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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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Gottschalk A, Sczakiel HL, Hülsemann W, Schwartzmann S, Abad-Perez AT, Grünhagen J, Ott CE, Spielmann M, Horn D, Mundlos S, Jamsheer A, Mensah MA. HOXD13-associated synpolydactyly: Extending and validating the genotypic and phenotypic spectrum with 38 new and 49 published families. Genet Med 2023; 25:100928. [PMID: 37427568 DOI: 10.1016/j.gim.2023.100928] [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: 01/31/2023] [Revised: 07/02/2023] [Accepted: 07/02/2023] [Indexed: 07/11/2023] Open
Abstract
PURPOSE HOXD13 is an important regulator of limb development. Pathogenic variants in HOXD13 cause synpolydactyly type 1 (SPD1). How different types and positions of HOXD13 variants contribute to genotype-phenotype correlations, penetrance, and expressivity of SPD1 remains elusive. Here, we present a novel cohort and a literature review to elucidate HOXD13 phenotype-genotype correlations. METHODS Patients with limb anomalies suggestive of SPD1 were selected for analysis of HOXD13 by Sanger sequencing, repeat length analysis, and next-generation sequencing. Literature was reviewed for HOXD13 heterozygotes. Variants were annotated for phenotypic data. Severity was calculated, and cluster and decision-tree analyses were performed. RESULTS We identified 98 affected members of 38 families featuring 11 different (likely) causative variants and 4 variants of uncertain significance. The most frequent (25/38) were alanine repeat expansions. Phenotypes ranged from unaffected heterozygotes to severe osseous synpolydactyly, with intra- and inter-familial heterogeneity and asymmetry. A literature review provided 160 evaluable affected members of 49 families with SPD1. Computer-aided analysis only corroborated a positive correlation between alanine repeat length and phenotype severity. CONCLUSION Our findings support that HOXD13-protein condensation in addition to haploinsufficiency is the molecular pathomechanism of SPD1. Our data may, also, facilitate the interpretation of synpolydactyly radiographs by future automated tools.
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Affiliation(s)
- Annika Gottschalk
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Henrike L Sczakiel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Berlin, Germany
| | - Wiebke Hülsemann
- Handsurgery Department, Children's Hospital Wilhelmstift, Hamburg, Germany
| | - Sarina Schwartzmann
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Angela T Abad-Perez
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Johannes Grünhagen
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Labor Berlin Charité Vivantes GmbH, Department of Human Genetics, Berlin, Germany
| | - Claus-Eric Ott
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Human Molecular Genomics Group, Berlin, Germany; Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - Denise Horn
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Stefan Mundlos
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany
| | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland; Centers for Medical Genetics, GENESIS, Poznan, Poland
| | - Martin A Mensah
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Medizinische Genetik und Humangenetik, Berlin, Germany; Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, Germany; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Digital Clinician Scientist Program, Berlin, Germany.
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3
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Guo X, Shi T, Lin M, Liu B, Pan Y. Two Novel Frameshift Mutations in the GLI3 Gene Underlie Non-Syndromic Polydactyly in Chinese Families. Genet Test Mol Biomarkers 2023; 27:299-305. [PMID: 37768332 DOI: 10.1089/gtmb.2023.0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023] Open
Abstract
Objective: Polydactyly is characterized by multiple distinct heterogeneous phenotypes, the etiologies of which involve several genes. This study aimed to explore the genetic defects and further clarify the molecular mechanism of polydactyly in several Chinese families. Methods: Three families with diverse phenotypes of non-syndromic polydactyly were analyzed: two were cases of familial disease, whereas one was sporadic. PCR and Sanger sequencing were used to screen for pathogenic mutations in two known disease-associated genes, GLI3 and HOXD13, while bioinformatic analyses predicted the pathogenicity of the identified variants. Reverse transcription PCR was used to analyze the splicing effect of an intronic variant. Results: Two novel heterozygous frameshift mutations (c.4478delG/p.S1493Tfs*18; c.846_c.847insC/p.R283Qfs*21) were identified in the GLI3 gene from two of the pedigrees. Both c.4478delG and c.846_c.847insC were later confirmed in affected and unaffected members and normal controls, to truncate and disrupt the integrity of the GLI3 protein, reduce its level of expression, and disrupt its biological function through nonsense-mediated mRNA decay (NMD). In addition, a deep intron mutation (c.125-47 C>A) was detected in the GLI3 gene from the sporadic case, however, both bioinformatics analysis (HSF, splice AI, and CBS) and RT-PCR indicated that the variant c.125-47 C>A had minimal if any impact on splicing of the GLI3 gene. Conclusion: Two newly identified heterozygous frameshift mutations in the GLI3 gene were detected in two families with non-syndromic polydactyly, further extending the mutational spectrum of the GLI3 gene in non-syndromic polydactyly. Moreover, our study further expanded the phenotypic spectrum of non-syndromic polydactyly.
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Affiliation(s)
- Xiaoyan Guo
- Department of Laboratory Medicine, Fuzhou Second Hospital, Fuzhou, P.R. China
- Department of Laboratory Medicine, Fuzhou Second Hospital of Xiamen University, School of Medicine, Xiamen University, Fuzhou, P.R. China
- Department of Laboratory Medicine, The Third Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China
| | - Tengfei Shi
- Department of Laboratory Medicine, Fuzhou Second Hospital, Fuzhou, P.R. China
| | - Mingrui Lin
- Intensive Care Unit, The Affiliated People's Hospital of Fujian Traditional Medical University, Fuzhou, P.R. China
| | - Boling Liu
- Department of Orthopaedics, Fuzhou Second Hospital, Fuzhou, P.R. China
| | - Yuancheng Pan
- Department of Orthopaedics, Fuzhou Second Hospital, Fuzhou, P.R. China
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4
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Zhang L, Fang Z, Cheng G, He M, Lin Y. A novel Hoxd13 mutation causes synpolydactyly and promotes osteoclast differentiation by regulating pSmad5/p65/c-Fos/Rank axis. Cell Death Dis 2023; 14:145. [PMID: 36804539 PMCID: PMC9941469 DOI: 10.1038/s41419-023-05681-8] [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: 11/12/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
The mutations of HOXD13 gene have been involved in synpolydactyly (SPD), and the polyalanine extension mutation of Hoxd13 gene could lead to SPD in mice. In this study, a novel missense mutation of Hoxd13 (NM_000523: exon2: c.G917T: p.R306L) was identified in a Chinese family with SPD. The mice carrying the corresponding Hoxd13mutation were generated. The results showed that the homozygous mutation of Hoxd13 also caused SPD, but heterozygous mutation did not affect limbs development, which was different from that of SPD patients. With the increasing generation, the mice with homozygous Hoxd13 mutation presented more severe syndactyly. Western blotting showed that this mutation did not affect the protein expression of Hoxd13, suggesting that this mutation did not result in haploinsufficiency. Further analysis demonstrated that this homozygous Hoxd13mutation promoted osteoclast differentiation and bone loss, and enhanced the mRNA and protein expression of osteoclast-related genes Rank, c-Fos, and p65. Meanwhile, this homozygous Hoxd13 mutation elevated the level of phosphorylated Smad5 (pSmad5). Co-immunoprecipitation verified that this mutation attenuated the interaction between pSmad5 and HOXD13, suggesting that this mutation released more pSmad5. Inhibition of pSmad5 reduced the expression of Rank, c-Fos, and p65 despite in the mutation group. In addition, inhibition of pSmad5 repressed the osteoclast differentiation. ChIP assay confirmed that p65 and c-Fos could bind to the promoter of Rank. These results suggested that this novel Hoxd13 mutation promoted osteoclast differentiation by regulating Smad5/p65/c-Fos/Rank axis, which might provide a new insight into SPD development.
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Affiliation(s)
- Lishan Zhang
- grid.410638.80000 0000 8910 6733Department of Hand and Foot Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021 China
| | - Ziqi Fang
- grid.460018.b0000 0004 1769 9639Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250021 China
| | - Guangdong Cheng
- grid.410638.80000 0000 8910 6733Department of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021 China
| | - Mengting He
- grid.464402.00000 0000 9459 9325Department of Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, 250000 China
| | - Yanliang Lin
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250021, China. .,Department of Reproductive Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China.
