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Cova G, Glaser J, Schöpflin R, Prada-Medina CA, Ali S, Franke M, Falcone R, Federer M, Ponzi E, Ficarella R, Novara F, Wittler L, Timmermann B, Gentile M, Zuffardi O, Spielmann M, Mundlos S. Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve split-hand/foot malformation type 3. Nat Commun 2023; 14:1475. [PMID: 36928426 PMCID: PMC10020157 DOI: 10.1038/s41467-023-37057-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 03/01/2023] [Indexed: 03/18/2023] Open
Abstract
Split-Hand/Foot Malformation type 3 (SHFM3) is a congenital limb malformation associated with tandem duplications at the LBX1/FGF8 locus. Yet, the disease patho-mechanism remains unsolved. Here we investigate the functional consequences of SHFM3-associated rearrangements on chromatin conformation and gene expression in vivo in transgenic mice. We show that the Lbx1/Fgf8 locus consists of two separate, but interacting, regulatory domains. Re-engineering of a SHFM3-associated duplication and a newly reported inversion in mice results in restructuring of the chromatin architecture. This leads to ectopic activation of the Lbx1 and Btrc genes in the apical ectodermal ridge (AER) in an Fgf8-like pattern induced by AER-specific enhancers of Fgf8. We provide evidence that the SHFM3 phenotype is the result of a combinatorial effect on gene misexpression in the developing limb. Our results reveal insights into the molecular mechanism underlying SHFM3 and provide conceptual framework for how genomic rearrangements can cause gene misexpression and disease.
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Affiliation(s)
- Giulia Cova
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany.
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
- Department of Pathology, New York University School of Medicine, Langone Health Medical Center, New York, NY, 10016, USA.
| | - Juliane Glaser
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
| | - Robert Schöpflin
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Cesar Augusto Prada-Medina
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Salaheddine Ali
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Martin Franke
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, 41013, Spain
| | - Rita Falcone
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
| | - Miriam Federer
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany
- Universität Innsbruck, Innsbruck, 6020, Austria
| | - Emanuela Ponzi
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | - Romina Ficarella
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | | | - Lars Wittler
- Department of Developmental Genetics, Transgenic Unit, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Mattia Gentile
- Medical Genetics Unit, Department of Reproductive Medicine, ASL Bari, Bari, 70131, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, 27100, Italy
| | - Malte Spielmann
- Institute of Human Genetics, Universitätsklinikum Schleswig Holstein Campus Kiel and Christian-Albrechts-Universität, Kiel, 24118, Germany
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- Human Molecular Genomics Group, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany.
- Institute of Medical and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin Berlin, Berlin, 13353, Germany.
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Elliott AM, Scott WJ, Chudley AE, Reed MH, Evans JA. Classifications of split hand foot malformation (SHFM) should include transverse deficiencies: Why Maisels was correct. Am J Med Genet A 2021; 185:2809-2814. [PMID: 33955662 DOI: 10.1002/ajmg.a.62242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/02/2021] [Accepted: 04/03/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Alison M Elliott
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,BC Children's Research Institute, Vancouver, British Columbia, Canada
| | - William J Scott
- Division of Developmental Biology, University of Cincinnati, Cincinnati, Ohio, USA
| | - Albert E Chudley
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Martin H Reed
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Radiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Jane A Evans
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
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Holder-Espinasse M, Jamsheer A, Escande F, Andrieux J, Petit F, Sowinska-Seidler A, Socha M, Jakubiuk-Tomaszuk A, Gerard M, Mathieu-Dramard M, Cormier-Daire V, Verloes A, Toutain A, Plessis G, Jonveaux P, Baumann C, David A, Farra C, Colin E, Jacquemont S, Rossi A, Mansour S, Ghali N, Moncla A, Lahiri N, Hurst J, Pollina E, Patch C, Ahn JW, Valat AS, Mezel A, Bourgeot P, Zhang D, Manouvrier-Hanu S. Duplication of 10q24 locus: broadening the clinical and radiological spectrum. Eur J Hum Genet 2019; 27:525-534. [PMID: 30622331 PMCID: PMC6460637 DOI: 10.1038/s41431-018-0326-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/25/2017] [Accepted: 12/04/2018] [Indexed: 01/21/2023] Open
