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Weiss B, Ott T, Vick P, Lui JC, Roeth R, Vogel S, Waldmüller S, Hoffmann S, Baron J, Wit JM, Rappold GA. Identification of novel genes including NAV2 associated with isolated tall stature. Front Endocrinol (Lausanne) 2023; 14:1258313. [PMID: 38152138 PMCID: PMC10752378 DOI: 10.3389/fendo.2023.1258313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/07/2023] [Indexed: 12/29/2023] Open
Abstract
Very tall people attract much attention and represent a clinically and genetically heterogenous group of individuals. Identifying the genetic etiology can provide important insights into the molecular mechanisms regulating linear growth. We studied a three-generation pedigree with five isolated (non-syndromic) tall members and one individual with normal stature by whole exome sequencing; the tallest man had a height of 211 cm. Six heterozygous gene variants predicted as damaging were shared among the four genetically related tall individuals and not present in a family member with normal height. To gain insight into the putative role of these candidate genes in bone growth, we assessed the transcriptome of murine growth plate by microarray and RNA Seq. Two (Ift140, Nav2) of the six genes were well-expressed in the growth plate. Nav2 (p-value 1.91E-62) as well as Ift140 (p-value of 2.98E-06) showed significant downregulation of gene expression between the proliferative and hypertrophic zone, suggesting that these genes may be involved in the regulation of chondrocyte proliferation and/or hypertrophic differentiation. IFT140, NAV2 and SCAF11 have also significantly associated with height in GWAS studies. Pathway and network analysis indicated functional connections between IFT140, NAV2 and SCAF11 and previously associated (tall) stature genes. Knockout of the all-trans retinoic acid responsive gene, neuron navigator 2 NAV2, in Xenopus supports its functional role as a growth promotor. Collectively, our data expand the spectrum of genes with a putative role in tall stature phenotypes and, among other genes, highlight NAV2 as an interesting gene to this phenotype.
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Affiliation(s)
- Birgit Weiss
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Tim Ott
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Philipp Vick
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Julian C. Lui
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Ralph Roeth
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Sebastian Vogel
- Department of Zoology, University of Hohenheim, Stuttgart, Germany
| | - Stephan Waldmüller
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Sandra Hoffmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Jeffrey Baron
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, United States
| | - Jan M. Wit
- Division of Pediatric Endocrinology, Department of Pediatrics, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, Netherlands
| | - Gudrun A. Rappold
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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2
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Pleuger C, Lehti MS, Dunleavy JE, Fietz D, O'Bryan MK. Haploid male germ cells-the Grand Central Station of protein transport. Hum Reprod Update 2020; 26:474-500. [PMID: 32318721 DOI: 10.1093/humupd/dmaa004] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/15/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The precise movement of proteins and vesicles is an essential ability for all eukaryotic cells. Nowhere is this more evident than during the remarkable transformation that occurs in spermiogenesis-the transformation of haploid round spermatids into sperm. These transformations are critically dependent upon both the microtubule and the actin cytoskeleton, and defects in these processes are thought to underpin a significant percentage of human male infertility. OBJECTIVE AND RATIONALE This review is aimed at summarising and synthesising the current state of knowledge around protein/vesicle transport during haploid male germ cell development and identifying knowledge gaps and challenges for future research. To achieve this, we summarise the key discoveries related to protein transport using the mouse as a model system. Where relevant, we anchored these insights to knowledge in the field of human spermiogenesis and the causality of human male infertility. SEARCH METHODS Relevant studies published in English were identified using PubMed using a range of search terms related to the core focus of the review-protein/vesicle transport, intra-flagellar transport, intra-manchette transport, Golgi, acrosome, manchette, axoneme, outer dense fibres and fibrous sheath. Searches were not restricted to a particular time frame or species although the emphasis within the review is on mammalian spermiogenesis. OUTCOMES Spermiogenesis is the final phase of sperm development. It results in the transformation of a round cell into a highly polarised sperm with the capacity for fertility. It is critically dependent on the cytoskeleton and its ability to transport protein complexes and vesicles over long distances and often between distinct cytoplasmic compartments. The development of the acrosome covering the sperm head, the sperm tail within the ciliary lobe, the manchette and its role in sperm head shaping and protein transport into the tail, and the assembly of mitochondria into the mid-piece of sperm, may all be viewed as a series of overlapping and interconnected train tracks. Defects in this redistribution network lead to male infertility characterised by abnormal sperm morphology (teratozoospermia) and/or abnormal sperm motility (asthenozoospermia) and are likely to be causal of, or contribute to, a significant percentage of human male infertility. WIDER IMPLICATIONS A greater understanding of the mechanisms of protein transport in spermiogenesis offers the potential to precisely diagnose cases of male infertility and to forecast implications for children conceived using gametes containing these mutations. The manipulation of these processes will offer opportunities for male-based contraceptive development. Further, as increasingly evidenced in the literature, we believe that the continuous and spatiotemporally restrained nature of spermiogenesis provides an outstanding model system to identify, and de-code, cytoskeletal elements and transport mechanisms of relevance to multiple tissues.
