1
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Chen Z, Snetkova V, Bower G, Jacinto S, Clock B, Dizehchi A, Barozzi I, Mannion BJ, Alcaina-Caro A, Lopez-Rios J, Dickel DE, Visel A, Pennacchio LA, Kvon EZ. Increased enhancer-promoter interactions during developmental enhancer activation in mammals. Nat Genet 2024; 56:675-685. [PMID: 38509385 PMCID: PMC11203181 DOI: 10.1038/s41588-024-01681-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/06/2024] [Indexed: 03/22/2024]
Abstract
Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.
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Affiliation(s)
- Zhuoxin Chen
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Valentina Snetkova
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Grace Bower
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Sandra Jacinto
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Benjamin Clock
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Atrin Dizehchi
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA
| | - Iros Barozzi
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Brandon J Mannion
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
| | - Ana Alcaina-Caro
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
| | - Javier Lopez-Rios
- Centro Andaluz de Biología del Desarrollo, CSIC, Universidad Pablo de Olavide, Junta de Andalucía, Seville, Spain
- School of Health Sciences, Universidad Loyola Andalucía, Seville, Spain
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Octant, Inc, Emeryville, CA, USA
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- School of Natural Sciences, University of California, Merced, CA, USA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Comparative Biochemistry Program, University of California, Berkeley, CA, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Evgeny Z Kvon
- Department of Developmental and Cell Biology, School of the Biological Sciences, University of California, Irvine, CA, USA.
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2
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Nim HT, Dang L, Thiyagarajah H, Bakopoulos D, See M, Charitakis N, Sibbritt T, Eichenlaub MP, Archer SK, Fossat N, Burke RE, Tam PPL, Warr CG, Johnson TK, Ramialison M. A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease. Genome Biol 2021; 22:335. [PMID: 34906219 PMCID: PMC8672579 DOI: 10.1186/s13059-021-02539-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/10/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development. RESULTS We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes. CONCLUSIONS Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.
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Affiliation(s)
- Hieu T. Nim
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
| | - Louis Dang
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Harshini Thiyagarajah
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Daniel Bakopoulos
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Michael See
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Natalie Charitakis
- Murdoch Children’s Research Institute, Parkville, VIC Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC Australia
| | - Tennille Sibbritt
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Michael P. Eichenlaub
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
| | - Stuart K. Archer
- Monash Bioinformatics Platform, Monash University, Clayton, VIC Australia
| | - Nicolas Fossat
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
- Present address: Copenhagen Hepatitis C Program, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
- Present address: Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | - Richard E. Burke
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Patrick P. L. Tam
- Embryology Research Unit, Children’s Medical Research Institute, and School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales Australia
| | - Coral G. Warr
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
- School of Molecular Sciences, La Trobe University, Bundoora, Victoria 3083 Australia
| | - Travis K. Johnson
- School of Biological Sciences, Faculty of Science, Monash University, Clayton, VIC Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute and Systems Biology Institute Australia, Monash University, Clayton, VIC Australia
- Murdoch Children’s Research Institute, Parkville, VIC Australia
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3
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Prickett AR, Montibus B, Barkas N, Amante SM, Franco MM, Cowley M, Puszyk W, Shannon MF, Irving MD, Madon-Simon M, Ward A, Schulz R, Baldwin HS, Oakey RJ. Imprinted Gene Expression and Function of the Dopa Decarboxylase Gene in the Developing Heart. Front Cell Dev Biol 2021; 9:676543. [PMID: 34239874 PMCID: PMC8258389 DOI: 10.3389/fcell.2021.676543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/19/2021] [Indexed: 11/13/2022] Open
Abstract
Dopa decarboxylase (DDC) synthesizes serotonin in the developing mouse heart where it is encoded by Ddc_exon1a, a tissue-specific paternally expressed imprinted gene. Ddc_exon1a shares an imprinting control region (ICR) with the imprinted, maternally expressed (outside of the central nervous system) Grb10 gene on mouse chromosome 11, but little else is known about the tissue-specific imprinted expression of Ddc_exon1a. Fluorescent immunostaining localizes DDC to the developing myocardium in the pre-natal mouse heart, in a region susceptible to abnormal development and implicated in congenital heart defects in human. Ddc_exon1a and Grb10 are not co-expressed in heart nor in brain where Grb10 is also paternally expressed, despite sharing an ICR, indicating they are mechanistically linked by their shared ICR but not by Grb10 gene expression. Evidence from a Ddc_exon1a gene knockout mouse model suggests that it mediates the growth of the developing myocardium and a thinning of the myocardium is observed in a small number of mutant mice examined, with changes in gene expression detected by microarray analysis. Comparative studies in the human developing heart reveal a paternal expression bias with polymorphic imprinting patterns between individual human hearts at DDC_EXON1a, a finding consistent with other imprinted genes in human.
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Affiliation(s)
- Adam R. Prickett
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Bertille Montibus
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Nikolaos Barkas
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Samuele M. Amante
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Maurício M. Franco
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Michael Cowley
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - William Puszyk
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Matthew F. Shannon
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - Melita D. Irving
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
- Department of Clinical Genetics, Guy’s and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Marta Madon-Simon
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Andrew Ward
- Department of Biology and Biochemistry and Centre for Regenerative Medicine, University of Bath, Bath, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
| | - H. Scott Baldwin
- Department of Pediatrics (Cardiology), Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rebecca J. Oakey
- Department of Medical and Molecular Genetics, King’s College London, London, United Kingdom
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4
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Choi KYG, Wu BC, Lee AHY, Baquir B, Hancock REW. Utilizing Organoid and Air-Liquid Interface Models as a Screening Method in the Development of New Host Defense Peptides. Front Cell Infect Microbiol 2020; 10:228. [PMID: 32509598 PMCID: PMC7251080 DOI: 10.3389/fcimb.2020.00228] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022] Open
Abstract
Host defense peptides (HDPs), also known as antimicrobial peptides, are naturally occurring polypeptides (~12–50 residues) composed of cationic and hydrophobic amino acids that adopt an amphipathic conformation upon folding usually after contact with membranes. HDPs have a variety of biological activities including immunomodulatory, anti-inflammatory, anti-bacterial, and anti-biofilm functions. Although HDPs have the potential to address the global threat of antibiotic resistance and to treat immune and inflammatory disorders, they have yet to achieve this promise. Indeed, there are several challenges associated with bringing peptide-based drug candidates from the lab bench to clinical practice, including identifying appropriate indications, stability, toxicity, and cost. These challenges can be addressed in part by the development of innate defense regulator (IDR) peptides and peptidomimetics, which are synthetic derivatives of HDPs with similar or better efficacy, increased stability, and reduced toxicity and cost of the original HDP. However, one of the largest gaps between basic research and clinical application is the validity and translatability of conventional model systems, such as cell lines and animal models, for screening HDPs and their derivatives as potential drug therapies. Indeed, such translation has often relied on animal models, which have only limited validity. Here we discuss the recent development of human organoids for disease modeling and drug screening, assisted by the use of omics analyses. Organoids, developed from primary cells, cell lines, or human pluripotent stem cells, are three-dimensional, self-organizing structures that closely resemble their corresponding in vivo organs with regards to immune responses, tissue organization, and physiological properties; thus, organoids represent a reliable method for studying efficacy, formulation, toxicity and to some extent drug stability and pharmacodynamics. The use of patient-derived organoids enables the study of patient-specific efficacy, toxicogenomics and drug response predictions. We outline how organoids and omics data analysis can be leveraged to aid in the clinical translation of IDR peptides.
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Affiliation(s)
- Ka-Yee Grace Choi
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Bing Catherine Wu
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Beverlie Baquir
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Robert E W Hancock
- Department of Microbiology and Immunology, Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
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5
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Roseman CC, Capellini TD, Jagoda E, Williams SA, Grabowski M, O'Connor C, Polk JD, Cheverud JM. Variation in mouse pelvic morphology maps to locations enriched in Sox9 Class II and Pitx1 regulatory features. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:100-112. [PMID: 32017444 DOI: 10.1002/jez.b.22926] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/12/2019] [Accepted: 12/21/2019] [Indexed: 11/10/2022]
Abstract
Variation in pelvic morphology has a complex genetic basis and its patterning and specification is governed by conserved developmental pathways. Whether the mechanisms underlying the differentiation and specification of the pelvis also produce the morphological covariation on which natural selection may act, is still an open question in evolutionary developmental biology. We use high-resolution quantitative trait locus (QTL) mapping in the F34 generation of an advanced intercross experiment (LG,SM-G34 ) to characterize the genetic architecture of the mouse pelvis. We test the prediction that genomic features linked to developmental patterning and differentiation of the hind limb and pelvis and the regulation of chondrogenesis are overrepresented in QTL. We find 31 single QTL trait associations at the genome- or chromosome-wise significance level coalescing to 27 pleiotropic loci. We recover further QTL at a more relaxed significance threshold replicating locations found in a previous experiment in an earlier generation of the same population. QTL were more likely than chance to harbor Pitx1 and Sox9 Class II chromatin immunoprecipitation-seq features active during development of skeletal features. There was weak or no support for the enrichment of seven more categories of developmental features drawn from the literature. Our results suggest that genotypic variation is channeled through a subset of developmental processes involved in the generation of phenotypic variation in the pelvis. This finding indicates that the evolvability of complex traits may be subject to biases not evident from patterns of covariance among morphological features or developmental patterning when either is considered in isolation.
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Affiliation(s)
- Charles C Roseman
- Victor E. Shelford Vivarium, Department of Animal Biology, School of Integrative Biology, University of Illinois, Urbana-Champaign, Illinois
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Evelyn Jagoda
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Scott A Williams
- Department of Anthropology, Center for the Study of Human Origins, New York University, New York, New York.,New York Consortium in Evolutionary Primatology, New York, New York
| | - Mark Grabowski
- Research Centre in Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Liverpool, UK
| | - Christine O'Connor
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota.,Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota
| | - John D Polk
- Department of Anthropology, University of Illinois, Urbana-Champaign, Illinois.,Department of Biomedical and Translational Sciences, Carle-Illinois College of Medicine, Urbana, Illinois
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6
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Yaro M, Munyard KA, Morgan E, Allcock RJN, Stear MJ, Groth DM. Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment. BMC Genomics 2019; 20:816. [PMID: 31699027 PMCID: PMC6836352 DOI: 10.1186/s12864-019-6198-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to these disease challenges. Haemonchosis and Trypanosomiasis collectively cost the worldwide animal industry billions of dollars in production losses annually. RESULTS Here, we separately sequenced and then pooled according to breed the genomes from five unrelated individuals from each of the Djallonke and Sahelian sheep breeds (sourced from Ghana), at greater than 22-fold combined coverage for each breed. A total of approximately 404 million (97%) and 343 million (97%) sequence reads from the Djallonke and Sahelian breeds respectively, were successfully mapped to the sheep reference genome Oar v3.1. We identified approximately 11.1 million and 10.9 million single nucleotide polymorphisms (SNPs) in the Djallonke and Sahelian breeds, with approximately 15 and 16% respectively of these not previously reported in sheep. Multiple regions of reduced heterozygosity were also found; 70 co-localised within genomic regions harbouring genes that mediate disease resistance, immune response and adaptation in sheep or cattle. Thirty- three of the regions of reduced heterozygosity co-localised with previously reported genes for resistance to haemonchosis and trypanosomiasis. CONCLUSIONS Our analyses suggest that these regions of reduced heterozygosity may be signatures of selection for these economically important diseases.
