphia translocation in chronic myeloid leukemia]. Schweiz Med Wochenschr 1996; 126:855-63. [PMID: 8685681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The Philadelphia chromosome (Ph) resulting from translocation t(9;22)(q34;q11) is observed in more than 90% of patients with chronic myeloid leukemia (CML). Its molecular consequence is the genesis of a fusion gene BCR-ABL between the 5' sequences of the BCR gene (chromosome 22) and the 3' end of the ABL gene (chromosome 9). Fluorescence in situ hybridization (FISH) using specific DNA probes provides a useful tool for the detection of t(9;22) and BCR-ABL rearrangement. We report our results using the FISH technique for t(9;22) assessment in the hematopoietic cells of patients with Ph-positive CML. The DNA libraries pBS 9 and pBS 22 containing multiple sequences derived from chromosomes 9 and 22 have been used to identify t(9;22) in metaphase cells. The cos bcr-51 and cos abl-18 probes that hybridize to unique sequences specific to the BCR and ABL genes have the ability to detect the BCR-ABL rearrangement in metaphase cells as well as in interphase nuclei. FISH is a sensitive and specific technique that represents a valuable complement to conventional cytogenetics. The BCR-ABL rearrangement can be detected in metaphase spreads of insufficient quality or from interphase nuclei in the case of terminally differentiated cells or of cells which do not divide in vitro. When the efficiency of hybridization and detection is good, a large number of cells can be analyzed. This is of major significance in assessment of response to treatment and definition of a cytogenetic remission. However, interphase cytogenetics may be difficult due to variations in signal resolution and background level. The FISH technique can also be used to detect the BCR-ABL rearrangement in cases of Ph negative BCR-ABL positive CML.
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Affiliation(s)
- D Martinet
- Division autonome de génétique médicale, Centre hospitalier universitaire vaudois (CHUV), Lausanne
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Dhier P, Martinet D. [Simplified impression technique for the IMZ antirotational implant system]. Chir Dent Fr 1991; 61:43-4. [PMID: 1935363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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