1
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Huang X, Henck J, Qiu C, Sreenivasan VKA, Balachandran S, Amarie OV, Hrabě de Angelis M, Behncke RY, Chan WL, Despang A, Dickel DE, Duran M, Feuchtinger A, Fuchs H, Gailus-Durner V, Haag N, Hägerling R, Hansmeier N, Hennig F, Marshall C, Rajderkar S, Ringel A, Robson M, Saunders LM, da Silva-Buttkus P, Spielmann N, Srivatsan SR, Ulferts S, Wittler L, Zhu Y, Kalscheuer VM, Ibrahim DM, Kurth I, Kornak U, Visel A, Pennacchio LA, Beier DR, Trapnell C, Cao J, Shendure J, Spielmann M. Single-cell, whole-embryo phenotyping of mammalian developmental disorders. Nature 2023; 623:772-781. [PMID: 37968388 PMCID: PMC10665194 DOI: 10.1038/s41586-023-06548-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 08/16/2023] [Indexed: 11/17/2023]
Abstract
Mouse models are a critical tool for studying human diseases, particularly developmental disorders1. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse2. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing3 to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions4,5. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution.
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Affiliation(s)
- Xingfan Huang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA, USA
| | - Jana Henck
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Varun K A Sreenivasan
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Freising, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Rose Yinghan Behncke
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Wing-Lee Chan
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Alexandra Despang
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Diane E Dickel
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Annette Feuchtinger
- Core Facility Pathology & Tissue Analytics, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Natja Haag
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Rene Hägerling
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Nils Hansmeier
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | | | - Cooper Marshall
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | | | - Alessa Ringel
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
| | - Michael Robson
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lauren M Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Patricia da Silva-Buttkus
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics, German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sascha Ulferts
- Institute of Medical Genetics and Human Genetics of the Charité, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Yiwen Zhu
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | | | - Daniel M Ibrahim
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BCRT, Berlin, Germany
| | - Ingo Kurth
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Uwe Kornak
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Axel Visel
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - David R Beier
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Malte Spielmann
- Institute of Human Genetics, University Medical Center Schleswig-Holstein, University of Lübeck & Kiel University, Lübeck, Germany.
- Max Planck Institute for Molecular Genetics, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck, Germany.
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2
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Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, Majesky MW, Millen KJ, Tollis M, Miller DE. Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3 (Bethesda) 2023; 13:jkad177. [PMID: 37552705 PMCID: PMC10542272 DOI: 10.1093/g3journal/jkad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/03/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023]
Abstract
There is increasing interest in the African spiny mouse (Acomys cahirinus) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality reference genome is needed to better understand these regenerative properties at the molecular level. Here, we present an improved reference genome for A. cahirinus generated from long Nanopore sequencing reads. We confirm the quality of our annotations using RNA sequencing data from 4 different tissues. Our genome is of higher contiguity and quality than previously reported genomes from this species and will facilitate ongoing efforts to better understand the regenerative properties of this organism.
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Affiliation(s)
- Elizabeth Dong Nguyen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Vahid Nikoonejad Fard
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Sarah Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Miranda Galey
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Branden R Nelson
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Paul Wakenight
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Aaron McKenna
- Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH 03755, USA
| | - Theo K Bammler
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jim MacDonald
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daryl M Okamura
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - David R Beier
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jan Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Mark W Majesky
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Kathleen J Millen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
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3
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Okamura DM, Nguyen ED, Collins SJ, Yoon K, Gere JB, Weiser-Evans MCM, Beier DR, Majesky MW. Mammalian organ regeneration in spiny mice. J Muscle Res Cell Motil 2023; 44:39-52. [PMID: 36131170 DOI: 10.1007/s10974-022-09631-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022]
Abstract
Fibrosis-driven solid organ failure is a major world-wide health burden with few therapeutic options. Spiny mice (genus: Acomys) are terrestrial mammals that regenerate severe skin wounds without fibrotic scars to evade predators. Recent studies have shown that spiny mice also regenerate acute ischemic and traumatic injuries to kidney, heart, spinal cord, and skeletal muscle. A common feature of this evolved wound healing response is a lack of formation of fibrotic scar tissue that degrades organ function, inhibits regeneration, and leads to organ failure. Complex tissue regeneration is an extremely rare property among mammalian species. In this article, we discuss the evidence that Acomys represents an emerging model organism that offers a unique opportunity for the biomedical community to investigate and clinically translate molecular mechanisms of scarless wound healing and regeneration of organ function in a mammalian species.
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Affiliation(s)
- Daryl M Okamura
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Elizabeth D Nguyen
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Sarah J Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Kevin Yoon
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Joshua B Gere
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Mary C M Weiser-Evans
- Department of Medicine, Division of Renal Diseases & Hypertension, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - David R Beier
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Mark W Majesky
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, 98195, USA.
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA.
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4
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Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, Majesky MW, Millen KJ, Tollis M, Miller DE. GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse ( Acomys cahirinus ). bioRxiv 2023:2023.04.03.535372. [PMID: 37066261 PMCID: PMC10103962 DOI: 10.1101/2023.04.03.535372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
There is increasing interest in the African spiny mouse ( Acomys cahirinus ) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality reference genome is needed to better understand these regenerative properties at the molecular level. Here, we present an improved reference genome for A. cahirinus generated from long Nanopore sequencing reads. We confirm the quality of our annotations using RNA sequencing data from four different tissues. Our genome is of higher contiguity and quality than previously reported genomes from this species and will facilitate ongoing efforts to better understand the regenerative properties of this organism.
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Affiliation(s)
- Elizabeth Dong Nguyen
- Department of Pediatrics, University of Washington, Seattle, WA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
| | - Vahid Nikoonejad Fard
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | - Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, CA
| | - Sarah Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | - Miranda Galey
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA
| | - Branden R. Nelson
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA
| | - Paul Wakenight
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA
| | - Simone M. Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | - Aaron McKenna
- Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH
| | - Theo K. Bammler
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA
| | - Jim MacDonald
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA
| | - Daryl M. Okamura
- Department of Pediatrics, University of Washington, Seattle, WA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA
| | - David R. Beier
- Department of Pediatrics, University of Washington, Seattle, WA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | - Jan Marino Ramirez
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Neurological Surgery, University of Washington, Seattle WA
| | - Mark W. Majesky
- Department of Pediatrics, University of Washington, Seattle, WA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
| | - Kathleen J. Millen
- Department of Pediatrics, University of Washington, Seattle, WA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | - Danny E. Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
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5
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Jamet S, Ha S, Ho TH, Houghtaling S, Timms A, Yu K, Paquette A, Maga AM, Greene NDE, Beier DR. The arginine methyltransferase Carm1 is necessary for heart development. G3 Genes|Genomes|Genetics 2022; 12:6613934. [PMID: 35736367 PMCID: PMC9339313 DOI: 10.1093/g3journal/jkac155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/27/2022] [Indexed: 11/28/2022]
Abstract
To discover genes implicated in human congenital disorders, we performed ENU mutagenesis in the mouse and screened for mutations affecting embryonic development. In this work, we report defects of heart development in mice homozygous for a mutation of coactivator-associated arginine methyltransferase 1 (Carm1). While Carm1 has been extensively studied, it has never been previously associated with a role in heart development. Phenotype analysis combining histology and microcomputed tomography imaging shows a range of cardiac defects. Most notably, many affected midgestation embryos appear to have cardiac rupture and hemorrhaging in the thorax. Mice that survive to late gestation show a variety of cardiac defects, including ventricular septal defects, double outlet right ventricle, and persistent truncus arteriosus. Transcriptome analyses of the mutant embryos by mRNA-seq reveal the perturbation of several genes involved in cardiac morphogenesis and muscle development and function. In addition, we observe the mislocalization of cardiac neural crest cells at E12.5 in the outflow tract. The cardiac phenotype of Carm1 mutant embryos is similar to that of Pax3 null mutants, and PAX3 is a putative target of CARM1. However, our analysis does not support the hypothesis that developmental defects in Carm1 mutant embryos are primarily due to a functional defect of PAX3.