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Duan R, Hijazi H, Gulec EY, Eker HK, Costa SR, Sahin Y, Ocak Z, Isikay S, Ozalp O, Bozdogan S, Aslan H, Elcioglu N, Bertola DR, Gezdirici A, Du H, Fatih JM, Grochowski CM, Akay G, Jhangiani SN, Karaca E, Gu S, Coban-Akdemir Z, Posey JE, Bayram Y, Sutton VR, Carvalho CM, Pehlivan D, Gibbs RA, Lupski JR. Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability. HGG ADVANCES 2022; 3:100132. [PMID: 36035248 PMCID: PMC9403727 DOI: 10.1016/j.xhgg.2022.100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic heterogeneity, reduced penetrance, and variable expressivity, the latter including asymmetric body axis plane presentations, have all been described in families with congenital limb malformations (CLMs). Interfamilial and intrafamilial heterogeneity highlight the complexity of the underlying genetic pathogenesis of these developmental anomalies. Family-based genomics by exome sequencing (ES) and rare variant analyses combined with whole-genome array-based comparative genomic hybridization were implemented to investigate 18 families with limb birth defects. Eleven of 18 (61%) families revealed explanatory variants, including 7 single-nucleotide variant alleles and 3 copy number variants (CNVs), at previously reported "disease trait associated loci": BHLHA9, GLI3, HOXD cluster, HOXD13, NPR2, and WNT10B. Breakpoint junction analyses for all three CNV alleles revealed mutational signatures consistent with microhomology-mediated break-induced replication, a mechanism facilitated by Alu/Alu-mediated rearrangement. Homozygous duplication of BHLHA9 was observed in one Turkish kindred and represents a novel contributory genetic mechanism to Gollop-Wolfgang Complex (MIM: 228250), where triplication of the locus has been reported in one family from Japan (i.e., 4n = 2n + 2n versus 4n = 3n + 1n allelic configurations). Genes acting on limb patterning are sensitive to a gene dosage effect and are often associated with an allelic series. We extend an allele-specific gene dosage model to potentially assist, in an adjuvant way, interpretations of interconnections among an allelic series, clinical severity, and reduced penetrance of the BHLHA9-related CLM spectrum.
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Affiliation(s)
- Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
| | | | - Silvia R. Costa
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
| | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
| | - Zeynep Ocak
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
| | - Débora R. Bertola
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Baylor-Hopkins Center for Mendelian Genomics
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
- Department of Medical Genetics, Konya City Hospital, Konya, Turkey
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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Starosta RT, Granadillo JL, Patel KR, Finegold MJ, Stoll J, Kulkarni S. Intrahepatic Cholestasis, Refractory Epilepsy, Skeletal Dysplasia, Endocrine Failure, and Dysmorphic Features in a Child With a Monoallelic 2q24-32.2 Deletion Encompassing ABCB11. Pediatr Dev Pathol 2022; 25:174-179. [PMID: 34428094 DOI: 10.1177/10935266211036084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We report a newborn who presented with multiple limb and facial anomalies, endocrine disorders, and progressively worsening low-GGT cholestasis. A liver biopsy revealed hepatocellular cholestasis with giant cell transformation. Immunohistochemical staining revealed complete absence of BSEP protein compared to control liver. A large 2q24-32.2 deletion leading to loss of 78 OMIM genes. Multiple structural anomalies, epilepsy and endocrine anomalies have been described with hemizygous loss of these genes. This deletion also resulted in complete heterozygous deletion of ABCB11, which encodes the bile salt export pump (BSEP). Genetic analysis did not reveal any pathogenic variants, deletions, or duplications in the other ABCB11 allele. A heterozygous variant in NR1H4, which causes the autosomal recessive progressive familial intrahepatic cholestasis type 5, was also detected. The possible explanations for the PFIC type 2 phenotype in heterozygous loss of ABCB11 include genetic modifiers or di-genic disease with a compound ABCB11 deletion and an NR1H4 missense variant; or undetected pathogenic variants in the other ABCB11 or NR1H4 alleles.
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Affiliation(s)
- Rodrigo Tzovenos Starosta
- Division of Genetics and Genomic Medicine, Department of Pediatrics, 7548Washington University in Saint Louis, Saint Louis Children's Hospital, Washington University in Saint Louis, Saint Louis, Missouri.,Department of Pediatrics, 7548Washington University in Saint Louis, Washington University in Saint Louis, St. Louis Children's Hospital, Saint Louis, Missouri
| | - Jorge Luis Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, 7548Washington University in Saint Louis, Saint Louis Children's Hospital, Washington University in Saint Louis, Saint Louis, Missouri
| | - Kalyani R Patel
- Department of Pathology and Immunology, Texas Children's Hospital, Houston, Texas
| | | | - Janis Stoll
- Department of Pediatrics, 7548Washington University in Saint Louis, Washington University in Saint Louis, St. Louis Children's Hospital, Saint Louis, Missouri
| | - Sakil Kulkarni
- Department of Pediatrics, 7548Washington University in Saint Louis, Washington University in Saint Louis, St. Louis Children's Hospital, Saint Louis, Missouri
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7
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Zhang M, Lu L, Wei B, Zhang Y, Li X, Shi Y, Ge W, Sun M. Brachydactyly type A3 is caused by a novel 13 bp HOXD13 frameshift deletion in a Chinese family. Am J Med Genet A 2020; 182:2432-2436. [PMID: 32789964 DOI: 10.1002/ajmg.a.61788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/01/2020] [Accepted: 07/11/2020] [Indexed: 12/13/2022]
Abstract
Brachydactyly type A (BDA) is defined as short middle phalanges of the affected digits and is subdivided into four types (BDA1-4). To date, the molecular cause is unknown. However, there is some evidence that pathogenic variants of HOXD13 could be associated with BDA3 and BDA4. Here, we report a Chinese autosomal dominant BDA3 pedigree with a novel HOXD13 mutation. The affected individuals presented with an obviously shorter fifth middle phalanx. The radial side of the middle phalanx was shorter than the ulnar side, and the terminal phalanx of the fifth finger inclined radially and formed classical clinodactyly. Interestingly, the index finger was normal. The initial diagnosis was BDA3. However, the distal third and fourth middle phalanges were also slightly affected, resulting in mild radial clinodactyly. Both feet showed shortening of the middle phalanges, which were fused to the distal phalanges of the second to the fifth toes, as reported in BDA4. Therefore, this pedigree had combined BDA3 and atypical BDA4. By direct sequencing, a 13 bp deletion within exon 1 of HOXD13 (NM_000523.4: c.708_720del13; NP_000514.2: p.Gly237fs) was identified. The 13 bp deletion resulted in a frameshift and premature termination of HOXD13. This study provides further evidences that variants in HOXD13 cause BDA3-BDA4 phenotypes.
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Affiliation(s)
- Mengshu Zhang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Likui Lu
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Bin Wei
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yingying Zhang
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiang Li
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yajun Shi
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Wei Ge
- Department of Neurology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Miao Sun
- Institute for Fetology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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8
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A heterozygous duplication variant of the HOXD13 gene caused synpolydactyly type 1 with variable expressivity in a Chinese family. BMC MEDICAL GENETICS 2019; 20:203. [PMID: 31870337 PMCID: PMC6929446 DOI: 10.1186/s12881-019-0908-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 10/15/2019] [Indexed: 11/19/2022]
Abstract
Background Synpolydactyly type 1 (SPD1), also known as syndactyly type II, is an autosomal dominant limb deformity generally results in webbing of 3rd and 4th fingers, duplication of 4th or 5th toes. It is most commonly caused by mutation in HOXD13 gene. In this study, a five-generation Chinese family affected with SPD1 disease were collected. We tried to identify the pathogenic variations associated with SPD1 involved in the family. Methods We used the whole genome sequencing (WGS) to identify the pathogenic variant in this family which was later confirmed by PCR-Sanger sequencing. The genetic variation were evaluated with the frequencies in the 1000 Genome Project and Exome Aggregation Consortium (ExAC) dataset. The significance of variants were assessed using different mutation predictor softwares like Mutation Taster, PROVEAN and SIFT. The classification of variants was assessed according to American College of Medical Genetics and Genomics (ACMG) guidelines. Results Our results showed the mutation of 24-base pair duplication (c.183_206dupAGCGGCGGCTGCGGCGGCGGCGGC) in exon one of HOXD13 in heterozygous form which was predicted to result in eight extra alanine (A) residues in N-terminal domain of HOXD13 protein. The mutation was detected in all affected members of the family. Conclusion Based on our mutation analysis of variant c.183_206dupAGCGGCGGCTGCGGCGGCGGCGGC in HOXD13 and its cosegregation in all affected family members, we found this variant as likely pathogenic to this SPD1 family. Our study highlights variable expressivity of HOXD13 mutation. Our results also widen the spectrum of HOXD13 mutation responsible for SPD1.
