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Zepeda-Olmos PM, Robles-Espinoza K, Esparza-García E, Magaña-Torres MT. The First Patient with Tibial Hemimelia-Polysyndactyly-Triphalangeal Thumb Syndrome Caused by De Novo c.423+4916 T>C ZRS Variant: A Case Report. Int J Mol Sci 2024; 25:9348. [PMID: 39273297 PMCID: PMC11394837 DOI: 10.3390/ijms25179348] [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: 06/28/2024] [Revised: 07/26/2024] [Accepted: 07/28/2024] [Indexed: 09/15/2024] Open
Abstract
Genetic variants in the zone of polarizing activity regulatory sequence (ZRS) that induce ectopic expression of the SHH gene have been associated with different ZRS-related phenotypes. We report the first patient with a de novo variant, c.423+4916 T>C, in ZRS (previously classified as a variant of uncertain significance) that causes tibial hemimelia-polysyndactyly-triphalangeal thumb syndrome (THPTTS). A two-month-old male patient presented with bilateral preaxial polydactyly, triphalangeal thumb, and tibial agenesis and was heterozygous for the variant c.423+4916T>C (neither of his parents was a carrier). The findings obtained from the family study were sufficient to reclassify the variant from "uncertain significance" to "likely pathogenic" according to three criteria from the American College of Medical Genetics and Genomics guidelines, as follows: (1) absence of gnomAD, (2) confirmation of paternity and maternity, and (3) strong phenotype-genotype association. In ZRS-associated syndromes, a wide clinical spectrum has been observed, ranging from polydactyly to THPTTS; our patient has the most severe and rare phenotype. We did not perform functional assays. However, the c.423+4916T>C variant is flanked by three variants, which have been proven not only to cause the phenotype but also to increase the expression of SHH. Through all this data gathering, we consider the c.423+4916T>C variant to be causative of THPTTS.
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Affiliation(s)
- Paola Montserrat Zepeda-Olmos
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Sierra Mojada 800, Independencia Oriente, Guadalajara 44340, Jalisco, Mexico
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Independencia Oriente, Guadalajara 44340, Jalisco, Mexico
| | - Kiabeth Robles-Espinoza
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Sierra Mojada 800, Independencia Oriente, Guadalajara 44340, Jalisco, Mexico
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Sierra Mojada 950, Independencia Oriente, Guadalajara 44340, Jalisco, Mexico
| | - Eduardo Esparza-García
- Unidad Médica de Alta Especialidad, Hospital de Pediatría del Centro Médico Nacional de Occidente, Instituto Mexicano del Seguro Social, Belisario Domínguez 735, La Perla, Guadalajara 44360, Jalisco, Mexico
| | - María Teresa Magaña-Torres
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Sierra Mojada 800, Independencia Oriente, Guadalajara 44340, Jalisco, Mexico
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2
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Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
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Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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3
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Lopez Soriano V, Dueñas Rey A, Mukherjee R, Coppieters F, Bauwens M, Willaert A, De Baere E. Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci. Nat Commun 2024; 15:1600. [PMID: 38383453 PMCID: PMC10881467 DOI: 10.1038/s41467-024-45381-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.
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Affiliation(s)
- Victor Lopez Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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4
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Ferrante C, Cavin L. Early Mesozoic burst of morphological disparity in the slow-evolving coelacanth fish lineage. Sci Rep 2023; 13:11356. [PMID: 37443368 PMCID: PMC10345187 DOI: 10.1038/s41598-023-37849-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Since the split of the coelacanth lineage from other osteichthyans 420 million years ago, the morphological disparity of this clade has remained remarkably stable. Only few outliers with peculiar body shape stood out over the evolutionary history, but they were phylogenetically and stratigraphically independent of each other. Here, we report the discovery of a new clade of ancient latimeriid coelacanths representing a small flock of species present in the Western Tethys between 242 and 241 million years ago. Among the four species, two show highly derived anatomy. A new genus shows reversal to plesiomorphic conditions in its skull and caudal fin organisation. The new genus and its sister Foreyia have anatomical modules that moved from the general coelacanth Bauplau either in the same direction or in opposite direction that affect proportions of the body, opercle and fins. Comparisons with extant genetic models shows that changes of the regulatory network of the Hedgehog signal gene family may account for most of the altered anatomy. This unexpected, short and confined new clade represents the only known example of a burst of morphological disparity over the long history of coelacanths at a recovery period after the Permian-Triassic Mass Extinction.
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Affiliation(s)
- Christophe Ferrante
- Department of Geology and Palaeontology, Natural History Museum of Geneva, CP 6434, 1211, Geneva 6, Switzerland.
- Department of Earth Sciences, University of Geneva, Rue des Maraîchers 13, 1205, Geneva, Switzerland.
| | - Lionel Cavin
- Department of Geology and Palaeontology, Natural History Museum of Geneva, CP 6434, 1211, Geneva 6, Switzerland
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5
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Kyriazis Z, Kollia P, Grivea I, Stefanou N, Sotiriou S, Dailiana ZH. Polydactyly: Clinical and molecular manifestations. World J Orthop 2023; 14:13-22. [PMID: 36686282 PMCID: PMC9850794 DOI: 10.5312/wjo.v14.i1.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/04/2022] [Accepted: 12/08/2022] [Indexed: 01/13/2023] Open
Abstract
Polydactyly is a malformation during the development of the human limb, which is characterized by the presence of more than the normal number of fingers or toes. It is considered to be one of the most common inherited hand disorders. It can be divided into two major groups: Non-syndromic polydactyly or syndromic polydactyly. According to the anatomical location of the duplicated digits, polydactyly can be generally subdivided into pre-, post-axial, and mesoaxial forms. Non-syndromic polydactyly is often inherited with an autosomal dominant trait and defects during the procedure of anterior-posterior patterning of limb development are incriminated for the final phenotype of the malformation. There are several forms of polydactyly, including hand and foot extra digit manifestations. The deformity affects upper limbs with a higher frequency than the lower, and the left foot is more often involved than the right. The treatment is always surgical. Since the clinical presentation is highly diverse, the treatment combines single or multiple surgical operations, depending on the type of polydactyly. The research attention that congenital limb deformities have recently attracted has resulted in broadening the list of isolated gene mutations associated with the disorders. Next generation sequencing technologies have contributed to the correlation of phenotype and genetic profile of the multiple polydactyly manifestations and have helped in early diagnosis and screening of most non-syndromic and syndromic disorders.
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Affiliation(s)
- Zisis Kyriazis
- Department of Orthopaedic Surgery, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa 41500, Greece
| | - Panagoula Kollia
- Department of Genetics and Biotechnology, Faculty of Biology, University of Athens, Athens 15701, Greece
| | - Ioanna Grivea
- Department of Paediatrics, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa 41500, Greece
| | - Nikolaos Stefanou
- Department of Orthopaedic Surgery, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa 41500, Greece
| | - Sotirios Sotiriou
- Laboratory of Histology and Embryology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa 41500, Greece
| | - Zoe H Dailiana
- Department of Orthopaedic Surgery, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa 41500, Greece
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6
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Zhou Q, Cheng S, Zheng S, Wang Z, Guan P, Zhu Z, Huang X, Zhou C, Li G. ChromLoops: a comprehensive database for specific protein-mediated chromatin loops in diverse organisms. Nucleic Acids Res 2023; 51:D57-D69. [PMID: 36243984 PMCID: PMC9825580 DOI: 10.1093/nar/gkac893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 01/29/2023] Open
Abstract
Chromatin loops (or chromatin interactions) are important elements of chromatin structures. Disruption of chromatin loops is associated with many diseases, such as cancer and polydactyly. A few methods, including ChIA-PET, HiChIP and PLAC-Seq, have been proposed to detect high-resolution, specific protein-mediated chromatin loops. With rapid progress in 3D genomic research, ChIA-PET, HiChIP and PLAC-Seq datasets continue to accumulate, and effective collection and processing for these datasets are urgently needed. Here, we developed a comprehensive, multispecies and specific protein-mediated chromatin loop database (ChromLoops, https://3dgenomics.hzau.edu.cn/chromloops), which integrated 1030 ChIA-PET, HiChIP and PLAC-Seq datasets from 13 species, and documented 1 491 416 813 high-quality chromatin loops. We annotated genes and regions overlapping with chromatin loop anchors with rich functional annotations, such as regulatory elements (enhancers, super-enhancers and silencers), variations (common SNPs, somatic SNPs and eQTLs), and transcription factor binding sites. Moreover, we identified genes with high-frequency chromatin interactions in the collected species. In particular, we identified genes with high-frequency interactions in cancer samples. We hope that ChromLoops will provide a new platform for studying chromatin interaction regulation in relation to biological processes and disease.
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Affiliation(s)
- Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheng Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shanshan Zheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenji Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Pengpeng Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhixian Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingyu Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Cong Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, Key Laboratory of Smart Farming for Agricultural Animals, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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7
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Bastide S, Chomsky E, Saudemont B, Loe-Mie Y, Schmutz S, Novault S, Marlow H, Tanay A, Spitz F. TATTOO-seq delineates spatial and cell type-specific regulatory programs in the developing limb. SCIENCE ADVANCES 2022; 8:eadd0695. [PMID: 36516250 PMCID: PMC9750149 DOI: 10.1126/sciadv.add0695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
The coordinated differentiation of progenitor cells into specialized cell types and their spatial organization into distinct domains is central to embryogenesis. Here, we developed and applied an unbiased spatially resolved single-cell transcriptomics method to identify the genetic programs underlying the emergence of specialized cell types during mouse limb development and their spatial integration. We identify multiple transcription factors whose expression patterns are predominantly associated with cell type specification or spatial position, suggesting two parallel yet highly interconnected regulatory systems. We demonstrate that the embryonic limb undergoes a complex multiscale reorganization upon perturbation of one of its spatial organizing centers, including the loss of specific cell populations, alterations of preexisting cell states' molecular identities, and changes in their relative spatial distribution. Our study shows how multidimensional single-cell, spatially resolved molecular atlases can allow the deconvolution of spatial identity and cell fate and reveal the interconnected genetic networks that regulate organogenesis and its reorganization upon genetic alterations.
