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Lyons PJ. Inactive metallopeptidase homologs: the secret lives of pseudopeptidases. Front Mol Biosci 2024; 11:1436917. [PMID: 39050735 PMCID: PMC11266112 DOI: 10.3389/fmolb.2024.1436917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024] Open
Abstract
Inactive enzyme homologs, or pseudoenzymes, are proteins, found within most enzyme families, that are incapable of performing catalysis. Rather than catalysis, they are involved in protein-protein interactions, sometimes regulating the activity of their active enzyme cousins, or scaffolding protein complexes. Pseudoenzymes found within metallopeptidase families likewise perform these functions. Pseudoenzymes within the M14 carboxypeptidase family interact with collagens within the extracellular space, while pseudopeptidase members of the M12 "a disintegrin and metalloprotease" (ADAM) family either discard their pseudopeptidase domains as unnecessary for their roles in sperm maturation or utilize surface loops to enable assembly of key complexes at neuronal synapses. Other metallopeptidase families contain pseudopeptidases involved in protein synthesis at the ribosome and protein import into organelles, sometimes using their pseudo-active sites for these interactions. Although the functions of these pseudopeptidases have been challenging to study, ongoing work is teasing out the secret lives of these proteins.
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Affiliation(s)
- Peter J. Lyons
- Department of Biology, Andrews University, Berrien Springs, MI, United States
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Faria JAD, Moraes DR, Kulikowski LD, Batista RL, Gomes NL, Nishi MY, Zanardo E, Nonaka CKV, de Freitas Souza BS, Mendonca BB, Domenice S. Cytogenomic Investigation of Syndromic Brazilian Patients with Differences of Sexual Development. Diagnostics (Basel) 2023; 13:2235. [PMID: 37443631 DOI: 10.3390/diagnostics13132235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Cytogenomic methods have gained space in the clinical investigation of patients with disorders/differences in sexual development (DSD). Here we evaluated the role of the SNP array in achieving a molecular diagnosis in Brazilian patients with syndromic DSD of unknown etiology. METHODS Twenty-two patients with DSD and syndromic features were included in the study and underwent SNP-array analysis. RESULTS In two patients, the diagnosis of 46,XX SRY + DSD was established. Additionally, two deletions were revealed (3q29 and Xp22.33), justifying the syndromic phenotype in these patients. Two pathogenic CNVs, a 10q25.3-q26.2 and a 13q33.1 deletion encompassing the FGFR2 and the EFNB2 gene, were associated with genital atypia and syndromic characteristics in two patients with 46,XY DSD. In a third 46,XY DSD patient, we identified a duplication in the 14q11.2-q12 region of 6.5 Mb associated with a deletion in the 21p11.2-q21.3 region of 12.7 Mb. In a 46,XY DSD patient with delayed neuropsychomotor development and congenital cataracts, a 12 Kb deletion on chromosome 10 was found, partially clarifying the syndromic phenotype, but not the genital atypia. CONCLUSIONS The SNP array is a useful tool for DSD patients, identifying the molecular etiology in 40% (2/5) of patients with 46,XX DSD and 17.6% (3/17) of patients with 46,XY DSD.
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Affiliation(s)
- José Antonio Diniz Faria
- Faculdade de Medicina, Universidade Federal da Bahia, Salvador 40110-909, Brazil
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Daniela R Moraes
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Leslie Domenici Kulikowski
- Laboratório de Citogenômica e Patologia Molecular LIM/03, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Rafael Loch Batista
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Nathalia Lisboa Gomes
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Mirian Yumie Nishi
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Evelin Zanardo
- Laboratório de Citogenômica e Patologia Molecular LIM/03, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Carolina Kymie Vasques Nonaka
- Centro de Biotecnologia e Terapia Celular, Hospital São Rafael, Salvador 41253-190, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Salvador 41253-190, Brazil
| | - Bruno Solano de Freitas Souza
- Centro de Biotecnologia e Terapia Celular, Hospital São Rafael, Salvador 41253-190, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Salvador 41253-190, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (FIOCRUZ), Salvador 40296-710, Brazil
| | - Berenice Bilharinho Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
| | - Sorahia Domenice
- Unidade de Endocrinologia do Desenvolvimento, Laboratório de Hormônios e Genética Molecular LIM/42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-010, Brazil
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Sumalde AAM, Scholes MA, Kalmanson OA, Terhune EA, Frejo L, Wethey CI, Roman-Naranjo P, Carry PM, Gubbels SP, Lopez-Escamez JA, Hadley-Miller N, Santos-Cortez RLP. Rare Coding Variants in Patients with Non-Syndromic Vestibular Dysfunction. Genes (Basel) 2023; 14:831. [PMID: 37107589 PMCID: PMC10137884 DOI: 10.3390/genes14040831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Vertigo due to vestibular dysfunction is rare in children. The elucidation of its etiology will improve clinical management and the quality of life of patients. Genes for vestibular dysfunction were previously identified in patients with both hearing loss and vertigo. This study aimed to identify rare, coding variants in children with peripheral vertigo but no hearing loss, and in patients with potentially overlapping phenotypes, namely, Meniere's disease or idiopathic scoliosis. Rare variants were selected from the exome sequence data of 5 American children with vertigo, 226 Spanish patients with Meniere's disease, and 38 European-American probands with scoliosis. In children with vertigo, 17 variants were found in 15 genes involved in migraine, musculoskeletal phenotypes, and vestibular development. Three genes, OTOP1, HMX3, and LAMA2, have knockout mouse models for vestibular dysfunction. Moreover, HMX3 and LAMA2 were expressed in human vestibular tissues. Rare variants within ECM1, OTOP1, and OTOP2 were each identified in three adult patients with Meniere's disease. Additionally, an OTOP1 variant was identified in 11 adolescents with lateral semicircular canal asymmetry, 10 of whom have scoliosis. We hypothesize that peripheral vestibular dysfunction in children may be due to multiple rare variants within genes that are involved in the inner ear structure, migraine, and musculoskeletal disease.
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Affiliation(s)
- Angelo Augusto M. Sumalde
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Otolaryngology-Head and Neck Surgery, University of the Philippines Manila College of Medicine, Philippine General Hospital, Manila 1000, Philippines
| | - Melissa A. Scholes
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO 80045, USA
- Department of Otolaryngology-Head and Neck Surgery, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Olivia A. Kalmanson
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Elizabeth A. Terhune
- Department of Orthopedics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lidia Frejo
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer-University of Granada-Junta de Andalucia, PTS, 18016 Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain
| | - Cambria I. Wethey
- Department of Orthopedics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Pablo Roman-Naranjo
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer-University of Granada-Junta de Andalucia, PTS, 18016 Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain
| | - Patrick M. Carry
- Department of Orthopedics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Musculoskeletal Research Center, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Samuel P. Gubbels
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jose A. Lopez-Escamez
- Otology and Neurotology Group CTS495, Department of Genomic Medicine, GENYO-Centre for Genomics and Oncological Research-Pfizer-University of Granada-Junta de Andalucia, PTS, 18016 Granada, Spain
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain
- Meniere’s Disease Neuroscience Research Program, Faculty of Medicine & Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Nancy Hadley-Miller
- Department of Orthopedics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Musculoskeletal Research Center, Children’s Hospital Colorado, Aurora, CO 80045, USA
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Center for Children’s Surgery, Children’s Hospital Colorado, Aurora, CO 80045, USA
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Popescu R, Grămescu M, Caba L, Pânzaru MC, Butnariu L, Braha E, Popa S, Rusu C, Cardos G, Zeleniuc M, Martiniuc V, Gug C, Păduraru L, Stamatin M, Diaconu CC, Gorduza EV. A Case of Inherited t(4;10)(q26;q26.2) Chromosomal Translocation Elucidated by Multiple Chromosomal and Molecular Analyses. Case Report and Review of the Literature. Genes (Basel) 2021; 12:genes12121957. [PMID: 34946906 PMCID: PMC8701147 DOI: 10.3390/genes12121957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 01/05/2023] Open
Abstract
We present a complex chromosomal anomaly identified using cytogenetic and molecular methods. The child was diagnosed during the neonatal period with a multiple congenital anomalies syndrome characterized by: flattened occipital region; slight turricephaly; tall and broad forehead; hypertelorism; deep-set eyes; down slanting and short palpebral fissures; epicanthic folds; prominent nose with wide root and bulbous tip; microstomia; micro-retrognathia, large, short philtrum with prominent reliefs; low set, prominent ears; and congenital heart disease. The GTG banding karyotype showed a 46,XY,der(10)(10pter→10q26.2::4q26→4qter) chromosomal formula and his mother presented an apparently balanced reciprocal translocation: 46,XX,t(4;10)(q26;q26.2). The chromosomal anomalies of the child were confirmed by MLPA, and supplementary investigation discovered a quadruplication of the 4q35.2 region. The mother has a triplication of the same chromosomal fragment (4q35.2). Using array-CGH, we described the anomalies completely. Thus, the boy has a 71,057 kb triplication of the 4q26-q35.2 region, a 562 kb microdeletion in the 10q26.3 region, and a 795 kb quadruplication of the 4q35.2 region, while the mother presents a 795 kb triplication of the 4q35.2 region. Analyzing these data, we consider that the boy's phenotype is influenced only by the 4q partial trisomy. We compare our case with similar cases, and we review the literature data.