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Affiliation(s)
- M. Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - K. A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - E. Morgan
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
| | - R. J. N. Allcock
- The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA Australia
- Pathwest Laboratory Medicine WA, QEII Medical Centre, Monash Avenue, Nedlands, 6009 Australia
| | - M. J. Stear
- Agribio centre for Agribioscience, La Trobe University, Melbourne, Australia
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow, Bearsden Road, Glasgow, G61 1QH UK
| | - D. M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth, WA 6845 Australia
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7
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Amrom D, Poduri A, Goldman JS, Dan B, Deconinck N, Pichon B, Nadaf J, Andermann F, Andermann E, Walsh CA, Dobyns WB. Duplication 2p16 is associated with perisylvian polymicrogyria. Am J Med Genet A 2019; 179:2343-2356. [PMID: 31660690 DOI: 10.1002/ajmg.a.61342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 07/01/2019] [Accepted: 08/12/2019] [Indexed: 11/07/2022]
Abstract
Polymicrogyria (PMG) is a heterogeneous brain malformation that may result from prenatal vascular disruption or infection, or from numerous genetic causes that still remain difficult to identify. We identified three unrelated patients with polymicrogyria and duplications of chromosome 2p, defined the smallest region of overlap, and performed gene pathway analysis using Cytoscape. The smallest region of overlap in all three children involved 2p16.1-p16.3. All three children have bilateral perisylvian polymicrogyria (BPP), intrauterine and postnatal growth deficiency, similar dysmorphic features, and poor feeding. Two of the three children had documented intellectual disability. Gene pathway analysis suggested a number of developmentally relevant genes and gene clusters that were over-represented in the critical region. We narrowed a rare locus for polymicrogyria to a region of 2p16.1-p16.3 that contains 33-34 genes, 23 of which are expressed in cerebral cortex during human fetal development. Using pathway analysis, we showed that several of the duplicated genes contribute to neurodevelopmental pathways including morphogen, cytokine, hormonal and growth factor signaling, regulation of cell cycle progression, cell morphogenesis, axonal guidance, and neuronal migration. These findings strengthen the evidence for a novel locus associated with polymicrogyria on 2p16.1-p16.3, and comprise the first step in defining the underlying genetic etiology.
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Affiliation(s)
- Dina Amrom
- Neurogenetics Unit, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Department of Neurology, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Annapurna Poduri
- Division of Epilepsy & Clinical Neurophysiology, Children's Hospital, Boston, Massachusetts.,Department of Neurology, Children's Hospital, Boston, Massachusetts
| | - Jennifer S Goldman
- Ludmer Centre for Neuroinformatics and Mental Health and the Department of Biomedical Engineering, McGill Centre for Integrative Neuroscience, McGill University, Montreal, Quebec, Canada
| | | | | | - Bruno Pichon
- Department of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Genome Quebec Innovation Center, McGill University, Montreal, Quebec, Canada
| | - Frederick Andermann
- Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Epilepsy Research Group, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Eva Andermann
- Neurogenetics Unit, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Epilepsy Research Group, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada
| | - Christopher A Walsh
- Department of Neurology, Children's Hospital, Boston, Massachusetts.,Division of Genetics and Manton Center for Orphan Disease Research, Children's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts
| | - William B Dobyns
- Department of Pediatrics (Genetics) and Neurology, University of Washington, and Seattle Children's Research Institute, Seattle, Washington
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8
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Rafi SK, Fernández-Jaén A, Álvarez S, Nadeau OW, Butler MG. High Functioning Autism with Missense Mutations in Synaptotagmin-Like Protein 4 (SYTL4) and Transmembrane Protein 187 (TMEM187) Genes: SYTL4- Protein Modeling, Protein-Protein Interaction, Expression Profiling and MicroRNA Studies. Int J Mol Sci 2019; 20:E3358. [PMID: 31323913 PMCID: PMC6651166 DOI: 10.3390/ijms20133358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 01/31/2023] Open
Abstract
We describe a 7-year-old male with high functioning autism spectrum disorder (ASD) and maternally-inherited rare missense variant of Synaptotagmin-like protein 4 (SYTL4) gene (Xq22.1; c.835C>T; p.Arg279Cys) and an unknown missense variant of Transmembrane protein 187 (TMEM187) gene (Xq28; c.708G>T; p. Gln236His). Multiple in-silico predictions described in our study indicate a potentially damaging status for both X-linked genes. Analysis of predicted atomic threading models of the mutant and the native SYTL4 proteins suggest a potential structural change induced by the R279C variant which eliminates the stabilizing Arg279-Asp60 salt bridge in the N-terminal half of the SYTL4, affecting the functionality of the protein's critical RAB-Binding Domain. In the European (Non-Finnish) population, the allele frequency for this variant is 0.00042. The SYTL4 gene is known to directly interact with several members of the RAB family of genes, such as, RAB27A, RAB27B, RAB8A, and RAB3A which are known autism spectrum disorder genes. The SYTL4 gene also directly interacts with three known autism genes: STX1A, SNAP25 and STXBP1. Through a literature-based analytical approach, we identified three of five (60%) autism-associated serum microRNAs (miRs) with high predictive power among the total of 298 mouse Sytl4 associated/predicted microRNA interactions. Five of 13 (38%) miRs were differentially expressed in serum from ASD individuals which were predicted to interact with the mouse equivalent Sytl4 gene. TMEM187 gene, like SYTL4, is a protein-coding gene that belongs to a group of genes which host microRNA genes in their introns or exons. The novel Q236H amino acid variant in the TMEM187 in our patient is near the terminal end region of the protein which is represented by multiple sequence alignments and hidden Markov models, preventing comparative structural analysis of the variant harboring region. Like SYTL4, the TMEM187 gene is expressed in the brain and interacts with four known ASD genes, namely, HCFC1; TMLHE; MECP2; and GPHN. TMM187 is in linkage with MECP2, which is a well-known determinant of brain structure and size and is a well-known autism gene. Other members of the TMEM gene family, TMEM132E and TMEM132D genes are associated with bipolar and panic disorders, respectively, while TMEM231 is a known syndromic autism gene. Together, TMEM187 and SYTL4 genes directly interact with recognized important ASD genes, and their mRNAs are found in extracellular vesicles in the nervous system and stimulate target cells to translate into active protein. Our evidence shows that both these genes should be considered as candidate genes for autism. Additional biological testing is warranted to further determine the pathogenicity of these gene variants in the causation of autism.
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Affiliation(s)
- Syed K Rafi
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | | | - Sara Álvarez
- Genomics and Medicine, NIM Genetics, 28108 Madrid, Spain
| | - Owen W Nadeau
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Merlin G Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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9
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Collins JE, White RJ, Staudt N, Sealy IM, Packham I, Wali N, Tudor C, Mazzeo C, Green A, Siragher E, Ryder E, White JK, Papatheodoru I, Tang A, Füllgrabe A, Billis K, Geyer SH, Weninger WJ, Galli A, Hemberger M, Stemple DL, Robertson E, Smith JC, Mohun T, Adams DJ, Busch-Nentwich EM. Common and distinct transcriptional signatures of mammalian embryonic lethality. Nat Commun 2019; 10:2792. [PMID: 31243271 PMCID: PMC6594971 DOI: 10.1038/s41467-019-10642-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 05/22/2019] [Indexed: 12/20/2022] Open
Abstract
The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.
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Affiliation(s)
- John E Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Richard J White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Nicole Staudt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Ian M Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Ian Packham
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Catherine Tudor
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Cecilia Mazzeo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Angela Green
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emma Siragher
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Edward Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Jacqueline K White
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - Irene Papatheodoru
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Amy Tang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, CB10 1SD, UK
| | - Stefan H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Wolfgang J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Waehringerstr. 13, 1090, Wien, Austria
| | - Antonella Galli
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Myriam Hemberger
- The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
- Departments of Biochemistry & Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Derek L Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Camena Bioscience, The Science Village, Chesterford Research Park, Cambridge, CB10 1XL, UK
| | - Elizabeth Robertson
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - James C Smith
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Timothy Mohun
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Elisabeth M Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
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10
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de Kroon LMG, van den Akker GGH, Brachvogel B, Narcisi R, Belluoccio D, Jenner F, Bateman JF, Little CB, Brama PAJ, Blaney Davidson EN, van der Kraan PM, van Osch GJVM. Identification of TGFβ-related genes regulated in murine osteoarthritis and chondrocyte hypertrophy by comparison of multiple microarray datasets. Bone 2018; 116:67-77. [PMID: 30010080 DOI: 10.1016/j.bone.2018.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 01/04/2023]
Abstract
OBJECTIVE Osteoarthritis (OA) is a joint disease characterized by progressive degeneration of articular cartilage. Some features of OA, including chondrocyte hypertrophy and focal calcification of articular cartilage, resemble the endochondral ossification processes. Alterations in transforming growth factor β (TGFβ) signaling have been associated with OA as well as with chondrocyte hypertrophy. Our aim was to identify novel candidate genes implicated in chondrocyte hypertrophy during OA pathogenesis by determining which TGFβ-related genes are regulated during murine OA and endochondral ossification. METHODS A list of 580 TGFβ-related genes, including TGFβ signaling pathway components and TGFβ-target genes, was generated. Regulation of these TGFβ-related genes was assessed in a microarray of murine OA cartilage: 1, 2 and 6 weeks after destabilization of the medial meniscus (DMM). Subsequently, genes regulated in the DMM model were studied in two independent murine microarray datasets on endochondral ossification: the growth plate and transient embryonic cartilage (joint development). RESULTS A total of 106 TGFβ-related genes were differentially expressed in articular cartilage of DMM-operated mice compared to sham-control. From these genes, 43 were similarly regulated during chondrocyte hypertrophy in the growth plate or embryonic joint development. Among these 43 genes, 18 genes have already been associated with OA. The remaining 25 genes were considered as novel candidate genes involved in OA pathogenesis and endochondral ossification. In supplementary data of published human OA microarrays we found indications that 15 of the 25 novel genes are indeed regulated in articular cartilage of human OA patients. CONCLUSION By focusing on TGFβ-related genes during OA and chondrocyte hypertrophy in mice, we identified 18 known and 25 new candidate genes potentially implicated in phenotypical changes in chondrocytes leading to OA. We propose that 15 of these candidates warrant further investigation as therapeutic target for OA as they are also regulated in articular cartilage of OA patients.