Abstract
Split-hand-split-foot malformation (SHFM) is a rare condition that occurs in 1 in 8500-25,000 newborns and accounts for 15% of all limb reduction defects. SHFM is heterogeneous and can be isolated, associated with other malformations, or syndromic. The mode of inheritance is mostly autosomal dominant with incomplete penetrance, but can be X-linked or autosomal recessive. Seven loci are currently known: SHFM1 at 7q21.2q22.1 (DLX5 gene), SHFM2 at Xq26, SHFM3 at 10q24q25, SHFM4 at 3q27 (TP63 gene), SHFM5 at 2q31 and SHFM6 as a result of variants in WNT10B (chromosome 12q13). Duplications at 17p13.3 are seen in SHFM when isolated or associated with long bone deficiency. Tandem genomic duplications at chromosome 10q24 involving at least the DACTYLIN gene are associated with SHFM3. No point variant in any of the genes residing within the region has been identified so far, but duplication of exon 1 of the BTRC gene may explain the phenotype, with likely complex alterations of gene regulation mechanisms that would impair limb morphogenesis. We report on 32 new index cases identified by array-CGH and/or by qPCR, including some prenatal ones, leading to termination for the most severe. Twenty-two cases were presenting with SHFM and 7 with monodactyly only. Three had an overlapping phenotype. Additional findings were identified in 5 (renal dysplasia, cutis aplasia, hypogonadism and agenesis of corpus callosum with hydrocephalus). We present their clinical and radiological findings and review the literature on this rearrangement that seems to be one of the most frequent cause of SHFM.
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MESH Headings
- Adult
- Child, Preschool
- Chromosomes, Human, Pair 10/genetics
- Comparative Genomic Hybridization/methods
- F-Box Proteins/genetics
- Female
- Gene Rearrangement/genetics
- Genetic Predisposition to Disease
- Hand Deformities, Congenital/diagnostic imaging
- Hand Deformities, Congenital/genetics
- Hand Deformities, Congenital/physiopathology
- Humans
- Infant
- Limb Deformities, Congenital/diagnostic imaging
- Limb Deformities, Congenital/genetics
- Limb Deformities, Congenital/physiopathology
- Male
- Pedigree
- Phenotype
- Proteasome Endopeptidase Complex/genetics
- Proto-Oncogene Proteins/genetics
- Radiography
- Segmental Duplications, Genomic/genetics
- Wnt Proteins/genetics
- Young Adult
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Affiliation(s)
| | - Aleksander Jamsheer
- Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Fabienne Escande
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille, France
- RADEME, EA 7364, Lille University, Lille, France
| | - Joris Andrieux
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille, France
| | - Florence Petit
- RADEME, EA 7364, Lille University, Lille, France
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
| | | | - Magdalena Socha
- Department of Medical Genetics, University of Medical Sciences, Poznan, Poland
| | - Anna Jakubiuk-Tomaszuk
- Department of Pediatric Neurology and Rehabilitation, Medical University of Bialystok, Bialystok, Poland
| | | | | | | | - Alain Verloes
- Service de Génétique, Hôpital Robert Debré, Paris, France
| | | | | | | | | | - Albert David
- Service de Génétique, CHU Nantes, Nantes, France
| | - Chantal Farra
- American University of Beirut Medical Centre, Beirut, Lebanon
| | | | - Sébastien Jacquemont
- Department of Paediatrics, Faculty of Medicine, University of Montréal, Montreal, Canada
| | - Annick Rossi
- Laboratoire de Cytogénétique, EFS Normandie, Bois Guillaume, France
| | | | - Neeti Ghali
- North West Thames Regional Genetics Service, Harrow, UK
| | - Anne Moncla
- Laboratoire de Génétique Chromosomique, CHU Marseille, Marseille, France
| | | | - Jane Hurst
- Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Elena Pollina
- Pathology Department, Queen Elizabeth Hospital, Woolwich, UK
| | | | - Joo Wook Ahn
- Genetics Laboratories, Guy's Hospital, London, UK
| | - Anne-Sylvie Valat
- Centre Pluridisciplinaire de Diagnostic Prénatal, CHRU Lille, Lille, France
| | - Aurélie Mezel
- Service de Chirurgie Orthopédique, CHRU Lille, Lille, France
| | - Philippe Bourgeot
- Centre Pluridisciplinaire de Diagnostic Prénatal, CHRU Lille, Lille, France
| | - David Zhang
- Institute of Neurology, University College London, London, UK
| | - Sylvie Manouvrier-Hanu
- RADEME, EA 7364, Lille University, Lille, France
- Clinique de Génétique Guy Fontaine, CHU Lille, Lille, France
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Carter TC, Sicko RJ, Kay DM, Browne ML, Romitti PA, Edmunds ZL, Liu A, Fan R, Druschel CM, Caggana M, Brody LC, Mills JL. Copy-number variants and candidate gene mutations in isolated split hand/foot malformation. J Hum Genet 2017; 62:877-884. [PMID: 28539665 PMCID: PMC5612852 DOI: 10.1038/jhg.2017.56] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/19/2017] [Accepted: 04/25/2017] [Indexed: 12/27/2022]