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Affiliation(s)
- Christiane Pleuger
- School of Biological Sciences, Monash University, Clayton 3800, Australia.,Institute for Veterinary Anatomy, Histology and Embryology, Justus-Liebig University Giessen, Giessen 35392, Germany.,Hessian Centre of Reproductive Medicine, Justus Liebig University Giessen, Giessen 35392, Germany
| | - Mari S Lehti
- School of Biological Sciences, Monash University, Clayton 3800, Australia.,Institute of Biomedicine, University of Turku, Turku 20520, Finland
| | | | - Daniela Fietz
- Institute for Veterinary Anatomy, Histology and Embryology, Justus-Liebig University Giessen, Giessen 35392, Germany.,Hessian Centre of Reproductive Medicine, Justus Liebig University Giessen, Giessen 35392, Germany
| | - Moira K O'Bryan
- School of Biological Sciences, Monash University, Clayton 3800, Australia
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3
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Suzuki A, Jun G, Abdallah N, Gajera M, Iwata J. Gene datasets associated with mouse cleft palate. Data Brief 2018; 18:655-673. [PMID: 29896534 PMCID: PMC5996166 DOI: 10.1016/j.dib.2018.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/01/2018] [Indexed: 12/20/2022] Open
Abstract
This article presents data on genes associated with cleft palate (CP), retrieved through both a full-text systematic review and a mouse genome informatics (MGI) database search. In order to group CP-associated genes according to function, pathway, biological process, and cellular component, the genes were analyzed using category enrichment bioinformatics tools, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). This approach provides invaluable opportunities for the identification of candidate pathways and genes in CP research.
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Affiliation(s)
- Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Goo Jun
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Nada Abdallah
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mona Gajera
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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4
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Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice. G3-GENES GENOMES GENETICS 2018; 8:401-409. [PMID: 29208648 PMCID: PMC5919724 DOI: 10.1534/g3.117.300292] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Positional cloning of ENU-induced mutations has traditionally relied on analysis of polymorphic variation between two strains. In contrast, the application of whole-genome sequencing (WGS) has enabled gene discovery in mutant lines maintained on an inbred genetic background. This approach utilizes genetic variation derived from ENU-induced variants for mapping and reduces the likelihood of phenotypic variation, making it an ideal method for genetic modifier screening. Here, we describe the results of such a screen, wherein we determined the minimal number of mutant genomic DNA samples to include in our analyses and improved the sensitivity of our screen by individually barcoding each genomic DNA library. We present several unique cases to illustrate this approach's efficacy, including the discovery of two distinct mutations that generate essentially identical mutant phenotypes, the ascertainment of a non-ENU-induced candidate variant through homozygosity mapping, and an approach for the identification of putative dominant genetic modifiers.