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Affiliation(s)
- Sébastien Bastide
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- École Doctorale “Complexité du Vivant”, Sorbonne Université, 75005 Paris, France
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Elad Chomsky
- Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel
- Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Baptiste Saudemont
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Yann Loe-Mie
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, Paris, France
| | - Sandrine Schmutz
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Sophie Novault
- Cytometry and Biomarkers, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Heather Marlow
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute, Rehovot, Israel
| | - François Spitz
- (Epi)genomics of Animal Development, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
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8
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The molecular genetics of human appendicular skeleton. Mol Genet Genomics 2022; 297:1195-1214. [PMID: 35907958 DOI: 10.1007/s00438-022-01930-1] [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: 07/07/2021] [Accepted: 07/09/2022] [Indexed: 10/16/2022]
Abstract
Disorders that result from de-arrangement of growth, development and/or differentiation of the appendages (limbs and digit) are collectively called as inherited abnormalities of human appendicular skeleton. The bones of appendicular skeleton have central role in locomotion and movement. The different types of appendicular skeletal abnormalities are well described in the report of "Nosology and Classification of Genetic skeletal disorders: 2019 Revision". In the current article, we intend to present the embryology, developmental pathways, disorders and the molecular genetics of the appendicular skeletal malformations. We mainly focused on the polydactyly, syndactyly, brachydactyly, split-hand-foot malformation and clubfoot disorders. To our knowledge, only nine genes of polydactyly, five genes of split-hand-foot malformation, nine genes for syndactyly, eight genes for brachydactyly and only single gene for clubfoot have been identified to be involved in disease pathophysiology. The current molecular genetic data will help life sciences researchers working on the rare skeletal disorders. Moreover, the aim of present systematic review is to gather the published knowledge on molecular genetics of appendicular skeleton, which would help in genetic counseling and molecular diagnosis.
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9
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Cassim A, Hettiarachchi D, Dissanayake VHW. Genetic determinants of syndactyly: perspectives on pathogenesis and diagnosis. Orphanet J Rare Dis 2022; 17:198. [PMID: 35549993 PMCID: PMC9097448 DOI: 10.1186/s13023-022-02339-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/26/2022] [Indexed: 12/04/2022] Open
Abstract
The formation of the digits is a tightly regulated process. During embryogenesis, disturbance of genetic pathways in limb development could result in syndactyly; a common congenital malformation consisting of webbing in adjacent digits. Currently, there is a paucity of knowledge regarding the exact developmental mechanism leading to this condition. The best studied canonical interactions of Wingless‐type–Bone Morphogenic Protein–Fibroblast Growth Factor (WNT–BMP–FGF8), plays a role in the interdigital cell death (ICD) which is thought to be repressed in human syndactyly. Animal studies have displayed other pathways such as the Notch signaling, metalloprotease and non-canonical WNT-Planar cell polarity (PCP), to also contribute to failure of ICD, although less prominence has been given. The current diagnosis is based on a clinical evaluation followed by radiography when indicated, and surgical release of digits at 6 months of age is recommended. This review discusses the interactions repressing ICD in syndactyly, and characterizes genes associated with non-syndromic and selected syndromes involving syndactyly, according to the best studied canonical WNT-BMP-FGF interactions in humans. Additionally, the controversies regarding the current syndactyly classification and the effect of non-coding elements are evaluated, which to our knowledge has not been previously highlighted. The aim of the review is to better understand the developmental process leading to this condition.
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Affiliation(s)
- Afraah Cassim
- Human Genetics Unit, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo, Sri Lanka.
| | - Dineshani Hettiarachchi
- Human Genetics Unit, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo, Sri Lanka
| | - Vajira H W Dissanayake
- Human Genetics Unit, Faculty of Medicine, University of Colombo, 25, Kynsey Road, Colombo, Sri Lanka
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10
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Zaib T, Rashid H, Khan H, Zhou X, Sun P. Recent Advances in Syndactyly: Basis, Current Status and Future Perspectives. Genes (Basel) 2022; 13:771. [PMID: 35627156 PMCID: PMC9141913 DOI: 10.3390/genes13050771] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 02/05/2023] Open
Abstract
A comprehensive summary of recent knowledge in syndactyly (SD) is important for understanding the genetic etiology of SD and disease management. Thus, this review article provides background information on SD, as well as insights into phenotypic and genetic heterogeneity, newly identified gene mutations in various SD types, the role of HOXD13 in limb deformities, and recently introduced modern surgical techniques for SD. This article also proposes a procedure for genetic analysis to obtain a clearer genotype-phenotype correlation for SD in the future. We briefly describe the classification of non-syndromic SD based on variable phenotypes to explain different phenotypic features and mutations in the various genes responsible for the pathogenesis of different types of SD. We describe how different types of mutation in HOXD13 cause various types of SD, and how a mutation in HOXD13 could affect its interaction with other genes, which may be one of the reasons behind the differential phenotypes and incomplete penetrance. Furthermore, we also discuss some recently introduced modern surgical techniques, such as free skin grafting, improved flap techniques, and dermal fat grafting in combination with the Z-method incision, which have been successfully practiced clinically with no post-operative complications.
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Affiliation(s)
- Tahir Zaib
- Stem Cell Research Center, Shantou University Medical College, Shantou 515041, China
- (T.Z.)
- (X.Z.)
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Hibba Rashid
- Department of Biotechnology and Microbiology, Abasyn University, Peshawar 25000, Pakistan
| | - Hanif Khan
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China
| | - Xiaoling Zhou
- Stem Cell Research Center, Shantou University Medical College, Shantou 515041, China
- (T.Z.)
- (X.Z.)
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
| | - Pingnan Sun
- Stem Cell Research Center, Shantou University Medical College, Shantou 515041, China
- (T.Z.)
- (X.Z.)
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou 515041, China
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11
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Zeng L, Jin JY, Luo FM, Sheng Y, Wu PF, Xiang R. ZPA Regulatory Sequence Variants in Chinese Patients With Preaxial Polydactyly: Genetic and Clinical Characteristics. Front Pediatr 2022; 10:797978. [PMID: 35652055 PMCID: PMC9149355 DOI: 10.3389/fped.2022.797978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/29/2022] [Indexed: 11/29/2022] Open
Abstract
Preaxial polydactyly (PPD) is a common congenital abnormality with an incidence of 0.8-1.4% in Asians, characterized by the presence of extra digit(s) on the preaxial side of the hand or foot. PPD is genetically classified into four subtypes, PPD type I-IV. Variants in six genes/loci [including GLI family zinc finger 3 (GLI3), ZPA regulatory sequence (ZRS), and pre-ZRS region] have been identified in PPD cases. Among these loci, ZRS is, perhaps, the most special and well known, but most articles only reported one or a few cases. There is a lack of reports on the ZRS-variant frequency in patients with PPD. In this study, we recruited 167 sporadic or familial cases (including 154 sporadic patients and 13 families) with PPD from Central-South China and identified four ZRS variants in four patients (2.40%, 4/167), including two novel variants (ZRS131A > T/chr7:g.156584439A > T and ZRS474C > G/chr7:g.156584096C > G) and two known variants (ZRS428T > A/chr7:g.156584142T > A and ZRS619C > T/chr7:g.156583951C > T). ZRS131A > T and ZRS428T > A were detected in PPD I cases and ZRS474C > G and ZRS619C > T combinedly acted to cause PPD II. The detectable rate of ZRS variants in PPD I was 1.60% (2/125), while PPD II was significantly higher (9.52%, 2/21). Three bilateral PPD cases harbored ZRS variants (13.64%, 3/22), suggesting that bilateral PPD was more possibly caused by genetic etiologies. This study identified two novel ZRS variants, further confirmed the association between ZRS and PPD I and reported a rare PPD II case resulted from the compound heterozygote of ZRS. This investigation preliminarily evaluated a ZRS variants rate in patients with PPD and described the general picture of PPD in Central-South China.
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Affiliation(s)
- Lei Zeng
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China
| | - Jie-Yuan Jin
- School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Fang-Mei Luo
- School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China
| | - Yue Sheng
- School of Life Sciences, Central South University, Changsha, China
| | - Pan-Feng Wu
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Rong Xiang
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
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12
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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13
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Xu J, Chen X, Teng X, Wang X, Chen H. Complex radial polydactyly in a Chinese family: inclusion of triphalangism, triplication, and syndactyly. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1296. [PMID: 34532433 PMCID: PMC8422142 DOI: 10.21037/atm-21-2773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/01/2021] [Indexed: 11/21/2022]
Abstract
Background Few studies have investigated families in which multiple individuals over three or more generations are affected by radial polydactyly and syndactyly. This report describes an extremely rare family in which nine individuals across six generations were affected by complex radial polydactyly. Methods We investigated a six-generation pedigree with radial polydactyly including triplication, triphalangism, hypoplasia, and symphalangism. There was a total of 34 individuals (including their spouses) in the family and 11 individuals had polydactyly. The average age of the patients ranged from 7 months to 96 years. The characteristic feature of the malformation in these patients was described. Two patients underwent surgical resection for radial supernumerary thumbs. The Bilhout-Cloquet technique and On-top-plasty technique were used to reconstruct the nail and the joints. Results The patients in this family presented with thumb duplication and triphalangism in both hands, including a variety of deformities, such as triplication, triphalangism, hypoplasia, and symphalangism. Syndactyly and ulnar polydactyly were also frequently observed. Two patients who underwent surgical treatment showed good hand and thumb function at the 8- and 2-year post-operative follow-up, respectively. Conclusions The present study reported various mixed phenotypes including triplication, triphalangism, hypoplasia, and symphalangism within the same family which may represent a rare type of polydactyly. Surgical resection of extra digits to achieve mobility of the thumb is the main treatment option for radial polydactyly. Given the ulnar thumb is better developed, the radial thumb is typically resected in patients with radial polydactyly. These reconstructive principles are fit for this Chinese family as well.