Abstract
Split hand/foot malformation (SHFM) is a congenital limb deficiency with missing or shortened central digits. Some SHFM genes have been identified but the cause of many SHFM cases is unknown. We used single-nucleotide polymorphism (SNP) microarray analysis to detect copy-number variants (CNVs) in 25 SHFM cases without other birth defects from New York State (NYS), prioritized CNVs absent from population CNV databases, and validated these CNVs using quantitative real-time polymerase chain reaction (qPCR). We tested for the validated CNVs in seven cases from Iowa using qPCR, and also sequenced 36 SHFM candidate genes in all the subjects. Seven NYS cases had a potentially deleterious variant: two had a p.R225H or p.R225L mutation in TP63, one had a 17q25 microdeletion, one had a 10q24 microduplication and three had a 17p13.3 microduplication. In addition, one Iowa case had a de novo 10q24 microduplication. The 17q25 microdeletion has not been reported previously in SHFM and included two SHFM candidate genes (SUMO2 and GRB2), while the 10q24 and 17p13.3 CNVs had breakpoints within genomic regions that contained putative regulatory elements and a limb development gene. In SHFM pathogenesis, the microdeletion may cause haploinsufficiency of SHFM genes and/or deletion of their regulatory regions, and the microduplications could disrupt regulatory elements that control transcription of limb development genes.
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Affiliation(s)
- Tonia C. Carter
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Building, Room 3117, Bethesda, MD 20892, USA
| | - Robert J. Sicko
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201-2002, USA
| | - Denise M. Kay
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201-2002, USA
| | - Marilyn L. Browne
- Congenital Malformations Registry, New York State Department of Health, Empire State Plaza-Corning Tower, Albany, NY 12237, USA
- University at Albany School of Public Health, One University Place, Rensselaer, NY 12144, USA
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, 145 N. Riverside Drive, Iowa City, IA 52242, USA
| | - Zoë L. Edmunds
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201-2002, USA
| | - Aiyi Liu
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Building, Room 3117, Bethesda, MD 20892, USA
| | - Ruzong Fan
- Department of Biostatistics, Bioinformatics, and Biomathematics, 4000 Reservoir Road NW, Building D-180, Georgetown University Medical Center, Washington DC 20057, USA
| | - Charlotte M. Druschel
- Congenital Malformations Registry, New York State Department of Health, Empire State Plaza-Corning Tower, Albany, NY 12237, USA
| | - Michele Caggana
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201-2002, USA
| | - Lawrence C. Brody
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 50, 50 South Drive, MSC 8004, Bethesda, MD 20892, USA
| | - James L. Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Building, Room 3117, Bethesda, MD 20892, USA
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5
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Cao L, Yang W, Wang S, Chen C, Zhang X, Luo Y. Molecular Genetic Characterization of a Chinese Family with Severe Split Hand/Foot Malformation. Genet Test Mol Biomarkers 2017; 21:357-362. [PMID: 28422522 DOI: 10.1089/gtmb.2016.0415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AIMS Split hand/foot malformation (SHFM) is a congenital limb malformation characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM is a genetically heterogeneous disease; the aim of this study was to identify pathogenic variations in a Chinese family with SHFM. MATERIALS AND METHODS Haplotype analyses with microsatellite markers covering the five SHFM loci were performed to localize the causative locus. Real-time quantitative polymerase chain reaction (qPCR) assays and inverse PCR were performed to determine the copy number variations and to amplify junction breakpoints in affected individuals. Candidate genes were further screened for mutations through Sanger sequencing. RESULTS A potential haplotype in the SHFM3 locus was shared by all affected individuals. qPCR and inverse PCR showed a microduplication at chromosome 10q24 spanning 488,859 bp and encompassing five entire genes, LBX1, BTRC, POLL, DPCD, and FBXW4, that co-segregated with the SHFM phenotype. No coding or splice-site mutations of these genes were found. CONCLUSION We determined the molecular basis of SHFM in a Chinese family by haplotype analysis, qPCR, inverse PCR, and Sanger sequencing. Our work extends the clinical spectrum of SHFM3; provides a fine-scale delineation of the chromosomal breakpoints helping to narrow the critical region of SHFM3; and facilitates an understanding of the mechanisms underlying abnormal limb development and extraskeletal anomalies.