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5
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Zhang Y, Liu H, Li W, Zhang Z, Zhang S, Teves ME, Stevens C, Foster JA, Campbell GE, Windle JJ, Hess RA, Pazour GJ, Zhang Z. Intraflagellar transporter protein 140 (IFT140), a component of IFT-A complex, is essential for male fertility and spermiogenesis in mice. Cytoskeleton (Hoboken) 2018; 75:70-84. [PMID: 29236364 DOI: 10.1002/cm.21427] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 11/11/2022]
Abstract
Intraflagellar transport (IFT) is a conserved mechanism essential for the assembly and maintenance of most eukaryotic cilia and flagella. However, little is known about its role in sperm flagella formation and male fertility. IFT140 is a component of IFT-A complex. In mouse, it is highly expressed in the testis. Ift140 gene was inactivated specifically in mouse spermatocytes/spermatids. The mutant mice did not show any gross abnormalities, but all were infertile and associated with significantly reduced sperm number and motility. Multiple sperm morphological abnormalities were discovered, including amorphous heads, short/bent flagella and swollen tail tips, as well as vesicles along the flagella due to spermiogenesis defects. The epididymides contained round bodies of cytoplasm derived from the sloughing of the cytoplasmic lobes and residual bodies. Knockout of Ift140 did not significantly affect testicular expression levels of selective IFT components but localization of IFT27 and IFT88, two components of IFT-B complex, was changed. Our findings demonstrate that IFT140 is a key regulator for male fertility and normal spermiogenesis in mice. It not only plays a role in sperm flagella assembling, but is also involved in critical assembly of proteins that interface between the germ cell plasma and the Sertoli cell.
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Affiliation(s)
- Yong Zhang
- Department of Dermatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Hong Liu
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia 23298.,School of Public Health, Wuhan University of Science and Technology, Wuhan 430060, Hubei
| | - Wei Li
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Zhengang Zhang
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia 23298.,Department of Gastroenterology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei
| | - Shiyang Zhang
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia 23298.,School of Public Health, Wuhan University of Science and Technology, Wuhan 430060, Hubei
| | - Maria E Teves
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Courtney Stevens
- Department of Biology, Randolph-Macon College, Ashland, Virginia 23005
| | - James A Foster
- Department of Biology, Randolph-Macon College, Ashland, Virginia 23005
| | - Gregory E Campbell
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Jolene J Windle
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298
| | - Rex A Hess
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois, 2001 S. Lincoln, Urbana, Illinois 61802-6199
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Zhibing Zhang
- Department of Obstetrics & Gynecology, Virginia Commonwealth University, Richmond, Virginia 23298.,School of Public Health, Wuhan University of Science and Technology, Wuhan 430060, Hubei
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6
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Hashimoto H, Kawabe T, Fukuda T, Kusakabe M. A Novel Ataxic Mutant Mouse Line Having Sensory Neuropathy Shows Heavy Iron Deposition in Kidney. NEURODEGENER DIS 2017; 17:181-198. [DOI: 10.1159/000457126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/20/2017] [Indexed: 01/11/2023] Open
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7
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Lan Y, Zhang N, Liu H, Xu J, Jiang R. Golgb1 regulates protein glycosylation and is crucial for mammalian palate development. Development 2016; 143:2344-55. [PMID: 27226319 DOI: 10.1242/dev.134577] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 05/09/2016] [Indexed: 12/14/2022]
Abstract
Cleft palate is a common major birth defect for which currently known causes account for less than 30% of pathology in humans. In this study, we carried out mutagenesis screening in mice to identify new regulators of palatogenesis. Through genetic linkage mapping and whole-exome sequencing, we identified a loss-of-function mutation in the Golgb1 gene that co-segregated with cleft palate in a new mutant mouse line. Golgb1 is a ubiquitously expressed large coiled-coil protein, also known as giantin, that is localized at the Golgi membrane. Using CRISPR/Cas9-mediated genome editing, we generated and analyzed developmental defects in mice carrying additional Golgb1 loss-of-function mutations, which supported a crucial requirement for Golgb1 in palate development. Through maxillary explant culture assays, we demonstrate that the Golgb1 mutant embryos have intrinsic defects in palatal shelf elevation. Just prior to the developmental stage of palatal shelf elevation in wild-type littermates, Golgb1 mutant embryos exhibit increased cell density, reduced hyaluronan accumulation and impaired protein glycosylation in the palatal mesenchyme. Together, these results demonstrate that, although it is a ubiquitously expressed Golgi-associated protein, Golgb1 has specific functions in protein glycosylation and tissue morphogenesis.
