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Qian W, Curtain BMM, Ryan JP, Navadgi S. Locally invasive cholangiocarcinoma causing gastric outlet obstruction in heterotaxy syndrome: A case report and review of literature. Radiol Case Rep 2024; 19:531-534. [PMID: 38044905 PMCID: PMC10686879 DOI: 10.1016/j.radcr.2023.10.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 12/05/2023] Open
Abstract
Heterotaxy syndrome is a disease of embryo development resulting in abnormal distribution of thoracic and abdominal organs across the left-right axis. In this case, A 77-year-old gentleman was admitted with gastric outlet obstruction secondary to cholangiocarcinoma. This is on a background of heterotaxy syndrome, specifically situs ambiguus. The patient's anatomical variations included a right-sided stomach, midline liver, and asplenia. Due to variant anatomy and risk of aspiration; endoscopy was abandoned in favor of surgical bypass via a gastrojejunostomy. Although technically challenging, complex upper abdominal surgery in heterotaxy syndrome has been described in the literature. Variations in anatomy observed in heterotaxy syndrome may render patients ineligible for resection of cholangiocarcinoma and increase the risk of complications. Careful preoperative planning with imaging and meticulous intraoperative dissection is required.
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Affiliation(s)
- Wanyang Qian
- Department of Surgery, St John of God Subiaco Hospital, Subiaco, Western Australia
| | | | - James P. Ryan
- Department of Radiology, St Vincent's University Hospital, Dublin, Ireland
| | - Suresh Navadgi
- Department of Surgery, St John of God Subiaco Hospital, Subiaco, Western Australia
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2
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Perrot A, Rickert-Sperling S. Human Genetics of Defects of Situs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1441:705-717. [PMID: 38884744 DOI: 10.1007/978-3-031-44087-8_42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Defects of situs are associated with complex sets of congenital heart defects in which the normal concordance of asymmetric thoracic and abdominal organs is disturbed. The cellular and molecular mechanisms underlying the formation of the embryonic left-right axis have been investigated extensively in the past decade. This has led to the identification of mutations in at least 33 different genes in humans with heterotaxy and situs defects. Those mutations affect a broad range of molecular components, from transcription factors, signaling molecules, and chromatin modifiers to ciliary proteins. A substantial overlap of these genes is observed with genes associated with other congenital heart diseases such as tetralogy of Fallot and double-outlet right ventricle, d-transposition of the great arteries, and atrioventricular septal defects. In this chapter, we present the broad genetic heterogeneity of situs defects including recent human genomics efforts.
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Affiliation(s)
- Andreas Perrot
- Experimental and Clinical Research Center, a cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité Universitätsmedizin Berlin, Berlin, Germany
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Nakai K, Lin H, Yamano S, Tanaka S, Kitamoto S, Saitoh H, Sakuma K, Kurauchi J, Akter E, Konno M, Ishibashi K, Kamata R, Ohashi A, Koseki J, Takahashi H, Yokoyama H, Shiraki Y, Enomoto A, Abe S, Hayakawa Y, Ushiku T, Mutoh M, Fujita Y, Kon S. Wnt activation disturbs cell competition and causes diffuse invasion of transformed cells through NF-κB-MMP21 pathway. Nat Commun 2023; 14:7048. [PMID: 37923722 PMCID: PMC10624923 DOI: 10.1038/s41467-023-42774-6] [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: 12/14/2022] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Normal epithelial cells exert their competitive advantage over RasV12-transformed cells and eliminate them into the apical lumen via cell competition. However, the internal or external factors that compromise cell competition and provoke carcinogenesis remain elusive. In this study, we examine the effect of sequential accumulation of gene mutations, mimicking multi-sequential carcinogenesis on RasV12-induced cell competition in intestinal epithelial tissues. Consequently, we find that the directionality of RasV12-cell extrusion in Wnt-activated epithelia is reversed, and transformed cells are delaminated into the basal lamina via non-cell autonomous MMP21 upregulation. Subsequently, diffusively infiltrating, transformed cells develop into highly invasive carcinomas. The elevated production of MMP21 is elicited partly through NF-κB signaling, blockage of which restores apical elimination of RasV12 cells. We further demonstrate that the NF-κB-MMP21 axis is significantly bolstered in early colorectal carcinoma in humans. Collectively, this study shows that cells with high mutational burdens exploit cell competition for their benefit by behaving as unfit cells, endowing them with an invasion advantage.
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Affiliation(s)
- Kazuki Nakai
- Division of Cancer Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, 278-0022, Japan
| | - Hancheng Lin
- Division of Cancer Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, 278-0022, Japan
| | - Shotaro Yamano
- Japan Bioassay Research Center, Japan Organization of Occupational Health and Safety, Kanagawa, 257-0015, Japan
| | - Shinya Tanaka
- Department of Molecular Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Sho Kitamoto
- Division of Microbiology and Immunology, The WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka, 565-0871, Japan
| | - Hitoshi Saitoh
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, 277-8577, Japan
| | - Kenta Sakuma
- Division of Cancer Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, 278-0022, Japan
| | - Junpei Kurauchi
- Division of Cancer Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, 278-0022, Japan
| | - Eilma Akter
- Division of Cancer Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, 278-0022, Japan
| | - Masamitsu Konno
- Division of Cancer Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, 278-0022, Japan
| | - Kojiro Ishibashi
- Division of Tumor Cell Biology and Bioimaging, Cancer Research Institute, Kanazawa University, Kakuma-Machi, Kanazawa, 920-1192, Japan
| | - Ryo Kamata
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, 277-8577, Japan
| | - Akihiro Ohashi
- Division of Translational Genomics, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, 277-8577, Japan
| | - Jun Koseki
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Hirotaka Takahashi
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Hideshi Yokoyama
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba, 278-8510, Japan
| | - Yukihiro Shiraki
- Department of Pathology, Nagoya University Hospital, Nagoya, 466-8550, Japan
| | - Atsushi Enomoto
- Department of Pathology, Nagoya University Hospital, Nagoya, 466-8550, Japan
| | - Sohei Abe
- Department of Gastroenterology, Graduate School of Medicine, University of Tokyo, Tokyo, 113-8655, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, University of Tokyo, Tokyo, 113-8655, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, University of Tokyo, Tokyo, 113-8655, Japan
| | - Michihiro Mutoh
- Department of Molecular-Targeting Prevention, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Yasuyuki Fujita
- Department of Molecular Oncology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Shunsuke Kon
- Division of Cancer Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, 278-0022, Japan.
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Safizadeh Shabestari SA, Nassir N, Sopariwala S, Karimov I, Tambi R, Zehra B, Kosaji N, Akter H, Berdiev BK, Uddin M. Overlapping pathogenic de novo CNVs in neurodevelopmental disorders and congenital anomalies impacting constraint genes regulating early development. Hum Genet 2023; 142:1201-1213. [PMID: 36383254 PMCID: PMC10449996 DOI: 10.1007/s00439-022-02482-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022]
Abstract
Neurodevelopmental disorders (NDDs) and congenital anomalies (CAs) are rare disorders with complex etiology. In this study, we investigated the less understood genomic overlap of copy number variants (CNVs) in two large cohorts of NDD and CA patients to identify de novo CNVs and candidate genes associated with both phenotypes. We analyzed clinical microarray CNV data from 10,620 NDD and 3176 CA cases annotated using Horizon platform of GenomeArc Analytics and applied rigorous downstream analysis to evaluate overlapping genes from NDD and CA CNVs. Out of 13,796 patients, only 195 cases contained 218 validated de novo CNVs. Eighteen percent (31/170) de novo CNVs in NDD cases and 40% (19/48) de novo CNVs in CA cases contained genomic overlaps impacting developmentally constraint genes. Seventy-nine constraint genes (10.1% non-OMIM entries) were found to have significantly enriched genomic overlap within rare de novo pathogenic deletions (P value = 0.01, OR = 1.58) and 45 constraint genes (13.3% non-OMIM entries) within rare de novo pathogenic duplications (P value = 0.01, OR = 1.97). Analysis of spatiotemporal transcriptome demonstrated both pathogenic deletion and duplication genes to be highly expressed during the prenatal stage in human developmental brain (P value = 4.95 X 10-6). From the list of overlapping genes, EHMT1, an interesting known NDD gene encompassed pathogenic deletion CNVs from both NDD and CA patients, whereas FAM189A1, and FSTL5 are new candidate genes from non-OMIM entries. In summary, we have identified constraint overlapping genes from CNVs (including de novo) in NDD and CA patients that have the potential to play a vital role in common disease etiology.
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Affiliation(s)
| | - Nasna Nassir
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | | | | | - Richa Tambi
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Binte Zehra
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Noor Kosaji
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Bakhrom K Berdiev
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
| | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE.
- GenomeArc Inc, Toronto, ON, Canada.
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Yuan L, Yu X, Xiao H, Deng S, Xia H, Xu H, Yang Y, Deng H. Identification of novel compound heterozygous variants in the DNAH1 gene of a Chinese family with left-right asymmetry disorder. Front Mol Biosci 2023; 10:1190162. [PMID: 37457836 PMCID: PMC10345202 DOI: 10.3389/fmolb.2023.1190162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
Most internal organs in humans and other vertebrates exhibit striking left-right asymmetry in position and structure. Variation of normal organ positioning results in left-right asymmetry disorders and presents as internal organ reversal or randomization. Up to date, at least 82 genes have been identified as the causative genetic factors of left-right asymmetry disorders. This study sought to discover potential pathogenic variants responsible for left-right asymmetry disorder present in a Han-Chinese family using whole exome sequencing combined with Sanger sequencing. Novel compound heterozygous variants, c.5690A>G (p.Asn1897Ser) and c.7759G>A (p.Val2587Met), in the dynein axonemal heavy chain 1 gene (DNAH1), were found in the proband and absent in unaffected family members. Conservation analysis has shown that the variants affect evolutionarily conserved residues, which may impact the tertiary structure of the DNAH1 protein. The novel compound heterozygous variants may potentially bear responsibility for left-right asymmetry disorder, which results from a perturbation of left-right axis coordination at the earliest embryonic development stages. This study broadens the variant spectrum of left-right asymmetry disorders and may be helpful for genetic counseling and healthcare management for the diagnosed individual, and promotes a greater understanding of the pathophysiology.