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Affiliation(s)
- Lihua Cao
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China
| | - Wei Yang
- 2 McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, China
| | - Shusen Wang
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China
| | - Chen Chen
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China
| | - Xue Zhang
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China .,2 McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing, China
| | - Yang Luo
- 1 The Research Center for Medical Genomics, Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University , Shenyang, China
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Li CF, Angione K, Milunsky JM. Identification of Critical Region Responsible for Split Hand/Foot Malformation Type 3 (SHFM3) Phenotype through Systematic Review of Literature and Mapping of Breakpoints Using Microarray Data. MICROARRAYS 2015; 5:microarrays5010002. [PMID: 27600068 PMCID: PMC5003447 DOI: 10.3390/microarrays5010002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/03/2015] [Accepted: 12/16/2015] [Indexed: 01/15/2023]
Abstract
Split hand/foot malformation (SHFM) is a limb malformation with underdeveloped or absent central digital rays, clefts of hands and feet, and variable syndactyly of the remaining digits. There are six types of SHFM. Here, we report a boy with SHFM type 3 having normal 4th and 5th digits, absent 2nd and 3rd digits, and a 4th finger flexion deformity, as well as absent 2nd, 3rd and 4th toes bilaterally. His father, two paternal uncles, and two paternal first cousins have similar phenotype. Chromosome analysis showed a normal male karyotype. A 514 kb gain at 10q24.31-q24.32 (chr10:102,962,134-103,476,346, hg19) was identified using 6.0 Single nucleotide polymorphism (SNP) microarray, resulting in the duplication of nine genes, including BTRC and FBXW4. A detailed systematic review of literature and mapping of breakpoints using microarray data from all reported cases in PubMed and DECIPHER were conducted, and exon 1 of BTRC gene was identified as the critical region responsible for the SHFM3 phenotype. The potential mechanism and future studies of this critical region causing the SHFM3 phenotype are discussed.
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Affiliation(s)
| | - Katie Angione
- Center for Human Genetics, Cambridge, MA 02139, USA.
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Japanese founder duplications/triplications involving BHLHA9 are associated with split-hand/foot malformation with or without long bone deficiency and Gollop-Wolfgang complex. Orphanet J Rare Dis 2014; 9:125. [PMID: 25351291 PMCID: PMC4205278 DOI: 10.1186/s13023-014-0125-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 07/22/2014] [Indexed: 11/10/2022] Open
Abstract
Background Limb malformations are rare disorders with high genetic heterogeneity. Although multiple genes/loci have been identified in limb malformations, underlying genetic factors still remain to be determined in most patients. Methods This study consisted of 51 Japanese families with split-hand/foot malformation (SHFM), SHFM with long bone deficiency (SHFLD) usually affecting the tibia, or Gollop-Wolfgang complex (GWC) characterized by SHFM and femoral bifurcation. Genetic studies included genomewide array comparative genomic hybridization and exome sequencing, together with standard molecular analyses. Results We identified duplications/triplications of a 210,050 bp segment containing BHLHA9 in 29 SHFM patients, 11 SHFLD patients, two GWC patients, and 22 clinically normal relatives from 27 of the 51 families examined, as well as in 2 of 1,000 Japanese controls. Families with SHFLD- and/or GWC-positive patients were more frequent in triplications than in duplications. The fusion point was identical in all the duplications/triplications and was associated with a 4 bp microhomology. There was no sequence homology around the two breakpoints, whereas rearrangement-associated motifs were abundant around one breakpoint. The rs3951819-D17S1174 haplotype patterns were variable on the duplicated/triplicated segments. No discernible genetic alteration specific to patients was detected within or around BHLHA9, in the known causative SHFM genes, or in the exome. Conclusions These results indicate that BHLHA9 overdosage constitutes the most frequent susceptibility factor, with a dosage effect, for a range of limb malformations at least in Japan. Notably, this is the first study revealing the underlying genetic factor for the development of GWC, and demonstrating the presence of triplications involving BHLHA9. It is inferred that a Japanese founder duplication was generated through a replication-based mechanism and underwent subsequent triplication and haplotype modification through recombination-based mechanisms, and that the duplications/triplications with various haplotypes were widely spread in Japan primarily via clinically normal carriers and identified via manifesting patients. Furthermore, genotype-phenotype analyses of patients reported in this study and the previous studies imply that clinical variability is ascribed to multiple factors including the size of duplications/triplications as a critical factor. Electronic supplementary material The online version of this article (doi:10.1186/s13023-014-0125-5) contains supplementary material, which is available to authorized users.