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Affiliation(s)
- Yu Lan
- Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Nian Zhang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Han Liu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jingyue Xu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Rulang Jiang
- Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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8
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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9
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Abstract
Primary cilia are essential cellular organelles projecting from the cell surface to sense and transduce developmental signaling. They are tiny but have complicated structures containing microtubule (MT)-based internal structures (the axoneme) and mother centriole formed basal body. Intraflagellar transport (Ift) operated by Ift proteins and motors are indispensable for cilia formation and function. Mutations in Ift proteins or Ift motors cause various human diseases, some of which have severe bone defects. Over the last few decades, major advances have occurred in understanding the roles of these proteins and cilia in bone development and remodeling by examining cilia/Ift protein-related human diseases and establishing mouse transgenic models. In this review, we describe current advances in the understanding of the cilia/Ift structure and function. We further summarize cilia/Ift-related human diseases and current mouse models with an emphasis on bone-related phenotypes, cilia morphology, and signaling pathways.
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Affiliation(s)
- Xue Yuan
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, 3435 Main Street, Buffalo, NY, 14214, USA
| | - Shuying Yang
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, The State University of New York, 3435 Main Street, Buffalo, NY, 14214, USA
- Developmental Genomics Group, New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, The State University of New York, 701 Ellicott St, Buffalo, NY, 14203, USA
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10
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Miller KA, Tan TY, Welfare MF, White SM, Stark Z, Savarirayan R, Burgess T, Heggie AA, Caruana G, Bertram JF, Bateman JF, Farlie PG. A mouse splice-site mutant and individuals with atypical chromosome 22q11.2 deletions demonstrate the crucial role for crkl in craniofacial and pharyngeal development. Mol Syndromol 2014; 5:276-86. [PMID: 25565927 DOI: 10.1159/000368865] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2014] [Indexed: 11/19/2022] Open
Abstract
The 22q11.2 deletion syndrome (22q11DS) is thought to be a contiguous gene syndrome caused by haploinsufficiency for a variable number of genes with overlapping function during the development of the craniofacial, pharyngeal and cardiac structures. The complexity of genetic and developmental anomalies resulting in 22q11DS has made attributing causation to specific genes difficult. The CRKL gene resides within the common 3-Mb region, most frequently affected in 22q11DS, and has been shown to play an essential role in the development of tissues affected in 22q11DS. Here, we report the characterisation of a mouse strain we named 'snoopy', harbouring a novel Crkl splice-site mutation that results in a loss of Crkl expression. The snoopy strain exhibits a variable phenotype that includes micrognathia, pharyngeal occlusion, aglossia and holoprosencephaly, and altered retinoic acid and endothelin signalling. Together, these features are reminiscent of malformations occurring in auriculocondylar syndrome and agnathia-otocephaly complex, 2 conditions not previously associated with the CRKL function. Comparison of the features of a cohort of patients harbouring small 22q11.2 deletions centred over the CRKL gene, but sparing TBX1, highlights the role of CRKL in contributing to the craniofacial features of 22q11DS. These analyses demonstrate the central role of Crkl in regulating signalling events in the developing oropharyngeal complex and its potential to contribute to dysmorphology.