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Affiliation(s)
- Lamei Yuan
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xuehui Yu
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Heng Xiao
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Sheng Deng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Hong Xia
- Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hongbo Xu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yan Yang
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Health Management Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
- Disease Genome Research Center, Central South University, Changsha, China
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
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Nandadasa S, Martin D, Deshpande G, Robert KL, Stack MS, Itoh Y, Apte SS. Degradomic Identification of Membrane Type 1-Matrix Metalloproteinase as an ADAMTS9 and ADAMTS20 Substrate. Mol Cell Proteomics 2023; 22:100566. [PMID: 37169079 PMCID: PMC10267602 DOI: 10.1016/j.mcpro.2023.100566] [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: 09/14/2022] [Revised: 05/05/2023] [Accepted: 05/07/2023] [Indexed: 05/13/2023] Open
Abstract
The secreted metalloproteases ADAMTS9 and ADAMTS20 are implicated in extracellular matrix proteolysis and primary cilium biogenesis. Here, we show that clonal gene-edited RPE-1 cells in which ADAMTS9 was inactivated, and which constitutively lack ADAMTS20 expression, have morphologic characteristics distinct from parental RPE-1 cells. To investigate underlying proteolytic mechanisms, a quantitative terminomics method, terminal amine isotopic labeling of substrates was used to compare the parental and gene-edited RPE-1 cells and their medium to identify ADAMTS9 substrates. Among differentially abundant neo-amino (N) terminal peptides arising from secreted and transmembrane proteins, a peptide with lower abundance in the medium of gene-edited cells suggested cleavage at the Tyr314-Gly315 bond in the ectodomain of the transmembrane metalloprotease membrane type 1-matrix metalloproteinase (MT1-MMP), whose mRNA was also reduced in gene-edited cells. This cleavage, occurring in the MT1-MMP hinge, that is, between the catalytic and hemopexin domains, was orthogonally validated both by lack of an MT1-MMP catalytic domain fragment in the medium of gene-edited cells and restoration of its release from the cell surface by reexpression of ADAMTS9 and ADAMTS20 and was dependent on hinge O-glycosylation. A C-terminally semitryptic MT1-MMP peptide with greater abundance in WT RPE-1 medium identified a second ADAMTS9 cleavage site in the MT1-MMP hemopexin domain. Consistent with greater retention of MT1-MMP on the surface of gene-edited cells, pro-MMP2 activation, which requires cell surface MT1-MMP, was increased. MT1-MMP knockdown in gene-edited ADAMTS9/20-deficient cells restored focal adhesions but not ciliogenesis. The findings expand the web of interacting proteases at the cell surface, suggest a role for ADAMTS9 and ADAMTS20 in regulating cell surface activity of MT1-MMP, and indicate that MT1-MMP shedding does not underlie their observed requirement in ciliogenesis.
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Affiliation(s)
- Sumeda Nandadasa
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA; Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA.
| | - Daniel Martin
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Gauravi Deshpande
- Imaging Core Facility, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA
| | - Karyn L Robert
- Department of Pediatrics, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - M Sharon Stack
- Department of Chemistry and Biochemistry and Harper Cancer Center, University of Notre Dame, Notre Dame, Indiana, USA
| | - Yoshifumi Itoh
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, UK
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, USA.
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Venditti M, Pedalino C, Rosello M, Fasano G, Serafini M, Revenu C, Del Bene F, Tartaglia M, Lauri A. A minimally invasive fin scratching protocol for fast genotyping and early selection of zebrafish embryos. Sci Rep 2022; 12:22597. [PMID: 36585409 PMCID: PMC9803660 DOI: 10.1038/s41598-022-26822-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022] Open
Abstract
Current genetic modification and phenotyping methods in teleost fish allow detailed investigation of vertebrate mechanisms of development, modeling of specific aspects of human diseases and efficient testing of drugs at an organ/organismal level in an unparalleled fast and large-scale mode. Fish-based experimental approaches have boosted the in vivo verification and implementation of scientific advances, offering the quality guaranteed by animal models that ultimately benefit human health, and are not yet fully replaceable by even the most sophisticated in vitro alternatives. Thanks to highly efficient and constantly advancing genetic engineering as well as non-invasive phenotyping methods, the small zebrafish is quickly becoming a popular alternative to large animals' experimentation. This approach is commonly associated to invasive procedures and increased burden. Here, we present a rapid and minimally invasive method to obtain sufficient genomic material from single zebrafish embryos by simple and precise tail fin scratching that can be robustly used for at least two rounds of genotyping already from embryos within 48 h of development. The described protocol betters currently available methods (such as fin clipping), by minimizing the relative animal distress associated with biopsy at later or adult stages. It allows early selection of embryos with desired genotypes for strategizing culturing or genotype-phenotype correlation experiments, resulting in a net reduction of "surplus" animals used for mutant line generation.
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Affiliation(s)
- Martina Venditti
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Catia Pedalino
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marion Rosello
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 Rue Moreau, 75012, Paris, France
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75005, Paris, France
| | - Giulia Fasano
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Malo Serafini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 Rue Moreau, 75012, Paris, France
| | - Céline Revenu
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75005, Paris, France
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 Rue Moreau, 75012, Paris, France
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, 75005, Paris, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Antonella Lauri
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy.
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Dong M, Liu J, Liu C, Wang H, Sun W, Liu B. CRISPR/CAS9: A promising approach for the research and treatment of cardiovascular diseases. Pharmacol Res 2022; 185:106480. [PMID: 36191879 DOI: 10.1016/j.phrs.2022.106480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/31/2022]
Abstract
The development of gene-editing technology has been one of the biggest advances in biomedicine over the past two decades. Not only can it be used as a research tool to build a variety of disease models for the exploration of disease pathogenesis at the genetic level, it can also be used for prevention and treatment. This is done by intervening with the expression of target genes and carrying out precise molecular targeted therapy for diseases. The simple and flexible clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene-editing technology overcomes the limitations of zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). For this reason, it has rapidly become a preferred method for gene editing. As a new gene intervention method, CRISPR/Cas9 has been widely used in the clinical treatment of tumours and rare diseases; however, its application in the field of cardiovascular diseases is currently limited. This article reviews the application of the CRISPR/Cas9 editing technology in cardiovascular disease research and treatment, and discusses the limitations and prospects of this technology.
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Affiliation(s)
- Mengying Dong
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Jiangen Liu
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Caixia Liu
- Department of Neurology, The Liaoning Province People's Hospital, 33 Wenyi Road, ShenYang, China, 110016
| | - He Wang
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041
| | - Wei Sun
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041.
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, 218 Ziqiang Road, Changchun, China, 130041.
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Qin XJ, Xu MM, Ye JJ, Niu YW, Wu YR, Xu R, Li F, Fu QH, Chen S, Sun K, Xu YJ. De novo disruptive heterozygous MMP21 variants are potential predisposing genetic risk factors in Chinese Han heterotaxy children. Hum Genomics 2022; 16:41. [PMID: 36123719 PMCID: PMC9484203 DOI: 10.1186/s40246-022-00409-9] [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: 05/31/2022] [Accepted: 08/12/2022] [Indexed: 11/25/2022] Open
Abstract
Background Heterotaxy syndrome (HTX) is caused by aberrant left–right patterning early in embryonic development, which results in abnormal positioning and morphology of the thoracic and abdominal organs. Currently, genetic testing discerns the underlying genetic cause in less than 20% of sporadic HTX cases, indicating that genetic pathogenesis remains poorly understood. In this study, we aim to garner a deeper understanding of the genetic factors of this disease by documenting the effect of different matrix metalloproteinase 21 (MMP21) variants on disease occurrence and pathogenesis. Methods Eighty-one HTX patients with complex congenital heart defects and 89 healthy children were enrolled, and we investigated the pathogenetic variants related to patients with HTX by exome sequencing. Zebrafish splice-blocking Morpholino oligo-mediated transient suppression assays were performed to confirm the potential pathogenicity of missense variants found in these patients with HTX. Results Three MMP21 heterozygous non-synonymous variants (c.731G > A (p.G244E), c.829C > T (p.L277F), and c.1459A > G (p.K487E)) were identified in three unrelated Chinese Han patients with HTX and complex congenital heart defects. Sanger sequencing confirmed that all variants were de novo. Cell transfection assay showed that none of the variants affect mRNA and protein expression levels of MMP21. Knockdown expression of mmp21 by splice-blocking Morpholino oligo in zebrafish embryos revealed a heart looping disorder, and mutant human MMP21 mRNA (c.731G > A, c.1459A > G, heterozygous mRNA (wild-type&c.731G > A), as well as heterozygous mRNA (wild-type& c.1459A > G) could not effectively rescue the heart looping defects. A patient with the MMP21 p.G244E variant was identified with other potential HTX-causing missense mutations, whereas the patient with the MMP21 p.K487E variant had no genetic mutations in other causative genes related to HTX. Conclusion Our study highlights the role of the disruptive heterozygous MMP21 variant (p.K487E) in the etiology of HTX with complex cardiac malformations and expands the current mutation spectrum of MMP21 in HTX. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00409-9.