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9
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Kashevarova AA, Skryabin NA, Nikitina TV, Lopatkina ME, Sazhenova EA, Zhigalina DI, Savchenko RR, Lebedev IN. Ontogenetic Pleiotropy of Genes Involved in CNVs in Human Spontaneous Abortions. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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WITHDRAWN: A 24-base pair duplication in exon one of HOXD13 gene linked to synpolydactyly type 1 in a Chinese family. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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11
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Zhu Y, Cheng Z, Wang J, Liu B, Cheng L, Chen B, Cao Y, Wang B. A novel mutation of HOXA11 in a patient with septate uterus. Orphanet J Rare Dis 2017; 12:178. [PMID: 29229001 PMCID: PMC5725892 DOI: 10.1186/s13023-017-0727-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/23/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The etiology of Müllerian duct anomalies (MDAs) is poorly understood at present. The HOXA11 gene is crucial for the development of the Müllerian duct. The objective of this study is to report a unique case of MDAs with a novel mutation in HOXA11. RESULTS We identified a potential disease-causing mutation (p. E255K) in a patient with a septate uterus. The mutation was not detected in 169 control subjects or listed in any databases of variations. Bioinformatic predictions and functional studies showed that the mutation reduces the DNA binding affinity and disrupts transactivation ability of HOXA11. CONCLUSION In conclusion, this is the first report to describe a HOXA11 mutation in Chinese women with MDAs. The results demonstrated that mutation in HOXA11 can contribute to the etiology of MDAs, especially the septate uterus, but might not be a common cause.
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Affiliation(s)
- Ying Zhu
- Reproductive Medicine Center, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Zhi Cheng
- School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, People's Republic of China.,National Research Institute for Family Planning, Beijing, 100081, People's Republic of China
| | - Jing Wang
- National Research Institute for Family Planning, Beijing, 100081, People's Republic of China
| | - Beihong Liu
- National Research Institute for Family Planning, Beijing, 100081, People's Republic of China
| | - Longfei Cheng
- National Research Institute for Family Planning, Beijing, 100081, People's Republic of China
| | - Beili Chen
- Reproductive Medicine Center, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, People's Republic of China
| | - Yunxia Cao
- Reproductive Medicine Center, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, People's Republic of China.
| | - Binbin Wang
- National Research Institute for Family Planning, Beijing, 100081, People's Republic of China. .,Center for Genetics, National Research Institute for Family Planning, 12, Dahuisi Road, Haidian, Beijing, 100081, China.
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12
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Radhakrishnan P, Nayak SS, Pai MV, Shukla A, Girisha KM. Occurrence of Synpolydactyly and Omphalocele in a Fetus with a HOXD13 Mutation. J Pediatr Genet 2017; 6:194-197. [PMID: 28794915 DOI: 10.1055/s-0037-1602142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/12/2017] [Indexed: 10/19/2022]
Abstract
Synpolydactyly (SPD) is an autosomal dominant congenital limb disorder due to mutations in HOXD13 . It is a phenotypically heterogeneous condition characterized by syndactyly of the third finger (F3), fourth finger (F4) and/or fourth toe (T4), and fifth toe (T5) with variably associated polydactyly. We report on a mother and fetus with SPD. The mother has a novel mutation (c.708_708delC) in the HOXD13 gene that was also seen in the fetus. However, the fetus had congenital omphalocele in addition to SPD that is an association not reported to date. A chromosomal microarray in the fetus was normal. We report a novel mutation in HOXD13 and document co-occurrence of an omphalocele and SPD in a fetus.
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Affiliation(s)
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Muralidhar V Pai
- Department of Obstetrics and Gynecology, Kasturba Medical College, Manipal University, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
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13
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Wang B, Li N, Geng J, Wang Z, Fu Q, Wang J, Xu Y. Exome sequencing identifies a novel nonsense mutation of HOXD13 in a Chinese family with synpolydactyly. Congenit Anom (Kyoto) 2017; 57:4-7. [PMID: 27254532 DOI: 10.1111/cga.12173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/24/2016] [Accepted: 05/30/2016] [Indexed: 12/30/2022]
Abstract
Synpolydactyly (SPD) is an autosomal dominant limb malformation with a distinctive combination of syndactyly and polydactyly. SPD is clinically heterogeneous and could be genetically classified into three types. The clinical phenotype of SPD is complicated by its variable expressivity. In the present study, whole exome sequencing (WES) was used to identify the affected gene(s) in a Chinese family with atypical SPD phenotype. Our results showed that a novel heterogenous nonsense mutation (c.556C > T, p.R186X) in HOXD13 was associated with this SPD case. Due to variable expressivity, the diagnosis of a clinical heterogenous disease such as SPD is usually difficult. Our results also suggested that WES is an efficient tool to assist with these diagnoses.
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Affiliation(s)
- Bo Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Niu Li
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juan Geng
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhigang Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qihua Fu
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yunlan Xu
- Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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14
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Greyvenstein OFC, Reich CM, van Marle-Koster E, Riley DG, Hayes BJ. Polyceraty (multi-horns) in Damara sheep maps to ovine chromosome 2. Anim Genet 2016; 47:263-6. [PMID: 26767563 DOI: 10.1111/age.12411] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2015] [Indexed: 01/08/2023]
Abstract
Polyceraty (presence of multiple horns) is rare in modern day ungulates. Although not found in wild sheep, polyceraty does occur in a small number of domestic sheep breeds covering a wide geographical region. Damara are fat-tailed hair sheep, from the south-western region of Africa, which display polyceraty, with horn number ranging from zero to four. We conducted a genome-wide association study for horn number with 43 Damara genotyped with 606 006 SNP markers. The analysis revealed a region with multiple significant SNPs on ovine chromosome 2, in a location different from the mutation for polled in sheep on chromosome 10. The causal mutation for polyceraty was not identified; however, the region associated with polyceraty spans nine HOXD genes, which are critical in embryonic development of appendages. Mutations in HOXD genes are implicated in polydactly phenotypes in mice and humans. There was no evidence for epistatic interactions contributing to polyceraty. This is the first report on the genetic mechanisms underlying polyceraty in the under-studied Damara.
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Affiliation(s)
- O F C Greyvenstein
- Department of Animal Science, Texas A&M University, College Station, TX, 77843, USA
| | - C M Reich
- BioSciences Research Division, Department of Economic Developments, Jobs, Transport and Resources, 5 Ring Road, Bundoora, Vic., 3083, Australia
| | - E van Marle-Koster
- Department of Animal and Wildlife Science, University of Pretoria, Hatfield, 0028, South Africa
| | - D G Riley
- Department of Animal Science, Texas A&M University, College Station, TX, 77843, USA
| | - B J Hayes
- BioSciences Research Division, Department of Economic Developments, Jobs, Transport and Resources, 5 Ring Road, Bundoora, Vic., 3083, Australia.,La Trobe University, Bundoora, Vic., 3083, Australia
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15
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Ibrahim DM, Tayebi N, Knaus A, Stiege AC, Sahebzamani A, Hecht J, Mundlos S, Spielmann M. A homozygous HOXD13 missense mutation causes a severe form of synpolydactyly with metacarpal to carpal transformation. Am J Med Genet A 2015; 170:615-21. [PMID: 26581570 DOI: 10.1002/ajmg.a.37464] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 10/22/2015] [Indexed: 11/06/2022]
Abstract
Synpolydactyly (SPD) is a rare congenital limb disorder characterized by syndactyly between the third and fourth fingers and an additional digit in the syndactylous web. In most cases SPD is caused by heterozygous mutations in HOXD13 resulting in the expansion of a N-terminal polyalanine tract. If homozygous, the mutation results in severe shortening of all metacarpals and phalanges with a morphological transformation of metacarpals to carpals. Here, we describe a novel homozygous missense mutation in a family with unaffected consanguineous parents and severe brachydactyly and metacarpal-to-carpal transformation in the affected child. We performed whole exome sequencing on the index patient, followed by Sanger sequencing of parents and patient to investigate cosegregation. The DNA-binding ability of the mutant protein was tested with electrophoretic mobility shift assays. We demonstrate that the c.938C>G (p.313T>R) mutation in the DNA-binding domain of HOXD13 prevents binding to DNA in vitro. Our results show to our knowledge for the first time that a missense mutation in HOXD13 underlies severe brachydactyly with metacarpal-to-carpal transformation. The mutation is non-penetrant in heterozygous carriers. In conjunction with the literature we propose the possibility that the metacarpal-to-carpal transformation results from a homozygous loss of functional HOXD13 protein in humans in combination with an accumulation of non-functional HOXD13 that might be able to interact with other transcription factors in the developing limb.