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Affiliation(s)
- Sophie Jamet
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
| | - Seungshin Ha
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
| | - Tzu-Hua Ho
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
| | - Scott Houghtaling
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
| | - Andrew Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
| | - Kai Yu
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine , Seattle, WA 98195, USA
| | - Alison Paquette
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine , Seattle, WA 98195, USA
| | - Ali Murat Maga
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine , Seattle, WA 98195, USA
| | - Nicholas D E Greene
- Developmental Biology & Cancer Department, UCL Great Ormond Street Institute of Child Health , London WC1N 1EH, UK
| | - David R Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute , Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine , Seattle, WA 98195, USA
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6
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Okamura DM, Nguyen ED, Collins SJ, Yoon K, Gere JB, Beier DR, Majesky MW. Abstract 480: Mammalian Organ Regeneration In Spiny Mice. Arterioscler Thromb Vasc Biol 2022. [DOI: 10.1161/atvb.42.suppl_1.480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Fibrosis-driven solid organ failure is a major global health burden. Spiny mice (genus:
Acomys
) are terrestrial mammals that regenerate severe skin wounds without scars to avoid predation. To test whether spiny mice can also regenerate internal organ injuries, we performed acute obstructive or ischemic surgeries on adult kidneys of
Acomys cahirinus
compared to
Mus musculus.
Despite equivalent acute tissue damage,
Acomys
fully regenerate nephron structure, vascular & lymphatic networks, and organ function without fibrosis by 14d while
Mus
(CD1 or C57BL/6) develop extensive interstitial fibrosis and progress to organ failure and death. Comparative transcriptomic, epigenetic, and single-cell assays revealed that the
Acomys
genome appears poised to initiate a regenerative response at the time of injury. In addition, we found the Hippo pathway effector protein YAP localized to the nucleus in renal tubular epithelial cells (RTEs) undergoing scarless wound healing in
Acomys
while it was either cytoplasmic or not detectable in
Mus
RTEs. Experiments
in vitro
revealed an accelerated PP2A-dependent YAP phosphatase activity that maintained nuclear YAP in
Acomys
RTEs and was not detected in
Mus
or human cells. Treatment of
Acomys in vivo
with the nuclear YAP-TEAD inhibitor verteporfin converted tissue regeneration to fibrosis in the dermis and similar experiments for the kidney are in progress. These results suggest that the spiny mouse genome evolved both transcriptional and post-translational adaptations important for scar-free regenerative wound healing
in vivo
.
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Affiliation(s)
| | | | | | - Kevin Yoon
- SEATTLE CHILDRENS RESEARCH INSTITU, Seattle, WA
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7
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Okamura DM, Nguyen ED, Beier DR, Majesky MW. Wound healing and regeneration in spiny mice (Acomys cahirinus). Curr Top Dev Biol 2022; 148:139-164. [DOI: 10.1016/bs.ctdb.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Okamura DM, Brewer CM, Wakenight P, Bahrami N, Bernardi K, Tran A, Olson J, Shi X, Yeh SY, Piliponsky A, Collins SJ, Nguyen ED, Timms AE, MacDonald JW, Bammler TK, Nelson BR, Millen KJ, Beier DR, Majesky MW. Spiny mice activate unique transcriptional programs after severe kidney injury regenerating organ function without fibrosis. iScience 2021; 24:103269. [PMID: 34849462 PMCID: PMC8609232 DOI: 10.1016/j.isci.2021.103269] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/02/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Fibrosis-driven solid organ failure is an enormous burden on global health. Spiny mice (Acomys) are terrestrial mammals that can regenerate severe skin wounds without scars to avoid predation. Whether spiny mice also regenerate internal organ injuries is unknown. Here, we show that despite equivalent acute obstructive or ischemic kidney injury, spiny mice fully regenerate nephron structure and organ function without fibrosis, whereas C57Bl/6 or CD1 mice progress to complete organ failure with extensive renal fibrosis. Two mechanisms for vertebrate regeneration have been proposed that emphasize either extrinsic (pro-regenerative macrophages) or intrinsic (surviving cells of the organ itself) controls. Comparative transcriptome analysis revealed that the Acomys genome appears poised at the time of injury to initiate regeneration by surviving kidney cells, whereas macrophage accumulation was not detected until about day 7. Thus, we provide evidence for rapid activation of a gene expression signature for regenerative wound healing in the spiny mouse kidney.
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Affiliation(s)
- Daryl M. Okamura
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Chris M. Brewer
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Paul Wakenight
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Nadia Bahrami
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Kristina Bernardi
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Amy Tran
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Jill Olson
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Xiaogang Shi
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Szu-Ying Yeh
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Adrian Piliponsky
- Center for Immunity & Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Sarah J. Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Elizabeth D. Nguyen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Andrew E. Timms
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - James W. MacDonald
- Department of Environmental & Occupational Health, University of Washington, Seattle, WA 98195, USA
| | - Theo K. Bammler
- Department of Environmental & Occupational Health, University of Washington, Seattle, WA 98195, USA
| | - Branden R. Nelson
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Kathleen J. Millen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - David R. Beier
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Mark W. Majesky
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
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9
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Weghorn D, Balick DJ, Cassa C, Kosmicki JA, Daly MJ, Beier DR, Sunyaev SR. Applicability of the Mutation-Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans. Mol Biol Evol 2020; 36:1701-1710. [PMID: 31004148 DOI: 10.1093/molbev/msz092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein-truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation-selection balance, as has been proposed earlier (Cassa et al. 2017). Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC data set (Lek et al. 2016). Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation-selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.
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Affiliation(s)
- Donate Weghorn
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA.,Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniel J Balick
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Christopher Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Jack A Kosmicki
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - David R Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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10
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Bittermann E, Abdelhamed Z, Liegel RP, Menke C, Timms A, Beier DR, Stottmann RW. Differential requirements of tubulin genes in mammalian forebrain development. PLoS Genet 2019; 15:e1008243. [PMID: 31386652 PMCID: PMC6697361 DOI: 10.1371/journal.pgen.1008243] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/16/2019] [Accepted: 06/12/2019] [Indexed: 11/24/2022] Open
Abstract
Tubulin genes encode a series of homologous proteins used to construct microtubules which are essential for multiple cellular processes. Neural development is particularly reliant on functional microtubule structures. Tubulin genes comprise a large family of genes with very high sequence similarity between multiple family members. Human genetics has demonstrated that a large spectrum of cortical malformations are associated with de novo heterozygous mutations in tubulin genes. However, the absolute requirement for many of these genes in development and disease has not been previously tested in genetic loss of function models. Here we directly test the requirement for Tuba1a, Tubb2a and Tubb2b in the mouse by deleting each gene individually using CRISPR-Cas9 genome editing. We show that loss of Tubb2a or Tubb2b does not impair survival but does lead to relatively mild cortical malformation phenotypes. In contrast, loss of Tuba1a is perinatal lethal and leads to significant forebrain dysmorphology. We also present a novel mouse ENU allele of Tuba1a with phenotypes similar to the null allele. This demonstrates the requirements for each of the tubulin genes and levels of functional redundancy are quite different throughout the gene family. The ability of the mouse to survive in the absence of some tubulin genes known to cause disease in humans suggests future intervention strategies for these devastating tubulinopathy diseases.