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Affiliation(s)
- Xi-Ji Qin
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Room 505, Scientific Building, Shanghai, 200092, China
| | - Meng-Meng Xu
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Room 505, Scientific Building, Shanghai, 200092, China.,Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jia-Jun Ye
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Room 505, Scientific Building, Shanghai, 200092, China
| | - Yi-Wei Niu
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Room 505, Scientific Building, Shanghai, 200092, China
| | - Yu-Rong Wu
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Room 505, Scientific Building, Shanghai, 200092, China
| | - Rang Xu
- Scientific Research Center, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Fen Li
- Department of Pediatric Cardiology, Shanghai Children's Medical Center, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Qi-Hua Fu
- Medical Laboratory, Shanghai Children's Medical Center, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Sun Chen
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Room 505, Scientific Building, Shanghai, 200092, China.
| | - Kun Sun
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Room 505, Scientific Building, Shanghai, 200092, China.
| | - Yue-Juan Xu
- Department of Pediatric Cardiology, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Room 505, Scientific Building, Shanghai, 200092, China.
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10
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Szenker-Ravi E, Ott T, Khatoo M, Moreau de Bellaing A, Goh WX, Chong YL, Beckers A, Kannesan D, Louvel G, Anujan P, Ravi V, Bonnard C, Moutton S, Schoen P, Fradin M, Colin E, Megarbane A, Daou L, Chehab G, Di Filippo S, Rooryck C, Deleuze JF, Boland A, Arribard N, Eker R, Tohari S, Ng AYJ, Rio M, Lim CT, Eisenhaber B, Eisenhaber F, Venkatesh B, Amiel J, Crollius HR, Gordon CT, Gossler A, Roy S, Attie-Bitach T, Blum M, Bouvagnet P, Reversade B. Discovery of a genetic module essential for assigning left-right asymmetry in humans and ancestral vertebrates. Nat Genet 2022; 54:62-72. [PMID: 34903892 DOI: 10.1038/s41588-021-00970-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 10/14/2021] [Indexed: 01/24/2023]
Abstract
The vertebrate left-right axis is specified during embryogenesis by a transient organ: the left-right organizer (LRO). Species including fish, amphibians, rodents and humans deploy motile cilia in the LRO to break bilateral symmetry, while reptiles, birds, even-toed mammals and cetaceans are believed to have LROs without motile cilia. We searched for genes whose loss during vertebrate evolution follows this pattern and identified five genes encoding extracellular proteins, including a putative protease with hitherto unknown functions that we named ciliated left-right organizer metallopeptide (CIROP). Here, we show that CIROP is specifically expressed in ciliated LROs. In zebrafish and Xenopus, CIROP is required solely on the left side, downstream of the leftward flow, but upstream of DAND5, the first asymmetrically expressed gene. We further ascertained 21 human patients with loss-of-function CIROP mutations presenting with recessive situs anomalies. Our findings posit the existence of an ancestral genetic module that has twice disappeared during vertebrate evolution but remains essential for distinguishing left from right in humans.
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Affiliation(s)
- Emmanuelle Szenker-Ravi
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore.
| | - Tim Ott
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Muznah Khatoo
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
| | - Anne Moreau de Bellaing
- Laboratoire de Cardiogénétique, Groupe Hospitalier Est, Hospices Civils de Lyon, Lyon, France
| | - Wei Xuan Goh
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
| | - Yan Ling Chong
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Anja Beckers
- Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
- REBIRTH Cluster of Excellence, Hannover, Germany
| | - Darshini Kannesan
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
| | - Guillaume Louvel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
- Écologie, Systématique et Évolution, UMR 8079 CNRS - Université Paris-Saclay - AgroParisTech, Orsay, France
| | - Priyanka Anujan
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
- Institute of Reproductive and Developmental Biology, Hammersmith Hospital, Imperial College, London, UK
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
| | - Carine Bonnard
- Skin Research Institute of Singapore (SRIS), A*STAR, Singapore, Singapore
| | - Sébastien Moutton
- CPDPN, Pôle mère enfant, Maison de Santé Protestante Bordeaux Bagatelle, Talence, France
| | | | - Mélanie Fradin
- Service de Génétique Médicale, Hôpital Sud, CHU de Rennes, Rennes, France
| | - Estelle Colin
- Service de Génétique Médicale, CHU d'Angers, Angers, France
| | - André Megarbane
- Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Institut Jérôme LEJEUNE, Paris, France
| | - Linda Daou
- Department of Pediatric Cardiology, Hôtel Dieu de France University Medical Center, Saint Joseph University, Alfred Naccache Boulevard, Achrafieh, Beirut, Lebanon
| | - Ghassan Chehab
- Department of Pediatric Cardiology, Hôtel Dieu de France University Medical Center, Saint Joseph University, Alfred Naccache Boulevard, Achrafieh, Beirut, Lebanon
- Department of Pediatrics, Lebanese University, Faculty of Medical Sciences, Hadath, Greater Beirut, Lebanon
| | - Sylvie Di Filippo
- Service de Cardiologie Pédiatrique, Groupe Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Caroline Rooryck
- Service de Génétique, University of Bordeaux, MRGM, INSERM U1211, CHU de Bordeaux, Bordeaux, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Nicolas Arribard
- Service de Cardiologie Pédiatrique, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Brussels, Belgium
| | - Rukiye Eker
- Pediatrics Department, Pediatric Cardiology Division, Istanbul Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Sumanty Tohari
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
| | - Alvin Yu-Jin Ng
- Molecular Diagnosis Centre (MDC), National University Hospital (NUH), Singapore, Singapore
| | - Marlène Rio
- Fédération de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Developmental Brain Disorders Laboratory, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Chun Teck Lim
- Bioinformatics Institute (BII), A*STAR, Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), A*STAR, Singapore, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute (BII), A*STAR, Singapore, Singapore
- Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), A*STAR, Singapore, Singapore
- Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
- Department of Pediatrics, National University of Singapore (NUS), Singapore, Singapore
| | - Jeanne Amiel
- Fédération de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Laboratory of Embryology and Genetics of Malformations, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Hugues Roest Crollius
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France
| | - Christopher T Gordon
- Laboratory of Embryology and Genetics of Malformations, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Achim Gossler
- Institute for Molecular Biology, Hannover Medical School, Hannover, Germany
- REBIRTH Cluster of Excellence, Hannover, Germany
| | - Sudipto Roy
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore
- Department of Pediatrics, National University of Singapore (NUS), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore (NUS), Singapore, Singapore
| | - Tania Attie-Bitach
- Fédération de Génétique, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Laboratory of Genetics and Development of the Cerebral Cortex, Université de Paris, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Martin Blum
- Institute of Biology, University of Hohenheim, Stuttgart, Germany.
| | | | - Bruno Reversade
- Laboratory of Human Genetics and Therapeutics, Genome Institute of Singapore (GIS), A*STAR, Singapore, Singapore.
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore, Singapore.
- Department of Pediatrics, National University of Singapore (NUS), Singapore, Singapore.
- Medical Genetics Department, Koç University School of Medicine (KUSOM), Istanbul, Turkey.
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11
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Harel T, Griffin JN, Arbogast T, Monroe TO, Palombo F, Martinelli M, Seri M, Pippucci T, Elpeleg O, Katsanis N. Loss of function mutations in CCDC32 cause a congenital syndrome characterized by craniofacial, cardiac and neurodevelopmental anomalies. Hum Mol Genet 2021; 29:1489-1497. [PMID: 32307552 DOI: 10.1093/hmg/ddaa073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/22/2020] [Accepted: 04/09/2020] [Indexed: 02/07/2023] Open
Abstract
Despite the wide use of genomics to investigate the molecular basis of rare congenital malformations, a significant fraction of patients remains bereft of diagnosis. As part of our continuous effort to recruit and perform genomic and functional studies on such cohorts, we investigated the genetic and mechanistic cause of disease in two independent consanguineous families affected by overlapping craniofacial, cardiac, laterality and neurodevelopmental anomalies. Using whole exome sequencing, we identified homozygous frameshift CCDC32 variants in three affected individuals. Functional analysis in a zebrafish model revealed that ccdc32 depletion recapitulates the human phenotypes. Because some of the patient phenotypes overlap defects common to ciliopathies, we asked if loss of CCDC32 might contribute to the dysfunction of this organelle. Consistent with this hypothesis, we show that ccdc32 is required for normal cilia formation in zebrafish embryos and mammalian cell culture, arguing that ciliary defects are at least partially involved in the pathomechanism of this disorder.