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Affiliation(s)
- Daniel M Ibrahim
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Naeimeh Tayebi
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexej Knaus
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Asita C Stiege
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Jochen Hecht
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), Berlin, Germany.,Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Malte Spielmann
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), Berlin, Germany
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16
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Christiaens AB, Deprez PML, Amyere M, Mendola A, Bernard P, Gillerot Y, Clapuyt P, Godfraind C, Lengelé BG, Vikkula M, Nyssen-Behets C. Isolated bilateral transverse agenesis of the distal segments of the lower limbs at the level of the knee joint in a human fetus. Am J Med Genet A 2015; 170A:523-530. [PMID: 26544544 DOI: 10.1002/ajmg.a.37462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 10/15/2015] [Indexed: 11/12/2022]
Abstract
Congenital limb anomalies occur in Europe with a prevalence of 3.81/1,000 births and can have a major impact on patients and their families. The present study concerned a female fetus aborted at 23 weeks of gestation because she was affected by non-syndromic bilateral absence of the zeugopod (leg) and autopod (foot). Autopsy of the aborted fetus, X-ray imaging, MRI, and histochemical analysis showed that the distal extremity of both femurs was continued by a cartilage-like mass, without joint cavitation. Karyotype was normal. Moreover, no damaging variant was detected by exome sequencing. The limb characteristics of the fetus, which to our knowledge have not yet been reported in humans, suggest a developmental arrest similar to anomalies described in chicks following surgical experiments on the apical ectodermal ridge of the lower limbs.
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Affiliation(s)
- Antoine B Christiaens
- Pôle de Morphologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium.,Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Pierre M L Deprez
- Ecole de Kinésiologie et Récréologie, Faculté des Sciences de la Santé et Services Communautaires, Université de Moncton, Moncton, New Brunswick, Canada.,Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Mustapha Amyere
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Antonella Mendola
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Pierre Bernard
- Department of Obstetrics, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Yves Gillerot
- Centre for Human Genetics, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Philippe Clapuyt
- Department of Radiology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Catherine Godfraind
- Laboratory of Pathology, Cliniques Universitaires Saint-Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Benoît G Lengelé
- Pôle de Morphologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Catherine Nyssen-Behets
- Pôle de Morphologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
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17
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Abstract
Despite extensive efforts to identify a clinically useful diagnostic biomarker in prostate cancer, no new test has been approved by regulatory authorities. As a result, this unmet need has shifted to biomarkers that additionally indicate presence or absence of "significant" disease. EN2 is a homeodomain-containing transcription factor secreted by prostate cancer into the urine and can be detected by enzyme-linked immunoassay. EN2 may be an ideal biomarker because normal prostate tissue and benign prostatic hypertrophic cells do not secrete EN2. This review discusses the enormous potential of EN2 to address this unmet need and provide the urologist with a simple, inexpensive, and reliable prostate cancer biomarker.
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Affiliation(s)
- Sophie E McGrath
- Faculty of Health & Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Agnieszka Michael
- Faculty of Health & Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Richard Morgan
- Faculty of Health & Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Hardev Pandha
- Faculty of Health & Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom.
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18
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Kember RL, Georgi B, Bailey-Wilson JE, Stambolian D, Paul SM, Bućan M. Copy number variants encompassing Mendelian disease genes in a large multigenerational family segregating bipolar disorder. BMC Genet 2015; 16:27. [PMID: 25887117 PMCID: PMC4382929 DOI: 10.1186/s12863-015-0184-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/19/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Bipolar affective disorder (BP) is a common, highly heritable psychiatric disorder characterized by periods of depression and mania. Using dense SNP genotype data, we characterized CNVs in 388 members of an Old Order Amish Pedigree with bipolar disorder. We identified CNV regions arising from common ancestral mutations by utilizing the pedigree information. By combining this analysis with whole genome sequence data in the same individuals, we also explored the role of compound heterozygosity. RESULTS Here we describe 541 inherited CNV regions, of which 268 are rare in a control population of European origin but present in a large number of Amish individuals. In addition, we highlight a set of CNVs found at higher frequencies in BP individuals, and within genes known to play a role in human development and disease. As in prior reports, we find no evidence for an increased burden of CNVs in BP individuals, but we report a trend towards a higher burden of CNVs in known Mendelian disease loci in bipolar individuals (BPI and BPII, p = 0.06). CONCLUSIONS We conclude that CNVs may be contributing factors in the phenotypic presentation of mood disorders and co-morbid medical conditions in this family. These results reinforce the hypothesis of a complex genetic architecture underlying BP disorder, and suggest that the role of CNVs should continue to be investigated in BP data sets.
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Affiliation(s)
- Rachel L Kember
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Benjamin Georgi
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Joan E Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, USA.
| | - Dwight Stambolian
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Steven M Paul
- Appel Alzheimer's Disease Research Institute, Mind and Brain Institute, Weill Cornell Medical College, New York, NY, USA.
| | - Maja Bućan
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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19
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Dai L, Liu D, Song M, Xu X, Xiong G, Yang K, Zhang K, Meng H, Guo H, Bai Y. Mutations in the homeodomain of HOXD13 cause syndactyly type 1-c in two Chinese families. PLoS One 2014; 9:e96192. [PMID: 24789103 PMCID: PMC4006867 DOI: 10.1371/journal.pone.0096192] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 04/04/2014] [Indexed: 11/18/2022] Open
Abstract
Background Syndactyly type 1 (SD1) is an autosomal dominant limb malformation characterized in its classical form by complete or partial webbing between the third and fourth fingers and/or the second and third toes. Its four subtypes (a, b, c, and d) are defined based on variable phenotypes, but the responsible gene is yet to be identified. SD1-a has been mapped to chromosome 3p21.31 and SD1-b to 2q34–q36. SD1-c and SD1-d are very rare and, to our knowledge, no gene loci have been identified. Methods and Results In two Chinese families with SD1-c, linkage and haplotype analyses mapped the disease locus to 2q31-2q32. Copy number variation (CNV) analysis, using array-based comparative genomic hybridization (array CGH), excluded the possibility of microdeletion or microduplication. Sequence analyses of related syndactyly genes in this region identified c.917G>A (p.R306Q) in the homeodomain of HOXD13 in family A. Analysis on family B identified the mutation c.916C>G (p.R306G) and therefore confirmed the genetic homogeneity. Luciferase assays indicated that these two mutations affected the transcriptional activation ability of HOXD13. The spectrum of HOXD13 mutations suggested a close genotype-phenotype correlation between the different types of HOXD13-Syndactyly. Overlaps of the various phenotypes were found both among and within families carrying the HOXD13 mutation. Conclusions Mutations (p.R306Q and p.R306G) in the homeodomain of HOXD13 cause SD1-c. There are affinities between SD1-c and synpolydactyly. Different limb malformations due to distinct classes of HOXD13 mutations should be considered as a continuum of phenotypes and further classification of syndactyly should be done based on phenotype and genotype.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Dan Liu
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Min Song
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Xueqing Xu
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Gang Xiong
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Kang Yang
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Kun Zhang
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hui Meng
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
- * E-mail: (YB); (HG)
| | - Yun Bai
- Department of Thoracic and Cardiac Surgery, Southwest Hospital, Third Military Medical University, Chongqing, China
- * E-mail: (YB); (HG)
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20
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Homeotic gene regulation: a paradigm for epigenetic mechanisms underlying organismal development. Subcell Biochem 2014; 61:177-207. [PMID: 23150252 DOI: 10.1007/978-94-007-4525-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The organization of eukaryotic genome into chromatin within the nucleus eventually dictates the cell type specific expression pattern of genes. This higher order of chromatin organization is established during development and dynamically maintained throughout the life span. Developmental mechanisms are conserved in bilaterians and hence they have body plan in common, which is achieved by regulatory networks controlling cell type specific gene expression. Homeotic genes are conserved in metazoans and are crucial for animal development as they specify cell type identity along the anterior-posterior body axis. Hox genes are the best studied in the context of epigenetic regulation that has led to significant understanding of the organismal development. Epigenome specific regulation is brought about by conserved chromatin modulating factors like PcG/trxG proteins during development and differentiation. Here we discuss the conserved epigenetic mechanisms relevant to homeotic gene regulation in metazoans.