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Wang X, Xin Q, Li L, Li J, Zhang C, Qiu R, Qian C, Zhao H, Liu Y, Shan S, Dang J, Bian X, Shao C, Gong Y, Liu Q. Exome sequencing reveals a heterozygous DLX5 mutation in a Chinese family with autosomal-dominant split-hand/foot malformation. Eur J Hum Genet 2014; 22:1105-10. [PMID: 24496061 DOI: 10.1038/ejhg.2014.7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 12/24/2013] [Accepted: 01/07/2014] [Indexed: 12/17/2022] Open
Abstract
Split-hand/foot malformation (SHFM) is a congenital limb deformity due to the absence or dysplasia of central rays of the autopod. Six SHFM loci have already been identified. Here we describe a Chinese family with autosomal-dominant SHFM1 that has previously been mapped to 7q21.2-21.3. The two affected family members, mother and son, showed deep median clefts between toes, ectrodactyly and syndactyly; the mother also showed triphalangeal thumbs. Exome sequencing and variant screening of candidate genes in the six loci known to be responsible for SHFM revealed a novel heterozygous mutation, c.558G>T (p.(Gln186His)), in distal-less homeobox 5 (DLX5). As DLX5 encodes a transcription factor capable of transactivating MYC, we also tested whether the mutation could affect DLX5 transcription acitivity. Results from luciferase reporter assay revealed that a mutation in DLX5 compromised its transcriptional activity. This is the first report of a mutation in DLX5 leading to autosomal-dominant SHFM1.
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Affiliation(s)
- Xue Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Qian Xin
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Lin Li
- Department of Medical Genetics, Linyi People's Hospital, Linyi, China
| | - Jiangxia Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Changwu Zhang
- Department of Orthopedics, Cangshan People's Hospital, Cangshan, China
| | - Rongfang Qiu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Chenmin Qian
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hailing Zhao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Yongchao Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Shan Shan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Jie Dang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Xianli Bian
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Changshun Shao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Yaoqin Gong
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
| | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, Shandong University School of Medicine, Jinan, China
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9
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Gurrieri F, Everman DB. Clinical, genetic, and molecular aspects of split-hand/foot malformation: an update. Am J Med Genet A 2013; 161A:2860-72. [PMID: 24115638 DOI: 10.1002/ajmg.a.36239] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 08/26/2013] [Indexed: 12/26/2022]
Abstract
We here provide an update on the clinical, genetic, and molecular aspects of split-hand/foot malformation (SHFM). This rare condition, affecting 1 in 8,500-25,000 newborns, is extremely complex because of its variability in clinical presentation, irregularities in its inheritance pattern, and the heterogeneity of molecular genetic alterations that can be found in affected individuals. Both syndromal and nonsyndromal forms are reviewed and the major molecular genetic alterations thus far reported in association with SHFM are discussed. This updated overview should be helpful for clinicians in their efforts to make an appropriate clinical and genetic diagnosis, provide an accurate recurrence risk assessment, and formulate a management plan.