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Affiliation(s)
- Tamar Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - John N Griffin
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Thomas Arbogast
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Tanner O Monroe
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Marcella Martinelli
- Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale, Alma Mater Studiorum - Università di Bologna, Bologna 40138, Italy
| | - Marco Seri
- Dipartimento di Scienze Mediche e Chirurgiche, Alma Mater Studiorum - Università di Bologna, Bologna 40138, Italy.,U.O. Genetica Medica, Policlinico S. Orsola-Malpighi, Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Tommaso Pippucci
- U.O. Genetica Medica, Policlinico S. Orsola-Malpighi, Azienda Ospedaliero-Universitaria di Bologna, Bologna 40138, Italy
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Nicholas Katsanis
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
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12
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Bolkier Y, Barel O, Marek-Yagel D, Atias-Varon D, Kagan M, Vardi A, Mishali D, Katz U, Salem Y, Tirosh-Wagner T, Jacobson JM, Raas-Rothschild A, Chorin O, Eliyahu A, Sarouf Y, Shlomovitz O, Veber A, Shalva N, Javasky E, Ben Moshe Y, Staretz-Chacham O, Rechavi G, Mane S, Anikster Y, Vivante A, Pode-Shakked B. Whole-exome sequencing reveals a monogenic cause in 56% of individuals with laterality disorders and associated congenital heart defects. J Med Genet 2021; 59:691-696. [PMID: 34215651 DOI: 10.1136/jmedgenet-2021-107775] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/19/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND The molecular basis of heterotaxy and congenital heart malformations associated with disruption of left-right asymmetry is broad and heterogenous, with over 25 genes implicated in its pathogenesis thus far. OBJECTIVE We sought to elucidate the molecular basis of laterality disorders and associated congenital heart defects in a cohort of 30 unrelated probands of Arab-Muslim descent, using next-generation sequencing techniques. METHODS Detailed clinical phenotyping followed by whole-exome sequencing (WES) was pursued for each of the probands and their parents (when available). Sanger sequencing was used for segregation analysis of disease-causing mutations in the families. RESULTS Using WES, we reached a molecular diagnosis for 17 of the 30 probands (56.7%). Genes known to be associated with heterotaxy and/or primary ciliary dyskinesia, in which homozygous pathogenic or likely pathogenic variants were detected, included CFAP53 (CCDC11), CFAP298 (C21orf59), CFAP300, LRRC6, GDF1, DNAAF1, DNAH5, CCDC39, CCDC40, PKD1L1 and TTC25. Additionally, we detected a homozygous disease causing mutation in DAND5, as a novel recessive monogenic cause for heterotaxy in humans. Three additional probands were found to harbour variants of uncertain significance. These included variants in DNAH6, HYDIN, CELSR1 and CFAP46. CONCLUSIONS Our findings contribute to the current knowledge regarding monogenic causes of heterotaxy and its associated congenital heart defects and underscore the role of next-generation sequencing techniques in the diagnostic workup of such patients, and especially among consanguineous families.
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Affiliation(s)
- Yoav Bolkier
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Ortal Barel
- Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Dina Marek-Yagel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Danit Atias-Varon
- Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Maayan Kagan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Amir Vardi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatric Cardiac Intensive Care, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - David Mishali
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatric Cardiac Intensive Care, Edmond Safra International Congenital Heart Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Uriel Katz
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yishay Salem
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tal Tirosh-Wagner
- Pediatric Heart Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jeffrey M Jacobson
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Imaging Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Annick Raas-Rothschild
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Odelia Chorin
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Yarden Sarouf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Omer Shlomovitz
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Alvit Veber
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Nechama Shalva
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Elisheva Javasky
- Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Yishay Ben Moshe
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Orna Staretz-Chacham
- Metabolic Clinic, Division of Pediatrics, Soroka Medical Center, Ben-Gurion University, Beer Sheva, Israel
| | - Gideon Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel.,Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yair Anikster
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,The Wohl Institute for Translational Medicine, Sheba Medical Center, Tel Hashomer, Israel
| | - Asaf Vivante
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Talpiot Medical Leadership Program, Sheba Medical Center, Tel Hashomer, Israel
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel .,Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel.,Talpiot Medical Leadership Program, Sheba Medical Center, Tel Hashomer, Israel
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13
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Xia H, Huang X, Deng S, Xu H, Yang Y, Liu X, Yuan L, Deng H. DNAH11 compound heterozygous variants cause heterotaxy and congenital heart disease. PLoS One 2021; 16:e0252786. [PMID: 34133440 PMCID: PMC8208527 DOI: 10.1371/journal.pone.0252786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/21/2021] [Indexed: 12/16/2022] Open
Abstract
Heterotaxy (HTX), a condition characterized by internal organs not being arranged as expected relative to each other and to the left-right axis, is often accompanied with congenital heart disease (CHD). The purpose was to detect the pathogenic variants in a Chinese family with HTX and CHD. A non-consanguineous Han Chinese family with HTX and CHD, and 200 unrelated healthy subjects were enlisted. Exome sequencing and Sanger sequencing were applied to identify the genetic basis of the HTX family. Compound heterozygous variants, c.3426-1G>A and c.4306C>T (p.(Arg1436Trp)), in the dynein axonemal heavy chain 11 gene (DNAH11) were identified in the proband via exome sequencing and further confirmed by Sanger sequencing. Neither c.3426-1G>A nor c.4306C>T variant in the DNAH11 gene was detected in 200 healthy controls. The DNAH11 c.3426-1G>A variant was predicted as altering the acceptor splice site and most likely affecting splicing. The DNAH11 c.4306C>T variant was predicted to be damaging, which may reduce the phenotype severity. The compound heterozygous variants, c.3426-1G>A and c.4306C>T, in the DNAH11 gene might be the pathogenic alterations resulting in HTX and CHD in this family. These findings broaden the variant spectrum of the DNAH11 gene and increase knowledge used in genetic counseling for the HTX family.
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Affiliation(s)
- Hong Xia
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Emergency, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangjun Huang
- Department of General Surgery, The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Sheng Deng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongbo Xu
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Yang
- Department of Neurology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Liu
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lamei Yuan
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- * E-mail: (HD); (LY)
| | - Hao Deng
- Center for Experimental Medicine, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- * E-mail: (HD); (LY)
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14
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Yuan ZZ, Fan LL, Jiang ZC, Yang YF, Tan ZP. A Novel Nonsense MMP21 Variant Causes Dextrocardia and Congenital Heart Disease in a Han Chinese Patient. Front Cardiovasc Med 2020; 7:582350. [PMID: 33240936 PMCID: PMC7680847 DOI: 10.3389/fcvm.2020.582350] [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: 07/11/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022] Open
Abstract
The position and morphology of human internal organs are asymmetrically distributed along the left-right axis. Aberrant left-right patterning in the developing embryo can lead to a series of congenital laterality defects, such as dextrocardia and heterotaxy syndrome. Laterality defects are a genetic condition; however, pathogenic genetic lesions are found in only one-fifth of patients. In this study, whole-exome sequencing was conducted for 78 patients with laterality defects. We identified a novel stopgain variant in MMP21 (c.G496T; p.G166*) in a Chinese patient with mirror-image dextrocardia. This variant caused a truncated MMP21 mRNA containing only the signal peptide and propeptide, while the coding sequence of matrix metalloproteinase-21 was almost entirely absent. To the best of our knowledge, this novel variant is the first homozygous stopgain variant identified in dextrocardia patients, and the first MMP21 variant found in East Asia. Our findings expand the spectrum of MMP21 variants and provide support for the critical role of MMP21 during left-right patterning in the Han Chinese population.
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Affiliation(s)
- Zhuang-Zhuang Yuan
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China.,Department of Cell Biology, 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
| | - Liang-Liang Fan
- Department of Cell Biology, 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
| | - Zi-Chen Jiang
- University of California, San Diego, San Diego, CA, United States
| | - Yi-Feng Yang
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhi-Ping Tan
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
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15
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Doello K, Conde V, Perez MC, Mendoza I, Mesas C, Prados J. Unusual long survival in a case of heterotaxy and polysplenia. Surg Radiol Anat 2020; 43:607-611. [PMID: 32995936 DOI: 10.1007/s00276-020-02586-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
Heterotaxy syndrome with polysplenia is an extremely rare congenital disorder caused by a disruption in the embryonic development that results in an abnormal arrangement of the abdominal and thoracic organs. We present the case of a 59-year-old female patient with invasive ductal carcinoma of the right breast (luminal A type) and CT findings of heterotaxy syndrome with polysplenia. The most remarkable anomalies identified were a left inferior vena cava draining into the hemiazygos vein, absent inferior vena cava at the thoracic level, and hepatic veins directly draining into the right atrium. Moreover, an atrial septal defect was identified, explaining the pulmonary hypertension of unknown cause previously detected in the patient. The relevance of this case lies in the unusual anatomical abnormalities found and the large patient survival, having in to account the great rate of heterotaxy syndrome mortality in the first years of life.
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Affiliation(s)
- Kevin Doello
- Medical Oncology Service, Virgen de las Nieves Hospital, 18014, Granada, Spain.,Institute of Biopathologyand Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100, Granada, Spain
| | - Veronica Conde
- Medical Oncology Service, Virgen de las Nieves Hospital, 18014, Granada, Spain
| | - Maria C Perez
- Radiological Service, Virgen de las Nieves Hospital, 18014, Granada, Spain
| | - Inmaculada Mendoza
- Radiological Service, Virgen de las Nieves Hospital, 18014, Granada, Spain
| | - Cristina Mesas
- Institute of Biopathologyand Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100, Granada, Spain.,Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071, Granada, Spain.,Instituto Biosanitario de Granada (Ibs. GRANADA), 18014, Granada, Spain
| | - José Prados
- Institute of Biopathologyand Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, 18100, Granada, Spain. .,Department of Anatomy and Embryology, Faculty of Medicine, University of Granada, 18071, Granada, Spain. .,Instituto Biosanitario de Granada (Ibs. GRANADA), 18014, Granada, Spain.
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16
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Turakhia Y, Chen HI, Marcovitz A, Bejerano G. A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals. Nucleic Acids Res 2020; 48:e91. [PMID: 32614390 PMCID: PMC7498332 DOI: 10.1093/nar/gkaa550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/23/2020] [Accepted: 06/23/2020] [Indexed: 01/20/2023] Open
Abstract
Gene losses provide an insightful route for studying the morphological and physiological adaptations of species, but their discovery is challenging. Existing genome annotation tools focus on annotating intact genes and do not attempt to distinguish nonfunctional genes from genes missing annotation due to sequencing and assembly artifacts. Previous attempts to annotate gene losses have required significant manual curation, which hampers their scalability for the ever-increasing deluge of newly sequenced genomes. Using extreme sequence erosion (amino acid deletions and substitutions) and sister species support as an unambiguous signature of loss, we developed an automated approach for detecting high-confidence gene loss events across a species tree. Our approach relies solely on gene annotation in a single reference genome, raw assemblies for the remaining species to analyze, and the associated phylogenetic tree for all organisms involved. Using human as reference, we discovered over 400 unique human ortholog erosion events across 58 mammals. This includes dozens of clade-specific losses of genes that result in early mouse lethality or are associated with severe human congenital diseases. Our discoveries yield intriguing potential for translational medical genetics and evolutionary biology, and our approach is readily applicable to large-scale genome sequencing efforts across the tree of life.