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Affiliation(s)
- Elizabeth Bittermann
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Zakia Abdelhamed
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Anatomy and Embryology, Faculty of Medicine (Girl’s Section), Al-Azhar University, Cairo, Egypt
| | - Ryan P. Liegel
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Chelsea Menke
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Andrew Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - David R. Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington Medical School, Seattle, Washington, United States of America
| | - Rolf W. Stottmann
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
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11
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Geister KA, Lopez-Jimenez AJ, Houghtaling S, Ho TH, Vanacore R, Beier DR. Loss of function of Colgalt1 disrupts collagen post-translational modification and causes musculoskeletal defects. Dis Model Mech 2019; 12:dmm.037176. [PMID: 31101663 PMCID: PMC6602307 DOI: 10.1242/dmm.037176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/13/2019] [Indexed: 12/11/2022] Open
Abstract
In a screen for organogenesis defects in N-ethyl-N-nitrosourea (ENU)-induced mutant mice, we discovered a line carrying a mutation in Colgalt1 [collagen beta(1-O)galactosyltransferase type 1], which is required for proper galactosylation of hydroxylysine residues in a number of collagens. Colgalt1 mutant embryos have not been previously characterized; here, we show that they exhibit skeletal and muscular defects. Analysis of mutant-derived embryonic fibroblasts reveals that COLGALT1 acts on collagen IV and VI, and, while collagen VI appears stable and its secretion is not affected, collagen IV accumulates inside of cells and within the extracellular matrix, possibly due to instability and increased degradation. We also generated mutant zebrafish that do not express the duplicated orthologs of mammalian Colgalt1. The double-homozygote mutants have muscle defects; they are viable through the larvae stage but do not survive to 10 days post-fertilization. We hypothesize that the Colgalt1 mutant could serve as a model of a human connective tissue disorder and/or congenital muscular dystrophy or myopathy. Summary: The authors characterized a novel mouse mutant that has a defect in collagen glycosylation, which appears to affect muscle development. There is very little functional characterization of the affected gene, but this study provides analysis of its embryonic phenotype and the biochemistry of the null mutant, as well as the phenotype of null-mutant zebrafish.
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Affiliation(s)
- Krista A Geister
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA.,Department of Pediatrics, Division of Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alberto Jose Lopez-Jimenez
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Scott Houghtaling
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Tzu-Hua Ho
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Roberto Vanacore
- Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.,Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David R Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA .,Department of Pediatrics, Division of Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
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12
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Strassman A, Schnütgen F, Dai Q, Jones JC, Gomez AC, Pitstick L, Holton NE, Moskal R, Leslie ER, von Melchner H, Beier DR, Bjork BC. Generation of a multipurpose Prdm16 mouse allele by targeted gene trapping. Dis Model Mech 2017; 10:909-922. [PMID: 28424158 PMCID: PMC5536910 DOI: 10.1242/dmm.029561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/18/2017] [Indexed: 12/17/2022] Open
Abstract
Gene trap mutagenesis is a powerful tool to create loss-of-function mutations in mice and other model organisms. Modifications of traditional gene trap cassettes, including addition of conditional features in the form of Flip-excision (FlEx) arrays to enable directional gene trap cassette inversions by Cre and Flpe site-specific recombinases, greatly enhanced their experimental potential. By taking advantage of these conditional gene trap cassettes, we developed a generic strategy for generating conditional mutations and validated this strategy in mice carrying a multipurpose allele of the Prdm16 transcription factor gene. We demonstrate that the gene trap insertion creates a null mutation replicating the Pierre Robin sequence-type cleft palate phenotype of other Prdm16 mutant mice. Consecutive breeding to Flpe and Emx1IREScre deleter mice spatially restricted Prdm16 loss to regions of the forebrain expressing the homeobox gene Emx1, demonstrating the utility of the technology for the analysis of tissue-specific gene functions. Summary: Described is the first targeting of an invertible gene trap to generate a conditional Prdm16 mouse allele and its use to assess phenotypic consequences of Prdm16 loss during craniofacial and brain development.
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Affiliation(s)
- Alexander Strassman
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Frank Schnütgen
- Department for Molecular Hematology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | - Qi Dai
- Department of Molecular Biosciences, The Wenner-Gren Institute, The University of Stockholm, SE-106 91 Stockholm, Sweden
| | - Jennifer C Jones
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Angela C Gomez
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Lenore Pitstick
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Nathan E Holton
- Department of Orthodontics, College of Dentistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Russell Moskal
- Department of Anatomy, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Erin R Leslie
- Department of Anatomy, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
| | - Harald von Melchner
- Department for Molecular Hematology, University Hospital Frankfurt, Goethe University, 60590 Frankfurt am Main, Germany
| | - David R Beier
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98105, USA.,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Bryan C Bjork
- Department of Biochemistry, Chicago College of Osteopathic Medicine, Midwestern University, Downers Grove, IL 60515, USA
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13
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Gallego-Llamas J, Timms AE, Pitstick R, Peters J, Carlson GA, Beier DR. Improvement of ENU Mutagenesis Efficiency Using Serial Injection and Mismatch Repair Deficiency Mice. PLoS One 2016; 11:e0159377. [PMID: 27441645 PMCID: PMC4956170 DOI: 10.1371/journal.pone.0159377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/03/2016] [Indexed: 12/05/2022] Open
Abstract
ENU mutagenesis is a powerful method for generating novel lines of mice that are informative with respect to both fundamental biological processes and human disease. Rapid developments in genomic technology have made the task of identifying causal mutations by positional cloning remarkably efficient. One limitation of this approach remains the mutation frequency achievable using standard treatment protocols, which currently generate approximately 1–2 sequence changes per megabase when optimized. In this study we used two strategies to attempt to increase the number of mutations induced by ENU treatment. One approach employed mice carrying a mutation in the DNA repair enzyme Msh6. The second strategy involved injection of ENU to successive generations of mice. To evaluate the number of ENU-induced mutations, single mice or pooled samples were analyzed using whole exome sequencing. The results showed that there is considerable variability in the induced mutation frequency using these approaches, but an overall increase in ENU-induced variants from one generation to another was observed. The analysis of the mice deficient for Msh6 also showed an increase in the ENU-induced variants compared to the wild-type ENU-treated mice. However, in both cases the increase in ENU-induced mutation frequency was modest.
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Affiliation(s)
- Jabier Gallego-Llamas
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States of America
| | - Andrew E. Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
| | - Rose Pitstick
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - Janet Peters
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - George A. Carlson
- McLaughlin Research Institute, Great Falls, MT, United States of America
| | - David R. Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States of America
- * E-mail:
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14
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Jacobs DT, Silva LM, Allard BA, Schonfeld MP, Chatterjee A, Talbott GC, Beier DR, Tran PV. Dysfunction of intraflagellar transport-A causes hyperphagia-induced obesity and metabolic syndrome. Dis Model Mech 2016; 9:789-98. [PMID: 27482817 PMCID: PMC4958314 DOI: 10.1242/dmm.025791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 04/29/2016] [Indexed: 12/15/2022] Open
Abstract
Primary cilia extend from the plasma membrane of most vertebrate cells and mediate signaling pathways. Ciliary dysfunction underlies ciliopathies, which are genetic syndromes that manifest multiple clinical features, including renal cystic disease and obesity. THM1 (also termed TTC21B or IFT139) encodes a component of the intraflagellar transport-A complex and mutations in THM1 have been identified in 5% of individuals with ciliopathies. Consistent with this, deletion of murine Thm1 during late embryonic development results in cystic kidney disease. Here, we report that deletion of murine Thm1 during adulthood results in obesity, diabetes, hypertension and fatty liver disease, with gender differences in susceptibility to weight gain and metabolic dysfunction. Pair-feeding of Thm1 conditional knock-out mice relative to control littermates prevented the obesity and related disorders, indicating that hyperphagia caused the obese phenotype. Thm1 ablation resulted in increased localization of adenylyl cyclase III in primary cilia that were shortened, with bulbous distal tips on neurons of the hypothalamic arcuate nucleus, an integrative center for signals that regulate feeding and activity. In pre-obese Thm1 conditional knock-out mice, expression of anorexogenic pro-opiomelanocortin (Pomc) was decreased by 50% in the arcuate nucleus, which likely caused the hyperphagia. Fasting of Thm1 conditional knock-out mice did not alter Pomc nor orexogenic agouti-related neuropeptide (Agrp) expression, suggesting impaired sensing of changes in peripheral signals. Together, these data indicate that the Thm1-mutant ciliary defect diminishes sensitivity to feeding signals, which alters appetite regulation and leads to hyperphagia, obesity and metabolic disease. Summary: Disruption of the IFT-A complex gene, Thm1, in adult mice misregulates response to feeding signals, altering appetite regulation and resulting in obesity through hyperphagia.