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Affiliation(s)
- Roxana Popescu
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Mihaela Grămescu
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Lavinia Caba
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
- Correspondence: (L.C.); (C.G.)
| | - Monica-Cristina Pânzaru
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Lăcrămioara Butnariu
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Elena Braha
- “C. I. Parhon” National Institute of Endocrinology, 34-35 Aviatorilor Avenue, 011853 Bucharest, Romania;
| | - Setalia Popa
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Cristina Rusu
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
| | - Georgeta Cardos
- Personal Genetics Laboratory Bucharest, 4 Strada Frumoasa Street, 010987 Bucharest, Romania; (G.C.); (M.Z.)
| | - Monica Zeleniuc
- Personal Genetics Laboratory Bucharest, 4 Strada Frumoasa Street, 010987 Bucharest, Romania; (G.C.); (M.Z.)
- Medical Genetics Department, “Carol Davila” University of Medicine and Pharmacy, 8 Eroii Sanitari Avenue, 050474 Bucharest, Romania
| | - Violeta Martiniuc
- Medical Genetics Department, “Cuza-Vodă” Obstetrics and Gynecology Hospital, 34 Cuza Voda Street, 700038 Iasi, Romania;
| | - Cristina Gug
- Microscopic Morphology Department, “Victor Babes” University of Medicine and Pharmacy, 2 Piata Eftimie Murgu, 300041 Timișoara, Romania
- Correspondence: (L.C.); (C.G.)
| | - Luminiţa Păduraru
- Neonatology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (L.P.); (M.S.)
| | - Maria Stamatin
- Neonatology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (L.P.); (M.S.)
| | - Carmen C. Diaconu
- Stefan S. Nicolau Institute of Virology, Romanian Academy, 285 Mihai Bravu, 030304 Bucharest, Romania;
| | - Eusebiu Vlad Gorduza
- Medical Genetics Department, “Grigore T. Popa” University of Medicine and Pharmacy, 16 University Street, 700115 Iasi, Romania; (R.P.); (M.G.); (M.-C.P.); (L.B.); (S.P.); (C.R.); (E.V.G.)
- Medical Genetics Department, “Cuza-Vodă” Obstetrics and Gynecology Hospital, 34 Cuza Voda Street, 700038 Iasi, Romania;
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Mackowetzky K, Yoon KH, Mackowetzky EJ, Waskiewicz AJ. Development and evolution of the vestibular apparatuses of the inner ear. J Anat 2021; 239:801-828. [PMID: 34047378 PMCID: PMC8450482 DOI: 10.1111/joa.13459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/07/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
The vertebrate inner ear is a labyrinthine sensory organ responsible for perceiving sound and body motion. While a great deal of research has been invested in understanding the auditory system, a growing body of work has begun to delineate the complex developmental program behind the apparatuses of the inner ear involved with vestibular function. These animal studies have helped identify genes involved in inner ear development and model syndromes known to include vestibular dysfunction, paving the way for generating treatments for people suffering from these disorders. This review will provide an overview of known inner ear anatomy and function and summarize the exciting discoveries behind inner ear development and the evolution of its vestibular apparatuses.
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Affiliation(s)
- Kacey Mackowetzky
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Kevin H. Yoon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | | | - Andrew J. Waskiewicz
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Women & Children’s Health Research InstituteUniversity of AlbertaEdmontonAlbertaCanada
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Li Q, Sun C, Guo J, Zhai W, Zhang L. Terminal 10q26.12 deletion is associated with neonatal asymmetric crying facies syndrome: a case report and literature review. Mol Cytogenet 2021; 14:36. [PMID: 34256807 PMCID: PMC8278754 DOI: 10.1186/s13039-021-00554-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/24/2021] [Indexed: 11/26/2022] Open
Abstract
Background The terminal 10q26 deletion syndrome is a clinically heterogeneous disorder without identified genotype–phenotype correlations. We reported a case of congenital asymmetric crying facies (ACF) syndrome with 10q26.12qter deletion and discussed their genotype–phenotype correlations and the potentially contributing genes involving the etiology of ACF. Methods and results We reported a case of neonatal 10q26.12qter deletion and summarized the genotype–phenotype correlations and contributing genes of 10q26.12qter deletion from DECIPHER database and published studies. Meanwhile, we analyzed the potential pathogenic genes contributing to 10q26 deletion syndrome. The female preterm infant harboring 10q26.12qter deletion showed symptoms of abnormal craniofacial appearance with rare congenital asymmetric crying facies, developmental retardation, congenital heart disease, and pulmonary artery hypertension. The deleted region was 13.28 Mb in size as detected by G-banding and array comparative genome hybridization, containing 62 Online Mendelian Inheritance in Man (OMIM) catalog genes. We summarized data from 17 other patients with 10q26.12qter deletion, 11 from the DECIPHER database and 6 from published studies. Patients with monoallelic WDR11 and FGFR2 deletions located in 10q26.12q26.2 were predisposed to craniofacial dysmorphisms, growth retardation, intellectual disability and cardiac diseases. Conclusion ACF is a facial dysmorphism frequently accompanied by other systemic deformities. It is a genetic abnormality that may associate with terminal 10q26.12 deletion. Early cardiac, audiologic, cranial examinations and genetic detection are needed to guide early diagnosis and treatment strategy.
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Affiliation(s)
- Qinghong Li
- Department of Neonatology, Northwest Women's and Children's Hospital, Yanta District, No. 1616, Yanxiang Road, Xi'an, 7100061, Shaanxi, People's Republic of China.
| | - Chunmei Sun
- Department of Neonatology, Northwest Women's and Children's Hospital, Yanta District, No. 1616, Yanxiang Road, Xi'an, 7100061, Shaanxi, People's Republic of China
| | - Jinzhen Guo
- Department of Neonatology, Northwest Women's and Children's Hospital, Yanta District, No. 1616, Yanxiang Road, Xi'an, 7100061, Shaanxi, People's Republic of China
| | - Wen Zhai
- Genetic Medical Center, Northwest Women's and Children's Hospital, Xi'an, 7100061, Shaanxi, People's Republic of China
| | - Liping Zhang
- Genetic Medical Center, Northwest Women's and Children's Hospital, Xi'an, 7100061, Shaanxi, People's Republic of China
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Cherik F, Lepage M, Remerand G, Francannet C, Delabaere A, Salaun G, Pebrel-Richard C, Gouas L, Vago P, Tchirkov A, Goumy C. Further refining the critical region of 10q26 microdeletion syndrome: A possible involvement of INSYN2 and NPS in the cognitive phenotype. Eur J Med Genet 2021; 64:104287. [PMID: 34252586 DOI: 10.1016/j.ejmg.2021.104287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/09/2021] [Accepted: 07/07/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND The 10q26 subtelomeric microdeletion syndrome is a rare and clinically heterogeneous disorder. The precise relationships between the causative genes and the phenotype are unclear. CASE PRESENTATION We report two new cases of 860 kb deletion of 10q26.2 identified by array CGH in a fetus with intrauterine growth retardation and his mother. The deleted region encompassed only four coding genes, DOCK1, INSYN2, NPS and FOX12. The proband had dysmorphic facies characterized by a high forehead, malformed ears, a prominent nose, and retrognathia. He had bilateral club feet, clinodactily and mild psychomotor retardation. His mother had a short stature, microcephaly, a long face with a high forehead and bitemporal narrowing, arched and sparse eyebrows, strabismus, prominent nose and chin, a thin upper lip and large protruding ears, and mild intellectual disability. CONCLUSIONS This study presents the smallest 10q26.2 deletion so far identified, which further refines the minimal critical region associated with the 10q26 microdeletion syndrome. It focuses on three genes potentially responsible for the phenotype: DOCK1, which is the major candidate gene, and INSYN2 and NPS, which could be involved in cognitive functions.
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Affiliation(s)
- Florian Cherik
- Service de Génétique Médicale, CHU, Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Mathis Lepage
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Ganaelle Remerand
- Service de Pédiatrie, CHU, Clermont-Ferrand, CHU Estaing, F-63000, France
| | - Christine Francannet
- Service de Génétique Médicale, CHU, Clermont-Ferrand, CHU Estaing, F-63000, France
| | | | - Gaëlle Salaun
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France; Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000, Clermont Ferrand, France
| | | | - Laetitia Gouas
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France; Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000, Clermont Ferrand, France
| | - Philippe Vago
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France; Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000, Clermont Ferrand, France
| | - Andrei Tchirkov
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France; Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000, Clermont Ferrand, France
| | - Carole Goumy
- Cytogénétique Médicale, CHU Clermont-Ferrand, CHU Estaing, F-63000, France; Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000, Clermont Ferrand, France.