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Affiliation(s)
- Jihai Xu
- Hand Surgery Department, Ningbo No. 6 Hospital, Ningbo, China
| | - Xiaokun Chen
- Department of Orthopedic Trauma, Peking University People Hospital, Beijing, China
| | - Xiaofeng Teng
- Hand Surgery Department, Ningbo No. 6 Hospital, Ningbo, China
| | - Xin Wang
- Hand Surgery Department, Ningbo No. 6 Hospital, Ningbo, China
| | - Hong Chen
- Hand Surgery Department, Ningbo No. 6 Hospital, Ningbo, China
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14
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Zhang SJ, Lin HB, Jiang QX, He SZ, Lyu GR. Prenatal diagnosis of triphalangeal thumb-polysyndactyly syndrome by ultrasonography combined with genetic testing: A case report. World J Clin Cases 2021; 9:6832-6838. [PMID: 34447832 PMCID: PMC8362503 DOI: 10.12998/wjcc.v9.i23.6832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/04/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Triphalangeal thumb-polysyndactyly syndrome (TPT-PS) is a rare type of congenital limb deformity, and most studies focus on the genetics. Case reports of the sonographic characteristics of TPT-PS during pregnancy are rare.
CASE SUMMARY A 30-year-old woman (G3P1) who had pregnancies with TPT-PS fetuses is presented. The possibility of TPT-PS was shown by ultrasound performed at the 19th wk of pregnancy, featuring hands with six metacarpals, an extra digit at the 5th finger side, and an abnormally widened thumb. Whole-exome sequencing was subsequently conducted. The results showed that exons 1-17 of the LMBR1 gene had a heterozygous duplication, with a length of approximately 253 kb.
CONCLUSION We suggest prenatal ultrasound examination combined with genetic testing to diagnose TPT-PS accurately and to help clinicians and patients make decisions.
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Affiliation(s)
- Shi-Jie Zhang
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, Fujian Province, China
| | - Hai-Bin Lin
- Department of Ultrasound, Jinjiang Municipal Hospital, Quanzhou 362000, Fujian Province, China
| | - Qiu-Xia Jiang
- Department of Ultrasound, Quanzhou Women’s and Children’s Hospital, Quanzhou 362000, Fujian Province, China
- Collaborative Innovation Center for Maternal and Infant Health Service, Application Technology of Education Ministry, Quanzhou Medical College, Quanzhou 362000, Fujian Province, China
| | - Shao-Zheng He
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, Fujian Province, China
| | - Guo-Rong Lyu
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, Fujian Province, China
- Department of Ultrasound, Jinjiang Municipal Hospital, Quanzhou 362000, Fujian Province, China
- Department of Ultrasound, Quanzhou Women’s and Children’s Hospital, Quanzhou 362000, Fujian Province, China
- Collaborative Innovation Center for Maternal and Infant Health Service, Application Technology of Education Ministry, Quanzhou Medical College, Quanzhou 362000, Fujian Province, China
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15
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Thirkannad SM, Patil R. The Story of the Hand. Indian J Plast Surg 2021; 54:106-113. [PMID: 34239230 PMCID: PMC8257305 DOI: 10.1055/s-0041-1729771] [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] [Indexed: 10/27/2022] Open
Abstract
This review describes the Story of the Human Hand. It traces the functional needs that led to evolution of the human hand as well as its embryological development. The various in utero stages of formation of the human hand are covered along with a description of the various molecular and genetic factors that control this process.
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Affiliation(s)
- Sunil M. Thirkannad
- Kleinert–Kutz Hand Care Center, Christine M. Kleinert Institute for Hand and Microsurgery, Louisville, Kentucky, United States
| | - Rahul Patil
- Kleinert–Kutz Hand Care Center, Christine M. Kleinert Institute for Hand and Microsurgery, Louisville, Kentucky, United States
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16
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A 300-kb microduplication of 7q36.3 in a patient with triphalangeal thumb-polysyndactyly syndrome combined with congenital heart disease and optic disc coloboma: a case report. BMC Med Genomics 2020; 13:175. [PMID: 33218365 PMCID: PMC7678048 DOI: 10.1186/s12920-020-00821-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/09/2020] [Indexed: 12/04/2022] Open
Abstract
Background Triphalangeal thumb-polysyndactyly syndrome (TPT-PS) is a rare well-defined autosomal dominant disorder characterized by long thumbs with three phalanges combined with pre- and postaxial polydactyly/syndactyly of limbs.
By now, the syndrome has been reported in several large families from different ethnic backgrounds, with a high degree of inter- and intrafamilial variability. The genome locus responsible for TPT-PS has been mapped to the 7q36.3 region harboring a long-range sonic hedgehog (SHH) regulatory sequence (ZRS). Both single-nucleotide variants and complete duplications of ZRS were shown to cause TPT-PS and similar limb phenotypes. TPT-PS usually forms as isolated limb pathology not associated with additional malformations, in particular, with cardiovascular abnormalities. Case presentation Here we report on a rare Russian neonatal case of TPT-PS combined with severe congenital heart disease, namely double outlet right ventricle, and microphthalmia with optic disc coloboma. Pedigree analysis revealed TPT-PS of various expressivity in 10 family members throughout five generations, while the cardiac defect and the eye pathology were detected only in the proband. To extend the knowledge on genotype–phenotype spectrum of TPT-PS, the careful clinical and genomic analysis of the family was performed. High-resolution array-based comparative genomic hybridization (array-CGH) revealed a ~ 300 kb microduplication of 7q36.3 locus (arr[GRCh37] 7q36.3(156385810_156684811) × 3) that co-segregated with TPT-PS in the proband and her mother. The duplication encompassed three genes including LMBR1, the intron 5 of which is known to harbor ZRS. Based on whole-exome sequencing data, no additional pathogenic mutations or variants of uncertain clinical significance were found in morbid cardiac genes or genes associated with a microphthalmia/anophthalmia/coloboma spectrum of ocular malformations. Conclusions The results support the previous data, indicating that complete ZRS duplication underlies TPT-PS, and suggest a broader phenotypic impact of the 7q36.3 microduplication. Potential involvement of the 7q36.3 microduplication in the patient’s cardiac and eye malformations is discussed. However, the contribution of some additional genetic/epigenetic factors to the complex patient`s phenotype cannot be excluded entirely. Further comprehensive functional studies are needed to prove the possible involvement of the 7q36.3 locus in congenital heart disease and eye pathology.
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17
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Chen HX, Yang ZY, Hou HT, Wang J, Wang XL, Yang Q, Liu L, He GW. Novel mutations of TCTN3/LTBP2 with cellular function changes in congenital heart disease associated with polydactyly. J Cell Mol Med 2020; 24:13751-13762. [PMID: 33098376 PMCID: PMC7753982 DOI: 10.1111/jcmm.15950] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/21/2020] [Accepted: 08/27/2020] [Indexed: 12/20/2022] Open
Abstract
Congenital heart disease (CHD) associated with polydactyly involves various genes. We aimed to identify variations from genes related to complex CHD with polydactyly and to investigate the cellular functions related to the mutations. Blood was collected from a complex CHD case with polydactyly, and whole exome sequencing (WES) was performed. The CRISPR/Cas9 system was used to generate human pluripotent stem cell with mutations (hPSCs-Mut) that were differentiated into cardiomyocytes (hPSC-CMs-Mut) and analysed by transcriptomics on day 0, 9 and 13. Two heterozygous mutations, LTBP2 (c.2206G>A, p.Asp736Asn, RefSeq NM_000428.2) and TCTN3 (c.1268G>A, p.Gly423Glu, RefSeq NM_015631.5), were identified via WES but no TBX5 mutations were found. The stable cell lines of hPSCs-LTBP2mu /TCTN3mu were constructed and differentiated into hPSC-CMs-LTBP2mu /TCTN3mu . Compared to the wild type, LTBP2 mutation delayed the development of CMs. The TCTN3 mutation consistently presented lower rate and weaker force of the contraction of CMs. For gene expression pattern of persistent up-regulation, pathways in cardiac development and congenital heart disease were enriched in hPSCs-CM-LTBP2mu , compared with hPSCs-CM-WT. Thus, the heterozygous mutations in TCTN3 and LTBP2 affect contractility (rate and force) of cardiac myocytes and may affect the development of the heart. These findings provide new insights into the pathogenesis of complex CHD with polydactyly.
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Affiliation(s)
- Huan-Xin Chen
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Zi-Yue Yang
- College of Life Sciences, Nankai University, Tianjin, China
| | - Hai-Tao Hou
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Jun Wang
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiu-Li Wang
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Qin Yang
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Lin Liu
- College of Life Sciences, Nankai University, Tianjin, China
| | - Guo-Wei He
- Center for Basic Medical Research & Department of Cardiovascular Surgery, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.,Zhejiang University, Hangzhou, Zhejiang, China.,Drug Research and Development Center, Wannan Medical College, Wuhu, Anhui, China.,Department of Surgery, Oregon Health and Science University, Portland, OR, USA
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18
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Xu J, Wu J, Teng X, Cai L, Yuan H, Chen X, Hu M, Wang X, Jiang N, Chen H. Large duplication in LMBR1 gene in a large Chinese pedigree with triphalangeal thumb polysyndactyly syndrome. Am J Med Genet A 2020; 182:2117-2123. [PMID: 32662247 DOI: 10.1002/ajmg.a.61757] [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: 10/16/2019] [Revised: 04/30/2020] [Accepted: 05/28/2020] [Indexed: 12/18/2022]
Abstract
Polydactyly and syndactyly are digital abnormalities in limb-associated birth defects usually caused by genetic disorders. In this study, a five-generation Chinese pedigree was found with triphalangeal thumb polysyndactyly syndrome (TPTPS), showing an autosomal dominant pattern of inheritance. We utilized linkage analysis and whole genome sequencing (WGS) for the genetic diagnosis of this pedigree. Linkage analysis was performed using a genome-wide single nucleotide polymorphism (SNP) chip and three genomic regions were identified in chromosomes 2, 6, and 7 with significant linkage signals. WGS discovered a copy number variation (CNV) mutation caused by a large duplication region at the tail of chromosome 7 located in exons 1-5 of the LMBR1 gene, including the zone of polarizing activity regulatory sequence (ZRS), with a length of approximately 180 kb. A real-time polymerase chain reaction (PCR) assay confirmed the duplication. The findings of our study supported the notion that large duplications including the ZRS caused TPTPS. Our study showed that linkage analysis in combination with WGS could successfully identify the disease locus and causative mutation in TPTPS, which could help elucidate the molecular mechanisms and genotype-phenotype correlations in polydactyly.