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21
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Abstract
The Hox genes are an evolutionarily conserved family of genes, which encode a class of important transcription factors that function in numerous developmental processes. Following their initial discovery, a substantial amount of information has been gained regarding the roles Hox genes play in various physiologic and pathologic processes. These processes range from a central role in anterior-posterior patterning of the developing embryo to roles in oncogenesis that are yet to be fully elucidated. In vertebrates there are a total of 39 Hox genes divided into 4 separate clusters. Of these, mutations in 10 Hox genes have been found to cause human disorders with significant variation in their inheritance patterns, penetrance, expressivity and mechanism of pathogenesis. This review aims to describe the various phenotypes caused by germline mutation in these 10 Hox genes that cause a human phenotype, with specific emphasis paid to the genotypic and phenotypic differences between allelic disorders. As clinical whole exome and genome sequencing is increasingly utilized in the future, we predict that additional Hox gene mutations will likely be identified to cause distinct human phenotypes. As the known human phenotypes closely resemble gene-specific murine models, we also review the homozygous loss-of-function mouse phenotypes for the 29 Hox genes without a known human disease. This review will aid clinicians in identifying and caring for patients affected with a known Hox gene disorder and help recognize the potential for novel mutations in patients with phenotypes informed by mouse knockout studies.
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Affiliation(s)
- Shane C Quinonez
- University of Michigan, Department of Pediatrics, Division of Pediatric Genetics, 1500 East Medical Center Drive, D5240 MPB/Box 5718, Ann Arbor, MI 48109-5718, USA.
| | - Jeffrey W Innis
- University of Michigan, Department of Pediatrics, Division of Pediatric Genetics, 1500 East Medical Center Drive, D5240 MPB/Box 5718, Ann Arbor, MI 48109-5718, USA; University of Michigan, Department of Human Genetics, 1241 E. Catherine, 4909 Buhl Building, Ann Arbor, MI 48109-5618, USA.
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22
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Shi X, Ji C, Cao L, Wu Y, Shang Y, Wang W, Luo Y. A splice donor site mutation in HOXD13 underlies synpolydactyly with cortical bone thinning. Gene 2013; 532:297-301. [PMID: 24055421 DOI: 10.1016/j.gene.2013.09.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 08/08/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022]
Abstract
Synpolydactyly 1(SPD1) is a dominantly inherited distal limb anomaly that is characterized by incomplete digit separation and increased number of digits. SPD1 is most commonly caused by polyalanine repeat expansions and mutations in the homeodomain of the HOXD13. We report a splice donor site mutation in HOXD13 associated in most cases with cortical bone thinning. In vitro study of transcripts and truncated protein analysis indicated that c.781+1G>A mutation results in truncated HOXD13 protein p.G190fsX4. Luciferase assay indicated that the truncated HOXD13 protein failed to bind to DNA. The mechanism for this phenotype was truncated protein loss of function.
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Affiliation(s)
- Xiuyan Shi
- The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
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23
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Brison N, Debeer P, Tylzanowski P. Joining the fingers: AHOXD13story. Dev Dyn 2013; 243:37-48. [DOI: 10.1002/dvdy.24037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 12/21/2022] Open
Affiliation(s)
- Nathalie Brison
- Center for Human Genetics; University Hospitals Leuven, University of Leuven; Belgium
| | - Philippe Debeer
- Department of Development and Regeneration; University of Leuven; Belgium
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Zhou X, Zheng C, He B, Zhu Z, Li P, He X, Zhu S, Yang C, Lao Z, Zhu Q, Liu X. A novel mutation outside homeodomain of HOXD13 causes synpolydactyly in a Chinese family. Bone 2013; 57:237-41. [PMID: 23948678 DOI: 10.1016/j.bone.2013.07.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 07/05/2013] [Accepted: 07/31/2013] [Indexed: 10/26/2022]
Abstract
INTRODUCTION Human synpolydactyly (SPD), belonging to syndactyly (SD) II, is caused by mutations in homeobox d13 (HOXD13). Here, we describe the study of a two-generation Chinese family with a variant form of synpolydactyly. MATERIALS AND METHODS The sequence of the HOXD13 gene was analyzed. Luciferase assays were conducted to determine whether the mutation affected the function of the HOXD13 protein. RESULTS We identified a novel c.659G>C (p.Gly220Ala) mutation outside the HOXD13 homeodomain responsible for the disease in this family. This mutation was not found in any of the unaffected family members and healthy control. Luciferase assays demonstrated that this mutation affected the transcriptional activation ability of HOXD13 (only approximately 84.7% of wild type, p<0.05). CONCLUSION Phenotypes displayed by individuals carrying the novel mutation present additional features, such as the fifth finger clinodactyly, which is not always associated with canonical SPD. This finding enhances our understanding about the phenotypic spectrum associated with HOXD13 mutations and advances our understanding of human limb development.
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Affiliation(s)
- Xiang Zhou
- Department of Microsurgery and Orthopedic Trauma, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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McGrath SE, Michael A, Pandha H, Morgan R. Engrailed homeobox transcription factors as potential markers and targets in cancer. FEBS Lett 2013; 587:549-54. [DOI: 10.1016/j.febslet.2013.01.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 01/10/2023]
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Illig R, Fritsch H, Schwarzer C. Spatio-temporal expression ofHOXgenes in human hindgut development. Dev Dyn 2012; 242:53-66. [DOI: 10.1002/dvdy.23893] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2012] [Indexed: 01/06/2023] Open
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A novel non-synonymous mutation in the homeodomain of HOXD13 causes synpolydactyly in a Chinese family. Clin Chim Acta 2012; 413:1049-52. [DOI: 10.1016/j.cca.2012.02.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 02/16/2012] [Accepted: 02/16/2012] [Indexed: 11/21/2022]
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Xin Q, Li L, Li J, Qiu R, Guo C, Gong Y, Liu Q. Eight-alanine duplication in homeobox D13 in a Chinese family with synpolydactyly. Gene 2012; 499:48-51. [PMID: 22406499 DOI: 10.1016/j.gene.2012.02.046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 02/15/2012] [Accepted: 02/21/2012] [Indexed: 11/30/2022]
Abstract
Human synpolydactyly (SPD), belonging to syndactyly (SD) II, is an inherited autosomal-dominant limb malformation characterized by SD of finger 3 or 4 or toe 4 or 5, usually with digit duplication. Previous studies have demonstrated that homeobox protein D13 (HOXD13) is responsible for this Mendelian disorder. In this paper, we report on a family with SPD - 7 members show typical SPD malformations. We used PCR and Sanger sequencing of DNA from peripheral blood samples and found an 8-Ala expansion in exon 1 of HOXD13 by mutation detection; this variant was absent in unaffected members and in 50 unaffected non-related subjects. This study further confirmed the correlation between SPD and alanine expansion in HOXD13.
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Affiliation(s)
- Qian Xin
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, Shandong University School of Medicine, Jinan 250012, PR China
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Jamsheer A, Sowińska A, Kaczmarek L, Latos-Bieleńska A. Isolated brachydactyly type E caused by a HOXD13 nonsense mutation: a case report. BMC MEDICAL GENETICS 2012; 13:4. [PMID: 22233338 PMCID: PMC3278352 DOI: 10.1186/1471-2350-13-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 01/10/2012] [Indexed: 11/10/2022]
Abstract
Background Brachydactyly type E (BDE; MIM#113300) is characterized by shortening of the metacarpal, metatarsal, and often phalangeal bones, and predominantly affects postaxial ray(s) of the limb. BDE may occur as an isolated trait or as part of a syndrome. Isolated BDE is rare and in the majority of cases the molecular pathogenesis has so far not been resolved. Originally, the molecular cause of isolated BDE has been unravelled in 2 families and shown to result from heterozygous missense mutations in the homeodomain of the HOXD13 gene. Since the initial manuscript, one further HOXD13 mutation has been reported only in a single family manifesting isolated BDE. Case Presentation In this paper, we report on a Polish family exhibiting isolated BDE caused by a novel nonsense heterozygous HOXD13 mutation. We investigated a Polish female proband and her father, both affected by isolated BDE, in whom we identified a nonsense heterozygous mutation c.820C > T(p.R274X) in the HOXD13 gene. So far, only two missense HOXD13 substitutions (p.S308C and p.I314L), localized within the homeodomain of the HOXD13 transcription factor, as well as a single nonsense mutation (p.E181X) were associated with BDE. Both missense changes were supposed to alter DNA binding affinity of the protein. Conclusion The variant p.R274X identified in our proband is the fourth HOXD13 mutation, and the second truncating (nonsense) mutation, reported to result in typical isolated BDE. We refer our clinical and molecular findings to the previously described HOXD13 associated phenotypes and mutations.