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Affiliation(s)
- Damon T Jacobs
- Department of Anatomy and Cell Biology and The Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Luciane M Silva
- Department of Anatomy and Cell Biology and The Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Bailey A Allard
- Department of Anatomy and Cell Biology and The Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Michael P Schonfeld
- Department of Anatomy and Cell Biology and The Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Anindita Chatterjee
- Department of Anatomy and Cell Biology and The Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - George C Talbott
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - David R Beier
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Pamela V Tran
- Department of Anatomy and Cell Biology and The Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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15
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Husson H, Moreno S, Smith LA, Smith MM, Russo RJ, Pitstick R, Sergeev M, Ledbetter SR, Bukanov NO, Lane M, Zhang K, Billot K, Carlson G, Shah J, Meijer L, Beier DR, Ibraghimov-Beskrovnaya O. Reduction of ciliary length through pharmacologic or genetic inhibition of CDK5 attenuates polycystic kidney disease in a model of nephronophthisis. Hum Mol Genet 2016; 25:2245-2255. [PMID: 27053712 PMCID: PMC5081056 DOI: 10.1093/hmg/ddw093] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/17/2016] [Indexed: 02/06/2023] Open
Abstract
Polycystic kidney diseases (PKDs) comprise a subgroup of ciliopathies characterized by the formation of fluid-filled kidney cysts and progression to end-stage renal disease. A mechanistic understanding of cystogenesis is crucial for the development of viable therapeutic options. Here, we identify CDK5, a kinase active in post mitotic cells, as a new and important mediator of PKD progression. We show that long-lasting attenuation of PKD in the juvenile cystic kidneys (jck) mouse model of nephronophthisis by pharmacological inhibition of CDK5 using either R-roscovitine or S-CR8 is accompanied by sustained shortening of cilia and a more normal epithelial phenotype, suggesting this treatment results in a reprogramming of cellular differentiation. Also, a knock down of Cdk5 in jck cells using small interfering RNA results in significant shortening of ciliary length, similar to what we observed with R-roscovitine. Finally, conditional inactivation of Cdk5 in the jck mice significantly attenuates cystic disease progression and is associated with shortening of ciliary length as well as restoration of cellular differentiation. Our results suggest that CDK5 may regulate ciliary length by affecting tubulin dynamics via its substrate collapsin response mediator protein 2. Taken together, our data support therapeutic approaches aimed at restoration of ciliogenesis and cellular differentiation as a promising strategy for the treatment of renal cystic diseases.
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Affiliation(s)
- Hervé Husson
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Sarah Moreno
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Laurie A Smith
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Mandy M Smith
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Ryan J Russo
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Rose Pitstick
- McLaughlin Research Institute, 1520 23rd Street South, Great Falls, Montana 59405, USA
| | - Mikhail Sergeev
- Harvard Institutes of Medicine, 4 Blackfan Circle HIM568, Boston, MA 02115, USA
| | - Steven R Ledbetter
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Nikolay O Bukanov
- Department of Rare Diseases, Sanofi-Genzyme R&D Center, 49 New York Avenue, Framingham, MA 01701, USA
| | - Monica Lane
- Department of Biological Mass Spectrometry & Biomarker Research, Sanofi-Genzyme R&D Center, 1 Mountain Road, Framingham, MA 01701, USA
| | - Kate Zhang
- Department of Biological Mass Spectrometry & Biomarker Research, Sanofi-Genzyme R&D Center, 1 Mountain Road, Framingham, MA 01701, USA
| | - Katy Billot
- ManRos Therapeutics, Hotel de Recherche-Centre de Perharidy, 29680 Roscoff, France
| | - George Carlson
- McLaughlin Research Institute, 1520 23rd Street South, Great Falls, Montana 59405, USA
| | - Jagesh Shah
- Harvard Institutes of Medicine, 4 Blackfan Circle HIM568, Boston, MA 02115, USA
| | - Laurent Meijer
- ManRos Therapeutics, Hotel de Recherche-Centre de Perharidy, 29680 Roscoff, France
| | - David R Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA 98101, USA
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16
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Gallego-Llamas J, Timms AE, Geister KA, Lindsay A, Beier DR. Variant mapping and mutation discovery in inbred mice using next-generation sequencing. BMC Genomics 2015; 16:913. [PMID: 26552429 PMCID: PMC4640199 DOI: 10.1186/s12864-015-2173-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/31/2015] [Indexed: 12/04/2022] Open
Abstract
Background The development of powerful new methods for DNA sequencing enable the discovery of sequence variants, their utilization for the mapping of mutant loci, and the identification of causal variants in a single step. We have applied this approach for the analysis of ENU-mutagenized mice maintained on an inbred background. Results We ascertained ENU-induced variants in four different phenotypically mutant lines. These were then used as informative markers for positional cloning of the mutated genes. We tested both whole genome (WGS) and whole exome (WES) datasets. Conclusion Both approaches were successful as a means to localize a region of homozygosity, as well as identifying mutations of candidate genes, which could be individually assessed. As expected, the WGS strategy was more reliable, since many more ENU-induced variants were ascertained. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2173-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jabier Gallego-Llamas
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA. .,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Krista A Geister
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - Anna Lindsay
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
| | - David R Beier
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA. .,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Ave., Seattle, WA, 98101, USA.