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Affiliation(s)
- Jihai Xu
- Department of Hand Surgery, Ningbo No. 6 Hospital, Ningbo, China
| | - Jing Wu
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaofeng Teng
- Department of Hand Surgery, Ningbo No. 6 Hospital, Ningbo, China
| | - Libing Cai
- Department of Hand Surgery, Ningbo No. 6 Hospital, Ningbo, China
| | - Huizong Yuan
- Department of Hand Surgery, Ningbo No. 6 Hospital, Ningbo, China
| | - Xiaokun Chen
- Department of Orthopedic Trauma, Peking University People Hospital, Beijing, China
| | - Mu Hu
- Department of Orthopedics, Ruijin Hospital North, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xin Wang
- Department of Hand Surgery, Ningbo No. 6 Hospital, Ningbo, China
| | - Ning Jiang
- Department of Biostatistics and Computational Biology, SKLG, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Chen
- Department of Hand Surgery, Ningbo No. 6 Hospital, Ningbo, China
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19
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Anderson RA, Schwalbach KT, Mui SR, LeClair EE, Topczewska JM, Topczewski J. Zebrafish models of skeletal dysplasia induced by cholesterol biosynthesis deficiency. Dis Model Mech 2020; 13:dmm042549. [PMID: 32430393 PMCID: PMC7328163 DOI: 10.1242/dmm.042549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 04/27/2020] [Indexed: 12/23/2022] Open
Abstract
Human disorders of the post-squalene cholesterol biosynthesis pathway frequently result in skeletal abnormalities, yet our understanding of the mechanisms involved is limited. In a forward-genetic approach, we have found that a late-onset skeletal mutant, named kolibernu7 , is the result of a cis-acting regulatory mutation leading to loss of methylsterol monooxygenase 1 (msmo1) expression within pre-hypertrophic chondrocytes. Generated msmo1nu81 knockdown mutation resulted in lethality at larval stage. We demonstrated that this is a result of both cholesterol deprivation and sterol intermediate accumulation by creating a mutation eliminating activity of Lanosterol synthase (Lss). Our results indicate that double lssnu60;msmo1nu81 and single lssnu60 mutants survive significantly longer than msmo1nu81 homozygotes. Liver-specific restoration of either Msmo1 or Lss in corresponding mutant backgrounds suppresses larval lethality. Rescued mutants develop dramatic skeletal abnormalities, with a loss of Msmo1 activity resulting in a more-severe patterning defect of a near-complete loss of hypertrophic chondrocytes marked by col10a1a expression. Our analysis suggests that hypertrophic chondrocytes depend on endogenous cholesterol synthesis, and blocking C4 demethylation exacerbates the cholesterol deficiency phenotype. Our findings offer new insight into the genetic control of bone development and provide new zebrafish models for human disorders of the cholesterol biosynthesis pathway.
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Affiliation(s)
- Rebecca A Anderson
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kevin T Schwalbach
- Developmental Biology Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Stephanie R Mui
- Developmental Biology Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Elizabeth E LeClair
- Department of Biological Sciences, DePaul University, Chicago, IL 60614, USA
| | - Jolanta M Topczewska
- Developmental Biology Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Jacek Topczewski
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Developmental Biology Program, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin 20-093, Poland
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20
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Kvon EZ, Zhu Y, Kelman G, Novak CS, Plajzer-Frick I, Kato M, Garvin TH, Pham Q, Harrington AN, Hunter RD, Godoy J, Meky EM, Akiyama JA, Afzal V, Tran S, Escande F, Gilbert-Dussardier B, Jean-Marçais N, Hudaiberdiev S, Ovcharenko I, Dobbs MB, Gurnett CA, Manouvrier-Hanu S, Petit F, Visel A, Dickel DE, Pennacchio LA. Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants. Cell 2020; 180:1262-1271.e15. [PMID: 32169219 PMCID: PMC7179509 DOI: 10.1016/j.cell.2020.02.031] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/13/2020] [Accepted: 02/12/2020] [Indexed: 12/17/2022]
Abstract
Establishing causal links between non-coding variants and human phenotypes is an increasing challenge. Here, we introduce a high-throughput mouse reporter assay for assessing the pathogenic potential of human enhancer variants in vivo and examine nearly a thousand variants in an enhancer repeatedly linked to polydactyly. We show that 71% of all rare non-coding variants previously proposed as causal lead to reporter gene expression in a pattern consistent with their pathogenic role. Variants observed to alter enhancer activity were further confirmed to cause polydactyly in knockin mice. We also used combinatorial and single-nucleotide mutagenesis to evaluate the in vivo impact of mutations affecting all positions of the enhancer and identified additional functional substitutions, including potentially pathogenic variants hitherto not observed in humans. Our results uncover the functional consequences of hundreds of mutations in a phenotype-associated enhancer and establish a widely applicable strategy for systematic in vivo evaluation of human enhancer variants.
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Affiliation(s)
- Evgeny Z Kvon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yiwen Zhu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Guy Kelman
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Catherine S Novak
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ingrid Plajzer-Frick
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Momoe Kato
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tyler H Garvin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Quan Pham
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anne N Harrington
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Riana D Hunter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Janeth Godoy
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eman M Meky
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jennifer A Akiyama
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veena Afzal
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Stella Tran
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | | | | - Sanjarbek Hudaiberdiev
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew B Dobbs
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Florence Petit
- CHU Lille, University of Lille, EA7364, F-59000, Lille, France
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; School of Natural Sciences, University of California, Merced, CA 95343, USA.
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; U.S. Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA; Comparative Biochemistry Program, University of California, Berkeley, CA 94720, USA.
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21
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Potuijt JWP, Hoogeboom J, de Graaff E, van Nieuwenhoven CA, Galjaard RJH. Variable expression of subclinical phenotypes instead of reduced penetrance in families with mild triphalangeal thumb phenotypes. J Med Genet 2020; 57:660-663. [PMID: 32179704 PMCID: PMC7525795 DOI: 10.1136/jmedgenet-2019-106685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 12/21/2022]
Abstract
Background The of zone of polarizing activity regulatory sequence (ZRS) is a regulatory element residing in intron 5 of LMBR1 and regulates Sonic Hedgehog expression in the limb bud. Variants in the ZRS are generally fully penetrant and can cause triphalangeal thumb (TPT) and polydactyly in affected families. Objective In this report, we describe two families with mild phenotypical presentation. Methods We performed a field study for clinical evaluation and sequenced the ZRS for variantsusing Sanger sequencing. Results In family I, a novel 165A>G variant in the ZRS (g.156584405A>G, GRCh37/Hg19) was found. In family II, we identified a 295T>C variant in the ZRS (g.156584535T>C, GRCh37/Hg19). Family members of both families who were presumed to be unaffected shared the variant in the ZRS with affected family members, suggesting reduced penetrance of the genotype. However, clinical examination of these unaffected family members revealed minor anomalies like broad thumbs and lack of thumb opposition. As the phenotype in affected patients is remarkably mild, we suggest that these ZRS variants are minimally disruptive for Sonic Hedgehog expression and therefore can result in subclinical phenotypes. Conclusion Our study underlines the importance of accurate clinical examination and appropriate genetic counselling in families with mild cases of TPT.
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Affiliation(s)
- Jacob W P Potuijt
- Plastic, Reconstructive and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jeannette Hoogeboom
- Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Esther de Graaff
- Division of Cell Biology, Neurobiology and Biophysics, Utrecht University, Utrecht, Utrecht, The Netherlands
| | | | - Robert Jan H Galjaard
- Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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22
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Shi L, Huang H, Jiang Q, Huang R, Fu W, Mao L, Wei X, Cui H, Lin K, Cai L, Yang Y, Wang Y, Wu J. Sub-Exome Target Sequencing in a Family With Syndactyly Type IV Due to a Novel Partial Duplication of the LMBR1 Gene: First Case Report in Fujian Province of China. Front Genet 2020; 11:130. [PMID: 32184803 PMCID: PMC7058806 DOI: 10.3389/fgene.2020.00130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/03/2020] [Indexed: 12/30/2022] Open
Abstract
Syndactyly is one of the most frequent hereditary limb malformations with clinical and genetical complexity. Autosomal dominant syndactyly type IV (SD4) is a rare form of syndactyly, caused by heterozygous mutations in a sonic hedgehog (SHH) regulatory element (ZRS) which resides in intron 5 of the LMBR1 gene on chromosome 7q36.3. SD4 is characterized by complete cutaneous syndactyly of the fingers, accompanied by cup-shaped hands due to flexion of the fingers and polydactyly. Here, for the first time, we reported a large Chinese family from Fujian province, manifesting cup-shaped hands consistent with SD4 and intrafamilial heterogeneity in clinical phenotype of tibial and fibulal shortening, triphalangeal thumb-polysyndactyly syndrome (TPTPS). We identified a novel duplication of ∼222 kb covering exons 2–17 of the LMBR1 gene in this family by sub-exome target sequencing. This case expands our new clinical understanding of SD4 phenotype and again confirms the feasibility to detect copy number variation by sub-exome target sequencing.