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Affiliation(s)
- Aleksander Jamsheer
- Department of Medical Genetics, University of Medical Sciences in Poznan, Poland, ul. Grunwaldzka 55 paw. 15, 60-352 Poznan, Poland.
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Limb skeletal malformations – What the HOX is going on? Eur J Med Genet 2012; 55:1-7. [DOI: 10.1016/j.ejmg.2011.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 06/10/2011] [Indexed: 11/21/2022]
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Abstract
Synpolydactyly 1 (SPD1; OMIM 186000), also known as type II syndactyly, is a dominantly inherited limb malformation that is characterized by an increased number of digits. SPD1 is most commonly caused by polyalanine repeat expansions in the coding region of the HOXD13 gene, which are believed to show a dominant-negative effect. In addition, missense and out-of-frame deletion mutations in the HOXD13 gene are also known to cause SPD, and the mechanism responsible for the phenotype appears to be haploinsufficiency. Here, we analyzed a large consanguineous family from Pakistan with SPD showing a wide variation in phenotype among affected individuals. We performed genetic linkage analysis, which identified a region on chromosome 2 containing the HOXD13 gene. Haplotype analysis with microsatellite markers suggested segregation of the phenotype with HOXD13 gene with incomplete penetrance. Direct sequencing analysis of HOXD13 gene revealed a nonsense mutation, designated Q248X. All affected individuals with the severe SPD phenotype are homozygous for the mutation, while those with the mild SPD phenotype are heterozygous for the mutation. Furthermore, some unaffected individuals also carry the mutation in the heterozygous state, showing incomplete penetrance. Our results demonstrate the first nonsense mutation in the HOXD13 gene underlying a severe form of SPD in the homozygous state, and a milder form of SPD with approximately 50% penetrance in the heterozygous state, most likely due to the production of 50% of protein compared to normal individuals..
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Theisen A, Rosenfeld JA, Shane K, McBride KL, Atkin JF, Gaba C, Hoo J, Kurczynski TW, Schnur RE, Coffey LB, Zackai EH, Schimmenti L, Friedman N, Zabukovec M, Ball S, Pagon R, Lucas A, Brasington CK, Spence JE, Sparks S, Banks V, Smith W, Friedberg T, Wyatt PR, Aust M, Tervo R, Crowley A, Skidmore D, Lamb AN, Ravnan B, Sahoo T, Schultz R, Torchia BS, Sgro M, Chitayat D, Shaffer LG. Refinement of the Region for Split Hand/Foot Malformation 5 on 2q31.1. Mol Syndromol 2011; 1:262-271. [PMID: 22140379 DOI: 10.1159/000328405] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2011] [Indexed: 12/23/2022] Open
Abstract
Background: Deletions that encompass 2q31.1 have been proposed as a microdeletion syndrome with common clinical features, including intellectual disability/developmental delay, microcephaly, cleft palate, growth delay, and hand/foot anomalies. In addition, several genes within this region have been proposed as candidates for split hand-foot malformation 5 (SHFM5). Methods: To delineate the genotype-phenotype correlation between deletions of this region, we identified 14 individuals with deletions at 2q31.1 detected by microarray analysis for physical and developmental disabilities. Results: All subjects for whom detailed clinical records were available had neurological deficits of varying degree. Seven subjects with deletions encompassing the HOXD cluster had hand/foot anomalies of varying severity, including syndactyly, brachydactyly, and ectrodactyly. Of 7 subjects with deletions proximal to the HOXD cluster, 5 of which encompassed DLX1/DLX2, none had clinically significant hand/foot anomalies. In contrast to previous reports, the individuals in our study did not display a characteristic gestalt of dysmorphic facial features. Conclusion: The absence of hand/foot anomalies in any of the individuals with deletions of DLX1/DLX2 but not the HOXD cluster supports the hypothesis that haploinsufficiency of the HOXD cluster, rather than DLX1/DLX2, accounts for the skeletal abnormalities in subjects with 2q31.1 microdeletions.
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Affiliation(s)
- A Theisen
- Signature Genomic Laboratories, Spokane, Wash
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Jun KR, Seo EJ, Lee JO, Yoo HW, Park IS, Yoon HK. Molecular cytogenetic and clinical characterization of a patient with a 5.6-Mb deletion in 7p15 including HOXA cluster. Am J Med Genet A 2011; 155A:642-7. [DOI: 10.1002/ajmg.a.33860] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Accepted: 11/29/2010] [Indexed: 11/06/2022]
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Fork stalling and template switching as a mechanism for polyalanine tract expansion affecting the DYC mutant of HOXD13, a new murine model of synpolydactyly. Genetics 2009; 183:23-30. [PMID: 19546318 DOI: 10.1534/genetics.109.104695] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyalanine expansion diseases are proposed to result from unequal crossover of sister chromatids that increases the number of repeats. In this report we suggest an alternative mechanism we put forward while we investigated a new spontaneous mutant that we named "Dyc" for "Digit in Y and Carpe" phenotype. Phenotypic analysis revealed an abnormal limb patterning similar to that of the human inherited congenital disease synpolydactyly (SPD) and to the mouse mutant model Spdh. Both human SPD and mouse Spdh mutations affect the Hoxd13 gene within a 15-residue polyalanine-encoding repeat in the first exon of the gene, leading to a dominant negative HOXD13. Genetic analysis of the Dyc mutant revealed a trinucleotide expansion in the polyalanine-encoding region of the Hoxd13 gene resulting in a 7-alanine expansion. However, unlike the Spdh mutation, this expansion cannot result from a simple duplication of a short segment. Instead, we propose the fork stalling and template switching (FosTeS) described for generation of nonrecurrent genomic rearrangements as a possible mechanism for the Dyc polyalanine extension, as well as for other polyalanine expansions described in the literature and that could not be explained by unequal crossing over.
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Tsai LP, Liao HM, Chen YJ, Fang JS, Chen CH. A novel microdeletion at chromosome 2q31.1-31.2 in a three-generation family presenting duplication of great toes with clinodactyly. Clin Genet 2009; 75:449-56. [DOI: 10.1111/j.1399-0004.2008.01147.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Malik S, Girisha KM, Wajid M, Roy AK, Phadke SR, Haque S, Ahmad W, Koch MC, Grzeschik KH. Synpolydactyly and HOXD13 polyalanine repeat: addition of 2 alanine residues is without clinical consequences. BMC MEDICAL GENETICS 2007; 8:78. [PMID: 18072967 PMCID: PMC2222244 DOI: 10.1186/1471-2350-8-78] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2007] [Accepted: 12/11/2007] [Indexed: 11/24/2022]
Abstract
BACKGROUND Type II syndactyly or synpolydactyly (SPD) is clinically very heterogeneous, and genetically three distinct SPD conditions are known and have been designated as SPD1, SPD2 and SPD3, respectively. SPD1 type is associated with expansion mutations in HOXD13, resulting in an addition of > or = 7 alanine residues to the polyalanine repeat. It has been suggested that expansions < or = 6 alanine residues go without medical attention, as no such expansion has ever been reported with the SPD1 phenotype. METHODS We describe a large Pakistani and an Indian family with SPD. We perform detailed clinical and molecular analyses to identify the genetic basis of this malformation. RESULTS We have identified four distinct clinical categories for the SPD1 phenotype observed in the affected subjects in both families. Next, we show that a milder foot phenotype, previously described as a separate entity, is in fact a part of the SPD1 phenotypic spectrum. Then, we demonstrate that the phenotype in both families segregates with an identical expansion mutation of 21 bp in HOXD13. Finally, we show that the HOXD13 polyalanine repeat is polymorphic, and the expansion of 2 alanine residues, evident in unaffected subjects of both families, is without clinical consequences. CONCLUSION It is the first molecular evidence supporting the hypothesis that expansion of < or = 6 alanine residues in the HOXD13 polyalanine repeat is not associated with the SPD1 phenotype.