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17
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Menke C, Cionni M, Siggers T, Bulyk ML, Beier DR, Stottmann RW. Grhl2 is required in nonneural tissues for neural progenitor survival and forebrain development. Genesis 2015; 53:573-582. [PMID: 26177923 PMCID: PMC4713386 DOI: 10.1002/dvg.22875] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 07/06/2015] [Accepted: 07/07/2015] [Indexed: 11/06/2022]
Abstract
Grainyhead-like genes are part of a highly conserved gene family that play a number of roles in ectoderm development and maintenance in mammals. Here we identify a novel allele of Grhl2, cleft-face 3 (clft3), in a mouse line recovered from an ENU mutagenesis screen for organogenesis defects. Homozygous clft3 mutants have a number of phenotypes in common with other alleles of Grhl2. We note a significant effect of genetic background on the clft3 phenotype. One of these is a reduction in size of the telencephalon where we find abnormal patterns of neural progenitor mitosis and apoptosis in mutant brains. Interestingly, Grhl2 is not expressed in the developing forebrain, suggesting this is a survival factor for neural progenitors exerting a paracrine effect on the neural tissue from the overlying ectoderm where Grhl2 is highly expressed. genesis 53:573-582, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Chelsea Menke
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Megan Cionni
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Trevor Siggers
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Biology, Boston University, Boston, MA
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Pathology, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
| | - David R. Beier
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Hospital, Seattle, WA
| | - Rolf W. Stottmann
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
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18
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Pooler AM, Polydoro M, Maury EA, Nicholls SB, Reddy SM, Wegmann S, William C, Saqran L, Cagsal-Getkin O, Pitstick R, Beier DR, Carlson GA, Spires-Jones TL, Hyman BT. Amyloid accelerates tau propagation and toxicity in a model of early Alzheimer's disease. Acta Neuropathol Commun 2015; 3:14. [PMID: 25853174 PMCID: PMC4371800 DOI: 10.1186/s40478-015-0199-x] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 12/25/2022] Open
Abstract
Introduction In early stages of Alzheimer’s disease (AD), neurofibrillary tangles (NFT) are largely restricted to the entorhinal cortex and medial temporal lobe. At later stages, when clinical symptoms generally occur, NFT involve widespread limbic and association cortices. At this point in the disease, amyloid plaques are also abundantly distributed in the cortex. This observation from human neuropathological studies led us to pose two alternative hypotheses: that amyloid in the cortex is permissive for the spread of tangles from the medial temporal lobe, or that these are co-occurring but not causally related events simply reflecting progression of AD pathology. Results We now directly test the hypothesis that cortical amyloid acts as an accelerant for spreading of tangles beyond the medial temporal lobe. We crossed rTgTauEC transgenic mice that demonstrate spread of tau from entorhinal cortex to other brain structures at advanced age with APP/PS1 mice, and examined mice with either NFTs, amyloid pathology, or both. We show that concurrent amyloid deposition in the cortex 1) leads to a dramatic increase in the speed of tau propagation and an extraordinary increase in the spread of tau to distal brain regions, and 2) significantly increases tau-induced neuronal loss. Conclusions These data strongly support the hypothesis that cortical amyloid accelerates the spread of tangles throughout the cortex and amplifies tangle-associated neural system failure in AD. Electronic supplementary material The online version of this article (doi:10.1186/s40478-015-0199-x) contains supplementary material, which is available to authorized users.
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19
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Czarnecki PG, Gabriel GC, Manning DK, Sergeev M, Lemke K, Klena NT, Liu X, Chen Y, Li Y, San Agustin JT, Garnaas MK, Francis RJ, Tobita K, Goessling W, Pazour GJ, Lo CW, Beier DR, Shah JV. ANKS6 is the critical activator of NEK8 kinase in embryonic situs determination and organ patterning. Nat Commun 2015; 6:6023. [PMID: 25599650 PMCID: PMC4361001 DOI: 10.1038/ncomms7023] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
The ciliary kinase NEK8 plays a critical role in situs determination and cystic kidney disease, yet its exact function remains unknown. In this study, we identify ANKS6 as a target and activator of NEK8. ANKS6 requires NEK8 for localizing to the ciliary inversin compartment (IC) and activates NEK8 by binding to its kinase domain. Here we demonstrate the functional importance of this interaction through the analysis of two novel mouse mutations, Anks6(Streaker) and Nek8(Roc). Both display heterotaxy, cardiopulmonary malformations and cystic kidneys, a syndrome also characteristic of mutations in Invs and Nphp3, the other known components of the IC. The Anks6(Strkr) mutation decreases ANKS6 interaction with NEK8, precluding NEK8 activation. The Nek8(Roc) mutation inactivates NEK8 kinase function while preserving ANKS6 localization to the IC. Together, these data reveal the crucial role of NEK8 kinase activation within the IC, promoting proper left-right patterning, cardiopulmonary development and renal morphogenesis.
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Affiliation(s)
- Peter G Czarnecki
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA [3] Renal Division, Beth Israel Deaconess Medical Center, Boston, Massachussetts 02215, USA
| | - George C Gabriel
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Danielle K Manning
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Mikhail Sergeev
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Kristi Lemke
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Nikolai T Klena
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Xiaoqin Liu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Yu Chen
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - You Li
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Jovenal T San Agustin
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachussetts 01655, USA
| | - Maija K Garnaas
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Richard J Francis
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Kimimasa Tobita
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - Wolfram Goessling
- Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachussetts 01655, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| | - David R Beier
- 1] Genetics Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA [2] Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington 98101, USA
| | - Jagesh V Shah
- 1] Department of Systems Biology, Harvard Medical School, 4 Blackfan Circle, HIM 568, Boston, Massachussetts 02115, USA [2] Renal Division, Brigham and Women's Hospital, Boston, Massachussetts 02115, USA
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20
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Abstract
This unit describes the treatment of laboratory mice with the mutagen N-ethyl-N-nitrosourea (ENU) to induce very highly increased rates of mutation throughout the genome. Further, it describes several popular mating schemes designed to produce animals displaying phenotypes associated with the induced mutations.
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Affiliation(s)
- Rolf Stottmann
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - David R. Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute
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21
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Tran PV, Talbott GC, Turbe-Doan A, Jacobs DT, Schonfeld MP, Silva LM, Chatterjee A, Prysak M, Allard BA, Beier DR. Downregulating hedgehog signaling reduces renal cystogenic potential of mouse models. J Am Soc Nephrol 2014; 25:2201-12. [PMID: 24700869 DOI: 10.1681/asn.2013070735] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Renal cystic diseases are a leading cause of renal failure. Mutations associated with renal cystic diseases reside in genes encoding proteins that localize to primary cilia. These cystoproteins can disrupt ciliary structure or cilia-mediated signaling, although molecular mechanisms connecting cilia function to renal cystogenesis remain unclear. The ciliary gene, Thm1(Ttc21b), negatively regulates Hedgehog signaling and is most commonly mutated in ciliopathies. We report that loss of murine Thm1 causes cystic kidney disease, with persistent proliferation of renal cells, elevated cAMP levels, and enhanced expression of Hedgehog signaling genes. Notably, the cAMP-mediated cystogenic potential of Thm1-null kidney explants was reduced by genetically deleting Gli2, a major transcriptional activator of the Hedgehog pathway, or by culturing with small molecule Hedgehog inhibitors. These Hedgehog inhibitors acted independently of protein kinase A and Wnt inhibitors. Furthermore, simultaneous deletion of Gli2 attenuated the renal cystic disease associated with deletion of Thm1. Finally, transcripts of Hedgehog target genes increased in cystic kidneys of two other orthologous mouse mutants, jck and Pkd1, and Hedgehog inhibitors reduced cystogenesis in jck and Pkd1 cultured kidneys. Thus, enhanced Hedgehog activity may have a general role in renal cystogenesis and thereby present a novel therapeutic target.
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Affiliation(s)
- Pamela V Tran
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Anatomy and Cell Biology and the Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas; and
| | - George C Talbott
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annick Turbe-Doan
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Damon T Jacobs
- Department of Anatomy and Cell Biology and the Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas; and
| | - Michael P Schonfeld
- Department of Anatomy and Cell Biology and the Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas; and
| | - Luciane M Silva
- Department of Anatomy and Cell Biology and the Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas; and
| | - Anindita Chatterjee
- Department of Anatomy and Cell Biology and the Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas; and
| | - Mary Prysak
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Bailey A Allard
- Department of Anatomy and Cell Biology and the Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas; and
| | - David R Beier
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington
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22
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Abstract
Formation of a 6-layered cortical plate and axon tract patterning are key features of cerebral cortex development. Abnormalities of these processes may be the underlying cause for a range of functional disabilities seen in human neurodevelopmental disorders. To identify mouse mutants with defects in cortical lamination or corticofugal axon guidance, N-ethyl-N-nitrosourea (ENU) mutagenesis was performed using mice expressing LacZ reporter genes in layers II/III and V of the cortex (Rgs4-lacZ) or in corticofugal axons (TAG1-tau-lacZ). Four lines with abnormal cortical lamination have been identified. One of these was a splice site mutation in reelin (Reln) that results in a premature stop codon and the truncation of the C-terminal region (CTR) domain of reelin. Interestingly, this novel allele of Reln did not display cerebellar malformation or ataxia, and this is the first report of a Reln mutant without a cerebellar defect. Four lines with abnormal cortical axon development were also identified, one of which was found by whole-genome resequencing to carry a mutation in Lrp2. These findings demonstrated that the application of ENU mutagenesis to mice carrying transgenic reporters marking cortical anatomy is a sensitive and specific method to identify mutations that disrupt patterning of the developing brain.