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Affiliation(s)
- Lijing Shi
- Department of Ultrasound, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Qiuxia Jiang
- Department of Ultrasound, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Rongsen Huang
- Department of Ultrasound, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Wanyu Fu
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Liangwei Mao
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, Wuhan, China
| | - Xiaoming Wei
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, Wuhan, China
| | | | - Keke Lin
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Licheng Cai
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, China
| | - You Yang
- BGI-Guangzhou Medical Laboratory, BGI-Shenzhen, Guangzhou, China
| | - Yuanbai Wang
- Prenatal Diagnosis Center, Quanzhou Women's and Children's Hospital, Quanzhou, China
| | - Jing Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
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23
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Lézot F, Corre I, Morice S, Rédini F, Verrecchia F. SHH Signaling Pathway Drives Pediatric Bone Sarcoma Progression. Cells 2020; 9:cells9030536. [PMID: 32110934 PMCID: PMC7140443 DOI: 10.3390/cells9030536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/19/2020] [Accepted: 02/23/2020] [Indexed: 02/07/2023] Open
Abstract
Primary bone tumors can be divided into two classes, benign and malignant. Among the latter group, osteosarcoma and Ewing sarcoma are the most prevalent malignant primary bone tumors in children and adolescents. Despite intensive efforts to improve treatments, almost 40% of patients succumb to the disease. Specifically, the clinical outcome for metastatic osteosarcoma or Ewing sarcoma remains poor; less than 30% of patients who present metastases will survive 5 years after initial diagnosis. One common and specific point of these bone tumors is their ability to deregulate bone homeostasis and remodeling and divert them to their benefit. Over the past years, considerable interest in the Sonic Hedgehog (SHH) pathway has taken place within the cancer research community. The activation of this SHH cascade can be done through different ways and, schematically, two pathways can be described, the canonical and the non-canonical. This review discusses the current knowledge about the involvement of the SHH signaling pathway in skeletal development, pediatric bone sarcoma progression and the related therapeutic options that may be possible for these tumors.
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24
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Su P, Xu C, Yang X, Zhou H, Li QZ. Response to Potuijt et al. Genet Med 2019; 22:819-820. [PMID: 31822852 DOI: 10.1038/s41436-019-0726-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- Peiqiang Su
- Department of Orthopedics, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China.
| | - Caixia Xu
- Research Center for Translational Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Xiaoming Yang
- Department of Orthopedics, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Hang Zhou
- Department of Orthopedics, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, P. R. China
| | - Quan-Zhen Li
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
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25
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Mortier GR, Cohn DH, Cormier-Daire V, Hall C, Krakow D, Mundlos S, Nishimura G, Robertson S, Sangiorgi L, Savarirayan R, Sillence D, Superti-Furga A, Unger S, Warman ML. Nosology and classification of genetic skeletal disorders: 2019 revision. Am J Med Genet A 2019; 179:2393-2419. [PMID: 31633310 DOI: 10.1002/ajmg.a.61366] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/01/2019] [Accepted: 09/05/2019] [Indexed: 01/23/2023]
Abstract
The application of massively parallel sequencing technology to the field of skeletal disorders has boosted the discovery of the underlying genetic defect for many of these diseases. It has also resulted in the delineation of new clinical entities and the identification of genes and pathways that had not previously been associated with skeletal disorders. These rapid advances have prompted the Nosology Committee of the International Skeletal Dysplasia Society to revise and update the last (2015) version of the Nosology and Classification of Genetic Skeletal Disorders. This newest and tenth version of the Nosology comprises 461 different diseases that are classified into 42 groups based on their clinical, radiographic, and/or molecular phenotypes. Remarkably, pathogenic variants affecting 437 different genes have been found in 425/461 (92%) of these disorders. By providing a reference list of recognized entities and their causal genes, the Nosology should help clinicians achieve accurate diagnoses for their patients and help scientists advance research in skeletal biology.
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Affiliation(s)
- Geert R Mortier
- Department of Medical Genetics, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Daniel H Cohn
- Department of Molecular, Cell and Developmental Biology and Department of Orthopaedic Surgery, University of California at Los Angeles, Los Angeles, California
| | | | - Christine Hall
- Department of Radiology, Great Ormond Street Hospital, London, UK
| | - Deborah Krakow
- Department of Obstetrics and Gynecology and Department of Orthopaedic Surgery and Human Genetics, University of California at Los Angeles, Los Angeles, California
| | - Stefan Mundlos
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Gen Nishimura
- Department of Radiology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Stephen Robertson
- Department of Paediatrics and Child Health, Dunedin School of Medicine, Otago University, Dunedin, New Zealand
| | - Luca Sangiorgi
- Department of Medical Genetics and Skeletal Rare Diseases, IRCCS Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Ravi Savarirayan
- Murdoch Childrens Research Institute and University of Melbourne, Parkville, Victoria, Australia
| | - David Sillence
- Discipline of Genomic Medicine, the Children's Hospital at Westmead, Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | | | - Sheila Unger
- Medical Genetics Service, CHUV, University of Lausanne, Lausanne, Switzerland
| | - Matthew L Warman
- Orthopaedic Research Laboratories, Boston Children's Hospital, Boston, Massachusetts
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26
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Guo X, Shi T, Lin M, Zhang Y. A Nonsense Mutation in HOXD13 Gene from A Chinese Family with Non-Syndromic Synpolydactyly. TOHOKU J EXP MED 2019; 249:93-100. [PMID: 31611522 DOI: 10.1620/tjem.249.93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Synpolydactyly is a congenital limb malformation characterized by incomplete separation and duplication in fingers and/or toes, which is mainly caused by mutations in the homeobox D13 (HOXD13) gene. Here, a four-generation family with variant phenotypes of synpolydactyly was analyzed, in which the proband had bilateral preaxial synpolydactyly in toes with normal fingers, the father had clinodactyly in the fifth fingers, while the mother and grandma was normal. Trio whole-exome sequencing (trio-WES) is a high throughput sequencing targeting whole genome for detecting exonic variants from the proband and the parents in a family. Through trio-WES followed by Sanger sequencing and enzyme digestion, a heterozygous nonsense mutation (c.859 C>T/p.Gln287Ter) was newly identified in the homeodomain of the HOXD13 gene from the proband and the affected father, but not from the unaffected mother, the unaffected grandma, or the normal control. Mutation Taster, Human Splicing Finder and EX-SKIP predicted that the heterozygous mutation (c.859 C>T) would result in haploinsufficiency of HOXD13 protein through nonsense-mediated mRNA decay (NMD) and splicing abnormality, which might disrupt the integrity and reduce the expression level of the HOXD13 protein (loss-of-function). In short, a heterozygous nonsense mutation in the HOXD13 gene was newly identified in two patients with mild phenotypes of synpolydactyly, which extends the mutation spectrum in HOXD13 gene. Moreover, the findings we presented here deepen our understanding of the clinical consequences of non-syndromic synpolydactyly and may provide a new clue for further studies of the pathogenic mechanism of the mutation that causes aberrant splicing of HOXD13 gene.
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Affiliation(s)
- Xiaoyan Guo
- Department of Laboratory Medicine, Fuzhou Second Hospital Affiliated to Xiamen University
| | - Tengfei Shi
- Department of Laboratory Medicine, Fuzhou Second Hospital Affiliated to Xiamen University
| | - Mingrui Lin
- Intensive Care Unit, The Affiliated People's Hospital of Fujian Traditional Medical University
| | - Yiyuan Zhang
- Department of Orthopedics, Fuzhou Second Hospital Affiliated to Xiamen University
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27
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Potuijt JWP, Galjaard RJH, van der Spek PJ, van Nieuwenhoven CA, Ahituv N, Oberg KC, Hovius SER. A multidisciplinary review of triphalangeal thumb. J Hand Surg Eur Vol 2019; 44:59-68. [PMID: 30318985 PMCID: PMC6297887 DOI: 10.1177/1753193418803521] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Despite being a rare congenital limb anomaly, triphalangeal thumb is a subject of research in various scientific fields, providing new insights in clinical research and evolutionary biology. The findings of triphalangeal thumb can be predictive for other congenital anomalies as part of an underlying syndrome. Furthermore, triphalangeal thumb is still being used as a model in molecular genetics to study gene regulation by long-range regulatory elements. We present a review that summarizes a number of scientifically relevant topics that involve the triphalangeal thumb phenotype. Future initiatives involving multidisciplinary teams collaborating in the field of triphalangeal thumb research can lead to a better understanding of the pathogenesis and molecular mechanisms of this condition as well as other congenital upper limb anomalies.
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Affiliation(s)
- Jacob W. P. Potuijt
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands,Jacob W. P. Potuijt, Department of Plastic, Reconstructive and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Ee-1589 Postbus 2040, 3015 GE Rotterdam, The Netherlands.
| | - Robert-Jan H. Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter J. van der Spek
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands,Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christianne A. van Nieuwenhoven
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, SF, USA,Institute for Human Genetics, University of California San Francisco, SF, USA
| | - Kerby C. Oberg
- Department of Pathology and Human Anatomy, Loma Linda University, Loma Linda, USA
| | - Steven E. R. Hovius
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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A novel ZRS variant causes preaxial polydactyly type I by increased sonic hedgehog expression in the developing limb bud. Genet Med 2019; 22:189-198. [PMID: 31395945 PMCID: PMC6944640 DOI: 10.1038/s41436-019-0626-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 07/22/2019] [Indexed: 02/06/2023] Open
Abstract
Purpose Preaxial polydactyly (PPD) is a common congenital hand malformation classified into four subtypes (PPD I–IV). Variants in the zone of polarizing activity regulatory sequence (ZRS) within intron 5 of the LMBR1 gene are linked to most PPD types. However, the genes responsible for PPD I and the underlying mechanisms are unknown. Methods A rare large four-generation family with isolated PPD I was subjected to genome-wide genotyping and sequence analysis. In vitro and in vivo functional studies were performed in Caco-2 cells, 293T cells, and a knockin transgenic mouse model. Results A novel g.101779T>A (reference sequence: NG_009240.2; position 446 of the ZRS) variant segregates with all PPD I–affected individuals. The knockin mouse with this ZRS variant exhibited PPD I phenotype accompanying ectopic and excess expression of Shh. We confirmed that HnRNP K can bind the ZRS and SHH promoters. The ZRS mutant enhanced the binding affinity for HnRNP K and upregulated SHH expression. Conclusion Our results identify the first PPD I disease-causing variant. The variant leading to PPD I may be associated with enhancing SHH expression mediated by HnRNP K. This study adds to the ZRS-associated syndromes classification system for PPD and clarifies the underlying molecular mechanisms.