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Affiliation(s)
- Sajid Malik
- Zentrum für Humangenetik, Philipps-Universität Marburg, Bahnhofstr. 7, 35037 Marburg, Germany
- Department of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - KM Girisha
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow-226014, Uttar Pradesh, India
| | - Muhammad Wajid
- Department of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - Akhilesh K Roy
- Division of Pediatric Surgery, Department of Surgery, Era's Lucknow Medical College, Hardoi Road, Sarfarazganj, Lucknow-226003, Uttar Pradesh, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow-226014, Uttar Pradesh, India
| | - Sayedul Haque
- Department of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biological Sciences, Quaid-I-Azam University, 45320 Islamabad, Pakistan
| | - Manuela C Koch
- Zentrum für Humangenetik, Philipps-Universität Marburg, Bahnhofstr. 7, 35037 Marburg, Germany
| | - Karl-Heinz Grzeschik
- Zentrum für Humangenetik, Philipps-Universität Marburg, Bahnhofstr. 7, 35037 Marburg, Germany
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Malik S, Abbasi AA, Ansar M, Ahmad W, Koch MC, Grzeschik KH. Genetic heterogeneity of synpolydactyly: a novel locus SPD3 maps to chromosome 14q11.2-q12. Clin Genet 2007; 69:518-24. [PMID: 16712704 DOI: 10.1111/j.1399-0004.2006.00620.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Syndactyly type II or synpolydactyly (SPD) is the second most frequent syndactyly type and is inherited in an autosomal dominant fashion. The cardinal features of this malformation are the cutaneous or bony fusion of third and fourth fingers, and fourth and fifth toes associated with additional digital elements within the web. It shows incomplete penetrance and high inter- and intrafamilial phenotypic variability. Two loci are known for SPD (MIM 186000, MIM 608180) associated with mutations in HOXD13 and FBLN1, respectively. Here, we report further genetic heterogeneity for SDP. Employing a whole genomic screen, we demonstrate, in a large Pakistani kindred, that the classical phenotype of SPD maps on a new locus at chromosome 14q11.2-q12. The highest LOD score (Z(max) = 4.06) was obtained with microsatellite marker D14S264, and the multipoint LOD score reached a maximum of 5.01. Haplotype analysis revealed that the disease interval is flanked by microsatellite markers D14S283 and D14S1060, encompassing a physical distance of 10.72 Mb. We propose to allocate to this locus the symbol SPD3 (synpolydactyly 3), and to name the loci associated with HOXD13 or FBLN1 mutations SPD1 and SPD2, respectively.
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Affiliation(s)
- S Malik
- Zentrum für Humangenetik, Philipps-Universität Marburg, Germany
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Luo T, Yu W, Yuan Z, Deng Y, Zhao Y, Yuan W, Xiao J, Wang Y, Luo N, Mo X, Li Y, Liu M, Wu X. A novel mutation of p63 in a Chinese family with inherited syndactyly and adactylism. Mutat Res 2007; 637:182-9. [PMID: 17915261 DOI: 10.1016/j.mrfmmm.2007.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 07/19/2007] [Accepted: 08/15/2007] [Indexed: 12/13/2022]
Abstract
p63 is a transcription factor homologous to p53 and p73; mutations in this gene have been identified in individuals with several types of developmental abnormalities, including EEC (ectrodactyly, ectodermal dysplasia, facial clefts) syndrome and split-hand/split-foot malformation (SHFM). Several mutations in the p63 gene have previously been shown to be related to SHFM. In this study, we report on a Chinese family with intrafamilial clinical variability of SHFM that have a novel heterozygous mutation in all four affected individuals. The mutation is in exon 8 of p63, 1046G --> A, which predicts an amino acid substitution G310E. SSCP analysis of the segregation pattern of the mutation strongly suggests a causal relationship to the SHFM phenotype in p63. This mutation has not been observed in other countries in the world.
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Affiliation(s)
- Tongxiu Luo
- The Center For Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, PR China
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Yue Y, Farcas R, Thiel G, Bommer C, Grossmann B, Galetzka D, Kelbova C, Küpferling P, Daser A, Zechner U, Haaf T. De novo t(12;17)(p13.3;q21.3) translocation with a breakpoint near the 5′ end of the HOXB gene cluster in a patient with developmental delay and skeletal malformations. Eur J Hum Genet 2007; 15:570-7. [PMID: 17327879 DOI: 10.1038/sj.ejhg.5201795] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A boy with severe mental retardation, funnel chest, bell-shaped thorax, and hexadactyly of both feet was found to have a balanced de novo t(12;17)(p13.3;q21.3) translocation. FISH with BAC clones and long-range PCR products assessed in the human genome sequence localized the breakpoint on chromosome 17q21.3 to a 21-kb segment that lies <30 kb upstream of the HOXB gene cluster and immediately adjacent to the 3' end of the TTLL6 gene. The breakpoint on chromosome 12 occurred within telomeric hexamer repeats and, therefore, is not likely to affect gene function directly. We propose that juxtaposition of the HOXB cluster to a repetitive DNA domain and/or separation from required cis-regulatory elements gave rise to a position effect.
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Affiliation(s)
- Ying Yue
- Institute for Human Genetics, Johannes Gutenberg University Mainz, Mainz, Germany
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Zhao X, Sun M, Zhao J, Leyva JA, Zhu H, Yang W, Zeng X, Ao Y, Liu Q, Liu G, Lo WHY, Jabs EW, Amzel LM, Shan X, Zhang X. Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. Am J Hum Genet 2007; 80:361-71. [PMID: 17236141 PMCID: PMC1785357 DOI: 10.1086/511387] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 11/22/2006] [Indexed: 11/03/2022] Open
Abstract
HOXD13, the homeobox-containing gene located at the most 5' end of the HOXD cluster, plays a critical role in limb development. It has been shown that mutations in human HOXD13 can give rise to limb malformations, with variable expressivity and a wide spectrum of clinical manifestations. Polyalanine expansions in HOXD13 cause synpolydactyly, whereas amino acid substitutions in the homeodomain are associated with brachydactyly types D and E. We describe two large Han Chinese families with different limb malformations, one with syndactyly type V and the other with limb features overlapping brachydactyly types A4, D, and E and mild syndactyly of toes 2 and 3. Two-point linkage analysis showed LOD scores >3 (theta =0) for markers within and/or flanking the HOXD13 locus in both families. In the family with syndactyly type V, we identified a missense mutation in the HOXD13 homeodomain, c.950A-->G (p.Q317R), which leads to substitution of the highly conserved glutamine that is important for DNA-binding specificity and affinity. In the family with complex brachydactyly and syndactyly, we detected a deletion of 21 bp in the imperfect GCN (where N denotes A, C, G, or T) triplet-containing exon 1 of HOXD13, which results in a polyalanine contraction of seven residues. Moreover, we found that the mutant HOXD13 with the p.Q317R substitution was unable to transactivate the human EPHA7 promoter. Molecular modeling data supported these experimental results. The calculated interactions energies were in agreement with the measured changes of the activity. Our data established the link between HOXD13 and two additional limb phenotypes--syndactyly type V and brachydactyly type A4--and demonstrated that a polyalanine contraction in HOXD13, most likely, led to other digital anomalies but not to synpolydactyly. We suggest the term "HOXD13 limb morphopathies" for the spectrum of limb disorders caused by HOXD13 mutations.
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Affiliation(s)
- Xiuli Zhao
- Department of Medical Genetics and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing China
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Horsnell K, Ali M, Malik S, Wilson L, Hall C, Debeer P, Crow Y. Clinical phenotype associated with homozygosity for a HOXD13 7-residue polyalanine tract expansion. Eur J Med Genet 2006; 49:396-401. [PMID: 16497573 DOI: 10.1016/j.ejmg.2006.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Revised: 01/11/2006] [Accepted: 01/11/2006] [Indexed: 11/29/2022]
Abstract
Synpolydactyly (SPD) is an autosomal dominant malformation of the distal limbs caused by mutations in the homeobox gene HOXD13 located on chromosome 2q31. We detail the clinical findings in a consanguineous Pakistani family segregating a HOXD13 7-residue polyalanine tract expansion. Three members of this pedigree were heterozygotes with features typical of SPD. Two further members demonstrate a more severe phenotype consistent with homozygosity for the familial mutation. We also report a child from a consanguineous Somali family homozygous for the same molecular lesion. Characteristic changes include a complex central polydactyly in the hands, abnormal modelling of the metacarpals and metatarsals, an increased number of carpal bones with abnormal shapes, hypoplasia or absence of the fifth digital rays in the feet, hypoplasia of the middle phalanges and abnormally long proximal phalanges in hands and feet. These cases illustrate the distinct phenotype associated with homozygosity for a HOXD13 mutation and also highlight the importance of considering homozygosity for a dominant mutation in consanguineous pedigrees.