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Whitman MC, Di Gioia SA, Chan WM, Gelber A, Pratt BM, Bell JL, Collins TE, Knowles JA, Armoskus C, Pato M, Pato C, Shaaban S, Staffieri S, MacKinnon S, Maconachie GDE, Elder JE, Traboulsi EI, Gottlob I, Mackey DA, Hunter DG, Engle EC. Recurrent Rare Copy Number Variants Increase Risk for Esotropia. Invest Ophthalmol Vis Sci 2021; 61:22. [PMID: 32780866 PMCID: PMC7443120 DOI: 10.1167/iovs.61.10.22] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To determine whether rare copy number variants (CNVs) increase risk for comitant esotropia. Methods CNVs were identified in 1614 Caucasian individuals with comitant esotropia and 3922 Caucasian controls from Illumina SNP genotyping using two Hidden Markov model (HMM) algorithms, PennCNV and QuantiSNP, which call CNVs based on logR ratio and B allele frequency. Deletions and duplications greater than 10 kb were included. Common CNVs were excluded. Association testing was performed with 1 million permutations in PLINK. Significant CNVs were confirmed with digital droplet polymerase chain reaction (ddPCR). Whole genome sequencing was performed to determine insertion location and breakpoints. Results Esotropia patients have similar rates and proportions of CNVs compared with controls but greater total length and average size of both deletions and duplications. Three recurrent rare duplications significantly (P = 1 × 10−6) increase the risk of esotropia: chromosome 2p11.2 (hg19, 2:87428677-87965359), spanning one long noncoding RNA (lncRNA) and two microRNAs (OR 14.16; 95% confidence interval [CI] 5.4–38.1); chromosome 4p15.2 (hg19, 4:25554332-25577184), spanning one lncRNA (OR 11.1; 95% CI 4.6–25.2); chromosome 10q11.22 (hg19, 10:47049547-47703870) spanning seven protein-coding genes, one lncRNA, and four pseudogenes (OR 8.96; 95% CI 5.4–14.9). Overall, 114 cases (7%) and only 28 controls (0.7%) had one of the three rare duplications. No case nor control had more than one of these three duplications. Conclusions Rare CNVs are a source of genetic variation that contribute to the genetic risk for comitant esotropia, which is likely polygenic. Future research into the functional consequences of these recurrent duplications may shed light on the pathophysiology of esotropia.
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Affiliation(s)
- Mary C Whitman
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Silvio Alessandro Di Gioia
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Wai-Man Chan
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Alon Gelber
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Brandon M Pratt
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Jessica L Bell
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Thomas E Collins
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - James A Knowles
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York, United States
| | - Christopher Armoskus
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, New York, United States
| | - Michele Pato
- Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, New York, United States
| | - Carlos Pato
- Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, New York, United States
| | - Sherin Shaaban
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,Present address: Department of Pathology and ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Sandra Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Sarah MacKinnon
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Gail D E Maconachie
- Department of Neuroscience, Psychology and Behavior, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - James E Elder
- Department of Ophthalmology, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Elias I Traboulsi
- Department of Pediatric Ophthalmology and Strabismus, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Irene Gottlob
- Department of Neuroscience, Psychology and Behavior, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, Australia.,Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia.,Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - David G Hunter
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Elizabeth C Engle
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
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9
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Osei-Owusu IA, Norris AL, Joynt AT, Thorpe J, Cho S, Tierney E, Schmidt J, Hagopian L, Harris J, Pevsner J. Characterization of an unbalanced translocation causing 3q28qter duplication and 10q26.2qter deletion in a patient with global developmental delay and self-injury. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005884. [PMID: 33335013 PMCID: PMC7784495 DOI: 10.1101/mcs.a005884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/08/2020] [Indexed: 01/17/2023] Open
Abstract
Chromosomal structural variation can cause severe neurodevelopmental and neuropsychiatric phenotypes. Here we present a nonverbal female adolescent with severe stereotypic movement disorder with severe problem behavior (e.g., self-injurious behavior, aggression, and disruptive and destructive behaviors), autism spectrum disorder, severe intellectual disability, attention deficit hyperactivity disorder, and global developmental delay. Previous cytogenetic analysis revealed balanced translocations present in the patient's apparently normal mother. We hypothesized the presence of unbalanced translocations in the patient due to maternal history of spontaneous abortions. Whole-genome sequencing and whole-genome optical mapping, complementary next-generation genomic technologies capable of the accurate and robust detection of structural variants, identified t(3;10), t(10;14), and t(3;14) three-way balanced translocations in the mother and der(10)t(3;14;10) and der(14)t(3;14;10) translocations in the patient. Instead of a t(3;10), she inherited a normal maternal copy of Chromosome 3, resulting in an unbalanced state of a 3q28qter duplication and 10q26.2qter deletion. Copy-imbalanced genes in one or both of these regions, such as DLG1, DOCK1, and EBF3, may contribute to the patient's phenotype that spans neurodevelopmental, musculoskeletal, and psychiatric domains, with the possible contribution of a maternally inherited 15q13.2q13.3 deletion.
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Affiliation(s)
- Ikeoluwa A Osei-Owusu
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Alexis L Norris
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Anya T Joynt
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Soonweng Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Elaine Tierney
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Jonathan Schmidt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Louis Hagopian
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Behavioral Psychology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA
| | - Jacqueline Harris
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
| | - Jonathan Pevsner
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA.,Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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10
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Chen CP, Huang JP, Chen SW, Chern SR, Wu PS, Wu FT, Chen WL, Chen LF, Wang W. Prenatal diagnosis of concomitant distal 5q duplication and terminal 10q deletion in a fetus with intrauterine growth restriction, congenital diaphragmatic hernia and congenital heart defects. Taiwan J Obstet Gynecol 2020; 59:135-139. [PMID: 32039782 DOI: 10.1016/j.tjog.2019.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2019] [Indexed: 10/25/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of concomitant distal 5q duplication and terminal 10q deletion in a fetus with intrauterine growth restriction (IUGR), congenital diaphragmatic hernia (CDH) and congenital heart defects (CHD). CASE REPORT A 34-year-old, gravida 4, para 2, woman was referred for amniocentesis at 21 weeks of gestation because of advanced maternal age and IUGR. There was no congenital malformation in the family. Amniocentesis revealed a derivative chromosome 10 with an additional maternal on the terminal region of 10q. Array comparative genomic hybridization (aCGH) analysis on the DNA extracted from the cultured amniocytes revealed a result of arr 5q31.3q35.5 (142, 548, 354-180,696,806) × 3.0, arr 10q26.3 (132, 932, 808-135,434,178) × 1.0 [GRCh37 (hg19)] with a 2.50-Mb deletion of 10q26.3 encompassing 19 [Online Mendelian Inheritance in Man (OMIM)] genes and a 38.15-Mb duplication of 5q31.3-q35.5 encompassing 195 OMIM genes including four CDH candidate genes of NDST1, ADAM19, NSD1 and MAML1. The mother was found to have a karyotype of 46,XX,t(5; 10) (q31.3; q26.3). Therefore, the fetal karyotype was 46,XX,der(10)t(5; 10)(q31.3; q26.3)mat. Prenatal ultrasound showed IUGR, right CDH, transposition of great artery, double outlet of right ventricle and right atrial isomerism. The pregnancy was terminated, and a malformed fetus was delivered with facial dysmorphism. CONCLUSION Fetuses with concomitant distal 5q duplication and terminal 10q deletion may present IUGR, CDH and CHD on prenatal ultrasound.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Jian-Pei Huang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; MacKay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
| | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Fang-Tzu Wu
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wen-Lin Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Li-Feng Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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11
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Skarp S, Kanervo L, Kotimäki J, Sorri M, Männikkö M, Hietikko E. Whole-exome sequencing suggests multiallelic inheritance for childhood-onset Ménière's disease. Ann Hum Genet 2019; 83:389-396. [PMID: 31106404 DOI: 10.1111/ahg.12327] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 03/18/2019] [Accepted: 04/29/2019] [Indexed: 01/22/2023]
Abstract
The genetic background of Ménière's disease (MD) was studied in one patient with childhood-onset MD and his grandfather affected with middle age-onset MD. Whole-exome sequencing was performed and the data were compared to 76 exomes from unrelated subjects without MD. Thirteen rare inner ear expressed variants with pathogenic estimations were observed in the case of childhood-onset MD. These variants were in genes involved in the formation of cell membranes or the cytoskeleton and in genes participating in cell death or gene-regulation pathways. His grandfather shared two of the variants: p.Y273N in HMX2 and p.L229F in TMEM55B. HMX2 p.Y273N was considered the more likely candidate for MD, as the gene is known to affect both hearing and vestibular function. The variant in the HMX2 gene may affect inner ear development and structural integrity and thus might predispose to the onset of MD. As there was a significant difference in onset between the patients, an accumulation of defects in several pathways is probably responsible for the exceptionally early onset of the disease, and the genetic etiology of childhood-onset MD is most likely multifactorial. This is the first molecular genetic study of childhood-onset MD.