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29
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Zhao X, Xu H, Liu X, Li L. Targeted exome sequencing reveals a novel
GLI3
mutation in a Chinese family with nonsyndromic polydactyly. Dev Dyn 2019; 248:942-947. [PMID: 31306531 DOI: 10.1002/dvdy.89] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/09/2019] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Xiangyu Zhao
- Department of Medical GeneticsLinyi People's Hospital Linyi Shandong Province China
| | - Hongyan Xu
- Department of Medical GeneticsLinyi People's Hospital Linyi Shandong Province China
| | - Xiaxia Liu
- Department of Medical GeneticsLinyi People's Hospital Linyi Shandong Province China
| | - Lin Li
- Department of Medical GeneticsLinyi People's Hospital Linyi Shandong Province China
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30
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Kumar Sahoo P, Sahu MM, Prasad Das S. Clinical spectrum of congenital tibial hemimelia in 35 limbs of 24 patients: A single center observational study from India. Eur J Med Genet 2019; 62:103666. [PMID: 31078790 DOI: 10.1016/j.ejmg.2019.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/04/2019] [Accepted: 05/04/2019] [Indexed: 11/29/2022]
Abstract
PURPOSE Considering the paucity of reports on large series of patients with tibial hemimelia, we assessed the clinical spectrum of this rare congenital disorder in patients seen at a single Indian center over 10 years. METHODS Retrospective review of medical records of patients seen at single center in 10 years. RESULTS Thirty-five cases of TH, mostly Jones types Ia (18) and II (10), were diagnosed in 24 patients (13 had unilateral TH). Associated foot deformities included equinovarus (22), varus foot (10), absence of the medial row of toes (5) and polydactyly (3). Upper limbs anomalies included split-hand deformity (five patients) and radial club hand (two patients). Nine limbs of seven patients were surgically reconstructed. Modified orthosis was provided to seven patients, custom designed prosthesis fitment in six and amputation with prosthesis fitment in one. Patients presenting at adolescence or later were habituated to their deformity for indoor ambulation; families declined amputation. CONCLUSION Reports of more TH cases will provide input to researchers to consider comprehensive rehabilitation for enhancing indoor and community ambulation.
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Affiliation(s)
- Pabitra Kumar Sahoo
- Swami Vivekananda National Institute of Rehabilitation Training and Research(SVNIRTAR), Olatpur, Cuttack, Odisha, 753014, India.
| | - Mamata Manjari Sahu
- Swami Vivekananda National Institute of Rehabilitation Training and Research(SVNIRTAR), Olatpur, Cuttack, Odisha, 753014, India.
| | - Sakti Prasad Das
- Swami Vivekananda National Institute of Rehabilitation Training and Research(SVNIRTAR), Olatpur, Cuttack, Odisha, 753014, India.
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31
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Yip RK, Chan D, Cheah KS. Mechanistic insights into skeletal development gained from genetic disorders. Curr Top Dev Biol 2019; 133:343-385. [DOI: 10.1016/bs.ctdb.2019.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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Pazzaglia UE, Sibilia V, Casati L, Salvi AG, Minini A, Reguzzoni M. The missing segment of the autopod 1st ray: new insights from a morphometric study of the human hand. J Anat 2018; 233:828-842. [PMID: 30368800 PMCID: PMC6231165 DOI: 10.1111/joa.12883] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2018] [Indexed: 12/16/2022] Open
Abstract
Whether the 1st segment of the human autopod 1st ray is a 'true' metapodial with loss of the proximal or mid phalanx or the original basal phalanx with loss of the metacarpal has been a long-lasting discussion. The actual knowledge of the developmental pattern of upper autopod segments at a fetal age of 20-22 weeks, combined with X-ray morphometry of normal long bones of the hand in the growing ages, was used for analysis of the parameters, percentage length, position of epiphyseal ossification centers and proximal/distal growth rate. The symmetric growth pattern in the fetal anlagen changed to unidirectional in the postnatal development in relation to epiphyseal ossification formation. The percentage length assessment, the distribution of the epiphyseal ossification centers, and differential proximal/distal growth rate among the growing hand segments supported homology of most proximal segment of the thumb with the 2nd-5th proximal phalanges and that of the proximal phalanx of the thumb with the 2nd-5th mid phalanges in the same hand. Published case reports of either metanalysis of 'triphalangeal thumb' and 'proximal/distal epiphyseal ossification centers' were used to support the applied morphometric methodology; in particular, the latter did not give evidence of growth pattern inversion of the proximal segment of the thumb. The presented data support the hypothesis that during evolution, the lost segment of the autopod 1st ray is the metacarpal.
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Affiliation(s)
- Ugo E. Pazzaglia
- Department of Medical and Surgical SpecialtiesRadiological Sciences and Public HealthUniversity of BresciaBresciaItaly
| | - Valeria Sibilia
- Department of Medical Biotechnology and Translational MedicineUniversity of MilanMilanoItaly
| | - Lavinia Casati
- Department of Medical Biotechnology and Translational MedicineUniversity of MilanMilanoItaly
| | - Andrea G. Salvi
- Department of Medical and Surgical SpecialtiesRadiological Sciences and Public HealthUniversity of BresciaBresciaItaly
| | - Andrea Minini
- Department of Medical and Surgical SpecialtiesRadiological Sciences and Public HealthUniversity of BresciaBresciaItaly
| | - Marcella Reguzzoni
- Department of Surgical and Morphological SciencesUniversity of InsubriaVareseItaly
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33
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Umair M, Ahmad F, Bilal M, Ahmad W, Alfadhel M. Clinical Genetics of Polydactyly: An Updated Review. Front Genet 2018; 9:447. [PMID: 30459804 PMCID: PMC6232527 DOI: 10.3389/fgene.2018.00447] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/14/2018] [Indexed: 01/17/2023] Open
Abstract
Polydactyly, also known as hyperdactyly or hexadactyly is the most common hereditary limb anomaly characterized by extra fingers or toes, with various associated morphologic phenotypes as part of a syndrome (syndromic polydactyly) or may occur as a separate event (non-syndromic polydactyly). Broadly, the non-syndromic polydactyly has been classified into three types, i.e.; preaxial polydactyly (radial), central polydactyly (axial), and postaxial polydactyly (ulnar). Mostly inherited as an autosomal dominant entity with variable penetrance and caused by defects that occur in the anterior-posterior patterning of limb development. In humans, to-date at least 10 loci and six genes causing non-syndromic polydactyly have been identified, including the ZNF141, GLI3, MIPOL1, IQCE, PITX1, and the GLI1. In the present review, clinical, genetic and molecular characterization of the polydactyly types has been presented including the recent genes and loci identified for non-syndromic polydactyly. This review provides an overview of the complex genetic mechanism underlie polydactyly and might help in genetic counseling and quick molecular diagnosis.
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Affiliation(s)
- Muhammad Umair
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Farooq Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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34
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Al-Qattan MM. The association between preaxial polydactyly and radial longitudinal deficiency in syndromic cases: a report on nine families. J Hand Surg Eur Vol 2018; 43:744-750. [PMID: 29451098 DOI: 10.1177/1753193418758862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
UNLABELLED Preaxial polydactyly and radial longitudinal deficiency are usually viewed as two different entities. We present nine families with different disorders in which both preaxial polydactyly and radial longitudinal deficiency were seen in the phenotype. This indicates that both entities may be caused by the same developmental error or insult. The pathogenesis is complex and may be related to the interactions of two signalling loops: the first loop (named as the radial longitudinal deficiency loop) contains genes/proteins responsible for the development of the radial ray; and the second loop (named as the preaxial polydactyly loop) contains the Sonic Hedgehog involved in the pathogenesis of preaxial polydactyly. This entity is named as the preaxial polydactyly-radial longitudinal deficiency association and should be included in the description of the preaxial polydactyly spectrum. LEVEL OF EVIDENCE IV.
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35
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Shh signaling influences the phenotype of Pitx1-/- hindlimbs. Dev Biol 2018; 439:65-68. [PMID: 29705333 DOI: 10.1016/j.ydbio.2018.04.024] [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: 08/22/2017] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 11/23/2022]
Abstract
Forelimbs (FLs) and hindlimbs (HLs) develop under the instructive and integrated guidance of signaling centers and transcription factor (TF) action. The development of structures specific to each limb type depends on the limb-specific modulation of these integrated components. Pitx1 is a transcription factor gene expressed in HL, absent in FL, and required for HL-specific patterning and development, in particular for formation of anterior HL skeletal elements. Pitx1 achieves this function by direct TF action on the core limb program, which is largely shared between FL and HL. Shh signaling plays a crucial role in anterior-posterior (AP) patterning in both FL and HL. The present work assessed the relationship between Shh signaling and Pitx1 action for AP patterning. We found that reducing the gene dosage of Shh in the context of the Pitx1-/- HL decreases the severity of the Pitx1-/- phenotype, in particular, the loss of anterior limb structures and the shortening of femur length. However, this did not rescue HL-specific patterning features. Thus, Pitx1 action integrates Shh signaling but not for limb-type-specific patterning.