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Affiliation(s)
- Seungshin Ha
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Rolf W Stottmann
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Divisions of Human Genetics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA and
| | - Andrew J Furley
- Department of Biomedical Science, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - David R Beier
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, University of Washington School of Medicine, Seattle, WA 98101, USA
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23
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Choi HJC, Lin JR, Vannier JB, Slaats GG, Kile AC, Paulsen RD, Manning DK, Beier DR, Giles RH, Boulton SJ, Cimprich KA. NEK8 links the ATR-regulated replication stress response and S phase CDK activity to renal ciliopathies. Mol Cell 2013; 51:423-39. [PMID: 23973373 PMCID: PMC3790667 DOI: 10.1016/j.molcel.2013.08.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/09/2013] [Accepted: 07/24/2013] [Indexed: 01/03/2023]
Abstract
Renal ciliopathies are a leading cause of kidney failure, but their exact etiology is poorly understood. NEK8/NPHP9 is a ciliary kinase associated with two renal ciliopathies in humans and mice, nephronophthisis (NPHP) and polycystic kidney disease. Here, we identify NEK8 as a key effector of the ATR-mediated replication stress response. Cells lacking NEK8 form spontaneous DNA double-strand breaks (DSBs) that further accumulate when replication forks stall, and they exhibit reduced fork rates, unscheduled origin firing, and increased replication fork collapse. NEK8 suppresses DSB formation by limiting cyclin A-associated CDK activity. Strikingly, a mutation in NEK8 that is associated with renal ciliopathies affects its genome maintenance functions. Moreover, kidneys of NEK8 mutant mice accumulate DNA damage, and loss of NEK8 or replication stress similarly disrupts renal cell architecture in a 3D-culture system. Thus, NEK8 is a critical component of the DNA damage response that links replication stress with cystic kidney disorders.
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Affiliation(s)
- Hyo Jei Claudia Choi
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Jia-Ren Lin
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Jean-Baptiste Vannier
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Gisela G. Slaats
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, the Netherlands
| | - Andrew C. Kile
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | - Renee D. Paulsen
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
| | | | - David R. Beier
- Brigham and Women's Hospital, Division of Genetics, Boston MA, 02115
| | - Rachel H. Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, the Netherlands
| | - Simon J. Boulton
- London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, EN6 3LD, UK
| | - Karlene A. Cimprich
- Stanford University School of Medicine, Department of Chemical and Systems Biology, Stanford, CA 94025
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24
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Stottmann RW, Donlin M, Hafner A, Bernard A, Sinclair DA, Beier DR. A mutation in Tubb2b, a human polymicrogyria gene, leads to lethality and abnormal cortical development in the mouse. Hum Mol Genet 2013; 22:4053-63. [PMID: 23727838 DOI: 10.1093/hmg/ddt255] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human cortical malformations, including lissencephaly, polymicrogyria and other diseases of neurodevelopment, have been associated with mutations in microtubule subunits and microtubule-associated proteins. Here we report our cloning of the brain dimple (brdp) mouse mutation, which we recovered from an ENU screen for recessive perinatal phenotypes affecting neurodevelopment. We identify the causal mutation in the tubulin, beta-2b (Tubb2b) gene as a missense mutation at a highly conserved residue (N247S). Brdp/brdp homozygous mutants have significant thinning of the cortical epithelium, which is markedly more severe in the caudo-lateral portion of the telencephalon, and do not survive past birth. The cortical defects are largely due to a major increase in apoptosis and we note abnormal proliferation of the basal progenitors. Adult brdp/+ mice are viable and fertile but exhibit behavioral phenotypes. This allele of Tubb2b represents the most severely affected mouse tubulin phenotype reported to date and this is the first report of a tubulin mutation affecting neuronal proliferation and survival.
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Affiliation(s)
- R W Stottmann
- Present address: Divisions of Human Genetics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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25
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Manning DK, Sergeev M, van Heesbeen RG, Wong MD, Oh JH, Liu Y, Henkelman RM, Drummond I, Shah JV, Beier DR. Loss of the ciliary kinase Nek8 causes left-right asymmetry defects. J Am Soc Nephrol 2013; 24:100-12. [PMID: 23274954 DOI: 10.1681/asn.2012050490] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A missense mutation in mouse Nek8, which encodes a ciliary kinase, produces the juvenile cystic kidneys (jck) model of polycystic kidney disease, but the functions of Nek8 are incompletely understood. Here, we generated a Nek8-null allele and found that homozygous mutant mice die at birth and exhibit randomization of left-right asymmetry, cardiac anomalies, and glomerular kidney cysts. The requirement for Nek8 in left-right patterning is conserved, as knockdown of the zebrafish ortholog caused randomized heart looping. Ciliogenesis was intact in Nek8-deficient embryos and cells, but we observed misexpression of left-sided marker genes early in development, suggesting that nodal ciliary signaling was perturbed. We also generated jck/Nek8 compound heterozygotes; these mutants developed less severe cystic disease than jck homozygotes and provided genetic evidence that the jck allele may encode a gain-of-function protein. Notably, NEK8 and polycystin-2 (PC2) proteins interact, and we found that Nek8(-/-) and Pkd2(-/-) embryonic phenotypes are strikingly similar. Nek8-deficient embryos and cells did express PC2 normally, which localized properly to the cilia. However, similar to cells lacking PC2, NEK8-depleted inner medullary collecting duct cells exhibited a defective response to fluid shear, suggesting that NEK8 may play a role in mediating PC2-dependent signaling.
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Affiliation(s)
- Danielle K Manning
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
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26
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Favero CB, Henshaw RN, Grimsley-Myers CM, Shrestha A, Beier DR, Dwyer ND. Mutation of the BiP/GRP78 gene causes axon outgrowth and fasciculation defects in the thalamocortical connections of the mammalian forebrain. J Comp Neurol 2013; 521:677-96. [PMID: 22821687 PMCID: PMC3515720 DOI: 10.1002/cne.23199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 05/13/2012] [Accepted: 07/13/2012] [Indexed: 02/05/2023]
Abstract
Proper development of axonal connections is essential for brain function. A forward genetic screen for mice with defects in thalamocortical development previously isolated a mutant called baffled. Here we describe the axonal defects of baffled in further detail and identify a point mutation in the Hspa5 gene, encoding the endoplasmic reticulum chaperone BiP/GRP78. This hypomorphic mutation of BiP disrupts proper development of the thalamocortical axon projection and other forebrain axon tracts, as well as cortical lamination. In baffled mutant brains, a reduced number of thalamic axons innervate the cortex by the time of birth. Thalamocortical and corticothalamic axons are delayed, overfasciculated, and disorganized along their pathway through the ventral telencephalon. Furthermore, dissociated mutant neurons show reduced axon extension in vitro. Together, these findings demonstrate a sensitive requirement for the endoplasmic reticulum chaperone BiP/GRP78 during axon outgrowth and pathfinding in the developing mammalian brain.