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Affiliation(s)
- Laurie M G de Kroon
- Department of Rheumatology, Experimental Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Orthopedics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.
| | - Guus G H van den Akker
- Department of Rheumatology, Experimental Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Bent Brachvogel
- Center for Biochemistry, Medical Faculty, University of Cologne, Cologne, Germany; Department of Pediatrics and Adolescent Medicine, Experimental Neonatology, Medical Faculty, University of Cologne, Cologne, Germany.
| | - Roberto Narcisi
- Department of Orthopedics, Erasmus MC University Medical Center, Rotterdam, the Netherlands.
| | - Daniele Belluoccio
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.
| | - Florien Jenner
- Equine University Hospital, University of Veterinary Medicine, Vienna, Austria.
| | - John F Bateman
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia.
| | - Christopher B Little
- Raymond Purves Bone and Joint Research Laboratories, Kolling Institute of Medical Research, University of Sydney, St Leonards, New South Wales, Australia.
| | - Pieter A J Brama
- Veterinary Clinical Sciences, School of Veterinary Medicine, University College Dublin, Dublin, Ireland.
| | - Esmeralda N Blaney Davidson
- Department of Rheumatology, Experimental Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Peter M van der Kraan
- Department of Rheumatology, Experimental Rheumatology, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Gerjo J V M van Osch
- Department of Orthopedics, Erasmus MC University Medical Center, Rotterdam, the Netherlands; Department of Otorhinolaryngology, Erasmus MC University Medical Center, Rotterdam, the Netherlands.
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11
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Hofer M, Hoferová Z, Remšík J, Nováková M, Procházková J, Fedr R, Kohoutek J, Dušek L, Hampl A, Souček K. Hematological findings in non-treated and gamma-irradiated mice deficient for MIC-1/GDF15. Physiol Res 2018; 67:623-636. [PMID: 29750874 DOI: 10.33549/physiolres.933810] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Several members of the TGF-beta family are known to effectively regulate the fate of hematopoietic progenitor cells in a complex and context-dependent manner. Growth differentiation factor-15 (GDF15) is a divergent member of the TGF-beta family. This stress-induced cytokine has been proposed to possess immunomodulatory functions and its high expression is often associated with progression of a variety of pathological conditions. GDF15 is also induced by chemotherapy and irradiation. Very few fundamental studies have been published regarding the effect of GDF15 in hematopoiesis. In this study, we analyzed the hematological status of untreated and gamma-irradiated mice deficient for GDF15 as a result of genetic knock-out (KO), in order to clarify the regulatory role of GDF15 in hematopoiesis. Significant differences between GDF15 KO mice and their pertinent WT controls were found in the parameters of blood monocyte numbers, blood platelet size, and distribution width, as well as in the values of bone marrow granulocyte/macrophage progenitor cells. Different tendencies of some hematological parameters in the GDF15 KO mice in normal conditions and those under exposure of the mice to ionizing radiation were registered. These findings are discussed in the context of the GDF15 gene function and its lack under conditions of radiation-induced damage.
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Affiliation(s)
- M Hofer
- Department of Molecular Cytology and Cytometry, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic. and Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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12
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Abernathy DG, Kim WK, McCoy MJ, Lake AM, Ouwenga R, Lee SW, Xing X, Li D, Lee HJ, Heuckeroth RO, Dougherty JD, Wang T, Yoo AS. MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. Cell Stem Cell 2018; 21:332-348.e9. [PMID: 28886366 DOI: 10.1016/j.stem.2017.08.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/26/2017] [Accepted: 08/09/2017] [Indexed: 12/19/2022]
Abstract
Directed reprogramming of human fibroblasts into fully differentiated neurons requires massive changes in epigenetic and transcriptional states. Induction of a chromatin environment permissive for acquiring neuronal subtype identity is therefore a major barrier to fate conversion. Here we show that the brain-enriched miRNAs miR-9/9∗ and miR-124 (miR-9/9∗-124) trigger reconfiguration of chromatin accessibility, DNA methylation, and mRNA expression to induce a default neuronal state. miR-9/9∗-124-induced neurons (miNs) are functionally excitable and uncommitted toward specific subtypes but possess open chromatin at neuronal subtype-specific loci, suggesting that such identity can be imparted by additional lineage-specific transcription factors. Consistently, we show that ISL1 and LHX3 selectively drive conversion to a highly homogeneous population of human spinal cord motor neurons. This study shows that modular synergism between miRNAs and neuronal subtype-specific transcription factors can drive lineage-specific neuronal reprogramming, providing a general platform for high-efficiency generation of distinct subtypes of human neurons.
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Affiliation(s)
- Daniel G Abernathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Developmental, Regenerative, and Stem Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Woo Kyung Kim
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Matthew J McCoy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Molecular Genetics & Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Allison M Lake
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca Ouwenga
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Seong Won Lee
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hyung Joo Lee
- Program in Molecular Genetics & Genomics, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Robert O Heuckeroth
- Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, and The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew S Yoo
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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13
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Genetic Dissection of a Supergene Implicates Tfap2a in Craniofacial Evolution of Threespine Sticklebacks. Genetics 2018; 209:591-605. [PMID: 29593029 DOI: 10.1534/genetics.118.300760] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023] Open
Abstract
In nature, multiple adaptive phenotypes often coevolve and can be controlled by tightly linked genetic loci known as supergenes. Dissecting the genetic basis of these linked phenotypes is a major challenge in evolutionary genetics. Multiple freshwater populations of threespine stickleback fish (Gasterosteus aculeatus) have convergently evolved two constructive craniofacial traits, longer branchial bones and increased pharyngeal tooth number, likely as adaptations to dietary differences between marine and freshwater environments. Prior QTL mapping showed that both traits are partially controlled by overlapping genomic regions on chromosome 21 and that a regulatory change in Bmp6 likely underlies the tooth number QTL. Here, we mapped the branchial bone length QTL to a 155 kb, eight-gene interval tightly linked to, but excluding the coding regions of Bmp6 and containing the candidate gene Tfap2a Further recombinant mapping revealed this bone length QTL is separable into at least two loci. During embryonic and larval development, Tfap2a was expressed in the branchial bone primordia, where allele specific expression assays revealed the freshwater allele of Tfap2a was expressed at lower levels relative to the marine allele in hybrid fish. Induced loss-of-function mutations in Tfap2a revealed an essential role in stickleback craniofacial development and show that bone length is sensitive to Tfap2a dosage in heterozygotes. Combined, these results suggest that closely linked but genetically separable changes in Bmp6 and Tfap2a contribute to a supergene underlying evolved skeletal gain in multiple freshwater stickleback populations.
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14
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Roux J, Liu J, Robinson-Rechavi M. Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. Mol Biol Evol 2018; 34:2773-2791. [PMID: 28981708 PMCID: PMC5850798 DOI: 10.1093/molbev/msx199] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The evolutionary history of vertebrates is marked by three ancient whole-genome duplications: two successive rounds in the ancestor of vertebrates, and a third one specific to teleost fishes. Biased loss of most duplicates enriched the genome for specific genes, such as slow evolving genes, but this selective retention process is not well understood. To understand what drives the long-term preservation of duplicate genes, we characterized duplicated genes in terms of their expression patterns. We used a new method of expression enrichment analysis, TopAnat, applied to in situ hybridization data from thousands of genes from zebrafish and mouse. We showed that the presence of expression in the nervous system is a good predictor of a higher rate of retention of duplicate genes after whole-genome duplication. Further analyses suggest that purifying selection against the toxic effects of misfolded or misinteracting proteins, which is particularly strong in nonrenewing neural tissues, likely constrains the evolution of coding sequences of nervous system genes, leading indirectly to the preservation of duplicate genes after whole-genome duplication. Whole-genome duplications thus greatly contributed to the expansion of the toolkit of genes available for the evolution of profound novelties of the nervous system at the base of the vertebrate radiation.
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Affiliation(s)
- Julien Roux
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jialin Liu
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Département d'Ecologie et d'Evolution, Université de Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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15
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de Bruin RG, Rabelink TJ, van Zonneveld AJ, van der Veer EP. Emerging roles for RNA-binding proteins as effectors and regulators of cardiovascular disease. Eur Heart J 2018; 38:1380-1388. [PMID: 28064149 DOI: 10.1093/eurheartj/ehw567] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/02/2016] [Indexed: 12/18/2022] Open
Abstract
The cardiovascular system comprises multiple cell types that possess the capacity to modulate their phenotype in response to acute or chronic injury. Transcriptional and post-transcriptional mechanisms play a key role in the regulation of remodelling and regenerative responses to damaged cardiovascular tissues. Simultaneously, insufficient regulation of cellular phenotype is tightly coupled with the persistence and exacerbation of cardiovascular disease. Recently, RNA-binding proteins such as Quaking, HuR, Muscleblind, and SRSF1 have emerged as pivotal regulators of these functional adaptations in the cardiovascular system by guiding a wide-ranging number of post-transcriptional events that dramatically impact RNA fate, including alternative splicing, stability, localization and translation. Moreover, homozygous disruption of RNA-binding protein genes is commonly associated with cardiac- and/or vascular complications. Here, we summarize the current knowledge on the versatile role of RNA-binding proteins in regulating the transcriptome during phenotype switching in cardiovascular health and disease. We also detail existing and potential DNA- and RNA-based therapeutic approaches that could impact the treatment of cardiovascular disease in the future.
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Affiliation(s)
- Ruben G de Bruin
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Ton J Rabelink
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Anton Jan van Zonneveld
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Eric P van der Veer
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
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16
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Hiyari S, Naghibi A, Wong R, Sadreshkevary R, Yi-Ling L, Tetradis S, Camargo PM, Pirih FQ. Susceptibility of different mouse strains to peri-implantitis. J Periodontal Res 2017; 53:107-116. [PMID: 29044525 DOI: 10.1111/jre.12493] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND OBJECTIVE Peri-implantitis (PI) is an inflammatory condition that affects the tissues surrounding dental implants. Although the pathogenesis of PI is not fully understood, evidence suggests that the etiology is multifactorial and may include a genetic component. The aim of this study was to investigate the role of genetics in the development of peri-implantitis. MATERIAL AND METHODS Four-week-old C57BL/6J, C3H/HeJ and A/J male mice had their left maxillary molars extracted. Implants were placed in the healed extraction sockets. Upon osseointegration, ligatures were placed around the implant head for 1 or 4 weeks to induce PI. Micro-computed tomography scanning was used to measure volumetric bone loss. Histological analyses were also performed to evaluate collagen organization and the presence of neutrophils and osteoclasts. RESULTS Radiographically, comparing the ligature-treated mice, C57BL/6J displayed the greatest amount of bone loss, followed by C3H/HeJ and A/J mice at 1 and 4 weeks. Histologically, at 1 week, C57BL/6J mice presented with the highest numbers of neutrophils and osteoclasts. At 4 weeks, C57BL/6J mice presented with the most active bone remodeling compared with the other two strains. CONCLUSION There were significant differences in the severity of peri-implantitis among the different mouse strains, suggesting that the genetic framework can affect implant survival and success. Future work is needed to dissect the genetic contribution to the development of peri-implantitis.