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Verdyck P, Blaumeiser B, Holder-Espinasse M, Van Hul W, Wuyts W. Adams-Oliver syndrome: clinical description of a four-generation family and exclusion of five candidate genes. Clin Genet 2006; 69:86-92. [PMID: 16451141 DOI: 10.1111/j.1399-0004.2006.00552.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a Belgian Adams-Oliver syndrome (AOS) family with 10 affected individuals over four generations, of which six were available for this study. Clinical symptoms observed in these patients were very variable as previously reported in other families and included large areas of alopecia on the vertex of the skull and serious limb reduction defects with agenesis of all toes of one foot. To identify the disease-causing gene, we sequenced the MSX1, CART1, P63 (P73L), RUNX2, and HOXD13 genes in this family and nine previously reported families, but no disease-causing mutations were found. Further investigation is ongoing in these families in order to identify the genetic cause of AOS.
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Affiliation(s)
- P Verdyck
- Department of Medical Genetics, University and University Hospital of Antwerp, Antwerp, Belgium
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Holder-Espinasse M, Herbaux B, Mezel A, Lacombe D, Devisme L, Boute-Bénéjean O, Dieux-Coeslier A, Escande F, Manouvrier-Hanu S. Société Française d’Orthopédie Pédiatrique. ACTA ACUST UNITED AC 2006; 92:83-94. [PMID: 16609623 DOI: 10.1016/s0035-1040(06)75680-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Limb malformations are frequent. These malformations are isolated or associated with anomalies of other developmental fields and accurate diagnostic is essential for prognosis evaluation, treatment and genetic counseling. Animal embryology and molecular biology techniques, have given us a better understanding of the processes of growth and patterning of the limb buds. The key genes that are involved in these processes have been identified and their interactions recognized. Human genetics has been able to identify, or at least localize, several genes implicated in limb development. We here review the present knowledge on these genes and their mutations responsible for limb anomalies.
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Affiliation(s)
- M Holder-Espinasse
- Service de Génétique Clinique Guy-Fontaine, Hôpital Jeanne-de-Flandre, avenue Eugène-Avinée, CHRU de Lille, 59037 Lille Cedex
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Abstract
The rapid generation of new shapes observed in the living world is the result of genetic variation, especially in "morphological" developmental genes. Many of these genes contain coding tandem repeats. Fondon and Garner have shown that expansions and contractions of these repeats are associated with the great diversity of morphologies observed in the domestic dog, Canis familiaris. In particular, they found that the repeat variations in two genes were significantly associated with changes in limb and skull morphology. These results open the possibility that such a mechanism contributes to the diversity of life.
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Dlugaszewska B, Silahtaroglu A, Menzel C, Kübart S, Cohen M, Mundlos S, Tümer Z, Kjaer K, Friedrich U, Ropers HH, Tommerup N, Neitzel H, Kalscheuer VM. Breakpoints around the HOXD cluster result in various limb malformations. J Med Genet 2005; 43:111-8. [PMID: 15980115 PMCID: PMC2564623 DOI: 10.1136/jmg.2005.033555] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Characterisation of disease associated balanced chromosome rearrangements is a promising starting point in the search for candidate genes and regulatory elements. METHODS We have identified and investigated three patients with limb abnormalities and breakpoints involving chromosome 2q31. Patient 1 with severe brachydactyly and syndactyly, mental retardation, hypoplasia of the cerebellum, scoliosis, and ectopic anus, carries a balanced t(2;10)(q31.1;q26.3) translocation. Patient 2, with translocation t(2;10)(q31.1;q23.33), has aplasia of the ulna, shortening of the radius, finger anomalies, and scoliosis. Patient 3 carries a pericentric inversion of chromosome 2, inv(2)(p15q31). Her phenotype is characterised by bilateral aplasia of the fibula and the radius, bilateral hypoplasia of the ulna, unossified carpal bones, and hypoplasia and dislocation of both tibiae. RESULTS By fluorescence in situ hybridisation, we have mapped the breakpoints to intervals of approximately 170 kb or less. None of the three 2q31 breakpoints, which all mapped close to the HOXD cluster, disrupted any known genes. CONCLUSIONS Hoxd gene expression in the mouse is regulated by cis-acting DNA elements acting over distances of several hundred kilobases. Moreover, Hoxd genes play an established role in bone development. It is therefore very likely that the three rearrangements disturb normal HOXD gene regulation by position effects.
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Affiliation(s)
- B Dlugaszewska
- Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany
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García-Ortiz JE, Banda-Espinoza F, Zenteno JC, Galván-Uriarte LM, Ruiz-Flores P, García-Cruz D. Split hand malformation, hypospadias, microphthalmia, distinctive face and short stature in two brothers suggest a new syndrome. Am J Med Genet A 2005; 135:21-7. [PMID: 15809993 DOI: 10.1002/ajmg.a.30696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Split hand/foot malformation (SHFM) is a genetically heterogeneous limb malformation that may be isolated or associated with other malformations. More than 50 recognizable entities with SHFM have been described and at least 5 mapped genetic loci have been implicated. Two brothers with intrauterine growth retardation, short stature, distinctive face, microphthalmia, genital anomalies, and SHFM are described. Molecular analyses of TP63, HOXA13, and HOXD13 genes were normal. We propose this pattern to be a newly recognized SHFM syndrome.
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Affiliation(s)
- Jose E García-Ortiz
- Departamento de Inmunobiología Molecular, CIB, Facultad de Medicina Universidad Autónoma de Coahuila, Torreón, Coahuila, México.
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Grier DG, Thompson A, Kwasniewska A, McGonigle GJ, Halliday HL, Lappin TR. The pathophysiology of HOX genes and their role in cancer. J Pathol 2005; 205:154-71. [PMID: 15643670 DOI: 10.1002/path.1710] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The HOM-C clustered prototype homeobox genes of Drosophila, and their counterparts, the HOX genes in humans, are highly conserved at the genomic level. These master regulators of development continue to be expressed throughout adulthood in various tissues and organs. The physiological and patho-physiological functions of this network of genes are being avidly pursued within the scientific community, but defined roles for them remain elusive. The order of expression of HOX genes within a cluster is co-ordinated during development, so that the 3' genes are expressed more anteriorly and earlier than the 5' genes. Mutations in HOXA13 and HOXD13 are associated with disorders of limb formation such as hand-foot-genital syndrome (HFGS), synpolydactyly (SPD), and brachydactyly. Haematopoietic progenitors express HOX genes in a pattern characteristic of the lineage and stage of differentiation of the cells. In leukaemia, dysregulated HOX gene expression can occur due to chromosomal translocations involving upstream regulators such as the MLL gene, or the fusion of a HOX gene to another gene such as the nucleoporin, NUP98. Recent investigations of HOX gene expression in leukaemia are providing important insights into disease classification and prediction of clinical outcome. Whereas the oncogenic potential of certain HOX genes in leukaemia has already been defined, their role in other neoplasms is currently being studied. Progress has been hampered by the experimental approach used in many studies in which the expression of small subsets of HOX genes was analysed, and complicated by the functional redundancy implicit in the HOX gene system. Attempts to elucidate the function of HOX genes in malignant transformation will be enhanced by a better understanding of their upstream regulators and downstream target genes.
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Affiliation(s)
- D G Grier
- Department of Child Health, Queen's University, Belfast, Grosvenor Road, Belfast BT12 6BA, UK
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Abstract
Drosophila melanogaster is emerging as one of the most effective tools for analyzing the function of human disease genes, including those responsible for developmental and neurological disorders, cancer, cardiovascular disease, metabolic and storage diseases, and genes required for the function of the visual, auditory and immune systems. Flies have several experimental advantages, including their rapid life cycle and the large numbers of individuals that can be generated, which make them ideal for sophisticated genetic screens, and in future should aid the analysis of complex multigenic disorders. The general principles by which D. melanogaster can be used to understand human disease, together with several specific examples, are considered in this review.
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Affiliation(s)
- Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92039, USA.
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Affiliation(s)
- Dian Donnai
- Academic Unit of Medical Genetics and Regional Genetics Service, St. Mary's Hospital, Manchester, United Kingdom.
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