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Affiliation(s)
- Yatish Turakhia
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Amir Marcovitz
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
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17
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Chen X, Deng S, Xia H, Yuan L, Xu H, Tang S, Deng H. Identification of a CCDC114 variant in a Han-Chinese patient with situs inversus. Exp Ther Med 2020; 20:3336-3342. [PMID: 32855706 DOI: 10.3892/etm.2020.9059] [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: 10/15/2019] [Accepted: 02/18/2020] [Indexed: 12/14/2022] Open
Abstract
The function and position of the internal organs within the human body are based on left-right (LR) asymmetry. Human LR asymmetry disorders are characterized by abnormal LR asymmetric arrangement of the internal organs resulting from defective embryonic nodal cilia and nodal signaling pathway. The coiled-coil domain containing 114 gene (CCDC114) is related to the biogenesis of cilia and attachment of the outer dynein arms (ODAs) to the axoneme of cilia. Mutations in the CCDC114 gene are reported to cause a subtype of primary ciliary dyskinesia (PCD) named ciliary dyskinesia, primary, 20 (CILD20). Patients with CCDC114 mutations present with a type of ciliopathy with high clinical heterogeneity. In the present study, a Han-Chinese patient with situs inversus was recruited. Exome sequencing was performed on this patient combined with variant validation by Sanger sequencing. A homozygous variant c.584T>C (p.L195P) in the CCDC114 gene was identified as the likely genetic cause for situs inversus in this patient. The findings of our study extend the mutational spectrum of the CCDC114 gene, and contribute to clarifying the pathogenesis of human ciliopathies and benefit genetic counseling.
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Affiliation(s)
- Xiangyu Chen
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Sheng Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China.,Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Hong Xia
- Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Hongbo Xu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Shiyu Tang
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China.,Neurology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
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18
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Gabriel GC, Young CB, Lo CW. Role of cilia in the pathogenesis of congenital heart disease. Semin Cell Dev Biol 2020; 110:2-10. [PMID: 32418658 DOI: 10.1016/j.semcdb.2020.04.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/22/2020] [Accepted: 04/25/2020] [Indexed: 12/13/2022]
Abstract
An essential role for cilia in the pathogenesis of congenital heart disease (CHD) has emerged from findings of a large-scale mouse forward genetic screen. High throughput screening with fetal ultrasound imaging followed by whole exome sequencing analysis recovered a preponderance of cilia related genes and cilia transduced cell signaling genes among mutations identified to cause CHD. The perturbation of left-right patterning in CHD pathogenesis is suggested by the association of CHD with heterotaxy, but also by the finding of the co-occurrence of laterality defects with CHD in birth defect registries. Many of the cilia and cilia cell signaling genes recovered were found to be related to Hedgehog signaling. Studies in mice showed cilia transduced hedgehog signaling coordinates left-right patterning with heart looping and differentiation of the heart tube. Cilia transduced Shh signaling also regulates later events in heart development, including outflow tract septation and formation of the atrioventricular septum. More recent work has shown mutations in cilia related genes may also contribute to valve disease that largely manifest in adult life. Overall, these and other findings show cilia play an important role in CHD and also in more common valve diseases.
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Affiliation(s)
- George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Cullen B Young
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15201, United States.
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19
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Marek‐Yagel D, Bolkier Y, Barel O, Vardi A, Mishali D, Katz U, Salem Y, Abudi S, Nayshool O, Kol N, Raas‐Rothschild A, Rechavi G, Anikster Y, Pode‐Shakked B. A founder truncating variant in
GDF1
causes autosomal‐recessive right isomerism and associated congenital heart defects in multiplex Arab kindreds. Am J Med Genet A 2020; 182:987-993. [DOI: 10.1002/ajmg.a.61509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/06/2019] [Accepted: 01/23/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Dina Marek‐Yagel
- Metabolic Disease UnitEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
| | - Yoav Bolkier
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- Pediatric Cardiology UnitEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
| | - Ortal Barel
- Sheba Cancer Research Center, Sheba Medical Center Tel‐Hashomer Israel
| | - Amir Vardi
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- Department of Pediatric Cardiac Intensive Care, Edmond Safra International Congenital Heart CenterEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
| | - David Mishali
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- Department of Pediatric Cardiac Intensive Care, Edmond Safra International Congenital Heart CenterEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
| | - Uriel Katz
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- Pediatric Cardiology UnitEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
| | - Yishay Salem
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- Pediatric Cardiology UnitEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
| | - Shachar Abudi
- Metabolic Disease UnitEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
| | - Omri Nayshool
- Sheba Cancer Research Center, Sheba Medical Center Tel‐Hashomer Israel
| | - Nitzan Kol
- Sheba Cancer Research Center, Sheba Medical Center Tel‐Hashomer Israel
| | - Annick Raas‐Rothschild
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- The Institute for Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
| | - Gideon Rechavi
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- Sheba Cancer Research Center, Sheba Medical Center Tel‐Hashomer Israel
- The Wohl Institute for Translational Medicine, Sheba Medical Center Tel‐Hashomer Israel
| | - Yair Anikster
- Metabolic Disease UnitEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- The Wohl Institute for Translational Medicine, Sheba Medical Center Tel‐Hashomer Israel
| | - Ben Pode‐Shakked
- Metabolic Disease UnitEdmond and Lily Safra Children's Hospital, Sheba Medical Center Tel‐Hashomer Israel
- Sackler Faculty of MedicineTel‐Aviv University Tel‐Aviv Israel
- Talpiot Medical Leadership ProgramSheba Medical Center Tel‐Hashomer Israel
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20
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Genetic architecture of laterality defects revealed by whole exome sequencing. Eur J Hum Genet 2019; 27:563-573. [PMID: 30622330 DOI: 10.1038/s41431-018-0307-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 10/29/2018] [Accepted: 11/07/2018] [Indexed: 01/24/2023] Open
Abstract
Aberrant left-right patterning in the developing human embryo can lead to a broad spectrum of congenital malformations. The causes of most laterality defects are not known, with variants in established genes accounting for <20% of cases. We sought to characterize the genetic spectrum of these conditions by performing whole-exome sequencing of 323 unrelated laterality cases. We investigated the role of rare, predicted-damaging variation in 1726 putative laterality candidate genes derived from model organisms, pathway analyses, and human phenotypes. We also evaluated the contribution of homo/hemizygous exon deletions and gene-based burden of rare variation. A total of 28 candidate variants (26 rare predicted-damaging variants and 2 hemizygous deletions) were identified, including variants in genes known to cause heterotaxy and primary ciliary dyskinesia (ACVR2B, NODAL, ZIC3, DNAI1, DNAH5, HYDIN, MMP21), and genes without a human phenotype association, but with prior evidence for a role in embryonic laterality or cardiac development. Sanger validation of the latter variants in probands and their parents revealed no de novo variants, but apparent transmitted heterozygous (ROCK2, ISL1, SMAD2), and hemizygous (RAI2, RIPPLY1) variant patterns. Collectively, these variants account for 7.1% of our study subjects. We also observe evidence for an excess burden of rare, predicted loss-of-function variation in PXDNL and BMS1- two genes relevant to the broader laterality phenotype. These findings highlight potential new genes in the development of laterality defects, and suggest extensive locus heterogeneity and complex genetic models in this class of birth defects.
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21
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Sarasamma S, Lai YH, Liang ST, Liu K, Hsiao CD. The Power of Fish Models to Elucidate Skin Cancer Pathogenesis and Impact the Discovery of New Therapeutic Opportunities. Int J Mol Sci 2018; 19:E3929. [PMID: 30544544 PMCID: PMC6321611 DOI: 10.3390/ijms19123929] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 01/21/2023] Open
Abstract
Animal models play important roles in investigating the pathobiology of cancer, identifying relevant pathways, and developing novel therapeutic tools. Despite rapid progress in the understanding of disease mechanisms and technological advancement in drug discovery, negative trial outcomes are the most frequent incidences during a Phase III trial. Skin cancer is a potential life-threatening disease in humans and might be medically futile when tumors metastasize. This explains the low success rate of melanoma therapy amongst other malignancies. In the past decades, a number of skin cancer models in fish that showed a parallel development to the disease in humans have provided important insights into the fundamental biology of skin cancer and future treatment methods. With the diversity and breadth of advanced molecular genetic tools available in fish biology, fish skin cancer models will continue to be refined and expanded to keep pace with the rapid development of skin cancer research. This review begins with a brief introduction of molecular characteristics of skin cancers, followed by an overview of teleost models that have been used in the last decades in melanoma research. Next, we will detail the importance of the zebrafish (Danio rerio) animal model and other emerging fish models including platyfish (Xiphophorus sp.), and medaka (Oryzias latipes) in future cutaneous malignancy studies. The last part of this review provides the recent development and genome editing applications of skin cancer models in zebrafish and the progress in small molecule screening.
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Affiliation(s)
- Sreeja Sarasamma
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
| | - Yu-Heng Lai
- Department of Chemistry, Chinese Culture University, Taipei 11114, Taiwan.
| | - Sung-Tzu Liang
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
| | - Kechun Liu
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China.
| | - Chung-Der Hsiao
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Department of Bioscience Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Taiwan Center for Biomedical Technology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
- Center for Nanotechnology, Chung Yuan Christian University, Chung-Li 32023, Taiwan.