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Affiliation(s)
- Sini Skarp
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Laura Kanervo
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Jouko Kotimäki
- Department of Otorhinolaryngology, Kainuu Central Hospital, Kajaani, Finland
| | - Martti Sorri
- Department of Otorhinolaryngology and Head and Neck Surgery, Oulu University Hospital, Finland & PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Minna Männikkö
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Infrastructure for Population Studies, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Elina Hietikko
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
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12
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Hartwell RD, England SJ, Monk NAM, van Hateren NJ, Baxendale S, Marzo M, Lewis KE, Whitfield TT. Anteroposterior patterning of the zebrafish ear through Fgf- and Hh-dependent regulation of hmx3a expression. PLoS Genet 2019; 15:e1008051. [PMID: 31022185 PMCID: PMC6504108 DOI: 10.1371/journal.pgen.1008051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 05/07/2019] [Accepted: 02/27/2019] [Indexed: 12/16/2022] Open
Abstract
In the zebrafish, Fgf and Hh signalling assign anterior and posterior identity, respectively, to the poles of the developing ear. Mis-expression of fgf3 or inhibition of Hh signalling results in double-anterior ears, including ectopic expression of hmx3a. To understand how this double-anterior pattern is established, we characterised transcriptional responses in Fgf gain-of-signalling or Hh loss-of-signalling backgrounds. Mis-expression of fgf3 resulted in rapid expansion of anterior otic markers, refining over time to give the duplicated pattern. Response to Hh inhibition was very different: initial anteroposterior asymmetry was retained, with de novo duplicate expression domains appearing later. We show that Hmx3a is required for normal anterior otic patterning, and that otic patterning defects in hmx3a-/- mutants are a close phenocopy to those seen in fgf3-/- mutants. However, neither loss nor gain of hmx3a function was sufficient to generate full ear duplications. Using our data to infer a transcriptional regulatory network required for acquisition of otic anterior identity, we can recapitulate both the wild-type and the double-anterior pattern in a mathematical model. Understanding how signalling molecules impart information to developing organ systems, and how this is interpreted through networks of gene activity, is a key goal of developmental genetic analysis. In the developing zebrafish inner ear, differences in gene expression arise between the anterior and posterior poles of the ear placode, ensuring that sensory structures in the ear develop in their correct positions. If signalling pathways are disrupted, a mirror-image ear can result, developing with two anterior poles. We have used genetic, pharmacological and mathematical modelling approaches to decipher the pathway of gene action required to specify anterior structures in the zebrafish ear. Patterns of gene expression are dynamic and plastic, with two different routes leading to the formation of duplicate anterior structures. Expression of the hmx3a gene is an early response to the anterior signalling molecule Fgf3, but is not sufficient to drive the formation of ectopic anterior structures at the posterior of the ear. The hmx3a gene codes for a protein that regulates other genes, and in humans, mutation of HMX genes results in diseases affecting inner ear function. Our work provides a framework for understanding the dynamics of early patterning events in the developing inner ear.
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Affiliation(s)
- Ryan D. Hartwell
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Samantha J. England
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Nicholas A. M. Monk
- School of Mathematics and Statistics, University of Sheffield, Sheffield, United Kingdom
| | - Nicholas J. van Hateren
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Sarah Baxendale
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Mar Marzo
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
| | - Katharine E. Lewis
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Tanya T. Whitfield
- Bateson Centre and Department of Biomedical Science, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
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13
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Yang Q, Zhang S, Li J, Wang X, Peng K, Lan X, Pan C. Development of a touch-down multiplex PCR method for simultaneously rapidly detecting three novel insertion/deletions (indels) within one gene: an example for goat GHR gene. Anim Biotechnol 2018; 30:366-371. [DOI: 10.1080/10495398.2018.1517770] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Qing Yang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Shaoli Zhang
- Innovation Experimental College, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jie Li
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xinyu Wang
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kun Peng
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xianyong Lan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chuanying Pan
- College of Animal Science and Technology, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A&F University, Yangling, Shaanxi, P. R. China
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14
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Urh K, Kolenc Ž, Hrovat M, Svet L, Dovč P, Kunej T. Molecular Mechanisms of Syndromic Cryptorchidism: Data Synthesis of 50 Studies and Visualization of Gene-Disease Network. Front Endocrinol (Lausanne) 2018; 9:425. [PMID: 30093884 PMCID: PMC6070605 DOI: 10.3389/fendo.2018.00425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/09/2018] [Indexed: 12/17/2022] Open
Abstract
Background: Cryptorchidism is one of the most frequent congenital birth defects in male children and is present in 2-4% of full-term male births. It has several possible health effects including reduced fertility, increased risk for testicular neoplasia, testicular torsion, and psychological consequences. Cryptorchidism is often diagnosed as comorbid; copresent with other diseases. It is also present in clinical picture of several syndromes. However, this field has not been systematically studied. The aim of the present study was to catalog published cases of syndromes which include cryptorchidism in the clinical picture and associated genomic information. Methods: The literature was extracted from Public/Publisher MEDLINE and Web of Science databases, using the keywords including: syndrome, cryptorchidism, undescended testes, loci, and gene. The obtained data was organized in a table according to the previously proposed standardized data format. The results of the study were visually represented using Gephi and karyotype view. Results: Fifty publications had sufficient data for analysis. Literature analysis resulted in 60 genomic loci, associated with 44 syndromes that have cryptorchidism in clinical picture. Genomic loci included 38 protein-coding genes and 22 structural variations containing microdeletions and microduplications. Loci, associated with syndromic cryptorchidism are located on 16 chromosomes. Visualization of retrieved data is presented in a gene-disease network. Conclusions: The study is ongoing and further studies will be needed to develop a complete catalog with the data from upcoming publications. Additional studies will also be needed for revealing of molecular mechanisms associated with syndromic cryptorchidism and revealing complete diseasome network.
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Affiliation(s)
| | | | | | | | | | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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15
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Urh K, Kunej T. Genome-wide screening for smallest regions of overlaps in cryptorchidism. Reprod Biomed Online 2018; 37:85-99. [PMID: 29631949 DOI: 10.1016/j.rbmo.2018.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 02/19/2018] [Accepted: 02/21/2018] [Indexed: 01/01/2023]
Abstract
Cryptorchidism is a urogenital abnormality associated with increased rates of testicular neoplasia and impaired spermatogenesis. The field is facing expansion of genomics data; however, it lacks protocols for biomarker prioritization. Identification of smallest regions of overlap (SRO) presents an approach for candidate gene identification but has not yet been systematically conducted in cryptorchidism. The aim of this study was to conduct a genome-wide screening for SRO (GW-SRO) associated with cryptorchidism development. We updated the Cryptorchidism Gene Database to version 3, remapped genomic coordinates of loci from older assemblies to the GRCh38 and performed genome-wide screening for overlapping regions associated with cryptorchidism risk. A total of 73 chromosomal loci (68 involved in chromosomal mutations and five copy number variations) described in 37 studies associated with cryptorchidism risk in humans were used for SRO identification. Analysis resulted in 18 SRO, based on deletions, duplications, inversions, derivations and copy number variations. Screening for SRO was challenging owing to heterogeneous reporting of genomic locations. To our knowledge, this is the first GW-SRO study for cryptorchidism and it presents the basis for further narrowing of critical regions for cryptorchidism and planning functional experiments. The developed protocol could also be applied to other multifactorial diseases.
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Affiliation(s)
- Kristian Urh
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, Slovenia.
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16
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Lacaria M, Srour M, Michaud JL, Doja A, Miller E, Schwartzentruber J, Goldsmith C, Majewski J, Boycott KM. Expansion of the clinical phenotype of the distal 10q26.3 deletion syndrome to include ataxia and hyperemia of the hands and feet. Am J Med Genet A 2017; 173:1611-1619. [PMID: 28432728 DOI: 10.1002/ajmg.a.38231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/05/2017] [Indexed: 12/23/2022]
Abstract
Distal deletion of the long arm of chromosome 10 is associated with a dysmorphic craniofacial appearance, microcephaly, behavioral issues, developmental delay, intellectual disability, and ocular, urogenital, and limb abnormalities. Herein, we present clinical, molecular, and cytogenetic investigations of four patients, including two siblings, with nearly identical terminal deletions of 10q26.3, all of whom have an atypical presentation of this syndrome. Their prominent features include ataxia, mild-to-moderate intellectual disability, and hyperemia of the hands and feet, and they do not display many of the other features commonly associated with deletions of this region. These results point to a novel gene locus associated with ataxia and highlight the variability of the clinical presentation of patients with deletions of this region.
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Affiliation(s)
- Melanie Lacaria
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario
| | - Myriam Srour
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec.,Department of Pediatrics, McGill University, Montreal, Quebec
| | - Jacques L Michaud
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec.,Department of Pediatrics, Universite de Montreal, Montreal, Quebec.,Department of Neurosciences, Universite de Montreal, Montreal, Quebec
| | - Asif Doja
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario.,Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Ontario.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario
| | - Elka Miller
- Department of Medical Imaging, Children's Hospital of Eastern Ontario, Ottawa, Ontario
| | | | - Claire Goldsmith
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec
| | | | - Kym M Boycott
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario.,Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario.,Faculty of Medicine, University of Ottawa, Ottawa, Ontario
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17
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Lin S, Zhou Y, Fang Q, Wu J, Zhang Z, Ji Y, Luo Y. Chromosome 10q26 deletion syndrome: Two new cases and a review of the literature. Mol Med Rep 2016; 14:5134-5140. [PMID: 27779662 PMCID: PMC5355737 DOI: 10.3892/mmr.2016.5864] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/06/2016] [Indexed: 01/16/2023] Open
Abstract
The current study presents the cases of two unrelated patients with similar clinical features, including craniofacial anomalies, developmental delay/intellectual disability and cardiac malformations, that are consistent with chromosome 10q26 deletion syndrome. High‑resolution single‑nucleotide polymorphism analysis revealed that 10q26 terminal deletions were present in these two patients. The locations and sizes of the 10q26 deletions in these two patients were compared with the locations and sizes of 10q26 deletions in 30 patients recorded in the DECIPHER database and 18 patients characterized in previous studies through chromosomal microarray analysis. The clinical features and locations of the 10q26 deletions of these patients were reviewed in an attempt to map or refine a critical region (CR) for phenotypes. Additionally, the association between previously suggested CRs and phenotypic variability was discussed. The current study emphasize that a distal 10q26 terminal deletion with a breakpoint at ~130 Mb may contribute to the common clinical features of 10q26 deletion syndrome.
