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Cabral de Almeida Cardoso L, Rodriguez-Laguna L, del Carmen Crespo M, Vallespín E, Palomares-Bralo M, Martin-Arenas R, Rueda-Arenas I, Silvestre de Faria PA, García-Miguel P, Lapunzina P, Regla Vargas F, Seuanez HN, Martínez-Glez V. Array CGH Analysis of Paired Blood and Tumor Samples from Patients with Sporadic Wilms Tumor. PLoS One 2015; 10:e0136812. [PMID: 26317783 PMCID: PMC4552764 DOI: 10.1371/journal.pone.0136812] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/07/2015] [Indexed: 11/24/2022] Open
Abstract
Wilms tumor (WT), the most common cancer of the kidney in infants and children, has a complex etiology that is still poorly understood. Identification of genomic copy number variants (CNV) in tumor genomes provides a better understanding of cancer development which may be useful for diagnosis and therapeutic targets. In paired blood and tumor DNA samples from 14 patients with sporadic WT, analyzed by aCGH, 22% of chromosome abnormalities were novel. All constitutional alterations identified in blood were segmental (in 28.6% of patients) and were also present in the paired tumor samples. Two segmental gains (2p21 and 20q13.3) and one loss (19q13.31) present in blood had not been previously described in WT. We also describe, for the first time, a small, constitutive partial gain of 3p22.1 comprising 2 exons of CTNNB1, a gene associated to WT. Among somatic alterations, novel structural chromosomal abnormalities were found, like gain of 19p13.3 and 20p12.3, and losses of 2p16.1-p15, 4q32.5-q35.1, 4q35.2-q28.1 and 19p13.3. Candidate genes included in these regions might be constitutively (SIX3, SALL4) or somatically (NEK1, PIAS4, BMP2) operational in the development and progression of WT. To our knowledge this is the first report of CNV in paired blood and tumor samples in sporadic WT.
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Affiliation(s)
| | - Lara Rodriguez-Laguna
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - María del Carmen Crespo
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Elena Vallespín
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - María Palomares-Bralo
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
| | - Rubén Martin-Arenas
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Inmaculada Rueda-Arenas
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | | | | | | | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- Section of Clinical Genetics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Fernando Regla Vargas
- Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Birth Defects Epidemiology Laboratory, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Hector N. Seuanez
- Genetics Division, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Víctor Martínez-Glez
- Section of Functional and Structural Genomics, Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, Madrid, Spain
- * E-mail:
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3
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Caparrós-Martín JA, De Luca A, Cartault F, Aglan M, Temtamy S, Otaify GA, Mehrez M, Valencia M, Vázquez L, Alessandri JL, Nevado J, Rueda-Arenas I, Heath KE, Digilio MC, Dallapiccola B, Goodship JA, Mill P, Lapunzina P, Ruiz-Perez VL. Specific variants in WDR35 cause a distinctive form of Ellis-van Creveld syndrome by disrupting the recruitment of the EvC complex and SMO into the cilium. Hum Mol Genet 2015; 24:4126-37. [PMID: 25908617 DOI: 10.1093/hmg/ddv152] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/21/2015] [Indexed: 12/13/2022] Open
Abstract
Most patients with Ellis-van Creveld syndrome (EvC) are identified with pathogenic changes in EVC or EVC2, however further genetic heterogeneity has been suggested. In this report we describe pathogenic splicing variants in WDR35, encoding retrograde intraflagellar transport protein 121 (IFT121), in three families with a clinical diagnosis of EvC but having a distinctive phenotype. To understand why WDR35 variants result in EvC, we analysed EVC, EVC2 and Smoothened (SMO) in IFT-A deficient cells. We found that the three proteins failed to localize to Wdr35(-/-) cilia, but not to the cilium of the IFT retrograde motor mutant Dync2h1(-/-), indicating that IFT121 is specifically required for their entry into the ciliary compartment. Furthermore expression of Wdr35 disease cDNAs in Wdr35(-/-) fibroblasts revealed that the newly identified variants lead to Hedgehog signalling defects resembling those of Evc(-/-) and Evc2(-/-) mutants. Together our data indicate that splicing variants in WDR35, and possibly in other IFT-A components, underlie a number of EvC cases by disrupting targeting of both the EvC complex and SMO to cilia.