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Affiliation(s)
- S Hiyari
- Section of Periodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - A Naghibi
- Section of Periodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - R Wong
- Section of Periodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - R Sadreshkevary
- Section of Periodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - L Yi-Ling
- Section of Oral Pathology, School of Dentistry, University of California, Los Angeles, CA, USA
| | - S Tetradis
- Section of Radiology, School of Dentistry, University of California, Los Angeles, CA, USA
| | - P M Camargo
- Section of Periodontics, School of Dentistry, University of California, Los Angeles, CA, USA
| | - F Q Pirih
- Section of Periodontics, School of Dentistry, University of California, Los Angeles, CA, USA
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17
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Galperin MY, Fernández-Suárez XM, Rigden DJ. The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res 2017; 45:D1-D11. [PMID: 28053160 PMCID: PMC5210597 DOI: 10.1093/nar/gkw1188] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 12/23/2022] Open
Abstract
This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein-protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as 'breakthrough' contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the 'golden set' of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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18
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Hooper JE, Feng W, Li H, Leach SM, Phang T, Siska C, Jones KL, Spritz RA, Hunter LE, Williams T. Systems biology of facial development: contributions of ectoderm and mesenchyme. Dev Biol 2017; 426:97-114. [PMID: 28363736 PMCID: PMC5530582 DOI: 10.1016/j.ydbio.2017.03.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 12/17/2022]
Abstract
The rapid increase in gene-centric biological knowledge coupled with analytic approaches for genomewide data integration provides an opportunity to develop systems-level understanding of facial development. Experimental analyses have demonstrated the importance of signaling between the surface ectoderm and the underlying mesenchyme are coordinating facial patterning. However, current transcriptome data from the developing vertebrate face is dominated by the mesenchymal component, and the contributions of the ectoderm are not easily identified. We have generated transcriptome datasets from critical periods of mouse face formation that enable gene expression to be analyzed with respect to time, prominence, and tissue layer. Notably, by separating the ectoderm and mesenchyme we considerably improved the sensitivity compared to data obtained from whole prominences, with more genes detected over a wider dynamic range. From these data we generated a detailed description of ectoderm-specific developmental programs, including pan-ectodermal programs, prominence- specific programs and their temporal dynamics. The genes and pathways represented in these programs provide mechanistic insights into several aspects of ectodermal development. We also used these data to identify co-expression modules specific to facial development. We then used 14 co-expression modules enriched for genes involved in orofacial clefts to make specific mechanistic predictions about genes involved in tongue specification, in nasal process patterning and in jaw development. Our multidimensional gene expression dataset is a unique resource for systems analysis of the developing face; our co-expression modules are a resource for predicting functions of poorly annotated genes, or for predicting roles for genes that have yet to be studied in the context of facial development; and our analytic approaches provide a paradigm for analysis of other complex developmental programs.
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Affiliation(s)
- Joan E Hooper
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Weiguo Feng
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Sonia M Leach
- Department of Biomedical Research, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA.
| | - Tzulip Phang
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Medicine, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Charlotte Siska
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, 12800 E 17th Avenue, Aurora, CO 80045, USA.
| | - Lawrence E Hunter
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
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19
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Holmes RS. Comparative studies of vertebrate iduronate 2-sulfatase (IDS) genes and proteins: evolution of A mammalian X-linked gene. 3 Biotech 2017; 7:22. [PMID: 28401457 PMCID: PMC5388652 DOI: 10.1007/s13205-016-0595-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 12/23/2016] [Indexed: 12/24/2022] Open
Abstract
IDS is responsible for the lysosomal degradation of heparan sulfate and dermatan sulfate and linked to an X-linked lysosomal storage disease, mucopolysaccharidosis 2 (MPS2), resulting in neurological damage and early death. Comparative IDS amino acid sequences and structures and IDS gene locations were examined using data from several vertebrate genome projects. Vertebrate IDS sequences shared 60–99% identities with each other. Human IDS showed 47% sequence identity with fruit fly (Drosophila melanogaster) IDS. Sequence alignments, key amino acid residues, N-glycosylation sites and conserved predicted secondary and tertiary structures were also studied, including signal peptide, propeptide and active site residues. Mammalian IDS genes usually contained 9 coding exons. The human IDS gene promoter contained a large CpG island (CpG46) and 5 transcription factor binding sites, whereas the 3′-UTR region contained 5 miRNA target sites. These may contribute to IDS gene regulation of expression in the brain and other neural tissues of the body. An IDS pseudogene (IDSP1) was located proximally to the IDS gene on the X-chromosome in primate genomes. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate IDS gene. These suggested that IDS has originated in an invertebrate ancestral genome and retained throughout vertebrate evolution and conserved on marsupial and eutherian X-chromosomes, with the exception of rat Ids on chromosome 8.
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20
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Carpenter AR, McHugh KM. Role of renal urothelium in the development and progression of kidney disease. Pediatr Nephrol 2017; 32:557-564. [PMID: 27115886 PMCID: PMC5081278 DOI: 10.1007/s00467-016-3385-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/11/2016] [Accepted: 03/31/2016] [Indexed: 10/21/2022]
Abstract
The clinical and financial impact of chronic kidney disease (CKD) is significant, while its progression and prognosis is variable and often poor. Studies using the megabladder (mgb -/- ) model of CKD show that renal urothelium plays a key role in modulating early injury responses following the development of congenital obstruction. The aim of this review is to examine the role that urothelium has in normal urinary tract development and pathogenesis. We discuss normal morphology of renal urothelium and then examine the role that uroplakins (Upks) play in its development. Histologic, biochemical, and molecular characterization of Upk1b RFP/RFP mice indicated Upk1b expression is essential for normal urinary tract development, apical plaque/asymmetric membrane unit (AUM) formation, and differentiation and functional integrity of the renal urothelium. Our studies provide the first evidence that Upk1b is directly associated with the development of congenital anomalies of the urinary tract (CAKUT), spontaneous age-dependent hydronephrosis, and dysplastic urothelia. These observations demonstrate the importance of proper urothelial differentiation in normal development and pathogenesis of the urinary tract and provide a unique working model to test the hypothesis that the complex etiology associated with CKD is dependent upon predetermined genetic susceptibilities that establish pathogenic thresholds for disease initiation and progression.
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Affiliation(s)
- Ashley R. Carpenter
- Biomedical Sciences Graduate Program, The Ohio State University,Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital
| | - Kirk M. McHugh
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital,Division of Anatomy, The Ohio State University
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21
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Armit C, Richardson L, Venkataraman S, Graham L, Burton N, Hill B, Yang Y, Baldock RA. eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis. Dev Biol 2017; 423:1-11. [PMID: 28161522 PMCID: PMC5442644 DOI: 10.1016/j.ydbio.2017.01.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 11/23/2022]
Abstract
The eMouseAtlas resource is an online database of 3D digital models of mouse development, an ontology of mouse embryo anatomy and a gene-expression database with about 30K spatially mapped gene-expression patterns. It is closely linked with the MGI/GXD database at the Jackson Laboratory and holds links to almost all available image-based gene-expression data for the mouse embryo. In this resource article we describe the novel web-based tools we have developed for 3D visualisation of embryo anatomy and gene expression. We show how mapping of gene expression data onto spatial models delivers a framework for capturing gene expression that enhances our understanding of development, and we review the exploratory tools utilised by the EMAGE gene expression database as a means of defining co-expression of in situ hybridisation, immunohistochemistry, and lacZ-omic expression patterns. We report on recent developments of the eHistology atlas and our use of web-services to support embedding of the online 'The Atlas of Mouse Development' in the context of other resources such as the DMDD mouse phenotype database. In addition, we discuss new developments including a cellular-resolution placental atlas, third-party atlas models, clonal analysis data and a new interactive eLearning resource for developmental processes.
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Affiliation(s)
- Chris Armit
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Lorna Richardson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Shanmugasundaram Venkataraman
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Liz Graham
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Nicholas Burton
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Bill Hill
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Yiya Yang
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
| | - Richard A Baldock
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, EH4 2XU, UK
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22
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Cai Y, Nogales-Cadenas R, Zhang Q, Lin JR, Zhang W, O’Brien K, Montagna C, Zhang ZD. Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model. BMC Genomics 2017; 18:185. [PMID: 28212608 PMCID: PMC5316186 DOI: 10.1186/s12864-017-3563-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 02/07/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Malignant breast cancer with complex molecular mechanisms of progression and metastasis remains a leading cause of death in women. To improve diagnosis and drug development, it is critical to identify panels of genes and molecular pathways involved in tumor progression and malignant transition. Using the PyMT mouse, a genetically engineered mouse model that has been widely used to study human breast cancer, we profiled and analyzed gene expression from four distinct stages of tumor progression (hyperplasia, adenoma/MIN, early carcinoma and late carcinoma) during which malignant transition occurs. RESULTS We found remarkable expression similarity among the four stages, meaning genes altered in the later stages showed trace in the beginning of tumor progression. We identified a large number of differentially expressed genes in PyMT samples of all stages compared with normal mammary glands, enriched in cancer-related pathways. Using co-expression networks, we found panels of genes as signature modules with some hub genes that predict metastatic risk. Time-course analysis revealed genes with expression transition when shifting to malignant stages. These may provide additional insight into the molecular mechanisms beyond pathways. CONCLUSIONS Thus, in this study, our various analyses with the PyMT mouse model shed new light on transcriptomic dynamics during breast cancer malignant progression.
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Affiliation(s)
- Ying Cai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | | | - Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Wen Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Kelly O’Brien
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY USA
| | - Zhengdong D. Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY USA
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23
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Rhee C, Edwards M, Dang C, Harris J, Brown M, Kim J, Tucker HO. ARID3A is required for mammalian placenta development. Dev Biol 2017; 422:83-91. [PMID: 27965054 PMCID: PMC5540318 DOI: 10.1016/j.ydbio.2016.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/17/2022]
Abstract
Previous studies in the mouse indicated that ARID3A plays a critical role in the first cell fate decision required for generation of trophectoderm (TE). Here, we demonstrate that ARID3A is widely expressed during mouse and human placentation and essential for early embryonic viability. ARID3A localizes to trophoblast giant cells and other trophoblast-derived cell subtypes in the junctional and labyrinth zones of the placenta. Conventional Arid3a knockout embryos suffer restricted intrauterine growth with severe defects in placental structural organization. Arid3a null placentas show aberrant expression of subtype-specific markers as well as significant alteration in cytokines, chemokines and inflammatory response-related genes, including previously established markers of human placentation disorders. BMP4-mediated induction of trophoblast stem (TS)-like cells from human induced pluripotent stem cells results in ARID3A up-regulation and cytoplasmic to nuclear translocation. Overexpression of ARID3A in BMP4-mediated TS-like cells up-regulates TE markers, whereas pluripotency markers are down-regulated. Our results reveal an essential, conserved function for ARID3A in mammalian placental development through regulation of both intrinsic and extrinsic developmental programs.
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Affiliation(s)
- Catherine Rhee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Melissa Edwards
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States; Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
| | - Christine Dang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - June Harris
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Mark Brown
- Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Haley O Tucker
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States.