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22
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Adamson KI, Sheridan E, Grierson AJ. Use of zebrafish models to investigate rare human disease. J Med Genet 2018; 55:641-649. [PMID: 30065072 DOI: 10.1136/jmedgenet-2018-105358] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 01/07/2023]
Abstract
Rare diseases are collectively common and often extremely debilitating. Following the emergence of next-generation sequencing (NGS) technologies, the variants underpinning rare genetic disorders are being unearthed at an accelerating rate. However, many rare conditions lack effective treatments due to their poorly understood pathophysiology. There is therefore a growing demand for the development of novel experimental models of rare genetic diseases, so that potentially causative variants can be validated, pathogenic mechanisms can be investigated and therapeutic targets can be identified. Animal models of rare diseases need to be genetically and physiologically similar to humans, and well-suited to large-scale experimental manipulation, considering the vast number of novel variants that are being identified through NGS. The zebrafish has emerged as a popular model system for investigating these variants, combining conserved vertebrate characteristics with a capacity for large-scale phenotypic and therapeutic screening. In this review, we aim to highlight the unique advantages of the zebrafish over other in vivo model systems for the large-scale study of rare genetic variants. We will also consider the generation of zebrafish disease models from a practical standpoint, by discussing how genome editing technologies, particularly the recently developed clustered regularly interspaced repeat (CRISPR)/CRISPR-associated protein 9 system, can be used to model rare pathogenic variants in zebrafish. Finally, we will review examples in the literature where zebrafish models have played a pivotal role in confirming variant causality and revealing the underlying mechanisms of rare diseases, often with wider implications for our understanding of human biology.
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Affiliation(s)
- Kathryn Isabel Adamson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Andrew James Grierson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK.,Department of Neuroscience, University of Sheffield, Sheffield, UK
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23
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Naert T, Vleminckx K. CRISPR/Cas9 disease models in zebrafish and Xenopus: The genetic renaissance of fish and frogs. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 28:41-52. [PMID: 30205880 DOI: 10.1016/j.ddtec.2018.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/29/2018] [Accepted: 07/13/2018] [Indexed: 12/11/2022]
Abstract
The speed by which clinical genomics is currently identifying novel potentially pathogenic variants is outperforming the speed by which these can be functionally (genotype-phenotype) annotated in animal disease models. However, over the past few years the emergence of CRISPR/Cas9 as a straight-forward genome editing technology has revolutionized disease modeling in vertebrate non-mammalian model organisms such as zebrafish, medaka and Xenopus. It is now finally possible, by CRISPR/Cas9, to rapidly establish clinically relevant disease models in these organisms. Interestingly, these can provide both cost-effective genotype-phenotype correlations for gene-(variants) and genomic rearrangements obtained from clinical practice, as well as be exploited to perform translational research to improve prospects of disease afflicted patients. In this review, we show an extensive overview of these new CRISPR/Cas9-mediated disease models and provide future prospects that will allow increasingly accurate modeling of human disease in zebrafish, medaka and Xenopus.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Belgium; Cancer Research Institute Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Belgium; Center for Medical Genetics, Ghent University, Belgium; Cancer Research Institute Ghent, Belgium.
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24
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Neurocristopathies: New insights 150 years after the neural crest discovery. Dev Biol 2018; 444 Suppl 1:S110-S143. [PMID: 29802835 DOI: 10.1016/j.ydbio.2018.05.013] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/12/2022]
Abstract
The neural crest (NC) is a transient, multipotent and migratory cell population that generates an astonishingly diverse array of cell types during vertebrate development. These cells, which originate from the ectoderm in a region lateral to the neural plate in the neural fold, give rise to neurons, glia, melanocytes, chondrocytes, smooth muscle cells, odontoblasts and neuroendocrine cells, among others. Neurocristopathies (NCP) are a class of pathologies occurring in vertebrates, especially in humans that result from the abnormal specification, migration, differentiation or death of neural crest cells during embryonic development. Various pigment, skin, thyroid and hearing disorders, craniofacial and heart abnormalities, malfunctions of the digestive tract and tumors can also be considered as neurocristopathies. In this review we revisit the current classification and propose a new way to classify NCP based on the embryonic origin of the affected tissues, on recent findings regarding the molecular mechanisms that drive NC formation, and on the increased complexity of current molecular embryology techniques.
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25
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Hodgson P, Ireland J, Grunow B. Fish, the better model in human heart research? Zebrafish Heart aggregates as a 3D spontaneously cardiomyogenic in vitro model system. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 138:132-141. [PMID: 29729327 DOI: 10.1016/j.pbiomolbio.2018.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/04/2018] [Accepted: 04/27/2018] [Indexed: 12/25/2022]
Abstract
The zebrafish (ZF) has become an essential model for biomedical, pharmacological and eco-toxicological heart research. Despite the anatomical differences between fish and human hearts, similarities in cellular structure and conservation of genes as well as pathways across vertebrates have led to an increase in the popularity of ZF as a model for human cardiac research. ZF research benefits from an entirely sequenced genome, which allows us to establish and study cardiovascular mutants to better understand cardiovascular diseases. In this review, we will discuss the importance of in vitro model systems for cardiac research and summarise results of in vitro 3D heart-like cell aggregates, consisting of myocardial tissue formed spontaneously from enzymatically digested whole embryonic ZF larvae (Zebrafish Heart Aggregate - ZFHA). We will give an overview of the similarities and differences of ZF versus human hearts and highlight why ZF complement established mammalian models (i.e. murine and large animal models) for cardiac research. At this stage, the ZFHA model system is being refined into a high-throughput (more ZFHA generated than larvae prepared) and stable in vitro test system to accomplish the same longevity of previously successful salmonid models. ZFHA have potential for the use of high-throughput-screenings of different factors like small molecules, nucleic acids, proteins and lipids which is difficult to achieve in the zebrafish in vivo screening models with lethal mutations as well as to explore ion channel disorders and to find appropriate drugs for safety screening.
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Affiliation(s)
- Patricia Hodgson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK; Salford Royal NHS Foundation Trust, Stott Lane, Salford M6 8HD, UK
| | - Jake Ireland
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK; School of Chemistry, Materials Science, and Engineering, Hilmer Building, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Bianka Grunow
- University Medicine Greifswald, Institute of Physiology, Greifswalder Str. 11C, 17495 Karlsburg, Germany; Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK.
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26
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Abstract
Prokaryotic type II adaptive immune systems have been developed into the versatile CRISPR technology, which has been widely applied in site-specific genome editing and has revolutionized biomedical research due to its superior efficiency and flexibility. Recent studies have greatly diversified CRISPR technologies by coupling it with various DNA repair mechanisms and targeting strategies. These new advances have significantly expanded the generation of genetically modified animal models, either by including species in which targeted genetic modification could not be achieved previously, or through introducing complex genetic modifications that take multiple steps and cost years to achieve using traditional methods. Herein, we review the recent developments and applications of CRISPR-based technology in generating various animal models, and discuss the everlasting impact of this new progress on biomedical research.
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Affiliation(s)
- Xun Ma
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Avery Sum-Yu Wong
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Hei-Yin Tam
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Samuel Yung-Kin Tsui
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Dittman Lai-Shun Chung
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Bo Feng
- Key Laboratory for Regenerative Medicine in Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China. .,Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Guangdong 510530, China.,SBS Core Laboratory, CUHK Shenzhen Research Institute, Shenzhen Guangdong 518057, China
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27
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Pagkratis S, Kryeziu S, Lin M, Hoque S, Bucobo JC, Buscaglia JM, Georgakis GV, Sasson AR, Kim J. Case report of intestinal non-rotation, heterotaxy, and polysplenia in a patient with pancreatic cancer. Medicine (Baltimore) 2017; 96:e8599. [PMID: 29245220 PMCID: PMC5728835 DOI: 10.1097/md.0000000000008599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
RATIONALE Heterotaxy with polysplenia is an extremely rare congenital condition resulting from abnormal arrangement of organs in the abdominal and thoracic cavities during embryologic development. When a malignancy such as pancreatic cancer develops under these conditions, surgical resection becomes particularly complex. This case report demonstrates successful pancreatic cancer resection despite the patient's complicated anatomy. PATIENT CONCERNS An 82-year-old female presented to our institution with complaints of mild right upper quadrant pain radiating to the mid-epigastric region. DIAGNOSES Physical examination revealed jaundice with scleral icterus consistent with obstructive jaundice. Radiographic imaging revealed hepatic duct dilation with several anatomic anomalies including small bowel location in the right upper abdomen, cecum, and appendix in the left lower quadrant, reversed superior mesenteric artery and superior mesenteric vein positions, and right-sided duodenal-jejunal flexture as well as an entirely right-sided pancreas, and left lower pelvis with ≥6 separate splenules. These findings resulted in a diagnosis of heterotaxy syndrome with polysplenia. INTERVENTIONS Careful preoperative planning and total pancreatectomy was performed without complication. OUTCOMES The patient recovered well. Pathologic examination of the pancreatic mass revealed moderately/poorly differentiated invasive pancreatic duct adenocarcinoma. The patient remains alive and well without signs of recurrent disease at the 2-year follow-up. LESSONS Given the wide range of anatomical variants observed in patients with heterotaxy syndrome, a thorough radiologic assessment is necessary before engaging in any surgical procedure. In our case, preoperative identification of the various anatomic anomalies, such as the short and vertically oriented pancreas, the porta hepatis position anterior to the duodenum, the nonrotation of the intestines and the anomalous origin of the right hepatic artery allowed us to perform a safe and uncomplicated total pancreatectomy.