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Affiliation(s)
- Shaobin Lin
- Fetal Medicine Center, Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yi Zhou
- Fetal Medicine Center, Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Qun Fang
- Fetal Medicine Center, Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Jianzhu Wu
- Fetal Medicine Center, Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Zhiqiang Zhang
- Fetal Medicine Center, Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yuanjun Ji
- Fetal Medicine Center, Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Yanmin Luo
- Fetal Medicine Center, Department of Obstetrics & Gynecology, The First Affiliated Hospital of Sun Yat‑Sen University, Guangzhou, Guangdong 510080, P.R. China
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18
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Sangu N, Okamoto N, Shimojima K, Ondo Y, Nishikawa M, Yamamoto T. A de novo microdeletion in a patient with inner ear abnormalities suggests that the 10q26.13 region contains the responsible gene. Hum Genome Var 2016; 3:16008. [PMID: 27274859 PMCID: PMC4871931 DOI: 10.1038/hgv.2016.8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 11/12/2022] Open
Abstract
Microdeletions in the 10q26.1 region are related to intellectual disability, growth delay, microcephaly, distinctive craniofacial features, cardiac defects, genital abnormalities and inner ear abnormalities. The genes responsible for inner ear abnormalities have been narrowed to fibroblast growth factor receptor 2 gene (FGFR2), H6 family homeobox 2 gene (HMX2) and H6 family homeobox 3 gene (HMX3). An additional patient with distinctive craniofacial features, congenital deafness and balance dysfunctions showed a de novo microdeletion of 10q26.11q26.13, indicating the existence of a gene responsible for inner ear abnormalities in this region.
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Affiliation(s)
- Noriko Sangu
- Tokyo Women's Medical University Institute for Integrated Medical Sciences, Tokyo, Japan; Department of Oral and Maxillofacial Surgery, Tokyo Women's Medical University, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health , Izumi, Japan
| | - Keiko Shimojima
- Tokyo Women's Medical University Institute for Integrated Medical Sciences , Tokyo, Japan
| | - Yumiko Ondo
- Tokyo Women's Medical University Institute for Integrated Medical Sciences , Tokyo, Japan
| | - Masanori Nishikawa
- Department of Radiology, Osaka Medical Center and Research Institute for Maternal and Child Health , Izumi, Japan
| | - Toshiyuki Yamamoto
- Tokyo Women's Medical University Institute for Integrated Medical Sciences , Tokyo, Japan
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19
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Ramos M, Wilkens A, Krantz ID, Wu Y. Hearing loss, coloboma and left ventricular enlargement in a boy with an interstitial 10q26 deletion. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:109-16. [PMID: 27125467 DOI: 10.1002/ajmg.c.31496] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Distal deletion of the long arm of chromosome 10 with breakpoints mapped at 10q26 is a well-recognized contiguous genomic disorder. A wide spectrum of clinical findings is seen in affected individuals and the common clinical features include craniofacial dysmorphia, developmental delay, intellectual disability, hypotonia, cardiovascular defects, and urogenital malformations. We report herein on a male patient with a 5.5 Mb interstitial deletion of 10q26.11q2613 and compare his clinical presentation to previously reported cases. Apart from characteristic phenotypes seen in 10q26 deletion syndrome, he presents with colobomas and left ventricle enlargement. These are cardiovascular and ophthalmological findings that have not been described in prior cases. © 2016 Wiley Periodicals, Inc.
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20
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Laudier B, Epiais T, Pâris A, Menuet A, Briault S, Ozsancak C, Perche O. Molecular and clinical analyses with neuropsychological assessment of a case of del(10)(q26.2qter) without intellectual disability: Genomic and transcriptomic combined approach and review of the literature. Am J Med Genet A 2016; 170:1806-12. [PMID: 27113058 DOI: 10.1002/ajmg.a.37677] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/03/2016] [Indexed: 11/10/2022]
Abstract
Terminal deletion of the long arm of the chromosome 10 is a rare but well known abnormality, with a large phenotypic variability. Very few data are available about subtelomeric deletion 10q26 patients without intellectual disability. Herein, we report the case of a young adult with a classical 10q26.2qter deletion. She exhibited mainly short stature at birth and in childhood/adulthood without intellectual disability or behavioral problems. After clinical and neuropsychological assessments, we performed genomic array and transcriptomic analysis and compared our results to the data available in the literature. The patient presents a 6.525 Mb heterozygous 10q26.2qter deletion, encompassed 48 genes. Among those genes, DOCK1, C10orf90, and CALY previously described as potential candidate genes for intellectual disability, were partially or completed deleted. Interestingly, they were not deregulated as demonstrated by transcriptomic analysis. This allowed us to suggest that the mechanism involved in the deletion 10qter phenotype is much more complex that only the haploinsufficiency of DOCK1 or other genes encompassed in the deletion. Genomic and transcriptomic combined approach has to be considered to understand this pathogenesis. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Béatrice Laudier
- UMR7355, CNRS, Orleans, France.,Experimental and Molecular Immunology and Neurogenetics, University of Orleans, Orleans, France.,Department of Genetics, Regional Hospital, Orleans, France
| | | | - Arnaud Pâris
- UMR7355, CNRS, Orleans, France.,Experimental and Molecular Immunology and Neurogenetics, University of Orleans, Orleans, France
| | - Arnaud Menuet
- UMR7355, CNRS, Orleans, France.,Experimental and Molecular Immunology and Neurogenetics, University of Orleans, Orleans, France
| | - Sylvain Briault
- UMR7355, CNRS, Orleans, France.,Experimental and Molecular Immunology and Neurogenetics, University of Orleans, Orleans, France.,Department of Genetics, Regional Hospital, Orleans, France
| | - Canan Ozsancak
- Department of Neurology, Regional Hospital, Orleans, France
| | - Olivier Perche
- UMR7355, CNRS, Orleans, France.,Experimental and Molecular Immunology and Neurogenetics, University of Orleans, Orleans, France.,Department of Genetics, Regional Hospital, Orleans, France
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21
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Patthey C, Clifford H, Haerty W, Ponting CP, Shimeld SM, Begbie J. Identification of molecular signatures specific for distinct cranial sensory ganglia in the developing chick. Neural Dev 2016; 11:3. [PMID: 26819088 PMCID: PMC4730756 DOI: 10.1186/s13064-016-0057-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/08/2016] [Indexed: 11/22/2022] Open
Abstract
Background The cranial sensory ganglia represent populations of neurons with distinct functions, or sensory modalities. The production of individual ganglia from distinct neurogenic placodes with different developmental pathways provides a powerful model to investigate the acquisition of specific sensory modalities. To date there is a limited range of gene markers available to examine the molecular pathways underlying this process. Results Transcriptional profiles were generated for populations of differentiated neurons purified from distinct cranial sensory ganglia using microdissection in embryonic chicken followed by FAC-sorting and RNAseq. Whole transcriptome analysis confirmed the division into somato- versus viscerosensory neurons, with additional evidence for subdivision of the somatic class into general and special somatosensory neurons. Cross-comparison of distinct ganglia transcriptomes identified a total of 134 markers, 113 of which are novel, which can be used to distinguish trigeminal, vestibulo-acoustic and epibranchial neuronal populations. In situ hybridisation analysis provided validation for 20/26 tested markers, and showed related expression in the target region of the hindbrain in many cases. Conclusions One hundred thirty-four high-confidence markers have been identified for placode-derived cranial sensory ganglia which can now be used to address the acquisition of specific cranial sensory modalities. Electronic supplementary material The online version of this article (doi:10.1186/s13064-016-0057-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cedric Patthey
- Department of Zoology, University of Oxford, Oxford, UK. .,Umeå Center for Molecular Medicine, Umeå University, Umeå, Sweden.
| | - Harry Clifford
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | - Wilfried Haerty
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | - Chris P Ponting
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK. .,MRC Functional Genomics, University of Oxford, Oxford, UK.
| | | | - Jo Begbie
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
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22
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Faria ÁC, Rabbi-Bortolini E, Rebouças MRGO, de S Thiago Pereira ALA, Frasson MGT, Atique R, Lourenço NCV, Rosenberg C, Kobayashi GS, Passos-Bueno MR, Errera FIV. Craniosynostosis in 10q26 deletion patients: A consequence of brain underdevelopment or altered suture biology? Am J Med Genet A 2015; 170A:403-409. [PMID: 26566760 DOI: 10.1002/ajmg.a.37448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 10/16/2015] [Indexed: 01/07/2023]
Abstract
Approximately a hundred patients with terminal 10q deletions have been described. They present with a wide range of clinical features always accompanied by delayed development, intellectual disability and craniofacial dysmorphisms. Here, we report a girl and a boy with craniosynostosis, developmental delay and other congenital anomalies. Karyotyping and molecular analysis including Multiplex Ligation dependent probe amplification (MLPA) and Array Comparative Genomic Hybridization (aCGH) were performed in both patients. We detected a 13.1 Mb pure deletion at 10q26.12-q26.3 in the girl and a 10.9 Mb pure deletion at 10q26.13-q26.3 in the boy, both encompassing about 100 genes. The clinical and molecular findings in these patients reinforce the importance of the DOCK1 smallest region of overlap I (SRO I), previously suggested to explain the clinical signs, and together with a review of the literature suggest a second 3.5 Mb region important for the phenotype (SRO II). Genotype-phenotype correlations and literature data suggest that the craniosynostosis is not directly related to dysregulated signaling in suture development, but may be secondary to alterations in brain development instead. Further, genes at 10q26 may be involved in the molecular crosstalk between brain and cranial vault.