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24
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Nguyen M, Singhal P, Piet JW, Shefelbine SJ, Maden M, Voss SR, Monaghan JR. Retinoic acid receptor regulation of epimorphic and homeostatic regeneration in the axolotl. Development 2017; 144:601-611. [PMID: 28087637 DOI: 10.1242/dev.139873] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/30/2016] [Indexed: 12/16/2023]
Abstract
Salamanders are capable of regenerating amputated limbs by generating a mass of lineage-restricted cells called a blastema. Blastemas only generate structures distal to their origin unless treated with retinoic acid (RA), which results in proximodistal (PD) limb duplications. Little is known about the transcriptional network that regulates PD duplication. In this study, we target specific retinoic acid receptors (RARs) to either PD duplicate (RA treatment or RARγ agonist) or truncate (RARβ antagonist) regenerating limbs. RARE-EGFP reporter axolotls showed divergent reporter activity in limbs undergoing PD duplication versus truncation, suggesting differences in patterning and skeletal regeneration. Transcriptomics identified expression patterns that explain PD duplication, including upregulation of proximal homeobox gene expression and silencing of distal-associated genes, whereas limb truncation was associated with disrupted skeletal differentiation. RARβ antagonism in uninjured limbs induced a loss of skeletal integrity leading to long bone regression and loss of skeletal turnover. Overall, mechanisms were identified that regulate the multifaceted roles of RARs in the salamander limb including regulation of skeletal patterning during epimorphic regeneration, skeletal tissue differentiation during regeneration, and homeostatic regeneration of intact limbs.
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Affiliation(s)
- Matthew Nguyen
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Pankhuri Singhal
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Judith W Piet
- Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA
| | - Sandra J Shefelbine
- Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA
| | - Malcolm Maden
- Department of Biology and UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - S Randal Voss
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
- Spinal Cord and Brain Injury Research Center, University of Kentucky, College of Medicine, Lexington, KY 40506, USA
| | - James R Monaghan
- Department of Biology, Northeastern University, Boston, MA 02115, USA
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25
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Abstract
In this chapter, we present an approach that allows a causal analysis of multiple "-omics" data with the help of an "upstream analysis" strategy. The goal of this approach is to identify master regulators in gene regulatory networks as potential drug targets for a pathological process. The data analysis strategy includes a state-of-the-art promoter analysis for potential transcription factor (TF)-binding sites using the TRANSFAC® database combined with an analysis of the upstream signal transduction pathways that control the activity of these TFs. When applied to genes that are associated with a switch to a pathological process, the approach identifies potential key molecules (master regulators) that may exert major control over and maintenance of transient stability of the pathological state. We demonstrate this approach on examples of analysis of multi-omics data sets that contain transcriptomics and epigenomics data in cancer. The results of this analysis helped us to better understand the molecular mechanisms of cancer development and cancer drug resistance. Such an approach promises to be very effective for rapid and accurate identification of cancer drug targets with true potential. The upstream analysis approach is implemented as an automatic workflow in the geneXplain platform ( www.genexplain.com ) using the open-source BioUML framework ( www.biouml.org ).
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Affiliation(s)
- Alexander E Kel
- Institute of Chemical Biology and Fundamental Medicine, SBRAN, Novosibirsk, Russia. .,Biosoft.ru, Ltd., Novosibirsk, Russia. .,geneXplain GmbH, Am Exer 10B, D-38302, Wolfenbüttel, Germany.
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26
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Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. Curr Environ Health Rep 2016; 3:53-63. [PMID: 26809562 DOI: 10.1007/s40572-016-0079-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The adverse outcome pathway (AOP) concept links molecular perturbations with organism and population-level outcomes to support high-throughput toxicity (HTT) testing. International efforts are underway to define AOPs and store the information supporting these AOPs in a central knowledge base; however, this process is currently labor-intensive and time-consuming. Publicly available data sources provide a wealth of information that could be used to define computationally predicted AOPs (cpAOPs), which could serve as a basis for creating expert-derived AOPs in a much more efficient way. Computational tools for mining large datasets provide the means for extracting and organizing the information captured in these public data sources. Using cpAOPs as a starting point for expert-derived AOPs should accelerate AOP development. Coupling this with tools to coordinate and facilitate the expert development efforts will increase the number and quality of AOPs produced, which should play a key role in advancing the adoption of HTT testing, thereby reducing the use of animals in toxicity testing and greatly increasing the number of chemicals that can be tested.
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27
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Ben-Ari Fuchs S, Lieder I, Stelzer G, Mazor Y, Buzhor E, Kaplan S, Bogoch Y, Plaschkes I, Shitrit A, Rappaport N, Kohn A, Edgar R, Shenhav L, Safran M, Lancet D, Guan-Golan Y, Warshawsky D, Shtrichman R. GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:139-51. [PMID: 26983021 PMCID: PMC4799705 DOI: 10.1089/omi.2015.0168] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from “data-to-knowledge-to-innovation,” a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data. Prominent among the emerging remedies to this challenge are the gene set enrichment tools. This study reports on GeneAnalytics™ (geneanalytics.genecards.org), a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics' differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science's GeneCards suite, including the GeneCards®—the human gene database; the MalaCards—the human diseases database; and the PathCards—the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®—the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene–tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell “cards” in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics, and others yet to emerge on the postgenomics horizon.
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Affiliation(s)
| | | | - Gil Stelzer
- 1 LifeMap Sciences Ltd. , Tel Aviv, Israel .,2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
| | | | - Ella Buzhor
- 3 Institute of Oncology, Sheba Medical Center , Tel Hashomer, Israel
| | | | - Yoel Bogoch
- 4 Surgical Department, Sourasky Medical Centre , Tel Aviv, Israel
| | | | - Alina Shitrit
- 2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
| | - Noa Rappaport
- 2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
| | - Asher Kohn
- 5 LifeMap Sciences, Inc. , Marshfield, Massachusetts, USA
| | - Ron Edgar
- 6 Venividi Solutions LLC , Rockville, Maryland, USA
| | | | - Marilyn Safran
- 2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
| | - Doron Lancet
- 2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
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28
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Fang Q, George AS, Brinkmeier ML, Mortensen AH, Gergics P, Cheung LYM, Daly AZ, Ajmal A, Pérez Millán MI, Ozel AB, Kitzman JO, Mills RE, Li JZ, Camper SA. Genetics of Combined Pituitary Hormone Deficiency: Roadmap into the Genome Era. Endocr Rev 2016; 37:636-675. [PMID: 27828722 PMCID: PMC5155665 DOI: 10.1210/er.2016-1101] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/31/2016] [Indexed: 02/08/2023]
Abstract
The genetic basis for combined pituitary hormone deficiency (CPHD) is complex, involving 30 genes in a variety of syndromic and nonsyndromic presentations. Molecular diagnosis of this disorder is valuable for predicting disease progression, avoiding unnecessary surgery, and family planning. We expect that the application of high throughput sequencing will uncover additional contributing genes and eventually become a valuable tool for molecular diagnosis. For example, in the last 3 years, six new genes have been implicated in CPHD using whole-exome sequencing. In this review, we present a historical perspective on gene discovery for CPHD and predict approaches that may facilitate future gene identification projects conducted by clinicians and basic scientists. Guidelines for systematic reporting of genetic variants and assigning causality are emerging. We apply these guidelines retrospectively to reports of the genetic basis of CPHD and summarize modes of inheritance and penetrance for each of the known genes. In recent years, there have been great improvements in databases of genetic information for diverse populations. Some issues remain that make molecular diagnosis challenging in some cases. These include the inherent genetic complexity of this disorder, technical challenges like uneven coverage, differing results from variant calling and interpretation pipelines, the number of tolerated genetic alterations, and imperfect methods for predicting pathogenicity. We discuss approaches for future research in the genetics of CPHD.
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Affiliation(s)
- Qing Fang
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Akima S George
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Michelle L Brinkmeier
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Amanda H Mortensen
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Peter Gergics
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Leonard Y M Cheung
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Alexandre Z Daly
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Adnan Ajmal
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - María Ines Pérez Millán
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - A Bilge Ozel
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Jacob O Kitzman
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Ryan E Mills
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Jun Z Li
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
| | - Sally A Camper
- Department of Human Genetics (Q.F., A.S.G., M.L.B., A.H.M., P.G., L.Y.M.C., A.Z.D., M.I.P.M., A.B.O., J.O.K., R.E.M., J.Z.L., S.A.C.), Graduate Program in Bioinformatics (A.S.G.), Endocrine Division, Department of Internal Medicine (A.A.), and Department of Computational Medicine and Bioinformatics (J.O.K., R.E.M., J.Z.L.), University of Michigan, Ann Arbor, Michigan 48109
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29
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Finger JH, Smith CM, Hayamizu TF, McCright IJ, Xu J, Law M, Shaw DR, Baldarelli RM, Beal JS, Blodgett O, Campbell JW, Corbani LE, Lewis JR, Forthofer KL, Frost PJ, Giannatto SC, Hutchins LN, Miers DB, Motenko H, Stone KR, Eppig JT, Kadin JA, Richardson JE, Ringwald M. The mouse Gene Expression Database (GXD): 2017 update. Nucleic Acids Res 2016; 45:D730-D736. [PMID: 27899677 PMCID: PMC5210556 DOI: 10.1093/nar/gkw1073] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/21/2016] [Accepted: 10/28/2016] [Indexed: 12/14/2022] Open
Abstract
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches. At present, GXD includes over 1.5 million expression results and more than 300 000 images, all annotated with detailed and standardized metadata. Since our last report in 2014, we have added a large amount of data, we have enhanced data and database infrastructure, and we have implemented many new search and display features. Interface enhancements include: a new Mouse Developmental Anatomy Browser; interactive tissue-by-developmental stage and tissue-by-gene matrix views; capabilities to filter and sort expression data summaries; a batch search utility; gene-based expression overviews; and links to expression data from other species.
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Affiliation(s)
| | | | - Terry F Hayamizu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Jingxia Xu
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Meiyee Law
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - David R Shaw
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Jon S Beal
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Olin Blodgett
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jeff W Campbell
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Lori E Corbani
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Jill R Lewis
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Kim L Forthofer
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Pete J Frost
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Lucie N Hutchins
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Dave B Miers
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Howie Motenko
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Kevin R Stone
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Janan T Eppig
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - James A Kadin
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | | | - Martin Ringwald
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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30
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DeLaughter DM, Bick AG, Wakimoto H, McKean D, Gorham JM, Kathiriya IS, Hinson JT, Homsy J, Gray J, Pu W, Bruneau BG, Seidman JG, Seidman CE. Single-Cell Resolution of Temporal Gene Expression during Heart Development. Dev Cell 2016; 39:480-490. [PMID: 27840107 PMCID: PMC5198784 DOI: 10.1016/j.devcel.2016.10.001] [Citation(s) in RCA: 317] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 03/30/2016] [Accepted: 09/30/2016] [Indexed: 12/29/2022]
Abstract
Activation of complex molecular programs in specific cell lineages governs mammalian heart development, from a primordial linear tube to a four-chamber organ. To characterize lineage-specific, spatiotemporal developmental programs, we performed single-cell RNA sequencing of >1,200 murine cells isolated at seven time points spanning embryonic day 9.5 (primordial heart tube) to postnatal day 21 (mature heart). Using unbiased transcriptional data, we classified cardiomyocytes, endothelial cells, and fibroblast-enriched cells, thus identifying markers for temporal and chamber-specific developmental programs. By harnessing these datasets, we defined developmental ages of human and mouse pluripotent stem-cell-derived cardiomyocytes and characterized lineage-specific maturation defects in hearts of mice with heterozygous mutations in Nkx2.5 that cause human heart malformations. This spatiotemporal transcriptome analysis of heart development reveals lineage-specific gene programs underlying normal cardiac development and congenital heart disease.