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28
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Reijnders MRF, Kousi M, van Woerden GM, Klein M, Bralten J, Mancini GMS, van Essen T, Proietti-Onori M, Smeets EEJ, van Gastel M, Stegmann APA, Stevens SJC, Lelieveld SH, Gilissen C, Pfundt R, Tan PL, Kleefstra T, Franke B, Elgersma Y, Katsanis N, Brunner HG. Variation in a range of mTOR-related genes associates with intracranial volume and intellectual disability. Nat Commun 2017; 8:1052. [PMID: 29051493 PMCID: PMC5648772 DOI: 10.1038/s41467-017-00933-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/08/2017] [Indexed: 11/09/2022] Open
Abstract
De novo mutations in specific mTOR pathway genes cause brain overgrowth in the context of intellectual disability (ID). By analyzing 101 mMTOR-related genes in a large ID patient cohort and two independent population cohorts, we show that these genes modulate brain growth in health and disease. We report the mTOR activator gene RHEB as an ID gene that is associated with megalencephaly when mutated. Functional testing of mutant RHEB in vertebrate animal models indicates pathway hyperactivation with a concomitant increase in cell and head size, aberrant neuronal migration, and induction of seizures, concordant with the human phenotype. This study reveals that tight control of brain volume is exerted through a large community of mTOR-related genes. Human brain volume can be altered, by either rare disruptive events causing hyperactivation of the pathway, or through the collective effects of common alleles.
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Affiliation(s)
- M R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - M Kousi
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - G M van Woerden
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - M Klein
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - J Bralten
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - G M S Mancini
- Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, 3000 CA, Rotterdam, The Netherlands
| | - T van Essen
- Department of Genetics, University of Groningen, University Medical Center of Groningen, 9700 RB, Groningen, The Netherlands
| | - M Proietti-Onori
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - E E J Smeets
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - M van Gastel
- Department of Medical Care, SWZ zorg, 5691 AG, Son, The Netherlands
| | - A P A Stegmann
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - S J C Stevens
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands
| | - S H Lelieveld
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 GA, Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - R Pfundt
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - P L Tan
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - T Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands
| | - B Franke
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands.,Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 GA, Nijmegen, The Netherlands
| | - Y Elgersma
- Department of Neuroscience and ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - N Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC, 27701, USA
| | - H G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, 6500 GA, The Netherlands. .,Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ, Maastricht, The Netherlands.
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29
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Reijnders MR, Ansor NM, Kousi M, Yue WW, Tan PL, Clarkson K, Clayton-Smith J, Corning K, Jones JR, Lam WW, Mancini GM, Marcelis C, Mohammed S, Pfundt R, Roifman M, Cohn R, Chitayat D, Millard TH, Katsanis N, Brunner HG, Banka S, Banka S. RAC1 Missense Mutations in Developmental Disorders with Diverse Phenotypes. Am J Hum Genet 2017; 101:466-477. [PMID: 28886345 DOI: 10.1016/j.ajhg.2017.08.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/01/2017] [Indexed: 01/01/2023] Open
Abstract
RAC1 is a widely studied Rho GTPase, a class of molecules that modulate numerous cellular functions essential for normal development. RAC1 is highly conserved across species and is under strict mutational constraint. We report seven individuals with distinct de novo missense RAC1 mutations and varying degrees of developmental delay, brain malformations, and additional phenotypes. Four individuals, each harboring one of c.53G>A (p.Cys18Tyr), c.116A>G (p.Asn39Ser), c.218C>T (p.Pro73Leu), and c.470G>A (p.Cys157Tyr) variants, were microcephalic, with head circumferences between -2.5 to -5 SD. In contrast, two individuals with c.151G>A (p.Val51Met) and c.151G>C (p.Val51Leu) alleles were macrocephalic with head circumferences of +4.16 and +4.5 SD. One individual harboring a c.190T>G (p.Tyr64Asp) allele had head circumference in the normal range. Collectively, we observed an extraordinary spread of ∼10 SD of head circumferences orchestrated by distinct mutations in the same gene. In silico modeling, mouse fibroblasts spreading assays, and in vivo overexpression assays using zebrafish as a surrogate model demonstrated that the p.Cys18Tyr and p.Asn39Ser RAC1 variants function as dominant-negative alleles and result in microcephaly, reduced neuronal proliferation, and cerebellar abnormalities in vivo. Conversely, the p.Tyr64Asp substitution is constitutively active. The remaining mutations are probably weakly dominant negative or their effects are context dependent. These findings highlight the importance of RAC1 in neuronal development. Along with TRIO and HACE1, a sub-category of rare developmental disorders is emerging with RAC1 as the central player. We show that ultra-rare disorders caused by private, non-recurrent missense mutations that result in varying phenotypes are challenging to dissect, but can be delineated through focused international collaboration.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK.
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30
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Bootorabi F, Manouchehri H, Changizi R, Barker H, Palazzo E, Saltari A, Parikka M, Pincelli C, Aspatwar A. Zebrafish as a Model Organism for the Development of Drugs for Skin Cancer. Int J Mol Sci 2017; 18:ijms18071550. [PMID: 28718799 PMCID: PMC5536038 DOI: 10.3390/ijms18071550] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022] Open
Abstract
Skin cancer, which includes melanoma and squamous cell carcinoma, represents the most common type of cutaneous malignancy worldwide, and its incidence is expected to rise in the near future. This condition derives from acquired genetic dysregulation of signaling pathways involved in the proliferation and apoptosis of skin cells. The development of animal models has allowed a better understanding of these pathomechanisms, with the possibility of carrying out toxicological screening and drug development. In particular, the zebrafish (Danio rerio) has been established as one of the most important model organisms for cancer research. This model is particularly suitable for live cell imaging and high-throughput drug screening in a large-scale fashion. Thanks to the recent advances in genome editing, such as the clustered regularly-interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) methodologies, the mechanisms associated with cancer development and progression, as well as drug resistance can be investigated and comprehended. With these unique tools, the zebrafish represents a powerful platform for skin cancer research in the development of target therapies. Here, we will review the advantages of using the zebrafish model for drug discovery and toxicological and phenotypical screening. We will focus in detail on the most recent progress in the field of zebrafish model generation for the study of melanoma and squamous cell carcinoma (SCC), including cancer cell injection and transgenic animal development. Moreover, we will report the latest compounds and small molecules under investigation in melanoma zebrafish models.
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Affiliation(s)
- Fatemeh Bootorabi
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, 14114 Tehran, Iran.
| | - Hamed Manouchehri
- Department of Aquaculture, Babol Branch, Islamic Azad University, 47134 Babol, Iran.
| | - Reza Changizi
- Department of Aquaculture, Babol Branch, Islamic Azad University, 47134 Babol, Iran.
| | - Harlan Barker
- Faculty of Medicine and Life Sciences, University of Tampere, 33014 Tampere, Finland.
| | - Elisabetta Palazzo
- Laboratory of Cutaneous Biology, Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, 41100 Modena, Italy.
| | - Annalisa Saltari
- Laboratory of Cutaneous Biology, Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, 41100 Modena, Italy.
| | - Mataleena Parikka
- Faculty of Medicine and Life Sciences, University of Tampere, Oral and Maxillofacial Unit, Tampere University Hospital, 33014 Tampere, Finland.
| | - Carlo Pincelli
- Laboratory of Cutaneous Biology, Department of Surgical, Medical, Dental and Morphological Sciences, University of Modena and Reggio Emilia, 41100 Modena, Italy.
| | - Ashok Aspatwar
- Faculty of Medicine and Life Sciences, University of Tampere, 33014 Tampere, Finland.
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31
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Gut P, Reischauer S, Stainier DYR, Arnaout R. LITTLE FISH, BIG DATA: ZEBRAFISH AS A MODEL FOR CARDIOVASCULAR AND METABOLIC DISEASE. Physiol Rev 2017; 97:889-938. [PMID: 28468832 PMCID: PMC5817164 DOI: 10.1152/physrev.00038.2016] [Citation(s) in RCA: 194] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 12/17/2022] Open
Abstract
The burden of cardiovascular and metabolic diseases worldwide is staggering. The emergence of systems approaches in biology promises new therapies, faster and cheaper diagnostics, and personalized medicine. However, a profound understanding of pathogenic mechanisms at the cellular and molecular levels remains a fundamental requirement for discovery and therapeutics. Animal models of human disease are cornerstones of drug discovery as they allow identification of novel pharmacological targets by linking gene function with pathogenesis. The zebrafish model has been used for decades to study development and pathophysiology. More than ever, the specific strengths of the zebrafish model make it a prime partner in an age of discovery transformed by big-data approaches to genomics and disease. Zebrafish share a largely conserved physiology and anatomy with mammals. They allow a wide range of genetic manipulations, including the latest genome engineering approaches. They can be bred and studied with remarkable speed, enabling a range of large-scale phenotypic screens. Finally, zebrafish demonstrate an impressive regenerative capacity scientists hope to unlock in humans. Here, we provide a comprehensive guide on applications of zebrafish to investigate cardiovascular and metabolic diseases. We delineate advantages and limitations of zebrafish models of human disease and summarize their most significant contributions to understanding disease progression to date.