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Affiliation(s)
- Kerry A Miller
- Murdoch Childrens Research Institute, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia
| | - Tiong Y Tan
- Murdoch Childrens Research Institute, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Victorian Clinical Genetics Services, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Department of Paediatrics, University of Melbourne, Parkville, Vic., Australia
| | - Megan F Welfare
- Murdoch Childrens Research Institute, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia
| | - Susan M White
- Murdoch Childrens Research Institute, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Victorian Clinical Genetics Services, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia
| | - Zornitza Stark
- Murdoch Childrens Research Institute, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Victorian Clinical Genetics Services, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia
| | - Ravi Savarirayan
- Murdoch Childrens Research Institute, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Victorian Clinical Genetics Services, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Department of Paediatrics, University of Melbourne, Parkville, Vic., Australia
| | - Trent Burgess
- Victorian Clinical Genetics Services, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia
| | - Andrew A Heggie
- Section of Oral and Maxillofacial Surgery, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Department of Paediatrics, University of Melbourne, Parkville, Vic., Australia
| | - Georgina Caruana
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Clayton, Vic., Australia
| | - John F Bertram
- Department of Anatomy and Developmental Biology, School of Biomedical Sciences, Monash University, Clayton, Vic., Australia
| | - John F Bateman
- Murdoch Childrens Research Institute, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic., Australia
| | - Peter G Farlie
- Murdoch Childrens Research Institute, Department of Plastic and Maxillofacial Surgery, Royal Children's Hospital, Parkville, Vic., Australia ; Department of Paediatrics, University of Melbourne, Parkville, Vic., Australia
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11
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Belizário JE. The humankind genome: from genetic diversity to the origin of human diseases. Genome 2014; 56:705-16. [PMID: 24433206 DOI: 10.1139/gen-2013-0125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have failed to establish common variant risk for the majority of common human diseases. The underlying reasons for this failure are explained by recent studies of resequencing and comparison of over 1200 human genomes and 10 000 exomes, together with the delineation of DNA methylation patterns (epigenome) and full characterization of coding and noncoding RNAs (transcriptome) being transcribed. These studies have provided the most comprehensive catalogues of functional elements and genetic variants that are now available for global integrative analysis and experimental validation in prospective cohort studies. With these datasets, researchers will have unparalleled opportunities for the alignment, mining, and testing of hypotheses for the roles of specific genetic variants, including copy number variations, single nucleotide polymorphisms, and indels as the cause of specific phenotypes and diseases. Through the use of next-generation sequencing technologies for genotyping and standardized ontological annotation to systematically analyze the effects of genomic variation on humans and model organism phenotypes, we will be able to find candidate genes and new clues for disease's etiology and treatment. This article describes essential concepts in genetics and genomic technologies as well as the emerging computational framework to comprehensively search websites and platforms available for the analysis and interpretation of genomic data.
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Affiliation(s)
- Jose E Belizário
- Departamento de Farmacologia, Instituto de Ciências Biomédicas da Universidade de São Paulo, Avenida Lineu Prestes, 1524 CEP 05508-900, São Paulo, SP, Brazil
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12
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Damerla RR, Chatterjee B, Li Y, Francis RJB, Fatakia SN, Lo CW. Ion Torrent sequencing for conducting genome-wide scans for mutation mapping analysis. Mamm Genome 2013; 25:120-8. [PMID: 24306492 DOI: 10.1007/s00335-013-9494-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/08/2013] [Indexed: 01/08/2023]
Abstract
Mutation mapping in mice can be readily accomplished by genome wide segregation analysis of polymorphic DNA markers. In this study, we showed the efficacy of Ion Torrent next generation sequencing for conducting genome-wide scans to map and identify a mutation causing congenital heart disease in a mouse mutant, Bishu, recovered from a mouse mutagenesis screen. The Bishu mutant line generated in a C57BL/6J (B6) background was intercrossed with another inbred strain, C57BL/10J (B10), and the resulting B6/B10 hybrid offspring were intercrossed to generate mutants used for the mapping analysis. For each mutant sample, a panel of 123 B6/B10 polymorphic SNPs distributed throughout the mouse genome was PCR amplified, bar coded, and then pooled to generate a single library used for Ion Torrent sequencing. Sequencing carried out using the 314 chip yielded >600,000 usable reads. These were aligned and mapped using a custom bioinformatics pipeline. Each SNP was sequenced to a depth >500×, allowing accurate automated calling of the B6/B10 genotypes. This analysis mapped the mutation in Bishu to an interval on the proximal region of mouse chromosome 4. This was confirmed by parallel capillary sequencing of the 123 polymorphic SNPs. Further analysis of genes in the map interval identified a splicing mutation in Dnaic1(c.204+1G>A), an intermediate chain dynein, as the disease causing mutation in Bishu. Overall, our experience shows Ion Torrent amplicon sequencing is high throughput and cost effective for conducting genome-wide mapping analysis and is easily scalable for other high volume genotyping analyses.