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Affiliation(s)
| | - Alexander G. Bick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - David McKean
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Irfan S. Kathiriya
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA
- Department of Anesthesia and Perioperative Care, University of California, San Francisco
| | - John T. Hinson
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jesse Gray
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - William Pu
- Department of Cardiology, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Benoit G. Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA
- Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute and Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
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31
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Reutter H, Hilger AC, Hildebrandt F, Ludwig M. Underlying genetic factors of the VATER/VACTERL association with special emphasis on the "Renal" phenotype. Pediatr Nephrol 2016; 31:2025-33. [PMID: 26857713 PMCID: PMC5207487 DOI: 10.1007/s00467-016-3335-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 12/18/2022]
Abstract
The acronym VATER/VACTERL association (OMIM #192350) refers to the rare non-random co-occurrence of the following component features (CFs): vertebral defects (V), anorectal malformations (A), cardiac defects (C), tracheoesophageal fistula with or without esophageal atresia (TE), renal malformations (R), and limb defects (L). According to epidemiological studies, the majority of patients with VATER/VACTERL association present with a "Renal" phenotype comprising a large spectrum of congenital renal anomalies. This finding is supported by evidence linking all of the human disease genes for the VATER/VACTERL association identified to date, namely, FGF8, FOXF1, HOXD13, LPP, TRAP1, and ZIC3, with renal malformations. Here we review these genotype-phenotype correlations and suggest that the elucidation of the genetic causes of the VATER/VACTERL association will ultimately provide insights into the genetic causes of the complete spectrum of congenital renal anomalies per se.
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Affiliation(s)
- Heiko Reutter
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany. .,Department of Neonatology and Pediatric Intensive Care, Children's Hospital-University of Bonn, Bonn, Germany.
| | - Alina C Hilger
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital-Harvard Medical School, Boston, MA, USA
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
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32
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Kel AE, Stegmaier P, Valeev T, Koschmann J, Poroikov V, Kel-Margoulis OV, Wingender E. Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. EUPA OPEN PROTEOMICS 2016; 13:1-13. [PMID: 29900117 PMCID: PMC5988513 DOI: 10.1016/j.euprot.2016.09.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 09/05/2016] [Accepted: 09/08/2016] [Indexed: 11/25/2022]
Abstract
Upstream analysis strategy for multi-omics data is proposed. Drug targets are predicted by search for TFBS and analysis of signaling network. Methotrexate resistance data include transcriptomics, proteomics and epigenomics. Predicted targets are: TGFalpha, IGFBP7, alpha9-integrin. Predicted drugs are: zardaverine, divalproex and human metabolite nicotinamide N-oxide.
We present an “upstream analysis” strategy for causal analysis of multiple “-omics” data. It analyzes promoters using the TRANSFAC database, combines it with an analysis of the upstream signal transduction pathways and identifies master regulators as potential drug targets for a pathological process. We applied this approach to a complex multi-omics data set that contains transcriptomics, proteomics and epigenomics data. We identified the following potential drug targets against induced resistance of cancer cells towards chemotherapy by methotrexate (MTX): TGFalpha, IGFBP7, alpha9-integrin, and the following chemical compounds: zardaverine and divalproex as well as human metabolites such as nicotinamide N-oxide.
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Affiliation(s)
- Alexander E Kel
- Institute of Chemical Biology and Fundamental Medicine, SBRAS, Novosibirsk, Russia.,Biosoft.ru, Ltd, Novosibirsk, Russia.,geneXplain GmbH, D-38302 Wolfenbüttel, Germany
| | | | - Tagir Valeev
- Biosoft.ru, Ltd, Novosibirsk, Russia.,A.P. Ershov Institute of Informatics Systems, SB RAS, Novosibirsk, Russia
| | | | | | | | - Edgar Wingender
- geneXplain GmbH, D-38302 Wolfenbüttel, Germany.,Institute of Bioinformatics, University Medical Center Göttingen, D-37077 Göttingen, Germany
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33
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Qu Y, Zhou B, Yang W, Han B, Yu-Rice Y, Gao B, Johnson J, Svendsen CN, Freeman MR, Giuliano AE, Sareen D, Cui X. Transcriptome and proteome characterization of surface ectoderm cells differentiated from human iPSCs. Sci Rep 2016; 6:32007. [PMID: 27550649 PMCID: PMC4994084 DOI: 10.1038/srep32007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/01/2016] [Indexed: 12/11/2022] Open
Abstract
Surface ectoderm (SE) cells give rise to structures including the epidermis and ectodermal associated appendages such as hair, eye, and the mammary gland. In this study, we validate a protocol that utilizes BMP4 and the γ-secretase inhibitor DAPT to induce SE differentiation from human induced pluripotent stem cells (hiPSCs). hiPSC-differentiated SE cells expressed markers suggesting their commitment to the SE lineage. Computational analyses using integrated quantitative transcriptomic and proteomic profiling reveal that TGFβ superfamily signaling pathways are preferentially activated in SE cells compared with hiPSCs. SE differentiation can be enhanced by selectively blocking TGFβ-RI signaling. We also show that SE cells and neural ectoderm cells possess distinct gene expression patterns and signaling networks as indicated by functional Ingenuity Pathway Analysis. Our findings advance current understanding of early human SE cell development and pave the way for modeling of SE-derived tissue development, studying disease pathogenesis, and development of regenerative medicine approaches.
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Affiliation(s)
- Ying Qu
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Bo Zhou
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Wei Yang
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Bingchen Han
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Yi Yu-Rice
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Bowen Gao
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Jeffery Johnson
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Clive N Svendsen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Michael R Freeman
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Armando E Giuliano
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
| | - Dhruv Sareen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.,iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Los Angeles, CA, 90048, USA.,Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Xiaojiang Cui
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, 90048, USA
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34
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Makrythanasis P, Guipponi M, Santoni FA, Zaki M, Issa MY, Ansar M, Hamamy H, Antonarakis SE. Exome sequencing discloses KALRN homozygous variant as likely cause of intellectual disability and short stature in a consanguineous pedigree. Hum Genomics 2016; 10:26. [PMID: 27421267 PMCID: PMC4947303 DOI: 10.1186/s40246-016-0082-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/05/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The recent availability of whole-exome sequencing has opened new possibilities for the evaluation of individuals with genetically undiagnosed intellectual disability. RESULTS We report two affected siblings, offspring of first-cousin parents, with intellectual disability, hypotonia, short stature, growth hormone deficiency, and delayed bone age. All members of the nuclear family were genotyped, and exome sequencing was performed in one of the affected individuals. We used an in-house algorithm (CATCH v1.1) that combines homozygosity mapping with exome sequencing results and provides a list of candidate variants. One identified novel homozygous missense variant in KALRN (NM_003947.4:c.3644C>A: p.(Thr1215Lys)) was predicted to be pathogenic by all pathogenicity prediction software used (SIFT, PolyPhen, Mutation Taster). KALRN encodes the protein kalirin, which is a GTP-exchange factor protein with a reported role in cytoskeletal remodeling and dendritic spine formation in neurons. It is known that mice with ablation of Kalrn exhibit age-dependent functional deficits and behavioral phenotypes. CONCLUSION Exome sequencing provided initial evidence linking KALRN to monogenic intellectual disability in man, and we propose that KALRN is the causative gene for the autosomal recessive phenotype in this family.
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Affiliation(s)
- Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland.,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Michel Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Maha Zaki
- Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Mahmoud Y Issa
- Department of Clinical Genetics, National Research Centre, Cairo, Egypt
| | - Muhammad Ansar
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Hanan Hamamy
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1 Rue Michel-Servet, 1211, Geneva, Switzerland. .,Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland. .,iGE3, Institute of Genetics and Genomics of Geneva, Geneva, Switzerland.
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35
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Aylward A, Cai Y, Lee A, Blue E, University of Washington Center for Mendelian Genomics, Rabinowitz D, Haddad J. Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate. Genet Epidemiol 2016; 40:432-41. [PMID: 27229527 PMCID: PMC4985012 DOI: 10.1002/gepi.21972] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 02/28/2016] [Accepted: 03/07/2016] [Indexed: 11/06/2022]
Abstract
Studies suggest that nonsyndromic cleft lip and palate (NSCLP) is polygenic with variable penetrance, presenting a challenge in identifying all causal genetic variants. Despite relatively high prevalence of NSCLP among Amerindian populations, no large whole exome sequencing (WES) studies have been completed in this population. Our goal was to identify candidate genes with rare genetic variants for NSCLP in a Honduran population using WES. WES was performed on two to four members of 27 multiplex Honduran families. Genetic variants with a minor allele frequency > 1% in reference databases were removed. Heterozygous variants consistent with dominant disease with incomplete penetrance were ascertained, and variants with predicted functional consequence were prioritized for analysis. Pedigree-specific P-values were calculated as the probability of all affected members in the pedigree being carriers, given that at least one is a carrier. Preliminary results identified 3,727 heterozygous rare variants; 1,282 were predicted to be functionally consequential. Twenty-three genes had variants of interest in ≥3 families, where some genes had different variants in each family, giving a total of 50 variants. Variant validation via Sanger sequencing of the families and unrelated unaffected controls excluded variants that were sequencing errors or common variants not in databases, leaving four genes with candidate variants in ≥3 families. Of these, candidate variants in two genes consistently segregate with NSCLP as a dominant variant with incomplete penetrance: ACSS2 and PHYH. Rare variants found at the same gene in all affected individuals in several families are likely to be directly related to NSCLP.