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Affiliation(s)
- Ágatha Cristhina Faria
- Programa de Graduação em Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Espírito Santo (UFES), Vitória, Espírito Santo, Brasil.,Laboratório de Genética Humana e Molecular, Centro de Pesquisa ICALP, Escola Superior de Ciências da Santa Casa de Misericórdia (EMESCAM), Vitória, Espírito Santo, Brasil
| | - Eliete Rabbi-Bortolini
- Laboratório de Genética e Biologia Molecular, Associação Educacional de Vitória, Vitória, Espírito Santo, Brasil
| | - Maria R G O Rebouças
- Divisão de Genética Clínica, Hospital Estadual Infantil Nossa Senhora da Glória (HEINSG), Vitória, Espírito Santo, Brasil
| | | | - Milena G Tonini Frasson
- Unidade de Neonatologia, Hospital Santa Casa de Misericórdia, Vitória, Espírito Santo, Brasil
| | - Rodrigo Atique
- Centro de Pesquisas Sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto De Biociências, Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Naila Cristina V Lourenço
- Centro de Pesquisas Sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto De Biociências, Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Carla Rosenberg
- Centro de Pesquisas Sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto De Biociências, Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Gerson S Kobayashi
- Centro de Pesquisas Sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto De Biociências, Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas Sobre o Genoma Humano e Células Tronco, Departamento de Genética e Biologia Evolutiva, Instituto De Biociências, Universidade de São Paulo (USP), São Paulo, São Paulo, Brasil
| | - Flávia Imbroisi Valle Errera
- Programa de Graduação em Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Espírito Santo (UFES), Vitória, Espírito Santo, Brasil.,Laboratório de Genética Humana e Molecular, Centro de Pesquisa ICALP, Escola Superior de Ciências da Santa Casa de Misericórdia (EMESCAM), Vitória, Espírito Santo, Brasil
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23
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Choucair N, Abou Ghoch J, Fawaz A, Mégarbané A, Chouery E. 10q26.1 Microdeletion: Redefining the critical regions for microcephaly and genital anomalies. Am J Med Genet A 2015; 167A:2707-13. [DOI: 10.1002/ajmg.a.37211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 06/04/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Nancy Choucair
- Unité de Génétique Médicale et Laboratoire Associé INSERM à l'Unité UMR_S 910; Faculté de Médecine; Université Saint-Joseph; Beirut Lebanon
- Faculté de Médecine de la Timone; Aix-Marseille Université; Marseille France
- Institut National de la Santé et de la Recherche Médicale; UMR_S910; Marseille France
| | - Joelle Abou Ghoch
- Unité de Génétique Médicale et Laboratoire Associé INSERM à l'Unité UMR_S 910; Faculté de Médecine; Université Saint-Joseph; Beirut Lebanon
| | - Ali Fawaz
- Neuropediatrics Department; Lebanese University; Beirut Lebanon
| | - André Mégarbané
- Unité de Génétique Médicale et Laboratoire Associé INSERM à l'Unité UMR_S 910; Faculté de Médecine; Université Saint-Joseph; Beirut Lebanon
- Institut Jérôme Lejeune; Paris France
| | - Eliane Chouery
- Unité de Génétique Médicale et Laboratoire Associé INSERM à l'Unité UMR_S 910; Faculté de Médecine; Université Saint-Joseph; Beirut Lebanon
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24
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Contribution of copy number variants (CNVs) to congenital, unexplained intellectual and developmental disabilities in Lebanese patients. Mol Cytogenet 2015; 8:26. [PMID: 25922617 PMCID: PMC4411788 DOI: 10.1186/s13039-015-0130-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Chromosomal microarray analysis (CMA) is currently the most widely adopted clinical test for patients with unexplained intellectual disability (ID), developmental delay (DD), and congenital anomalies. Its use has revealed the capacity to detect copy number variants (CNVs), as well as regions of homozygosity, that, based on their distribution on chromosomes, indicate uniparental disomy or parental consanguinity that is suggestive of an increased probability of recessive disease. Results We screened 149 Lebanese probands with ID/DD and 99 healthy controls using the Affymetrix Cyto 2.7 M and SNP6.0 arrays. We report all identified CNVs, which we divided into groups. Pathogenic CNVs were identified in 12.1% of the patients. We review the genotype/phenotype correlation in a patient with a 1q44 microdeletion and refine the minimal critical regions responsible for the 10q26 and 16q monosomy syndromes. Several likely causative CNVs were also detected, including new homozygous microdeletions (9p23p24.1, 10q25.2, and 8p23.1) in 3 patients born to consanguineous parents, involving potential candidate genes. However, the clinical interpretation of several other CNVs remains uncertain, including a microdeletion affecting ATRNL1. This CNV of unknown significance was inherited from the patient’s unaffected-mother; therefore, additional ethnically matched controls must be screened to obtain enough evidence for classification of this CNV. Conclusion This study has provided supporting evidence that whole-genome analysis is a powerful method for uncovering chromosomal imbalances, regardless of consanguinity in the parents of patients and despite the challenge presented by analyzing some CNVs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0130-y) contains supplementary material, which is available to authorized users.
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25
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Vera-Carbonell A, López-González V, Bafalliu JA, Ballesta-Martínez MJ, Fernández A, Guillén-Navarro E, López-Expósito I. Clinical comparison of 10q26 overlapping deletions: delineating the critical region for urogenital anomalies. Am J Med Genet A 2015; 167A:786-90. [PMID: 25655674 DOI: 10.1002/ajmg.a.36949] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/21/2014] [Indexed: 11/09/2022]
Abstract
The 10q26 deletion syndrome is a clinically heterogeneous disorder. The most common phenotypic characteristics include pre- and/or postnatal growth retardation, microcephaly, developmental delay/intellectual disability and a facial appearance consisting of a broad nasal bridge with a prominent nose, low-set malformed ears, strabismus, and a thin vermilion of the upper lip. In addition, limb and cardiac anomalies as well as urogenital anomalies are occasionally observed. In this report, we describe three unrelated females with 10q26 terminal deletions who shared clinical features of the syndrome, including urogenital defects. Cytogenetic studies showed an apparently de novo isolated deletion of the long arm of chromosome 10, with breakpoints in 10q26.1, and subsequent oligo array-CGH analysis confirmed the terminal location and defined the size of the overlapping deletions as ∼ 13.46, ∼ 9.31 and ∼ 9.17 Mb. We compared the phenotypic characteristics of the present patients with others reported to have isolated deletions and we suggest that small 10q26.2 terminal deletions may be associated with growth retardation, developmental delay/intellectual disability, craniofacial features and external genital anomalies whereas longer terminal deletions affecting the 10q26.12 and/or 10q26.13 regions may be responsible for renal/urinary tract anomalies. We propose that the haploinsufficiency of one or several genes located in the 10q26.12-q26.13 region may contribute to the renal or urinary tract pathogenesis and we highlight the importance of FGFR2 and probably of CTBP2 as candidate genes.
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Affiliation(s)
- Ascensión Vera-Carbonell
- Sección de Citogenética, Centro de Bioquímica y Genética Clínica, Hospital Clínico Universitario Virgen de la Arrixaca, El Palmar, Murcia, Spain; Instituto Murciano de Investigación Biosanitaria-Arrixaca (IMIB-Arrixaca); Centro de Investigación Biomédica de Red de Enfermedades Raras (CIBERER), Instituto de, Salud Carlos III (ISCIII), Madrid, Spain
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26
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Davies KTJ, Tsagkogeorga G, Rossiter SJ. Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals. BMC Evol Biol 2014; 14:261. [PMID: 25523630 PMCID: PMC4302572 DOI: 10.1186/s12862-014-0261-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 12/08/2014] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. RESULTS Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise frequency-modulated echolocation calls varying widely in frequency and intensity high levels of sequence divergence were found. CONCLUSIONS Levels of selective constraint acting on CNEs differed both across genomic locations and taxa, with observed variation in substitution rates of CNEs among bat species. More work is needed to determine whether this variation can be linked to echolocation, and wider taxonomic sampling is necessary to fully document levels of conservation in CNEs across diverse taxa.