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Affiliation(s)
- Fiorella Gurrieri
- Istituto di Genetica Medica, Università Cattolica del Sacro Cuore, Rome, Italy
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10
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Dai L, Deng Y, Li N, Xie L, Mao M, Zhu J. Discontinuous microduplications at chromosome 10q24.31 identified in a Chinese family with split hand and foot malformation. BMC MEDICAL GENETICS 2013; 14:45. [PMID: 23596994 PMCID: PMC3637097 DOI: 10.1186/1471-2350-14-45] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 04/08/2013] [Indexed: 02/05/2023]
Abstract
Background Split hand/foot malformation (SHFM) is a congenital disorder characterized by a cleft of the hands and/or feet due to dificiency of central rays. Genomic rearrangement at 10q24 has been found to cause nonsyndromic SHFM (SHFM3). Methods Four patients and fourteen unaffected individuals from a four-generation Chinese pedigree with typical SHFM3 phenotypes were recruited for this study. After informed consent was obtained, genome-wide copy number analysis was performed on all patients and two normal family members using the Affymetrix Cytogenetics Whole-Genome 2.7M Array. The results were then confirmed by real-time quantitative polymerase chain reaction in all available individuals of this pedigree. Candidate genes were further screened for mutation through sequence analyses. Results Copy number analysis showed a microduplication at chromosome 10q24.31-q24.32 co-segregating with the SHFM phenotype. Compared to other known genomic duplications for SHFM3, the duplication described here contains two discontinuous DNA fragments. The minimal centromeric duplicated segment of 259 kb involves LBX1, POLL and a disrupted BTRC. The minimal telomeric duplication of 114 kb encompasses DPCD and one part of FBXW4. No coding and splice-site mutations of candidate genes in the region were found. Conclusions Genomic duplications at chromosome 10q24.3, which were identified in the current study, provide further evidence for limb-specific cis-regulatory sequences in this region, highlighting the importance of chromosome 10q24.31-q24.32 in limb development and SHFM pathogenesis.
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Affiliation(s)
- Li Dai
- National Center for Birth Defects Monitoring, Chengdu, China.
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11
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Occurrence of central polydactyly, syndactyly, and cleft hand in a single family: report of five hands in three cases. J Hand Surg Am 2009; 34:1700-3. [PMID: 19762166 DOI: 10.1016/j.jhsa.2009.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 06/08/2009] [Accepted: 06/10/2009] [Indexed: 02/02/2023]
Abstract
Central polydactyly, syndactyly, and cleft hand are categorized separately in the International Federation of Societies for Surgery of the Hand classification. However, some investigators have proposed that these malformations should be classified into a single category: abnormal induction of finger rays. In this article, we report 5 hands with central polydactyly, syndactyly, and cleft hand in 3 patients from the same family and discuss the phenotypes in each hand.
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12
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Saitsu H, Kurosawa K, Kawara H, Eguchi M, Mizuguchi T, Harada N, Kaname T, Kano H, Miyake N, Toda T, Matsumoto N. Characterization of the complex 7q21.3 rearrangement in a patient with bilateral split-foot malformation and hearing loss. Am J Med Genet A 2009; 149A:1224-30. [PMID: 19449426 DOI: 10.1002/ajmg.a.32877] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We report on complex rearrangements of the 7q21.3 region in a female patient with bilateral split-foot malformation and hearing loss. G-banding karyotype was 46,XX,t(7;15)(q21;q15),t(9;14)(q21;q11.2)dn. By fluorescence, in situ hybridization (FISH), Southern hybridization, and inverse PCR, the 7q21.3 translocation breakpoint was determined at the nucleotide level. The breakpoint did not disrupt any genes, but was mapped to 38-kb telomeric to the DSS1 gene, and 258- and 272-kb centromeric to the DLX6 and DLX5 genes, respectively. It remains possible that the translocation would disrupt the interaction between these genes and their regulatory elements. Interestingly, microarray analysis also revealed an interstitial deletion close to (but not continuous to) the 7q21.3 breakpoint, indicating complex rearrangements within the split-hand/foot malformation 1 (SHFM1) locus in this patient. Furthermore, a 4.6-Mb deletion at 15q21.1-q21.2 adjacent to the 15q15 breakpoint was also identified. Cloning of the deletion junction at 7q21.3 revealed that the 0.8-Mb deletion was located 750-kb telomeric to the translocation breakpoint, encompassing TAC1, ASNS, OCM, and a part of LMTK2. Because TAC1, ASNS, and OCM genes were located on the reported copy number variation regions, it was less likely that the three genes were related to the split-foot malformation. LMTK2 appeared to be a potential candidate gene for SHFM1, but no LMTK2 mutations were found in 29 individuals with SHFM. Further LMTK2 analysis of SHFM patients together with hearing loss is warranted.
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Affiliation(s)
- Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Japan.