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Affiliation(s)
- José A Caparrós-Martín
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain, CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Alessandro De Luca
- Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo, Italy
| | - François Cartault
- CHU de la Réunion Hôpital Félix Guyon, Saint-Denis, Île de la Réunion, France
| | - Mona Aglan
- Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Samia Temtamy
- Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Ghada A Otaify
- Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - Mennat Mehrez
- Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - María Valencia
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain, CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Laura Vázquez
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain
| | - Jean-Luc Alessandri
- CHU de la Réunion Hôpital Félix Guyon, Saint-Denis, Île de la Réunion, France
| | - Julián Nevado
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain, Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Inmaculada Rueda-Arenas
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Karen E Heath
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain, Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | | | | | - Judith A Goodship
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK and
| | - Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Pablo Lapunzina
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain, Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IdiPAZ, Universidad Autónoma de Madrid, Madrid, Spain
| | - Victor L Ruiz-Perez
- Instituto de Investigaciones Biomédicas, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Madrid, Spain, CIBER de Enfermedades Raras (CIBERER), Madrid, Spain,
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4
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Nevado J, Rosenfeld JA, Mena R, Palomares-Bralo M, Vallespín E, Ángeles Mori M, Tenorio JA, Gripp KW, Denenberg E, Del Campo M, Plaja A, Martín-Arenas R, Santos-Simarro F, Armengol L, Gowans G, Orera M, Sanchez-Hombre MC, Corbacho-Fernández E, Fernández-Jaén A, Haldeman-Englert C, Saitta S, Dubbs H, Bénédicte DB, Li X, Devaney L, Dinulos MB, Vallee S, Crespo MC, Fernández B, Fernández-Montaño VE, Rueda-Arenas I, de Torres ML, Ellison JW, Raskin S, Venegas-Vega CA, Fernández-Ramírez F, Delicado A, García-Miñaúr S, Lapunzina P. PIAS4 is associated with macro/microcephaly in the novel interstitial 19p13.3 microdeletion/microduplication syndrome. Eur J Hum Genet 2015; 23:1615-26. [PMID: 25853300 DOI: 10.1038/ejhg.2015.51] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/23/2014] [Accepted: 02/17/2015] [Indexed: 12/24/2022] Open
Abstract
Array comparative genomic hybridization (aCGH) is a powerful genetic tool that has enabled the identification of novel imbalances in individuals with intellectual disability (ID), autistic disorders and congenital malformations. Here we report a 'genotype first' approach using aCGH on 13 unrelated patients with 19p13.3 submicroscopic rearrangement (11 deletions and 2 duplications) and review cases in the literature and in public databases. Shared phenotypic features suggest that these patients represent an interstitial microdeletion/microduplication syndrome at 19p13.3. Common features consist of abnormal head circumference in most patients (macrocephaly with the deletions and microcephaly with the duplications), ID with developmental delay (DD), hypotonia, speech delay and common dysmorphic features. The phenotype is associated with at least a ~0.113 Mb critical region harboring three strong candidate genes probably associated with DD, ID, speech delay and other dysmorphic features: MAP2K2, ZBTB7A and PIAS4, an E3 ubiquitin ligase involved in the ubiquitin signaling pathways, which we hypothesize for the first time to be associated with head size in humans.
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Affiliation(s)
- Julián Nevado
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Jill A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer Inc., Spokane, WA, USA
| | - Rocío Mena
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - María Palomares-Bralo
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Elena Vallespín
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - María Ángeles Mori
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.,CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Jair A Tenorio
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Karen W Gripp
- AI DuPont Hospital for Children, Wilmington, DE, USA
| | | | | | | | - Rubén Martín-Arenas
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | | | | | | | | | | | | | | | | | - Sulagna Saitta
- Medical Genetics Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Holly Dubbs
- The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Xia Li
- Ameripath Northeast, Shelton, CT, USA
| | - Lani Devaney
- Henry Ford Health System, Sterling Heights, Michigan, USA
| | | | | | - M Carmen Crespo
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Blanca Fernández
- Section Cytogenetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Victoria E Fernández-Montaño
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Inmaculada Rueda-Arenas
- Section of Functional and Structural Genomics Instituto de Genética Médica y Molecular (INGEMM)-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - María Luisa de Torres
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Section Cytogenetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | | | - Salmo Raskin
- Center for Health and Biological Sciences, Pontifícia Universidade Católica do Paraná (PUC-PR), Curitiba, Brazil
| | - Carlos A Venegas-Vega
- Genetic Unit Hospital General de México, México, México.,School of Medicine. Universidad Autónoma de México, México, México
| | | | - Alicia Delicado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Section Cytogenetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Sixto García-Miñaúr
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Section of Clinical Genetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Section of Clinical Genetics, INGEMM-IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
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