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Hinreiner S, Wieczorek D, Mueller D, Roedl T, Thiel G, Grasshoff U, Chaoui R, Hehr U. Further evidence for complex inheritance of holoprosencephaly: Lessons learned from pre- and postnatal diagnostic testing in Germany. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2018; 178:198-205. [PMID: 30182445 DOI: 10.1002/ajmg.c.31625] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/19/2018] [Accepted: 04/20/2018] [Indexed: 01/02/2023]
Abstract
Holoprosencephaly (HPE) has been defined as a distinct clinical entity with characteristic facial gestalt, which may-or may not-be associated with the true brain malformation observed postmortem in autopsy or in pre- or postnatal imaging. Affected families mainly show autosomal dominant inheritance with markedly reduced penetrance and extremely broad clinical variability even between mutation carriers within the same families. We here present advances in prenatal imaging over the last years, increasing the proportion of individuals with HPE identified prenatally including milder HPE forms and more frequently allowing to detect more severe forms already in early gestation. We report the results of diagnostic genetic testing of 344 unrelated patients for HPE at our lab in Germany since the year 2000, which currently with the application of next generation sequencing (NGS) panel sequencing identifies causal mutations for about 31% (12/38) of unrelated individuals with normal chromosomes when compared to about 15% (46/306) using conventional Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA). More comprehensive genetic testing by our in house NGS panel sequencing of 10 HPE associated genes (MiSeq™ and NextSeq™500, Illumina, Inc., San Diego, CA) not only allowed to include genes with smaller contribution to the phenotype, but may also unravel additional low frequency or more common genetic variants potentially contributing to the observed large intrafamiliar variability and may ultimately guide our understanding of the individual clinical manifestation of this complex developmental disorder.
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Affiliation(s)
| | - Dagmar Wieczorek
- Medical Faculty, Institute of Human Genetics, Heinrich-Heine-University Duesseldorf, Duesseldorf, Germany
| | - Dietmar Mueller
- Department of Medical Genetics, Children's Hospital Chemnitz, Chemnitz, Germany
| | - Tanja Roedl
- Center for Human Genetics Regensburg, Regensburg, Germany
| | - Gundula Thiel
- Center for Prenatal Diagnosis and Human Genetics, Berlin, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University Hospital Tuebingen, Tuebingen, Germany
| | - Rabih Chaoui
- Center for Prenatal Diagnosis and Human Genetics, Berlin, Germany
| | - Ute Hehr
- Center for Human Genetics Regensburg, Regensburg, Germany
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Lettice LA, Devenney P, De Angelis C, Hill RE. The Conserved Sonic Hedgehog Limb Enhancer Consists of Discrete Functional Elements that Regulate Precise Spatial Expression. Cell Rep 2018; 20:1396-1408. [PMID: 28793263 PMCID: PMC5561167 DOI: 10.1016/j.celrep.2017.07.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 05/17/2017] [Accepted: 07/13/2017] [Indexed: 12/21/2022] Open
Abstract
Expression of sonic hedgehog (Shh) in the limb bud is regulated by an enhancer called the zone of polarizing activity regulatory sequence (ZRS), which, in evolution, belongs to an ancient group of highly conserved cis regulators found in all classes of vertebrates. Here, we examined the endogenous ZRS in mice, using genome editing to establish the relationship between enhancer composition and embryonic phenotype. We show that enhancer activity is a consolidation of distinct activity domains. Spatial restriction of Shh expression is mediated by a discrete repressor module, whereas levels of gene expression are controlled by large overlapping domains containing varying numbers of HOXD binding sites. The number of HOXD binding sites regulates expression levels incrementally. Substantial portions of conserved sequence are dispensable, indicating the presence of sequence redundancy. We propose a collective model for enhancer activity in which function is an integration of discrete expression activities and redundant components that drive robust expression. The ancient vertebrate enhancer, the ZRS, shows sequence plasticity Discrete regulatory activities are assigned to specific sites in the enhancer The number of HOXD binding sites determines the level of Shh expression Robust expression is a collective of regulatory and redundant information
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Affiliation(s)
- Laura A Lettice
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Paul Devenney
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Carlo De Angelis
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Robert E Hill
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
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Zone of Polarizing Activity Regulatory Sequence Mutations/Duplications with Preaxial Polydactyly and Longitudinal Preaxial Ray Deficiency in the Phenotype: A Review of Human Cases, Animal Models, and Insights Regarding the Pathogenesis. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1573871. [PMID: 29651423 PMCID: PMC5832050 DOI: 10.1155/2018/1573871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/19/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023]
Abstract
Clinicians and scientists interested in developmental biology have viewed preaxial polydactyly (PPD) and longitudinal preaxial ray deficiency (LPAD) as two different entities. Point mutations and duplications in the zone of polarizing activity regulatory sequence (ZRS) are associated with anterior ectopic expression of Sonic Hedgehog (SHH) in the limb bud and usually result in a PPD phenotype. However, some of these mutations/duplications also have LPAD in the phenotype. This unusual PPD-LPAD association in ZRS mutations/duplications has not been specifically reviewed in the literature. The author reviews this unusual entity and gives insights regarding its pathogenesis.
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Thenar Dysplasia in Radial Polydactyly Depends on the Level of Bifurcation. Plast Reconstr Surg 2018; 141:85e-90e. [DOI: 10.1097/prs.0000000000003937] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Zhang Z, Yi D, Xie R, Hamilton JL, Kang QL, Chen D. Postaxial limb hypoplasia (PALH): the classification, clinical features, and related developmental biology. Ann N Y Acad Sci 2017; 1409:67-78. [PMID: 28990185 PMCID: PMC5730483 DOI: 10.1111/nyas.13440] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/18/2017] [Accepted: 06/28/2017] [Indexed: 12/29/2022]
Abstract
Postaxial limb hypoplasia (PALH) is a group of nonhereditary diseases with congenital lower limb deficiency affecting the fibular ray, including fibular hemimelia, proximal femoral focal deficiency, and tarsal coalition. The etiology and the developmental biology of the anomaly are still not fully understood. Here, we review the previous classification systems, present the clinical features, and discuss the developmental biology of PALH.
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Affiliation(s)
- Zeng Zhang
- Department of Orthopedic Surgery, Shanghai Jiao-Tong University Affiliated the Sixth People’s Hospital, Shanghai, China
| | - Dan Yi
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, Illinois
| | - Rong Xie
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, Illinois
| | - John L. Hamilton
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, Illinois
| | - Qing-Lin Kang
- Department of Orthopedic Surgery, Shanghai Jiao-Tong University Affiliated the Sixth People’s Hospital, Shanghai, China
| | - Di Chen
- Department of Orthopedic Surgery, Rush University Medical Center, Chicago, Illinois
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Bedard T, Lowry RB, Sibbald B, Crawford S, Kiefer GN. Congenital limb deficiencies and major associated anomalies in Alberta for the years 1980-2012. Am J Med Genet A 2017; 176:19-28. [PMID: 29168277 DOI: 10.1002/ajmg.a.38513] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/23/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
Abstract
There is a wide range of the proportion of congenital anomalies associated with limb deficiencies reported in the literature. This variation is primarily attributed to methodology and classification differences. The distribution of associated anomalies among cases with congenital limb deficiencies in Alberta born between January 1, 1980 and December 31, 2012 is described. Of the 170 cases identified, most were live born (75.3%), male (61.8%), had longitudinal limb deficiencies (78.8%), and had associated anomalies outside the musculoskeletal system (77.6%). Significant associations between the preaxial longitudinal group and the central nervous, gastrointestinal, and cardiovascular systems are reported as well as between the postaxial longitudinal group and congenital hip and foot anomalies. Probable and possible syndrome diagnoses are described for cases with recognized malformation patterns.
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Affiliation(s)
- Tanya Bedard
- Alberta Congenital Anomalies Surveillance System, Alberta Health, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - R Brian Lowry
- Alberta Congenital Anomalies Surveillance System, Alberta Health, Alberta Children's Hospital, Calgary, Alberta, Canada.,Departments of Pediatrics and Medical Genetics, University of Calgary, Alberta Children's Hospital, Calgary, Alberta, Canada.,Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
| | - Barbara Sibbald
- Alberta Congenital Anomalies Surveillance System, Alberta Health, Alberta Children's Hospital, Calgary, Alberta, Canada
| | - Susan Crawford
- Alberta Perinatal Health Program, Calgary, Alberta, Canada
| | - Gerhard N Kiefer
- Alberta Congenital Anomalies Surveillance System, Alberta Health, Alberta Children's Hospital, Calgary, Alberta, Canada.,Department of Surgery, University of Calgary, Alberta Children's Hospital, Calgary, Alberta, Canada
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Peluso S, Douglas A, Hill A, De Angelis C, Moore BL, Grimes G, Petrovich G, Essafi A, Hill RE. Fibroblast growth factors (FGFs) prime the limb specific Shh enhancer for chromatin changes that balance histone acetylation mediated by E26 transformation-specific (ETS) factors. eLife 2017; 6:28590. [PMID: 28949289 PMCID: PMC5659820 DOI: 10.7554/elife.28590] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/25/2017] [Indexed: 01/12/2023] Open
Abstract
Sonic hedgehog (Shh) expression in the limb bud organizing centre called the zone of polarizing activity is regulated by the ZRS enhancer. Here, we examine in mouse and in a mouse limb-derived cell line the dynamic events that activate and restrict the spatial activity of the ZRS. Fibroblast growth factor (FGF) signalling in the distal limb primes the ZRS at early embryonic stages maintaining a poised, but inactive state broadly across the distal limb mesenchyme. The E26 transformation-specific transcription factor, ETV4, which is induced by FGF signalling and acts as a repressor of ZRS activity, interacts with the histone deacetylase HDAC2 and ensures that the poised ZRS remains transcriptionally inactive. Conversely, GABPα, an activator of the ZRS, recruits p300, which is associated with histone acetylation (H3K27ac) indicative of an active enhancer. Hence, the primed but inactive state of the ZRS is induced by FGF signalling and in combination with balanced histone modification events establishes the restricted, active enhancer responsible for patterning the limb bud during development. As an animal embryo develops, specific genes need to be switched on and off at the right time and place to ensure that the embryo’s tissues and organs form properly. Proteins called transcription factors control the activity of individual genes by binding to regions of DNA known as enhancers. Changes in the way DNA is packaged inside cells can affect the ability of transcription factors to access the enhancers, and therefore also influence when particular genes are switched on or off. Sonic hedgehog (or Shh for short) is a gene that helps to control various aspects of development including the formation of the limbs and brain. The limb forms from a structure in the embryo referred to as the limb bud. An enhancer called ZRS regulates the precise position within the limb bud where the Shh gene is active in a region designated as the “zone of polarizing activity”. Yet, it was not known how the enhancer is controlled to ensure this pattern is achieved. Peluso et al. investigated the events that lead to ZRS becoming active in mice embryos. The experiments show that the ZRS enhancer exists in three different states in cells across the limb bud: poised, active and inactive. The enhancer is poised in a broad region of the limb bud in cells that are potentially able to switch on the Shh gene. Proteins called fibroblast growth factors drive the enhancer to enter this poised state by altering the way the DNA containing the enhancer is packaged in the cell. Specific transcription factors are able to bind to the poised enhancer and it is the balance between these different transcription factors that activates the enhancer in the zone of polarizing activity. Furthermore in the region of the limb bud where the fibroblast growth factors are not present the ZRS is inactive. These findings show that fibroblast growth factors, in combination with other changes to the ZRS enhancer, restrict the area in which the enhancer is active to a particular region of the limb bud. Differences in enhancer elements are known to underlie a range of inherited characteristics and may influence whether an individual develops many common diseases. In the future, investigating how cells control the activity of enhancers may provide clues to identifying new targets for drugs to treat some of these diseases.