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Affiliation(s)
- Alana Aylward
- Columbia University College of Physicians and Surgeons Otolaryngology Department, New York, NY
| | - Yi Cai
- Columbia University College of Physicians and Surgeons Otolaryngology Department, New York, NY
| | - Andrew Lee
- Columbia University College of Physicians and Surgeons Otolaryngology Department, New York, NY
| | - Elizabeth Blue
- University of Washington Department of Medicine, Division of Medical Genetics, Seattle, WA
| | | | | | - Joseph Haddad
- Columbia University College of Physicians and Surgeons Otolaryngology Department, New York, NY
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36
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Budnick I, Hamburg-Shields E, Chen D, Torre E, Jarrell A, Akhtar-Zaidi B, Cordovan O, Spitale RC, Scacheri P, Atit RP. Defining the identity of mouse embryonic dermal fibroblasts. Genesis 2016; 54:415-30. [PMID: 27265328 DOI: 10.1002/dvg.22952] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 01/14/2023]
Abstract
Embryonic dermal fibroblasts in the skin have the exceptional ability to initiate hair follicle morphogenesis and contribute to scarless wound healing. Activation of the Wnt signaling pathway is critical for dermal fibroblast fate selection and hair follicle induction. In humans, mutations in Wnt pathway components and target genes lead to congenital focal dermal hypoplasias with diminished hair. The gene expression signature of embryonic dermal fibroblasts during differentiation and its dependence on Wnt signaling is unknown. Here we applied Shannon entropy analysis to identify the gene expression signature of mouse embryonic dermal fibroblasts. We used available human DNase-seq and histone modification ChiP-seq data on various cell-types to demonstrate that genes in the fibroblast cell identity signature can be epigenetically repressed in other cell-types. We found a subset of the signature genes whose expression is dependent on Wnt/β-catenin activity in vivo. With our approach, we have defined and validated a statistically derived gene expression signature that may mediate dermal fibroblast identity and function in development and disease. genesis 54:415-430, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Isadore Budnick
- Department of Biology, Case Western Reserve University, Cleveland, Ohio
| | | | - Demeng Chen
- Department of Biology, Case Western Reserve University, Cleveland, Ohio
| | - Eduardo Torre
- Epithelial Biology Program, Department of Dermatology, Stanford University, California
| | - Andrew Jarrell
- Department of Biology, Case Western Reserve University, Cleveland, Ohio
| | - Batool Akhtar-Zaidi
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | - Olivia Cordovan
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | - Rob C Spitale
- Epithelial Biology Program, Department of Dermatology, Stanford University, California.,Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Peter Scacheri
- Department of Pharmaceutical Sciences, University of California, Irvine, California
| | - Radhika P Atit
- Department of Biology, Case Western Reserve University, Cleveland, Ohio.,Department of Pharmaceutical Sciences, University of California, Irvine, California.,Department of Dermatology, Case Western Reserve University, Cleveland, Ohio
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37
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Lesch BJ, Silber SJ, McCarrey JR, Page DC. Parallel evolution of male germline epigenetic poising and somatic development in animals. Nat Genet 2016; 48:888-94. [PMID: 27294618 DOI: 10.1038/ng.3591] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
Changes in gene regulation frequently underlie changes in morphology during evolution, and differences in chromatin state have been linked with changes in anatomical structure and gene expression across evolutionary time. Here we assess the relationship between evolution of chromatin state in germ cells and evolution of gene regulatory programs governing somatic development. We examined the poised (H3K4me3/H3K27me3 bivalent) epigenetic state in male germ cells from five mammalian and one avian species. We find that core genes poised in germ cells from multiple amniote species are ancient regulators of morphogenesis that sit at the top of transcriptional hierarchies controlling somatic tissue development, whereas genes that gain poising in germ cells from individual species act downstream of core poised genes during development in a species-specific fashion. We propose that critical regulators of animal development gained an epigenetically privileged state in germ cells, manifested in amniotes by H3K4me3/H3K27me3 poising, early in metazoan evolution.
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Affiliation(s)
| | - Sherman J Silber
- Infertility Center of St. Louis, St. Luke's Hospital, St. Louis, Missouri, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, USA
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38
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Clarkson MD. Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design. BMC DEVELOPMENTAL BIOLOGY 2016; 16:18. [PMID: 27206491 PMCID: PMC4875762 DOI: 10.1186/s12861-016-0116-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND A large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. In addition, attention to the design of the interfaces is critical to make online resources useful and usable. RESULTS I first present a survey of online atlases and gene expression resources for model organisms, with a focus on methods of semantic and spatial representation of anatomy. A total of 14 anatomical atlases and 21 gene expression resources are included. This survey demonstrates how choices in semantic representation, in the form of ontologies, can enhance interface search functions and provide links between relevant information. This survey also reviews methods for spatially representing anatomy in online resources. I then provide a collection of patterns for interface design based on the atlases and databases surveyed. These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures. CONCLUSIONS This collection of patterns for interface design will assist biologists and software developers in planning the interfaces of new atlases and databases or enhancing existing ones. They also show the benefits of standardizing semantic and spatial representations of anatomy by demonstrating how interfaces can use standardization to provide enhanced functionality.
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Affiliation(s)
- Melissa D Clarkson
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA, USA.
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Dececchi TA, Mabee PM, Blackburn DC. Data Sources for Trait Databases: Comparing the Phenomic Content of Monographs and Evolutionary Matrices. PLoS One 2016; 11:e0155680. [PMID: 27191170 PMCID: PMC4871461 DOI: 10.1371/journal.pone.0155680] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 05/03/2016] [Indexed: 01/17/2023] Open
Abstract
Databases of organismal traits that aggregate information from one or multiple sources can be leveraged for large-scale analyses in biology. Yet the differences among these data streams and how well they capture trait diversity have never been explored. We present the first analysis of the differences between phenotypes captured in free text of descriptive publications ('monographs') and those used in phylogenetic analyses ('matrices'). We focus our analysis on osteological phenotypes of the limbs of four extinct vertebrate taxa critical to our understanding of the fin-to-limb transition. We find that there is low overlap between the anatomical entities used in these two sources of phenotype data, indicating that phenotypes represented in matrices are not simply a subset of those found in monographic descriptions. Perhaps as expected, compared to characters found in matrices, phenotypes in monographs tend to emphasize descriptive and positional morphology, be somewhat more complex, and relate to fewer additional taxa. While based on a small set of focal taxa, these qualitative and quantitative data suggest that either source of phenotypes alone will result in incomplete knowledge of variation for a given taxon. As a broader community develops to use and expand databases characterizing organismal trait diversity, it is important to recognize the limitations of the data sources and develop strategies to more fully characterize variation both within species and across the tree of life.
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Affiliation(s)
- T. Alex Dececchi
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - Paula M. Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America
| | - David C. Blackburn
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
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McGlinchey JCP, Tummala H, Lester DH. Correction of the Pathogenic Alternative Splicing, Caused by the Common GNB3 c.825C>T Allele, Using a Novel, Antisense Morpholino. Nucleic Acid Ther 2016; 26:257-65. [PMID: 27028457 DOI: 10.1089/nat.2015.0571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The very common GNB3 c.825C>T polymorphism (rs5443) is present in approximately half of all human chromosomes. Significantly, the presence of the GNB3 825T allele has been strongly associated with predisposition to essential hypertension. Paradoxically the presence of the GNB3 825T allele, in exon 10, introduces a pathogenic alternative RNA splice site into the middle of exon 9. To attempt to correct this pathogenic aberrant splicing, we, therefore, bioinformatically designed, using a Gene Tools(®) algorithm, a GNB3-specific, antisense morpholino. It was hoped that this morpholino would behave in vitro as either a potential splice blocker and/or exon skipper, to both bind and inhibit/reduce the aberrant splicing of the GNB3 825T allele. On transfecting a human lymphoblast cell line homozygous for the 825T allele, with this antisense morpholino, we encouragingly observed both a significant reduction (from ∼58% to ∼5%) in the production of the aberrant smaller GNB3 transcript, and a subsequent increase in the normal GNB3 transcript (from ∼42% to ∼95%). Our results demonstrate the potential use of a GNB3-specific antisense morpholino, as a pharmacogenetic therapy for essential hypertension.
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Affiliation(s)
- Jonathan C P McGlinchey
- 1 School of Science, Engineering & Technology, Abertay University , Dundee, United Kingdom .,2 Blood Sciences Laboratory, Department of Haematology, Ninewells Hospital , Dundee, United Kingdom
| | - Hemanth Tummala
- 3 Centre for Paediatrics, Barts and The London School of Medicine and Dentistry, Queen Mary University of London , Barts and The London Children's Hospital, London, United Kingdom
| | - Douglas H Lester
- 1 School of Science, Engineering & Technology, Abertay University , Dundee, United Kingdom
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Proteomics of reproductive systems: Towards a molecular understanding of postmating, prezygotic reproductive barriers. J Proteomics 2016; 135:26-37. [DOI: 10.1016/j.jprot.2015.10.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/28/2015] [Accepted: 10/11/2015] [Indexed: 11/20/2022]
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Filipova D, Walter AM, Gaspar JA, Brunn A, Linde NF, Ardestani MA, Deckert M, Hescheler J, Pfitzer G, Sachinidis A, Papadopoulos S. Gene profiling of embryonic skeletal muscle lacking type I ryanodine receptor Ca(2+) release channel. Sci Rep 2016; 6:20050. [PMID: 26831464 PMCID: PMC4735524 DOI: 10.1038/srep20050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 12/22/2015] [Indexed: 12/20/2022] Open
Abstract
In mature skeletal muscle, the intracellular Ca2+ concentration rises dramatically upon membrane depolarization, constituting the link between excitation and contraction. This process requires Ca2+ release from the sarcoplasmic reticulum via the type 1 ryanodine receptor (RYR1). However, RYR1’s potential roles in muscle development remain obscure. We used an established RyR1- null mouse model, dyspedic, to investigate the effects of the absence of a functional RYR1 and, consequently, the lack of RyR1-mediated Ca2+ signaling, during embryogenesis. Homozygous dyspedic mice die after birth and display small limbs and abnormal skeletal muscle organization. Skeletal muscles from front and hind limbs of dyspedic fetuses (day E18.5) were subjected to microarray analyses, revealing 318 differentially expressed genes. We observed altered expression of multiple transcription factors and members of key signaling pathways. Differential regulation was also observed for genes encoding contractile as well as muscle-specific structural proteins. Additional qRT-PCR analysis revealed altered mRNA levels of the canonical muscle regulatory factors Six1, Six4, Pax7, MyoD, MyoG and MRF4 in mutant muscle, which is in line with the severe developmental retardation seen in dyspedic muscle histology analyses. Taken together, these findings suggest an important non-contractile role of RyR1 or RYR1-mediated Ca2+ signaling during muscle organ development.