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Affiliation(s)
- Carlita B. Favero
- Department of Cell Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | - Rasha N. Henshaw
- Department of Cell Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | | | - Ayushma Shrestha
- Department of Cell Biology, University of Virginia, Charlottesville, VA, 22908, USA
| | - David R. Beier
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Noelle D. Dwyer
- Department of Cell Biology, University of Virginia, Charlottesville, VA, 22908, USA
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27
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Leshchiner I, Alexa K, Kelsey P, Adzhubei I, Austin-Tse CA, Cooney JD, Anderson H, King MJ, Stottmann RW, Garnaas MK, Ha S, Drummond IA, Paw BH, North TE, Beier DR, Goessling W, Sunyaev SR. Mutation mapping and identification by whole-genome sequencing. Genome Res 2012; 22:1541-8. [PMID: 22555591 PMCID: PMC3409267 DOI: 10.1101/gr.135541.111] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetic mapping of mutations in model systems has facilitated the identification of genes contributing to fundamental biological processes including human diseases. However, this approach has historically required the prior characterization of informative markers. Here we report a fast and cost-effective method for genetic mapping using next-generation sequencing that combines single nucleotide polymorphism discovery, mutation localization, and potential identification of causal sequence variants. In contrast to prior approaches, we have developed a hidden Markov model to narrowly define the mutation area by inferring recombination breakpoints of chromosomes in the mutant pool. In addition, we created an interactive online software resource to facilitate automated analysis of sequencing data and demonstrate its utility in the zebrafish and mouse models. Our novel methodology and online tools will make next-generation sequencing an easily applicable resource for mutation mapping in all model systems.
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Affiliation(s)
- Ignaty Leshchiner
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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28
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Stottmann RW, Turbe-Doan A, Tran P, Kratz LE, Moran JL, Kelley RI, Beier DR. Cholesterol metabolism is required for intracellular hedgehog signal transduction in vivo. PLoS Genet 2011; 7:e1002224. [PMID: 21912524 PMCID: PMC3164675 DOI: 10.1371/journal.pgen.1002224] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 06/20/2011] [Indexed: 12/20/2022] Open
Abstract
We describe the rudolph mouse, a mutant with striking defects in both central nervous system and skeletal development. Rudolph is an allele of the cholesterol biosynthetic enzyme, hydroxysteroid (17-beta) dehydrogenase 7, which is an intriguing finding given the recent implication of oxysterols in mediating intracellular Hedgehog (Hh) signaling. We see an abnormal sterol profile and decreased Hh target gene induction in the rudolph mutant, both in vivo and in vitro. Reduced Hh signaling has been proposed to contribute to the phenotypes of congenital diseases of cholesterol metabolism. Recent in vitro and pharmacological data also indicate a requirement for intracellular cholesterol synthesis for proper regulation of Hh activity via Smoothened. The data presented here are the first in vivo genetic evidence supporting both of these hypotheses, revealing a role for embryonic cholesterol metabolism in both CNS development and normal Hh signaling. The molecules and signaling pathways that regulate growth and patterning of the developing embryo are still being elucidated, and one valuable experimental approach is the use of animal models, such as the mouse. We have identified a recessive mutation in the mouse, rudolph, that causes abnormal forebrain development and have determined that the mutated gene encodes hydroxysteroid (17-beta) dehydrogenase 7 gene, an enzyme necessary for cholesterol biosynthesis. Cholesterol is essential for proper signal transduction of the hedgehog family of proteins, key regulators of both developmental biology and tumor progression. We show that hedgehog signaling is diminished in our rudolph mutant. Our conclusions from studying this mouse mutant support two recent hypotheses in developmental biology. First, several human malformation syndromes are known to be caused by defects in cholesterol metabolism, but support linking the malformation to abnormal hedgehog signaling has not definitively been made. Second, while in vitro studies have shown that proper levels of metabolic by-products of cholesterol are necessary for proper hedgehog signaling, our studies offer the strongest genetic animal model evidence to support this idea.
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Affiliation(s)
- Rolf W. Stottmann
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annick Turbe-Doan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Pamela Tran
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lisa E. Kratz
- Kennedy Krieger Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jennifer L. Moran
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Richard I. Kelley
- Kennedy Krieger Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - David R. Beier
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Zheng Y, Yin H, Boeglin WE, Elias PM, Crumrine D, Beier DR, Brash AR. Lipoxygenases mediate the effect of essential fatty acid in skin barrier formation: a proposed role in releasing omega-hydroxyceramide for construction of the corneocyte lipid envelope. J Biol Chem 2011; 286:24046-56. [PMID: 21558561 DOI: 10.1074/jbc.m111.251496] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A barrier to water loss is vital to maintaining life on dry land. Formation of the mammalian skin barrier requires both the essential fatty acid linoleate and the two lipoxygenases 12R-lipoxygenase (12R-LOX) and epidermal lipoxygenase-3 (eLOX3), although their roles are poorly understood. Linoleate occurs in O-linoleoyl-ω-hydroxyceramide, which, after hydrolysis of the linoleate moiety, is covalently attached to protein via the free ω-hydroxyl of the ceramide, forming the corneocyte lipid envelope, a scaffold between lipid and protein that helps seal the barrier. Here we show using HPLC-UV, LC-MS, GC-MS, and (1)H NMR that O-linoleoyl-ω-hydroxyceramide is oxygenated in a regio- and stereospecific fashion by the consecutive actions of 12R-LOX and eLOX3 and that these products occur naturally in pig and mouse epidermis. 12R-LOX forms 9R-hydroperoxy-linoleoyl-ω-hydroxyceramide, further converted by eLOX3 to specific epoxyalcohol (9R,10R-trans-epoxy-11E-13R-hydroxy) and 9-keto-10E,12Z esters of the ceramide; an epoxy-ketone derivative (9R,10R-trans-epoxy-11E-13-keto) is the most prominent oxidized ceramide in mouse skin. These products are absent in 12R-LOX-deficient mice, which crucially display a near total absence of protein-bound ω-hydroxyceramides and of the corneocyte lipid envelope and die shortly after birth from transepidermal water loss. We conclude that oxygenation of O-linoleoyl-ω-hydroxyceramide is required to facilitate the ester hydrolysis and allow bonding of the ω-hydroxyceramide to protein, providing a coherent explanation for the roles of multiple components in epidermal barrier function. Our study uncovers a hitherto unknown biochemical pathway in which the enzymic oxygenation of ceramides is involved in building a crucial structure of the epidermal barrier.