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Affiliation(s)
- Silvia Peluso
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam Douglas
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison Hill
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Carlo De Angelis
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Benjamin L Moore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Giulia Petrovich
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Abdelkader Essafi
- School of Cellular and Molecular Medicine, Faculty of Biomedical Sciences, University of Bristol, Bristol, United Kingdom
| | - Robert E Hill
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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43
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Baas M, Potuijt JWP, Hovius SER, Hoogeboom AJM, Galjaard RJH, van Nieuwenhoven CA. Intrafamilial variability of the triphalangeal thumb phenotype in a Dutch population: Evidence for phenotypic progression over generations? Am J Med Genet A 2017; 173:2898-2905. [PMID: 28889454 PMCID: PMC5698718 DOI: 10.1002/ajmg.a.38398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/21/2017] [Accepted: 07/22/2017] [Indexed: 02/06/2023]
Abstract
Triphalangeal thumbs (TPTs) are regularly caused by mutations in the ZRS in LMBR1. Phenotypic variability can be present in TPT‐families. However, recent observations suggest an increased occurrence of severe phenotypes in the Dutch TPT‐population. Therefore, the aim of this study is to investigate the progression of the clinical severity of TPT‐phenotype through generations. Index patients from a Dutch TPT‐population were identified. A 105C>G mutation in the ZRS has previously been confirmed in this population. Questionnaires regarding family occurrence and phenotypes were distributed. Subsequently, families were visited to validate the phenotype. Both occurrence and inheritance patterns of the TPT‐phenotype were analyzed through multiple generations. One hundred seventy patients with TPT were identified from 11 families. When considering all 132 segregations (parent‐to‐child transmission), 54% of the segregations produced a stable phenotype, 38% produced a more severe phenotype while only 8% of the phenotype was less severe when compared to the affected parents. Overall, 71% of the index patients had a more severe phenotype compared to their great‐grandparent. Although all family members share an identical mutation in the ZRS (105C>G), it does not explain the wide phenotypic range of anomalies. Our observational study provides better estimations for counseling and provides new insights in the long‐range regulation of SHH by the ZRS‐enhancer. In the current study, we provide evidence that the assumed variability in TPT‐phenotype is not random, but in fact it is more likely that the expression becomes more severe in the next generation. Therefore, we observe a pattern that resembles phenotypic anticipation in TPT‐families.
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Affiliation(s)
- Martijn Baas
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jacob W P Potuijt
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Steven E R Hovius
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - A Jeannette M Hoogeboom
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Robert-Jan H Galjaard
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christianne A van Nieuwenhoven
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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Yang X, Shen Q, Sulaiman X, Liu H, Peng M, Zhang Y. Identity-by-descent refines mapping of candidate regions for preaxial polydactyly II /III in a large Chinese pedigree. Hereditas 2017; 155:2. [PMID: 28690477 PMCID: PMC5496229 DOI: 10.1186/s41065-017-0040-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022] Open
Abstract
Preaxial polydactyly (PPD) is congenital hand malformation characterized by the duplication of digit. Herein, we scan the genome-wide SNPs for a large Chinese family with PPD-II/III. We employ the refined IBD algorithm to identify the identity-by-decent (IBD) segments and compare the frequency among the patients and normal relatives. A total of 72 markers of 0.01 percentile of the permutation are identified as the peak signals. Among of them, 57markers locate on chromosome 7q36 which is associated with PPD. Further analyses refine the mapping of candidate region in chromosome 7q36 into two 380 Kb fragments within LMBR1 and SHH respectively. IBD approach is a suitable method for mapping causal gene of human disease. Target-enrichment sequencing as well as functional experiments are required to illustrate the pathogenic mechanisms for PPD in the future.
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Affiliation(s)
- Xingyan Yang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Quankuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ /CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming, China
| | | | - Hequn Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| | - Minsheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ /CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223 China
| | - Yaping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ /CUHK Joint Laboratory of Bio-resources and Molecular Research in Common Diseases, Kunming, China.,Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, 650223 China
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45
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Complex postaxial polydactyly types A and B with camptodactyly, hypoplastic third toe, zygodactyly and other digit anomalies caused by a novel GLI3 mutation. Eur J Med Genet 2017; 60:268-274. [DOI: 10.1016/j.ejmg.2017.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/07/2017] [Accepted: 03/11/2017] [Indexed: 11/21/2022]
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46
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Tao H, Kawakami Y, Hui CC, Hopyan S. The two domain hypothesis of limb prepattern and its relevance to congenital limb anomalies. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28319333 DOI: 10.1002/wdev.270] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 11/06/2022]
Abstract
Functional annotation of mutations that cause human limb anomalies is enabled by basic developmental studies. In this study, we focus on the prepatterning stage of limb development and discuss a recent model that proposes anterior and posterior domains of the early limb bud generate two halves of the future skeleton. By comparing phenotypes in humans with those in model organisms, we evaluate whether this prepatterning concept helps to annotate human disease alleles. WIREs Dev Biol 2017, 6:e270. doi: 10.1002/wdev.270 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Hirotaka Tao
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Sevan Hopyan
- Program in Developmental and Stem Cell Biology, Research Institute, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Division of Orthopaedic Surgery, Hospital for Sick Children and University of Toronto, Toronto, Canada
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47
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Wang B, Wang W, Ni F. Classification of Congenital Deformities of Hands and Upper Limbs and Selection of Surgery Timing. Plast Reconstr Surg 2017. [DOI: 10.1007/978-981-10-5101-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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48
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Abstract
Tibial hemimelia is a rare congenital lower limb deficiency presenting with a wide spectrum of associated congenital anomalies, deficiencies and duplications. Reconstructive options have been limited, and the gold standard for treatment has remained amputation with prosthetic fitting. There is now a better understanding of the genetics, etiology and pathoanatomy of tibial hemimelia. Armed with this knowledge, I present here a new classification to guide treatment and prognosis and then discuss new treatment strategies and techniques for limb reconstruction based on this new classification scheme.
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49
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Abstract
Genetic variation associated with disease often appears in non-coding parts of the genome. Understanding the mechanisms by which this phenomenon leads to disease is necessary to translate results from genetic association studies to the clinic. Assigning function to this type of variation is notoriously difficult because the human genome harbours a complex regulatory landscape with a dizzying array of transcriptional regulatory sequences, such as enhancers that have unpredictable, promiscuous and context-dependent behaviour. In this Review, we discuss how technological advances have provided increasingly detailed information on genome folding; for example, genome folding forms loops that bring enhancers and target genes into close proximity. We also now know that enhancers function within topologically associated domains, which are structural and functional units of chromosomes. Studying disease-associated mutations and chromosomal rearrangements in the context of the 3D genome will enable the identification of dysregulated target genes and aid the progression from descriptive genetic association results to discovering molecular mechanisms underlying disease.
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50
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Wu PF, Guo S, Fan XF, Fan LL, Jin JY, Tang JY, Xiang R. A Novel ZRS Mutation in a Chinese Patient with Preaxial Polydactyly and Triphalangeal Thumb. Cytogenet Genome Res 2016; 149:171-175. [PMID: 27592358 DOI: 10.1159/000448820] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2016] [Indexed: 11/19/2022] Open
Abstract
Preaxial polydactyly (PPD; OMIM 603596), which is characterized as having supernumerary fingers, is an unusual congenital hand abnormality. Triphalangeal thumb (TPT; OMIM 190600) is identified by an extra phalangeal bone and is often found in association with PPD. When in combination, the disease is referred to as PPD type II (PPD II; OMIM 174500). Previous studies have demonstrated that variations in the zone of polarizing activity regulatory sequence (ZRS; chr7:156,583,796-156,584,569; hg19) region are associated with PPD II. In this study, our patient was diagnosed with PPD II, having bilateral thumb duplication and unilateral TPT (on the right hand). Further investigation of possible causative genes identified a de novo heterozygous ZRS mutation (ZRS 428T>A). This novel mutation was neither found in 200 normal controls nor reported in online databases. Moreover, the bioinformatics program Genomic Evolutionary Rate Profiling (GERP) revealed this site (ZRS428) to be evolutionarily highly conserved, and the 428T>A point mutation was predicted to be deleterious by MutationTaster. In conclusion, the affected individual shows bilateral thumb duplication, but unilateral TPT making this case special. Thus, our findings not only further support the important role of ZRS in limb morphogenesis and expand the spectrum of ZRS mutations, but also emphasize the significance of genetic diagnosis and counseling of families with digit number and identity alterations as well.
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Affiliation(s)
- Pan-Feng Wu
- Department of Orthopaedics, Xiangya Hospital, Changsha, PR China
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