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Affiliation(s)
- Rama Rao Damerla
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Rangos Research Center Rm 8120, 530 45 St., Pittsburgh, PA, 15201, USA,
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13
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Miller KA, Gordon CT, Welfare MF, Caruana G, Bertram JF, Bateman JF, Farlie PG. bfb, a novel ENU-induced blebs mutant resulting from a missense mutation in Fras1. PLoS One 2013; 8:e76342. [PMID: 24143185 PMCID: PMC3797057 DOI: 10.1371/journal.pone.0076342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/23/2013] [Indexed: 12/28/2022] Open
Abstract
Fras1 is an extracellular matrix associated protein with essential roles in adhesion of epithelia and mesenchyme during early embryonic development. The adhesive function of Fras1 is achieved through interaction with a group of related proteins, Frem 1–3, and a cytoplasmic adaptor protein Grip1. Mutation of each of these proteins results in characteristic epithelial blistering and have therefore become known as “blebs” proteins. Human Fraser syndrome presents with a similar phenotype and the blebs mice have been instrumental in identification of the genetic basis of Fraser syndrome. We have identified a new ENU-induced blebs allele resulting from a novel missense mutation in Fras1. The resulting mouse strain, blood filled blisters (bfb), presents with a classic blebs phenotype but does not exhibit embryonic lethality typical of other blebs mutants and in addition, we report novel palate and sternal defects. Analysis of the bfb phenotype confirms the presence of epithelial-mesenchymal adhesion defects but also supports the emerging role of blebs proteins in regulating signalling during organogenesis. The bfb strain provides new opportunities to investigate the role of Fras1 in development.
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Affiliation(s)
- Kerry A. Miller
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Christopher T. Gordon
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Megan F. Welfare
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Georgina Caruana
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - John F. Bertram
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - John F. Bateman
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- Departments of Paediatrics, Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Peter G. Farlie
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
- * E-mail:
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Cauli: a mouse strain with an Ift140 mutation that results in a skeletal ciliopathy modelling Jeune syndrome. PLoS Genet 2013; 9:e1003746. [PMID: 24009529 PMCID: PMC3757063 DOI: 10.1371/journal.pgen.1003746] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 07/10/2013] [Indexed: 02/01/2023] Open
Abstract
Cilia are architecturally complex organelles that protrude from the cell membrane and have signalling, sensory and motility functions that are central to normal tissue development and homeostasis. There are two broad categories of cilia; motile and non-motile, or primary, cilia. The central role of primary cilia in health and disease has become prominent in the past decade with the recognition of a number of human syndromes that result from defects in the formation or function of primary cilia. This rapidly growing class of conditions, now known as ciliopathies, impact the development of a diverse range of tissues including the neural axis, craniofacial structures, skeleton, kidneys, eyes and lungs. The broad impact of cilia dysfunction on development reflects the pivotal position of the primary cilia within a signalling nexus involving a growing number of growth factor systems including Hedgehog, Pdgf, Fgf, Hippo, Notch and both canonical Wnt and planar cell polarity. We have identified a novel ENU mutant allele of Ift140, which causes a mid-gestation embryonic lethal phenotype in homozygous mutant mice. Mutant embryos exhibit a range of phenotypes including exencephaly and spina bifida, craniofacial dysmorphism, digit anomalies, cardiac anomalies and somite patterning defects. A number of these phenotypes can be attributed to alterations in Hedgehog signalling, although additional signalling systems are also likely to be involved. We also report the identification of a homozygous recessive mutation in IFT140 in a Jeune syndrome patient. This ENU-induced Jeune syndrome model will be useful in delineating the origins of dysmorphology in human ciliopathies. Skeletal ciliopathies are an emerging field of human disease in which skeletal birth defects arise due to abnormal communication between cells. This failure in communication arises following mutation in components of the primary cilia, a hair-like structure present on every cell. The skeletal ciliopathies are debilitating and in severe cases lead to death in early infancy. However, the mechanisms by which these malformations come about remains unclear. Mouse models are often used to delineate the causes of human birth defects and we have identified a model that mimics one of these conditions known as Jeune syndrome. It is the first mouse model with a mutation in the Ift140 gene, and these mice exhibit phenotypes that are often seen in this set of human syndromes. We have complimented this study with the discovery of a patient that presents with Jeune Syndrome resulting from mutation of human IFT140. This model will allow us to explore the role of IFT140 and the primary cilia in normal human development and provide insight into the field of human skeletal ciliopathies.
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