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Affiliation(s)
- Philipp Gut
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sven Reischauer
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Didier Y R Stainier
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
| | - Rima Arnaout
- Nestlé Institute of Health Sciences, EPFL Innovation Park, Lausanne, Switzerland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany; and Cardiovascular Research Institute and Division of Cardiology, Department of Medicine, University of California San Francisco, San Francisco, California
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32
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Zaidi S, Brueckner M. Genetics and Genomics of Congenital Heart Disease. Circ Res 2017; 120:923-940. [PMID: 28302740 DOI: 10.1161/circresaha.116.309140] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 11/16/2022]
Abstract
Congenital heart disease is the most common birth defect, and because of major advances in medical and surgical management, there are now more adults living with congenital heart disease (CHD) than children. Until recently, the cause of the majority of CHD was unknown. Advances in genomic technologies have discovered the genetic causes of a significant fraction of CHD, while at the same time pointing to remarkable complexity in CHD genetics. This review will focus on the evidence for genetic causes underlying CHD and discuss data supporting both monogenic and complex genetic mechanisms underlying CHD. The discoveries from CHD genetic studies draw attention to biological pathways that simultaneously open the door to a better understanding of cardiac development and affect clinical care of patients with CHD. Finally, we address clinical genetic evaluation of patients and families affected by CHD.
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Affiliation(s)
- Samir Zaidi
- From the Departments of Genetics (S.Z.) and Pediatrics and Genetics (M.B.), Yale University School of Medicine, New Haven CT
| | - Martina Brueckner
- From the Departments of Genetics (S.Z.) and Pediatrics and Genetics (M.B.), Yale University School of Medicine, New Haven CT.
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33
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Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome. Am J Hum Genet 2017; 100:666-675. [PMID: 28318500 DOI: 10.1016/j.ajhg.2017.02.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 02/17/2017] [Indexed: 01/27/2023] Open
Abstract
Despite the accelerated discovery of genes associated with syndromic traits, the majority of families affected by such conditions remain undiagnosed. Here, we employed whole-exome sequencing in two unrelated consanguineous kindreds with central nervous system (CNS), cardiac, renal, and digit abnormalities. We identified homozygous truncating mutations in TMEM260, a locus predicted to encode numerous splice isoforms. Systematic expression analyses across tissues and developmental stages validated two such isoforms, which differ in the utilization of an internal exon. The mutations in both families map uniquely to the long isoform, raising the possibility of an isoform-specific disorder. Consistent with this notion, RT-PCR of lymphocyte cell lines from one of the kindreds showed reduced levels of only the long isoform, which could be ameliorated by emetine, suggesting that the mutation induces nonsense-mediated decay. Subsequent in vivo testing supported this hypothesis. First, either transient suppression or CRISPR/Cas9 genome editing of zebrafish tmem260 recapitulated key neurological phenotypes. Second, co-injection of morphants with the long human TMEM260 mRNA rescued CNS pathology, whereas the short isoform was significantly less efficient. Finally, immunocytochemical and biochemical studies showed preferential enrichment of the long TMEM260 isoform to the plasma membrane. Together, our data suggest that there is overall reduced, but not ablated, functionality of TMEM260 and that attenuation of the membrane-associated functions of this protein is a principal driver of pathology. These observations contribute to an appreciation of the roles of splice isoforms in genetic disorders and suggest that dissection of the functions of these transcripts will most likely inform pathomechanism.
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34
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Doetschman T, Georgieva T. Gene Editing With CRISPR/Cas9 RNA-Directed Nuclease. Circ Res 2017; 120:876-894. [DOI: 10.1161/circresaha.116.309727] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 01/30/2017] [Accepted: 02/06/2017] [Indexed: 12/22/2022]
Abstract
Genetic engineering of model organisms and cultured cells has for decades provided important insights into the mechanisms underlying cardiovascular development and disease. In the past few years the development of several nuclease systems has broadened the range of model/cell systems that can be engineered. Of these, the CRISPR (clustered regularly interspersed short palindromic repeats)/Cas9 (CRISPR-associated protein 9) system has become the favorite for its ease of application. Here we will review this RNA-guided nuclease system for gene editing with respect to its usefulness for cardiovascular studies and with an eye toward potential therapy. Studies on its off-target activity, along with approaches to minimize this activity will be given. The advantages of gene editing versus gene targeting in embryonic stem cells, including the breadth of species and cell types to which it is applicable, will be discussed. We will also cover its use in iPSC for research and possible therapeutic purposes; and we will review its use in muscular dystrophy studies where considerable progress has been made toward dystrophin correction in mice. The CRISPR/Ca9s system is also being used for high-throughput screening of genes, gene regulatory regions, and long noncoding RNAs. In addition, the CRISPR system is being used for nongene-editing purposes such as activation and inhibition of gene expression, as well as for fluorescence tagging of chromosomal regions and individual mRNAs to track their cellular location. Finally, an approach to circumvent the inability of post-mitotic cells to support homologous recombination-based gene editing will be presented. In conclusion, applications of the CRISPR/Cas system are expanding at a breath-taking pace and are revolutionizing approaches to gain a better understanding of human diseases.
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Affiliation(s)
- Thomas Doetschman
- From the BIO5 Institute (T.D., T.G.) and Department of Cellular and Molecular Medicine (T.D.), University of Arizona, Tucson
| | - Teodora Georgieva
- From the BIO5 Institute (T.D., T.G.) and Department of Cellular and Molecular Medicine (T.D.), University of Arizona, Tucson
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35
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Duboué ER, Halpern ME. Genetic and Transgenic Approaches to Study Zebrafish Brain Asymmetry and Lateralized Behavior. LATERALIZED BRAIN FUNCTIONS 2017. [DOI: 10.1007/978-1-4939-6725-4_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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36
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Liu J, Zhou Y, Qi X, Chen J, Chen W, Qiu G, Wu Z, Wu N. CRISPR/Cas9 in zebrafish: an efficient combination for human genetic diseases modeling. Hum Genet 2016; 136:1-12. [PMID: 27807677 PMCID: PMC5214880 DOI: 10.1007/s00439-016-1739-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/17/2016] [Indexed: 12/26/2022]
Abstract
The next-generation sequencing identifies a growing number of candidate genes associated with human genetic diseases, which inevitably requires efficient methods to validate the causal links between genotype and phenotype. Recently, zebrafish, with sufficiently high-throughput capabilities, has become a favored option to study human pathogenesis. In addition, CRISPR/Cas9-based approaches have radically reduced the efforts to introduce targeted genome engineering in various organisms. Here, we systemically review the basic considerations in the design of gene editing in zebrafish with CRISPR/Cas9, and explore the potential of the combination of these two to support efficient functional analysis of human genetic variants.
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Affiliation(s)
- Jiaqi Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China.,Tsinghua University Medical School, Beijing, China
| | - Xiaolong Qi
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jia Chen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Weisheng Chen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China. .,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China.
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37
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Vetrini F, D'Alessandro LCA, Akdemir ZC, Braxton A, Azamian MS, Eldomery MK, Miller K, Kois C, Sack V, Shur N, Rijhsinghani A, Chandarana J, Ding Y, Holtzman J, Jhangiani SN, Muzny DM, Gibbs RA, Eng CM, Hanchard NA, Harel T, Rosenfeld JA, Belmont JW, Lupski JR, Yang Y. Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans. Am J Hum Genet 2016; 99:886-893. [PMID: 27616478 DOI: 10.1016/j.ajhg.2016.07.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023] Open
Abstract
Disruption of the establishment of left-right (L-R) asymmetry leads to situs anomalies ranging from situs inversus totalis (SIT) to situs ambiguus (heterotaxy). The genetic causes of laterality defects in humans are highly heterogeneous. Via whole-exome sequencing (WES), we identified homozygous mutations in PKD1L1 from three affected individuals in two unrelated families. PKD1L1 encodes a polycystin-1-like protein and its loss of function is known to cause laterality defects in mouse and medaka fish models. Family 1 had one fetus and one deceased child with heterotaxy and complex congenital heart malformations. WES identified a homozygous splicing mutation, c.6473+2_6473+3delTG, which disrupts the invariant splice donor site in intron 42, in both affected individuals. In the second family, a homozygous c.5072G>C (p.Cys1691Ser) missense mutation was detected in an individual with SIT and congenital heart disease. The p.Cys1691Ser substitution affects a highly conserved cysteine residue and is predicted by molecular modeling to disrupt a disulfide bridge essential for the proper folding of the G protein-coupled receptor proteolytic site (GPS) motif. Damaging effects associated with substitutions of this conserved cysteine residue in the GPS motif have also been reported in other genes, namely GPR56, BAI3, and PKD1 in human and lat-1 in C. elegans, further supporting the likely pathogenicity of p.Cys1691Ser in PKD1L1. The identification of bi-allelic PKD1L1 mutations recapitulates previous findings regarding phenotypic consequences of loss of function of the orthologous genes in mice and medaka fish and further expands our understanding of genetic contributions to laterality defects in humans.
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Affiliation(s)
| | - Lisa C A D'Alessandro
- Division of Cardiology, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia Braxton
- Baylor Genetics, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahshid S Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohammad K Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | | | | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Judy Holtzman
- Genetics Department, Kaiser Permanente Medical Group, San Jose, CA 95123, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M Eng
- Baylor Genetics, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Neil A Hanchard
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - John W Belmont
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yaping Yang
- Baylor Genetics, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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38
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Bouvagnet P, Guimier A, Amiel J, Gordon CT. [A gene coding for a metalloprotease for the first time implied in heterotaxy]. Med Sci (Paris) 2016; 32:551-3. [PMID: 27406754 DOI: 10.1051/medsci/20163206007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Patrice Bouvagnet
- Inserm U1217, CNRS 5310, Université Lyon 1, 8, avenue Rockefeller, 69008 Lyon, France
| | - Anne Guimier
- Inserm U 1163, Institut Imagine, 24, boulevard Montparnasse, 75014 Paris, France
| | - Jeanne Amiel
- Inserm U 1163, Institut Imagine, 24, boulevard Montparnasse, 75014 Paris, France
| | - Christopher T Gordon
- Inserm U 1163, Institut Imagine, 24, boulevard Montparnasse, 75014 Paris, France
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