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Saeki N, Inui-Yamamoto C, Ikeda Y, Kanai R, Hata K, Itoh S, Inubushi T, Akiyama S, Ohba S, Abe M. Deletion of Trps1 regulatory elements recapitulates postnatal hip joint abnormalities and growth retardation of Trichorhinophalangeal syndrome in mice. Hum Mol Genet 2024:ddae102. [PMID: 38899779 DOI: 10.1093/hmg/ddae102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/09/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
Trichorhinophalangeal syndrome (TRPS) is a genetic disorder caused by point mutations or deletions in the gene-encoding transcription factor TRPS1. TRPS patients display a range of skeletal dysplasias, including reduced jaw size, short stature, and a cone-shaped digit epiphysis. Certain TRPS patients experience early onset coxarthrosis that leads to a devastating drop in their daily activities. The etiologies of congenital skeletal abnormalities of TRPS were revealed through the analysis of Trps1 mutant mouse strains. However, early postnatal lethality in Trps1 knockout mice has hampered the study of postnatal TRPS pathology. Here, through epigenomic analysis we identified two previously uncharacterized candidate gene regulatory regions in the first intron of Trps1. We deleted these regions, either individually or simultaneously, and examined their effects on skeletal morphogenesis. Animals that were deleted individually for either region displayed only modest phenotypes. In contrast, the Trps1Δint/Δint mouse strain with simultaneous deletion of both genomic regions exhibit postnatal growth retardation. This strain displayed delayed secondary ossification center formation in the long bones and misshaped hip joint development that resulted in acetabular dysplasia. Reducing one allele of the Trps1 gene in Trps1Δint mice resulted in medial patellar dislocation that has been observed in some patients with TRPS. Our novel Trps1 hypomorphic strain recapitulates many postnatal pathologies observed in human TRPS patients, thus positioning this strain as a useful animal model to study postnatal TRPS pathogenesis. Our observations also suggest that Trps1 gene expression is regulated through several regulatory elements, thus guaranteeing robust expression maintenance in skeletal cells.
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Affiliation(s)
- Naoya Saeki
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
- Department of Special Needs Dentistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Chizuko Inui-Yamamoto
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Yuki Ikeda
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Rinna Kanai
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
- Department of Fixed Prosthodontics and Orofacial Function, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Kenji Hata
- Department of Molecular and Cellular Biochemistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shousaku Itoh
- Department of Restorative Dentistry and Endodontology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Toshihiro Inubushi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shigehisa Akiyama
- Department of Special Needs Dentistry, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
| | - Makoto Abe
- Department of Tissue and Developmental Biology, Osaka University Graduate School of Dentistry, Yamada-oka 1-8, Suita, Osaka 565-0871, Japan
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Abrar M, Ali S, Hussain I, Khatoon H, Batool F, Ghazanfar S, Corcoran D, Kawakami Y, Abbasi AA. Cis-regulatory control of mammalian Trps1 gene expression. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38369890 DOI: 10.1002/jez.b.23246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.
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Affiliation(s)
- Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Center of Regenerative Medicine and Stem Cells Research, Aga Khan University Hospital, Karachi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agriculture Research Centre (NARC), Islamabad, Pakistan
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Kamar A, Fahed AC, Shibbani K, El-Hachem N, Bou-Slaiman S, Arabi M, Kurban M, Seidman JG, Seidman CE, Haidar R, Baydoun E, Nemer G, Bitar F. A Novel Role for CSRP1 in a Lebanese Family with Congenital Cardiac Defects. Front Genet 2017; 8:217. [PMID: 29326753 PMCID: PMC5741687 DOI: 10.3389/fgene.2017.00217] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022] Open
Abstract
Despite an obvious role for consanguinity in congenital heart disease (CHD), most studies fail to document a monogenic model of inheritance except for few cases. We hereby describe a first-degree cousins consanguineous Lebanese family with 7 conceived children: 2 died in utero of unknown causes, 3 have CHD, and 4 have polydactyly. The aim of the study is to unveil the genetic variant(s) causing these phenotypes using next generation sequencing (NGS) technology. Targeted exome sequencing identified a heterozygous duplication in CSRP1 which leads to a potential frameshift mutation at position 154 of the protein. This mutation is inherited from the father, and segregates only with the CHD phenotype. The in vitro characterization demonstrates that the mutation dramatically abrogates its transcriptional activity over cardiac promoters like NPPA. In addition, it differentially inhibits the physical association of CSRP1 with SRF, GATA4, and with the newly described partner herein TBX5. Whole exome sequencing failed to show any potential variant linked to polydactyly, but revealed a novel missense mutation in TRPS1. This mutation is inherited from the healthy mother, and segregating only with the cardiac phenotype. Both TRPS1 and CSRP1 physically interact, and the mutations in each abrogate their partnership. Our findings add fundamental knowledge into the molecular basis of CHD, and propose the di-genic model of inheritance as responsible for such malformations.
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Affiliation(s)
- Amina Kamar
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Akl C Fahed
- Department of Genetics, Harvard Medical School, Boston, MA, United States.,Department of Medicine, Massachusetts General Hospital, Boston, MA, United States.,Division of Cardiology, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Kamel Shibbani
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Nehme El-Hachem
- Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Salim Bou-Slaiman
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon
| | - Mariam Arabi
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon
| | - Mazen Kurban
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut, Lebanon.,Department of Dermatology, American University of Beirut, Beirut, Lebanon.,Department of Dermatology, Columbia University, New York, NY, United States
| | - Jonathan G Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, United States
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, United States.,Division of Cardiology, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, United States
| | - Rachid Haidar
- Department of Surgery, American University of Beirut, Beirut, Lebanon
| | - Elias Baydoun
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Georges Nemer
- Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Fadi Bitar
- Department of Pediatrics and Adolescent Medicine, American University of Beirut, Beirut, Lebanon
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