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Affiliation(s)
- Kalina T J Davies
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Georgia Tsagkogeorga
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Stephen J Rossiter
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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27
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Peltekova IT, Hurteau-Millar J, Armour CM. Novel interstitial deletion of 10q24.3-25.1 associated with multiple congenital anomalies including lobar holoprosencephaly, cleft lip and palate, and hypoplastic kidneys. Am J Med Genet A 2014; 164A:3132-6. [DOI: 10.1002/ajmg.a.36740] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 07/31/2014] [Indexed: 01/19/2023]
Affiliation(s)
- Iskra T. Peltekova
- Department of Developmental Pediatrics; Montréal Children's Hospital; Montreal Québec
| | - Julie Hurteau-Millar
- Division of Radiology; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
| | - Christine M. Armour
- Division of Clinical Genetics; Children's Hospital of Eastern Ontario; Ottawa Ontario Canada
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28
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Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P, Davey Smith G, Dermitzakis ET. Cis and trans effects of human genomic variants on gene expression. PLoS Genet 2014; 10:e1004461. [PMID: 25010687 PMCID: PMC4091791 DOI: 10.1371/journal.pgen.1004461] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/12/2014] [Indexed: 11/18/2022] Open
Abstract
Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation. In order to detect genetic variations affecting gene expression, we performed association analysis of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with gene expression measured in 869 lymphoblastoid cell lines of the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort in cis and in trans. We discovered that 3,534 genes (false discovery rate (FDR) = 5%) are affected by an expression quantitative trait locus (eQTL) in cis and 48 genes are affected in trans. We observed that CNVs are more likely to be eQTLs than SNPs. In addition, we found that variants associated to complex traits and diseases are enriched for trans-eQTLs and that trans-eQTLs are enriched for cis-eQTLs. As a variant affecting both a gene in cis and in trans suggests that the cis gene is functionally linked to the trans gene expression, we looked specifically for trans effects of cis-eQTLs. We discovered that 26 cis-eQTLs are associated to 92 genes in trans with the cis-eQTLs of the transcriptions factors BATF3 and HMX2 affecting the most genes. We then explored if the variation of the level of expression of the cis genes were causally affecting the level of expression of the trans genes and discovered several causal relationships between variation in the level of expression of the cis gene and variation of the level of expression of the trans gene. This analysis shows that a large sample size allows the discovery of secondary effects of human variations on gene expression that can be used to construct short directed gene regulatory networks.
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Affiliation(s)
- Julien Bryois
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - Alfonso Buil
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
| | - David M. Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland, Australia
| | - John P. Kemp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Stephen B. Montgomery
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Department of Pathology and Genetics, Stanford University, Stanford, California, United States of America
| | | | - Karen M. Ho
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Susan Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kindom
- Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
- Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland
- Center of Excellence for Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail:
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Piard J, Mignot B, Arbez-Gindre F, Aubert D, Morel Y, Roze V, McElreavey K, Jonveaux P, Valduga M, Van Maldergem L. Severe sex differentiation disorder in a boy with a 3.8 Mb 10q25.3-q26.12 microdeletion encompassing EMX2. Am J Med Genet A 2014; 164A:2618-22. [DOI: 10.1002/ajmg.a.36662] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 05/30/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Juliette Piard
- Centre de Génétique Humaine; Université de Franche-Comté; Besançon France
| | - Brigitte Mignot
- Service de Pédiatrie; Université de Franche-Comté; Besançon France
| | | | - Didier Aubert
- Service de Chirurgie Pédiatrique; Université de Franche-Comté; Besançon France
| | - Yves Morel
- Service d'Endocrinologie Moléculaire et Maladies Rares; Université de Lyon; Lyon France
| | - Virginie Roze
- Laboratoire de Génétique; Histologie et Biologie de la Reproduction; Université de Franche-Comté; Besançon France
| | | | | | - Mylène Valduga
- Laboratoire de Génétique; Université de Nancy; Nancy France
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Abstract
Bipolar disorder is a common, complex genetic disorder, but the mode of transmission remains to be discovered. Many researchers assume that common genomic variants carry some risk for manifesting the disease. The research community has celebrated the first genome-wide significant associations between common single nucleotide polymorphisms (SNPs) and bipolar disorder. Currently, attempts are under way to translate these findings into clinical practice, genetic counseling, and predictive testing. However, some experts remain cautious. After all, common variants explain only a very small percentage of the genetic risk, and functional consequences of the discovered SNPs are inconclusive. Furthermore, the associated SNPs are not disease specific, and the majority of individuals with a "risk" allele are healthy. On the other hand, population-based genome-wide studies in psychiatric disorders have rediscovered rare structural variants and mutations in genes, which were previously known to cause genetic syndromes and monogenic Mendelian disorders. In many Mendelian syndromes, psychiatric symptoms are prevalent. Although these conditions do not fit the classic description of any specific psychiatric disorder, they often show nonspecific psychiatric symptoms that cross diagnostic boundaries, including intellectual disability, behavioral abnormalities, mood disorders, anxiety disorders, attention deficit, impulse control deficit, and psychosis. Although testing for chromosomal disorders and monogenic Mendelian disorders is well established, testing for common variants is still controversial. The standard concept of genetic testing includes at least three broad criteria that need to be fulfilled before new genetic tests should be introduced: analytical validity, clinical validity, and clinical utility. These criteria are currently not fulfilled for common genomic variants in psychiatric disorders. Further work is clearly needed before genetic testing for common variants in psychiatric disorders should be established.
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Affiliation(s)
- Berit Kerner
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
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31
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Castiglione A, Guaran V, Astolfi L, Orioli E, Zeri G, Gemmati D, Bovo R, Montaldi A, Alghisi A, Martini A. Karyotype-phenotype correlation in partial trisomies of the short arm of chromosome 6: a family case report and review of the literature. Cytogenet Genome Res 2013; 141:243-59. [PMID: 23942271 DOI: 10.1159/000353846] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2013] [Indexed: 11/19/2022] Open
Abstract
The first child (proband) of nonconsanguineous Caucasian parents underwent genetic investigation because she was affected with congenital choanal atresia, heart defects and kidney hyposplasia with mild transient renal insufficiency. The direct DNA sequencing after PCR of the CHD7 gene, which is thought to be responsible for approximately 60-70% of the cases of CHARGE syndrome/association, found no mutations. The cytogenetic analysis (standard GTG banding karyotype) revealed the presence of extrachromosomal material on 10q. The chromosome analysis was completed with array CGH (30 kb resolution), MLPA and FISH, which allowed the identification of three 6p regions (6p.25.3p23 × 3): 2 of these regions are normally located on chromosome 6, and the third region is translocated to the long arm of chromosome 10. The same chromosomal rearrangement was subsequently found in the father, who was affected with congenital ptosis and progressive hearing loss, and in the proband's sister, the second child, who presented at birth with choanal atresia and congenital heart defects. The mutated karyotypes, which were directly inherited, are thought to be responsible for a variable phenotype, including craniofacial dysmorphisms, choanal atresia, congenital ptosis, sensorineural hearing loss, heart defects, developmental delay, and renal dysfunction. Nevertheless, to achieve a complete audiological assessment of the father, he underwent further investigation that revealed an increased level of the coagulation factor XIII (300% increased activity), fluctuating levels of fibrin D-dimer degradation products (from 296 to 1,587 ng/ml) and a homoplasmic mitochondrial DNA mutation: T961G in the MTRNR1 (12S rRNA) gene. He was made a candidate for cochlear implantation. Preoperative high-resolution computed tomography and magnetic resonance imaging of the temporal bone revealed the presence of an Arnold-Chiari malformation type I. To the best of our knowledge, this study is the second report on partial 6p trisomy that involves the 10q terminal region. Furthermore, we report the first case of documented Arnold-Chiari malformation type I and increased factor XIII activity associated with 6p trisomy. We present a comprehensive report of the familial cases and an exhaustive literature review.
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Affiliation(s)
- A Castiglione
- Department of Neurosciences, Complex Operative Unit of Otorhinolaryngology and Otosurgery, Padua University Hospital, Padua, Italy
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Buniello A, Hardisty-Hughes RE, Pass JC, Bober E, Smith RJ, Steel KP. Headbobber: a combined morphogenetic and cochleosaccular mouse model to study 10qter deletions in human deafness. PLoS One 2013; 8:e56274. [PMID: 23457544 PMCID: PMC3572983 DOI: 10.1371/journal.pone.0056274] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/08/2013] [Indexed: 02/07/2023] Open
Abstract
The recessive mouse mutant headbobber (hb) displays the characteristic behavioural traits associated with vestibular defects including headbobbing, circling and deafness. This mutation was caused by the insertion of a transgene into distal chromosome 7 affecting expression of native genes. We show that the inner ear of hb/hb mutants lacks semicircular canals and cristae, and the saccule and utricle are fused together in a single utriculosaccular sac. Moreover, we detect severe abnormalities of the cochlear sensory hair cells, the stria vascularis looks severely disorganised, Reissner's membrane is collapsed and no endocochlear potential is detected. Myo7a and Kcnj10 expression analysis show a lack of the melanocyte-like intermediate cells in hb/hb stria vascularis, which can explain the absence of endocochlear potential. We use Trp2 as a marker of melanoblasts migrating from the neural crest at E12.5 and show that they do not interdigitate into the developing strial epithelium, associated with abnormal persistence of the basal lamina in the hb/hb cochlea. We perform array CGH, deep sequencing as well as an extensive expression analysis of candidate genes in the headbobber region of hb/hb and littermate controls, and conclude that the headbobber phenotype is caused by: 1) effect of a 648 kb deletion on distal Chr7, resulting in the loss of three protein coding genes (Gpr26, Cpmx2 and Chst15) with expression in the inner ear but unknown function; and 2) indirect, long range effect of the deletion on the expression of neighboring genes on Chr7, associated with downregulation of Hmx3, Hmx2 and Nkx1.2 homeobox transcription factors. Interestingly, deletions of the orthologous region in humans, affecting the same genes, have been reported in nineteen patients with common features including sensorineural hearing loss and vestibular problems. Therefore, we propose that headbobber is a useful model to gain insight into the mechanisms underlying deafness in human 10qter deletion syndrome.