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Affiliation(s)
- Dilyana Filipova
- Center of Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
| | - Anna M Walter
- Center of Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
| | - John A Gaspar
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
| | - Anna Brunn
- Department of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Nina F Linde
- Center of Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
| | - Mostafa A Ardestani
- Center of Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
| | - Martina Deckert
- Department of Neuropathology, University Hospital of Cologne, Cologne, Germany
| | - Jürgen Hescheler
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
| | - Gabriele Pfitzer
- Center of Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
| | - Agapios Sachinidis
- Center of Physiology and Pathophysiology, Institute of Neurophysiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
| | - Symeon Papadopoulos
- Center of Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty of the University of Cologne, Robert-Koch-Str. 39, Cologne 50931, Germany
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Kim S, Schliekelman P. Prioritizing hypothesis tests for high throughput data. ACTA ACUST UNITED AC 2015; 32:850-8. [PMID: 26576654 DOI: 10.1093/bioinformatics/btv608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 10/16/2015] [Indexed: 11/14/2022]
Abstract
MOTIVATION The advent of high throughput data has led to a massive increase in the number of hypothesis tests conducted in many types of biological studies and a concomitant increase in stringency of significance thresholds. Filtering methods, which use independent information to eliminate less promising tests and thus reduce multiple testing, have been widely and successfully applied. However, key questions remain about how to best apply them: When is filtering beneficial and when is it detrimental? How good does the independent information need to be in order for filtering to be effective? How should one choose the filter cutoff that separates tests that pass the filter from those that don't? RESULT We quantify the effect of the quality of the filter information, the filter cutoff and other factors on the effectiveness of the filter and show a number of results: If the filter has a high probability (e.g. 70%) of ranking true positive features highly (e.g. top 10%), then filtering can lead to dramatic increase (e.g. 10-fold) in discovery probability when there is high redundancy in information between hypothesis tests. Filtering is less effective when there is low redundancy between hypothesis tests and its benefit decreases rapidly as the quality of the filter information decreases. Furthermore, the outcome is highly dependent on the choice of filter cutoff. Choosing the cutoff without reference to the data will often lead to a large loss in discovery probability. However, naïve optimization of the cutoff using the data will lead to inflated type I error. We introduce a data-based method for choosing the cutoff that maintains control of the family-wise error rate via a correction factor to the significance threshold. Application of this approach offers as much as a several-fold advantage in discovery probability relative to no filtering, while maintaining type I error control. We also introduce a closely related method of P-value weighting that further improves performance. AVAILABILITY AND IMPLEMENTATION R code for calculating the correction factor is available at http://www.stat.uga.edu/people/faculty/paul-schliekelman CONTACT pdschlie@stat.uga.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sangjin Kim
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Paul Schliekelman
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
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Jiminez JA, Uwiera TC, Douglas Inglis G, Uwiera RRE. Animal models to study acute and chronic intestinal inflammation in mammals. Gut Pathog 2015; 7:29. [PMID: 26561503 PMCID: PMC4641401 DOI: 10.1186/s13099-015-0076-y] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/22/2015] [Indexed: 02/06/2023] Open
Abstract
Acute and chronic inflammatory diseases of the intestine impart a significant and negative impact on the health and well-being of human and non-human mammalian animals. Understanding the underlying mechanisms of inflammatory disease is mandatory to develop effective treatment and prevention strategies. As inflammatory disease etiologies are multifactorial, the use of appropriate animal models and associated metrics of disease are essential. In this regard, animal models used alone or in combination to study acute and chronic inflammatory disease of the mammalian intestine paired with commonly used inflammation-inducing agents are reviewed. This includes both chemical and biological incitants of inflammation, and both non-mammalian (i.e. nematodes, insects, and fish) and mammalian (i.e. rodents, rabbits, pigs, ruminants, dogs, and non-human primates) models of intestinal inflammation including germ-free, gnotobiotic, as well as surgical, and genetically modified animals. Importantly, chemical and biological incitants induce inflammation via a multitude of mechanisms, and intestinal inflammation and injury can vary greatly according to the incitant and animal model used, allowing studies to ascertain both long-term and short-term effects of inflammation. Thus, researchers and clinicians should be aware of the relative strengths and limitations of the various animal models used to study acute and chronic inflammatory diseases of the mammalian intestine, and the scope and relevance of outcomes achievable based on this knowledge. The ability to induce inflammation to mimic common human diseases is an important factor of a successful animal model, however other mechanisms of disease such as the amount of infective agent to induce disease, invasion mechanisms, and the effect various physiologic changes can have on inducing damage are also important features. In many cases, the use of multiple animal models in combination with both chemical and biological incitants is necessary to answer the specific question being addressed regarding intestinal disease. Some incitants can induce acute responses in certain animal models while others can be used to induce chronic responses; this review aims to illustrate the strengths and weaknesses in each animal model and to guide the choice of an appropriate acute or chronic incitant to facilitate intestinal disease.
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Affiliation(s)
- Janelle A. Jiminez
- />Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB Canada
- />Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Trina C. Uwiera
- />Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB Canada
| | - G. Douglas Inglis
- />Agriculture and Agri-Food Canada Research Centre, Lethbridge, AB Canada
| | - Richard R. E. Uwiera
- />Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
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Richardson L, Graham L, Moss J, Burton N, Roochun Y, Armit C, Baldock RA. Developing the eHistology Atlas. Database (Oxford) 2015; 2015:bav105. [PMID: 26500249 PMCID: PMC4618478 DOI: 10.1093/database/bav105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 09/17/2015] [Accepted: 09/30/2015] [Indexed: 01/03/2023]
Abstract
The eMouseAtlas project has undertaken to generate a new resource providing access to high-resolution colour images of the slides used in the renowned textbook 'The Atlas of Mouse Development' by Matthew H. Kaufman. The original histology slides were digitized, and the associated anatomy annotations captured for display in the new resource. These annotations were assigned to objects in the standard reference anatomy ontology, allowing the eHistology resource to be linked to other data resources including the Edinburgh Mouse Atlas Gene-Expression database (EMAGE) an the Mouse Genome Informatics (MGI) gene-expression database (GXD). The provision of the eHistology Atlas resource was assisted greatly by the expertise of the eMouseAtlas project in delivering large image datasets within a web environment, using IIP3D technology. This technology also permits future extensions to the resource through the addition of further layers of data and annotations to the resource. Database URL: www.emouseatlas.org/emap/eHistology/index.php.
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Affiliation(s)
- Lorna Richardson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Liz Graham
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Julie Moss
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Nick Burton
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Yogmatee Roochun
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Chris Armit
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
| | - Richard A Baldock
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK
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Maziveyi M, Alahari SK. Breast Cancer Tumor Suppressors: A Special Emphasis on Novel Protein Nischarin. Cancer Res 2015; 75:4252-9. [PMID: 26392073 DOI: 10.1158/0008-5472.can-15-1395] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 07/02/2015] [Indexed: 11/16/2022]
Abstract
Tumor suppressor genes regulate cell growth and prevent spontaneous proliferation that could lead to aberrant tissue function. Deletions and mutations of these genes typically lead to progression through the cell-cycle checkpoints, as well as increased cell migration. Studies of these proteins are important as they may provide potential treatments for breast cancers. In this review, we discuss a comprehensive overview on Nischarin, a novel protein discovered by our laboratory. Nischarin, or imidazoline receptor antisera-selected protein, is a protein involved in a vast number of cellular processes, including neuronal protection and hypotension. The NISCH promoter experiences hypermethylation in several cancers, whereas some highly aggressive breast cancer cells exhibit genomic loss of the NISCH locus. Furthermore, we discuss data illustrating a novel role of Nischarin as a tumor suppressor in breast cancer. Analysis of this new paradigm may shed light on various clinical questions. Finally, the therapeutic potential of Nischarin is discussed.
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Affiliation(s)
- Mazvita Maziveyi
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - Suresh K Alahari
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana.
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Hofrichter MAH, Nanda I, Gräf J, Schröder J, Shehata-Dieler W, Vona B, Haaf T. A Novel de novo Mutation in CEACAM16 Associated with Postlingual Hearing Impairment. Mol Syndromol 2015; 6:156-63. [PMID: 26648831 DOI: 10.1159/000439576] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2015] [Indexed: 12/20/2022] Open
Abstract
Mutations in CEACAM16 cause autosomal dominant nonsyndromic hearing loss (DFNA4B). So far, 2 families have been reported with segregating missense mutations, both in the immunoglobulin constant domain A of the CEACAM16 protein. In this study, we used the TruSight One panel to investigate a parent-child trio without familial history of hearing loss and one affected child. When filtering for recessive inheritance and de novo events, we discovered a de novo CEACAM16 mutation (c.1094T>G, p.Leu365Arg) as the sole likely pathogenic variant. The de novo mutation was confirmed by Sanger sequencing and STR analysis. The proband's hearing loss closely matches the described onset and severity for DFNA4B. We present the third CEACAM16 variant and the first de novo mutation in CEACAM16. This de novo mutation is robustly described as a pathogenic mutation according to in silico mutation prediction tools and affects a highly conserved amino acid in the most strongly conserved CEACAM16 N2 domain. Our strategy of screening family trios enhances de novo mutation discovery and the exclusion of other variants of potential interest through pedigree filtering.
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Affiliation(s)
| | - Indrajit Nanda
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
| | - Jens Gräf
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
| | - Jörg Schröder
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
| | - Wafaa Shehata-Dieler
- Department of Otorhinolaryngology, Comprehensive Hearing Center, University Hospitals, Würzburg, Germany
| | - Barbara Vona
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
| | - Thomas Haaf
- Department of Human Genetics, Julius Maximilian University, Würzburg, Germany
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A mouse informatics platform for phenotypic and translational discovery. Mamm Genome 2015; 26:413-21. [PMID: 26314589 PMCID: PMC4602054 DOI: 10.1007/s00335-015-9599-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 08/17/2015] [Indexed: 01/05/2023]
Abstract
The International Mouse Phenotyping Consortium (IMPC) is providing the world's first functional catalogue of a mammalian genome by characterising a knockout mouse strain for every gene. A robust and highly structured informatics platform has been developed to systematically collate, analyse and disseminate the data produced by the IMPC. As the first phase of the project, in which 5000 new knockout strains are being broadly phenotyped, nears completion, the informatics platform is extending and adapting to support the increasing volume and complexity of the data produced as well as addressing a large volume of users and emerging user groups. An intuitive interface helps researchers explore IMPC data by giving overviews and the ability to find and visualise data that support a phenotype assertion. Dedicated disease pages allow researchers to find new mouse models of human diseases, and novel viewers provide high-resolution images of embryonic and adult dysmorphologies. With each monthly release, the informatics platform will continue to evolve to support the increased data volume and to maintain its position as the primary route of access to IMPC data and as an invaluable resource for clinical and non-clinical researchers.
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Manda P, Balhoff JP, Lapp H, Mabee P, Vision TJ. Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution. Genesis 2015. [PMID: 26220875 DOI: 10.1002/dvg.22878] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms. To illustrate the power of this approach, we review the use of the KB to find taxa showing evolutionary variation similar to that of a query gene. Matches are made between the full set of phenotypes described for a gene and an evolutionary profile, the latter of which is defined as the set of phenotypes that are variable among the daughters of any node on the taxonomic tree. Phenoscape's semantic similarity interface allows the user to assess the statistical significance of each match and flags matches that may only result from differences in annotation coverage between genetic and evolutionary studies. Tools such as this will help meet the challenge of relating the growing volume of genetic knowledge in model organisms to the diversity of phenotypes in nature. The Phenoscape KB is available at http://kb.phenoscape.org.
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Affiliation(s)
- Prashanti Manda
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
| | - James P Balhoff
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
| | - Hilmar Lapp
- US National Evolutionary Synthesis Center, Durham, North Carolina.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, South Dakota
| | - Todd J Vision
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina.,US National Evolutionary Synthesis Center, Durham, North Carolina
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Graham E, Moss J, Burton N, Roochun Y, Armit C, Richardson L, Baldock R. The atlas of mouse development eHistology resource. Development 2015; 142:1909-11. [PMID: 26015534 DOI: 10.1242/dev.124917] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Atlas of Mouse Development by Professor Mathew Kaufman is an essential text for understanding mouse developmental anatomy. This definitive and authoritative atlas is still in production and is essential for any biologist working with the mouse embryo, although the last revision dates back to 1994. Here, we announce the eHistology online resource that provides free access to high-resolution colour images digitized from the original histological sections (www.emouseatlas.org/emap/eHistology/index.php) used by Kaufman for the Atlas. The images are provided with the original annotations and plate numbering of the paper atlas and enable viewing the material to cellular resolution.
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Affiliation(s)
- Elizabeth Graham
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Julie Moss
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Nick Burton
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | | | - Chris Armit
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Lorna Richardson
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Richard Baldock
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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