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13
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Elliott AM, Evans JA. The association of split hand foot malformation (SHFM) and congenital heart defects. ACTA ACUST UNITED AC 2008; 82:425-34. [DOI: 10.1002/bdra.20452] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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14
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Lezirovitz K, Maestrelli SRP, Cotrim NH, Otto PA, Pearson PL, Mingroni-Netto RC. A novel locus for split-hand/foot malformation associated with tibial hemimelia (SHFLD syndrome) maps to chromosome region 17p13.1–17p13.3. Hum Genet 2008; 123:625-31. [DOI: 10.1007/s00439-008-0515-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Accepted: 05/12/2008] [Indexed: 12/01/2022]
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15
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Chen CP, Chen YJ, Chern SR, Tsai FJ, Chang TY, Lee CC, Town DD, Lee MS, Wang W. Prenatal diagnosis of concomitant Wolf–Hirschhorn syndrome and split hand-foot malformation associated with partial monosomy 4p (4p16.1→pter) and partial trisomy 10q (10q25.1→qter). Prenat Diagn 2008; 28:450-3. [DOI: 10.1002/pd.1993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Kikuta H, Fredman D, Rinkwitz S, Lenhard B, Becker TS. Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol 2007; 8 Suppl 1:S4. [PMID: 18047696 PMCID: PMC2106839 DOI: 10.1186/gb-2007-8-s1-s4] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A large-scale enhancer detection screen was performed in the zebrafish using a retroviral vector carrying a basal promoter and a fluorescent protein reporter cassette. Analysis of insertional hotspots uncovered areas around developmental regulatory genes in which an insertion results in the same global expression pattern, irrespective of exact position. These areas coincide with vertebrate chromosomal segments containing identical gene order; a phenomenon known as conserved synteny and thought to be a vestige of evolution. Genomic comparative studies have found large numbers of highly conserved noncoding elements (HCNEs) spanning these and other loci. HCNEs are thought to act as transcriptional enhancers based on the finding that many of those that have been tested direct tissue specific expression in transient or transgenic assays. Although gene order in hox and other gene clusters has long been known to be conserved because of shared regulatory sequences or overlapping transcriptional units, the chromosomal areas found through insertional hotspots contain only one or a few developmental regulatory genes as well as phylogenetically unrelated genes. We have termed these regions genomic regulatory blocks (GRBs), and show that they underlie the phenomenon of conserved synteny through all sequenced vertebrate genomes. After teleost whole genome duplication, a subset of GRBs were retained in two copies, underwent degenerative changes compared with tetrapod loci that exist as single copy, and that therefore can be viewed as representing the ancestral form. We discuss these findings in light of evolution of vertebrate chromosomal architecture and the identification of human disease mutations.
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Affiliation(s)
- Hiroshi Kikuta
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormoehlensgate, 5008 Bergen, Norway
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17
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Kano H, Kurahashi H, Toda T. Genetically regulated epigenetic transcriptional activation of retrotransposon insertion confers mouse dactylaplasia phenotype. Proc Natl Acad Sci U S A 2007; 104:19034-9. [PMID: 17984064 PMCID: PMC2141903 DOI: 10.1073/pnas.0705483104] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Indexed: 01/17/2023] Open
Abstract
Dactylaplasia, characterized by missing central digital rays, is an inherited mouse limb malformation that depends on two genetic loci. The first locus, Dac, is an insertional mutation around the dactylin gene that is inherited as a semidominant trait. The second locus is an unlinked modifier, mdac/Mdac, that is polymorphic among inbred strains. Mdac dominantly suppresses the dactylaplasia phenotype in mice carrying Dac. However, little is known about either locus or the nature of their interaction. Here we show that Dac is a LTR retrotransposon insertion caused by the type D mouse endogenous provirus element (MusD). This insertion exhibits different epigenetic states and spatiotemporally expresses depending on the mdac/Mdac modifier background. In dactylaplasia mutants (Dac/+ mdac/mdac), the LTRs of the insertion contained unmethylated CpGs and active chromatin. Furthermore, MusD elements expressed ectopically at the apical ectodermal ridge of limb buds, accompanying the dactylaplasia phenotype. On the other hand, in Dac mutants carrying Mdac (Dac/+ Mdac/mdac), the 5' LTR of the insertion was heavily methylated and enriched with inactive chromatin, correlating with inhibition of the dactylaplasia phenotype. Ectopic expression was not observed in the presence of Mdac, which we refined to a 9.4-Mb region on mouse chromosome 13. We report a pathogenic mutation caused by MusD. Our findings indicate that ectopic expression from the MusD insertion correlates with the dactylaplasia phenotype and that Mdac acts as a defensive factor to protect the host genome from pathogenic MusD insertions.