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Affiliation(s)
- Annalisa Buniello
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | | | - Johanna C. Pass
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
| | - Eva Bober
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | - Karen P. Steel
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Wolfson Centre for Age-Related Diseases, King's College London, London, United Kingdom
- MRC Institute of Hearing Research, Nottingham, United Kingdom
- * E-mail:
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Roknic N, Huber A, Hegemann SCA, Häusler R, Gürtler N. Mutation analysis of Netrin 1 and HMX3 genes in patients with superior semicircular canal dehiscence syndrome. Acta Otolaryngol 2012; 132:1061-5. [PMID: 22779713 PMCID: PMC3477893 DOI: 10.3109/00016489.2012.681797] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CONCLUSION In spite of its absence in the control population, there is questionable evidence for the alteration c.114C->T in the HMX3 gene being implicated in the development of superior semicircular canal dehiscence (SSCD). However, the concept of a complex disease is valid for SSCD and a possible molecular origin can neither be confirmed nor excluded by the results of this study. OBJECTIVES SSCD was first described in 1998 by Minor et al. While the etiology is not clear, findings from both temporal bone CT and histologic studies suggest a congenital or developmental origin. In recent years, a couple of genes regulating inner ear morphogenesis have been described. Specifically, Netrin-1 and HMX3 have been shown to be critically involved in the formation of the SCC. Molecular alterations in these two genes might lead to a disturbed development of this canal and might represent an explanation for SSCD. METHODS DNA was extracted from whole blood of 15 patients with SSCD. The coding sequences of Netrin-1 and HMX3 were amplified by PCR and sequenced. RESULTS One sequence alteration, heterozygous c.114C->T (conservative change without alteration of amino acid) in exon 1 of HMX3, was detected in 2 of 15 patients but not in 300 control chromosomes. The study was supported in part by the Emilia-Guggenheim-Schnurr-Foundation, Basel, Switzerland.
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Affiliation(s)
- Nikola Roknic
- Klinik für Hals-Nasen-Ohrenkrankheiten, Hals- und Gesichtschirurgie, Kantonsspital Aarau AG, Switzerland
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Pietiläinen OPH, Rehnström K, Jakkula E, Service SK, Congdon E, Tilgmann C, Hartikainen AL, Taanila A, Heikura U, Paunio T, Ripatti S, Jarvelin MR, Isohanni M, Sabatti C, Palotie A, Freimer NB, Peltonen L. Phenotype mining in CNV carriers from a population cohort. Hum Mol Genet 2011; 20:2686-95. [PMID: 21505072 DOI: 10.1093/hmg/ddr162] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Phenotype mining is a novel approach for elucidating the genetic basis of complex phenotypic variation. It involves a search of rich phenotype databases for measures correlated with genetic variation, as identified in genome-wide genotyping or sequencing studies. An initial implementation of phenotype mining in a prospective unselected population cohort, the Northern Finland 1966 Birth Cohort (NFBC1966), identifies neurodevelopment-related traits-intellectual deficits, poor school performance and hearing abnormalities-which are more frequent among individuals with large (>500 kb) deletions than among other cohort members. Observation of extensive shared single nucleotide polymorphism haplotypes around deletions suggests an opportunity to expand phenotype mining from cohort samples to the populations from which they derive.
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Affiliation(s)
- Olli P H Pietiläinen
- Institute for Molecular Medicine Finland, and Department of Medical Genetics, University of Helsinki, Helsinki, Finland
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Urness LD, Paxton CN, Wang X, Schoenwolf GC, Mansour SL. FGF signaling regulates otic placode induction and refinement by controlling both ectodermal target genes and hindbrain Wnt8a. Dev Biol 2010; 340:595-604. [PMID: 20171206 PMCID: PMC2854211 DOI: 10.1016/j.ydbio.2010.02.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 02/10/2010] [Accepted: 02/10/2010] [Indexed: 12/25/2022]
Abstract
The inner ear epithelium, with its complex array of sensory, non-sensory, and neuronal cell types necessary for hearing and balance, is derived from a thickened patch of head ectoderm called the otic placode. Mouse embryos lacking both Fgf3 and Fgf10 fail to initiate inner ear development because appropriate patterns of gene expression fail to be specified within the pre-otic field. To understand the transcriptional "blueprint" initiating inner ear development, we used microarray analysis to identify prospective placode genes that were differentially expressed in control and Fgf3(-)(/)(-);Fgf10(-)(/)(-) embryos. Several genes in the down-regulated class, including Hmx3, Hmx2, Foxg1, Sox9, Has2, and Slc26a9 were validated by in situ hybridization. We also assayed candidate target genes suggested by other studies of otic induction. Two placode markers, Fgf4 and Foxi3, were down-regulated in Fgf3(-)(/)(-);Fgf10(-)(/)(-) embryos, whereas Foxi2, a cranial epidermis marker, was expanded in double mutants, similar to its behavior when WNT responses are blocked in the otic placode. Assays of hindbrain Wnt genes revealed that only Wnt8a was reduced or absent in FGF-deficient embryos, and that even some Fgf3(-)(/)(-);Fgf10(-)(/+) and Fgf3(-)(/)(-) embryos failed to express Wnt8a, suggesting a key role for Fgf3, and a secondary role for Fgf10, in Wnt8a expression. Chick explant assays showed that FGF3 or FGF4, but not FGF10, were sufficient to induce Wnt8a. Collectively, our results suggest that Wnt8a provides the link between FGF-induced formation of the pre-otic field and restriction of the otic placode to ectoderm adjacent to the hindbrain.
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Affiliation(s)
- Lisa D. Urness
- Department of Human Genetics, University of Utah, 15 N 2030 E, RM 2100, Salt Lake City, UT 84112-5330, USA
| | - Christian N. Paxton
- Department of Neurobiology and Anatomy, University of Utah, 30 N 1900 E, RM 2R066 SOM, Salt Lake City, UT 84132-3401, USA
| | - Xiaofen Wang
- Department of Human Genetics, University of Utah, 15 N 2030 E, RM 2100, Salt Lake City, UT 84112-5330, USA
| | - Gary C. Schoenwolf
- Department of Neurobiology and Anatomy, University of Utah, 30 N 1900 E, RM 2R066 SOM, Salt Lake City, UT 84132-3401, USA
| | - Suzanne L. Mansour
- Department of Human Genetics, University of Utah, 15 N 2030 E, RM 2100, Salt Lake City, UT 84112-5330, USA
- Department of Neurobiology and Anatomy, University of Utah, 30 N 1900 E, RM 2R066 SOM, Salt Lake City, UT 84132-3401, USA
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36
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Roberson EDO, Pevsner J. Visualization of shared genomic regions and meiotic recombination in high-density SNP data. PLoS One 2009; 4:e6711. [PMID: 19696932 PMCID: PMC2725774 DOI: 10.1371/journal.pone.0006711] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 07/23/2009] [Indexed: 11/23/2022] Open
Abstract
Background A fundamental goal of single nucleotide polymorphism (SNP) genotyping is to determine the sharing of alleles between individuals across genomic loci. Such analyses have diverse applications in defining the relatedness of individuals (including unexpected relationships in nominally unrelated individuals, or consanguinity within pedigrees), analyzing meiotic crossovers, and identifying a broad range of chromosomal anomalies such as hemizygous deletions and uniparental disomy, and analyzing population structure. Principal Findings We present SNPduo, a command-line and web accessible tool for analyzing and visualizing the relatedness of any two individuals using identity by state. Using identity by state does not require prior knowledge of allele frequencies or pedigree information, and is more computationally tractable and is less affected by population stratification than calculating identity by descent probabilities. The web implementation visualizes shared genomic regions, and generates UCSC viewable tracks. The command-line version requires pedigree information for compatibility with existing software and determining specified relationships even though pedigrees are not required for IBS calculation, generates no visual output, is written in portable C++, and is well-suited to analyzing large datasets. We demonstrate how the SNPduo web tool identifies meiotic crossover positions in siblings, and confirm our findings by visualizing meiotic recombination in synthetic three-generation pedigrees. We applied SNPduo to 210 nominally unrelated Phase I / II HapMap samples and, consistent with previous findings, identified six undeclared pairs of related individuals. We further analyzed identity by state in 2,883 individuals from multiplex families with autism and identified a series of anomalies including related parents, an individual with mosaic loss of chromosome 18, an individual with maternal heterodisomy of chromosome 16, and unexplained replicate samples. Conclusions SNPduo provides the ability to explore and visualize SNP data to characterize the relatedness between individuals. It is compatible with, but distinct from, other established analysis software such as PLINK, and performs favorably in benchmarking studies for the analyses of genetic relatedness.
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Affiliation(s)
- Elisha D. O. Roberson
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland, United States of America
| | - Jonathan Pevsner
- Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, Maryland, United States of America
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: JP:
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