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Affiliation(s)
- Hiroki Kano
- *Division of Clinical Genetics, Department of Medical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; and
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan
| | - Tatsushi Toda
- *Division of Clinical Genetics, Department of Medical Genetics, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan; and
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Cardozo T, Pagano M. Wrenches in the works: drug discovery targeting the SCF ubiquitin ligase and APC/C complexes. BMC BIOCHEMISTRY 2007; 8 Suppl 1:S9. [PMID: 18047746 PMCID: PMC2106342 DOI: 10.1186/1471-2091-8-s1-s9] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Recently, the ubiquitin proteasome system (UPS) has matured as a drug discovery arena, largely on the strength of the proven clinical activity of the proteasome inhibitor Velcade in multiple myeloma. Ubiquitin ligases tag cellular proteins, such as oncogenes and tumor suppressors, with ubiquitin. Once tagged, these proteins are degraded by the proteasome. The specificity of this degradation system for particular substrates lies with the E3 component of the ubiquitin ligase system (ubiquitin is transferred from an E1 enzyme to an E2 enzyme and finally, thanks to an E3 enzyme, directly to a specific substrate). The clinical effectiveness of Velcade (as it theoretically should inhibit the output of all ubiquitin ligases active in the cell simultaneously) suggests that modulating specific ubiquitin ligases could result in an even better therapeutic ratio. At present, the only ubiquitin ligase leads that have been reported inhibit the degradation of p53 by Mdm2, but these have not yet been developed into clinical therapeutics. In this review, we discuss the biological rationale, assays, genomics, proteomics and three-dimensional structures pertaining to key targets within the UPS (SCFSkp2 and APC/C) in order to assess their drug development potential. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).
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Affiliation(s)
- Timothy Cardozo
- Department of Pharmacology NYU Cancer Institute, New York University School of Medicine, 550 First Avenue MSB 599, New York, NY 10016, USA.
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Everman DB, Morgan CT, Lyle R, Laughridge ME, Bamshad MJ, Clarkson KB, Colby R, Gurrieri F, Innes AM, Roberson J, Schrander-Stumpel C, van Bokhoven H, Antonarakis SE, Schwartz CE. Frequency of genomic rearrangements involving the SHFM3 locus at chromosome 10q24 in syndromic and non-syndromic split-hand/foot malformation. Am J Med Genet A 2006; 140:1375-83. [PMID: 16761290 DOI: 10.1002/ajmg.a.31246] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Split-hand/foot malformation (SHFM), or ectrodactyly, is characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM occurs as both an isolated finding and a component of many syndromes. SHFM is a heterogeneous condition caused by multiple loci, including SHFM1 (chromosome region 7q21-q22), SHFM2 (Xq26), SHFM3 (10q24), SHFM4 (3q27), and SHFM5 (2q31). Mutations in TP63 at the SHFM4 locus are known to underlie both syndromic and non-syndromic forms SHFM, but the causes of most non-syndromic SHFM cases remain unknown. The recent identification of submicroscopic tandem chromosome duplications affecting the SHFM3 locus in seven families with non-syndromic SHFM has helped to further unravel the molecular basis of this malformation. In our ongoing studies of the SHFM3 locus in 44 additional cases of syndromic and non-syndromic SHFM, we have identified similar chromosome rearrangements in eight additional cases (18%), using pulsed-field gel electrophoresis (PFGE). We have also utilized real-time quantitative PCR (qPCR) to test for the duplications. Seven of the cases with rearrangements were non-syndromic. The current findings bring the total of SHFM3-associated cases with chromosome rearrangements to 15, which constitute 29% (15 of 51) of the cases screened to date. This includes 9 of 9 cases (100%) with known linkage to the SHFM3 locus, all of whom have non-syndromic SHFM, and 6 of 42 additional cases (14%), four of whom have non-syndromic SHFM. Thus, SHFM3 abnormalities underlie a substantial proportion of SHFM cases and appear to be a more frequent cause of non-syndromic SHFM than mutations in TP63.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 10/genetics
- Electrophoresis, Gel, Pulsed-Field
- F-Box Proteins/genetics
- Foot Deformities, Congenital/diagnosis
- Foot Deformities, Congenital/genetics
- Gene Duplication
- Gene Frequency
- Gene Rearrangement
- Genetic Linkage
- Hand Deformities, Congenital/diagnosis
- Hand Deformities, Congenital/genetics
- Humans
- Polymerase Chain Reaction/methods
- Syndrome
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Affiliation(s)
- David B Everman
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, 113 Gregor Mendel Circle, Greenwood, SC 29646, USA.
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