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Affiliation(s)
- Yuxiang Zheng
- Department of Pharmacology and the Vanderbilt Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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30
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Dwyer ND, Manning DK, Moran JL, Mudbhary R, Fleming MS, Favero CB, Vock VM, O'Leary DDM, Walsh CA, Beier DR. A forward genetic screen with a thalamocortical axon reporter mouse yields novel neurodevelopment mutants and a distinct emx2 mutant phenotype. Neural Dev 2011; 6:3. [PMID: 21214893 PMCID: PMC3024922 DOI: 10.1186/1749-8104-6-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 01/07/2011] [Indexed: 12/02/2022] Open
Abstract
Background The dorsal thalamus acts as a gateway and modulator for information going to and from the cerebral cortex. This activity requires the formation of reciprocal topographic axon connections between thalamus and cortex. The axons grow along a complex multistep pathway, making sharp turns, crossing expression boundaries, and encountering intermediate targets. However, the cellular and molecular components mediating these steps remain poorly understood. Results To further elucidate the development of the thalamocortical system, we first created a thalamocortical axon reporter line to use as a genetic tool for sensitive analysis of mutant mouse phenotypes. The TCA-tau-lacZ reporter mouse shows specific, robust, and reproducible labeling of thalamocortical axons (TCAs), but not the overlapping corticothalamic axons, during development. Moreover, it readily reveals TCA pathfinding abnormalities in known cortical mutants such as reeler. Next, we performed an unbiased screen for genes involved in thalamocortical development using random mutagenesis with the TCA reporter. Six independent mutant lines show aberrant TCA phenotypes at different steps of the pathway. These include ventral misrouting, overfasciculation, stalling at the corticostriatal boundary, and invasion of ectopic cortical cell clusters. An outcross breeding strategy coupled with a genomic panel of single nucleotide polymorphisms facilitated genetic mapping with small numbers of mutant mice. We mapped a ventral misrouting mutant to the Emx2 gene, and discovered that some TCAs extend to the olfactory bulbs in this mutant. Mapping data suggest that other lines carry mutations in genes not previously known for roles in thalamocortical development. Conclusions These data demonstrate the feasibility of a forward genetic approach to understanding mammalian brain morphogenesis and wiring. A robust axonal reporter enabled sensitive analysis of a specific axon tract inside the mouse brain, identifying mutant phenotypes at multiple steps of the pathway, and revealing a new aspect of the Emx2 mutant. The phenotypes highlight vulnerable choice points and latent tendencies of TCAs, and will lead to a refined understanding of the elements and interactions required to form the thalamocortical system. See Commentary: http://www.biomedcentral.com/1741-7007/9/1
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Affiliation(s)
- Noelle D Dwyer
- Howard Hughes Medical Institute, Department of Neurology, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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31
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Bjork BC, Fujiwara Y, Davis SW, Qiu H, Saunders TL, Sandy P, Orkin S, Camper SA, Beier DR. A transient transgenic RNAi strategy for rapid characterization of gene function during embryonic development. PLoS One 2010; 5:e14375. [PMID: 21179568 PMCID: PMC3002952 DOI: 10.1371/journal.pone.0014375] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 11/24/2010] [Indexed: 01/14/2023] Open
Abstract
RNA interference (RNAi) is a powerful strategy for studying the phenotypic consequences of reduced gene expression levels in model systems. To develop a method for the rapid characterization of the developmental consequences of gene dysregulation, we tested the use of RNAi for “transient transgenic” knockdown of mRNA in mouse embryos. These methods included lentiviral infection as well as transposition using the Sleeping Beauty (SB) and PiggyBac (PB) transposable element systems. This approach can be useful for phenotypic validation of putative mutant loci, as we demonstrate by confirming that knockdown of Prdm16 phenocopies the ENU-induced cleft palate (CP) mutant, csp1. This strategy is attractive as an alternative to gene targeting in embryonic stem cells, as it is simple and yields phenotypic information in a matter of weeks. Of the three methodologies tested, the PB transposon system produced high numbers of transgenic embryos with the expected phenotype, demonstrating its utility as a screening method.
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Affiliation(s)
- Bryan C. Bjork
- Genetics Division, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yuko Fujiwara
- Division of Hematology and Oncology, Children's Hospital, Harvard Medical School/Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Shannon W. Davis
- Departments of Human Genetics and Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Haiyan Qiu
- Genetics Division, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas L. Saunders
- Departments of Human Genetics and Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter Sandy
- The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Stuart Orkin
- Division of Hematology and Oncology, Children's Hospital, Harvard Medical School/Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Sally A. Camper
- Departments of Human Genetics and Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - David R. Beier
- Genetics Division, Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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32
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Abstract
The utilization of homologous recombination in embryonic stem cells as a means to generate mice carrying pre-determined modifications of genomic sequences has revolutionized the study of developmental biology. Recognizing the potential efficiencies that can be obtained by high-throughput production at centralized technology centers, a number of large-scale efforts for generating mice with targeted mutations have been funded. These programs are reaching fruition, and a variety of libraries of embryonic stem cells with defined mutations are now available.
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Affiliation(s)
- David R Beier
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School New Research Building 77 Avenue Louis Pasteur, Boston, MA 02115 USA
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33
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Abstract
Mutations in Interferon Regulatory Factor 6 (IRF6) have been identified in two human allelic syndromes with cleft lip and/or palate: Van der Woude (VWS) and Popliteal Pterygium syndromes (PPS). Furthermore, common IRF6 haplotypes and single nucleotide polymorphisms (SNP) alleles are strongly associated with nonsyndromic clefting defects in multiple ethnic populations. Mutations in the mouse often provide good models for the study of human diseases and developmental processes. We identified the cleft palate 1 (clft1) mouse mutant in a forward genetic screen for phenotypes modeling human congenital disease. In the clft1 mutant, we have identified a novel missense point mutation in the mouse Irf6 gene, which confers an amino acid alteration that has been found in a VWS family. Phenotypic comparison of clft1 mutants to previously reported Irf6 mutant alleles demonstrates the Irf6(clft1) allele is a hypomorphic allele. The cleft palate seen in these mutants appears to be due to abnormal adhesion between the palate and tongue. The Irf6(clft1) allele provides the first mouse model for the study of an etiologic IRF6 missense mutation observed in a human VWS family.
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Kamp A, Peterson MA, Svenson KL, Bjork BC, Hentges KE, Rajapaksha TW, Moran J, Justice MJ, Seidman JG, Seidman CE, Moskowitz IP, Beier DR. Genome-wide identification of mouse congenital heart disease loci. Hum Mol Genet 2010; 19:3105-13. [PMID: 20511334 DOI: 10.1093/hmg/ddq211] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Empirical evidence supporting a genetic basis for the etiology of congenital heart disease (CHD) is limited and few disease-causing mutations have been identified. To identify novel CHD genes, we performed a forward genetic screen to identify mutant mouse lines with heritable CHD. Lines with recessive N-ethyl-N-nitrsourea-induced CHD-causing mutations were identified using a three-generation backcross. A hierarchical screening protocol was used to test the hypothesis that the fetal-to-neonatal circulatory transition unmasks the specific structural heart defects observed in CHD. Mice with heart defects were efficiently ascertained by selecting for pups exhibiting perinatal lethality and characterizing their cardiac pathology. A marked increase of perinatal lethality was observed in the mutagen-treated cohort compared with an untreated backcross population. Cardiac pathology on perinatal lethals revealed cardiovascular defects in 79 pups from 47 of 321 mutagenized lines. All identified structural abnormalities were analogous to previously described forms of human CHD. Furthermore, the phenotypic recurrence and variance patterns across all lines were similar to human CHD prevalence and recurrence patterns. We mapped the locus responsible for heritable atrioventricular septal defects in six lines (avc1-6). Our screen demonstrated that 'sporadic' CHD may have major genetic component and established a practical, efficient approach for identifying CHD candidate genes.
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Affiliation(s)
- Anna Kamp
- Department of Pediatrics, The University of Chicago, Chicago, IL 60637, USA
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35
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Shiba D, Manning DK, Koga H, Beier DR, Yokoyama T. Inv acts as a molecular anchor for Nphp3 and Nek8 in the proximal segment of primary cilia. Cytoskeleton (Hoboken) 2010; 67:112-9. [PMID: 20169535 DOI: 10.1002/cm.20428] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A primary cilium is an antenna-like structure extending from the surface of most vertebrate cells. It is structurally divided along its vertical axis into sub-compartments that include the ciliary tip, the shaft, the ciliary necklace segment, the transitional zone and the basal body. We recently discovered that the shaft of the primary cilia has a distinct molecular compartment, termed the "Inv compartment", which is characterized by the accumulation of Inv at the base of primary cilia. Inv was discovered as a causative gene in inv mutant mice. It was later found to be responsible for the infantile type of nephronophthisis (NPHP2). Nephronophthisis (NPHP) is an autosomal recessive kidney disease. Nine causative genes have been identified, with all examined products thought to function in cilia, basal body and/or centrioles. However, their exact intra-ciliary localization and relationship have not been clear. Here, we report that products of Nphp3 and Nek8 (the mouse orthologs of the causative genes for NPHP3 and NPHP9, respectively) localize to the Inv compartment. We also show that Inv is essential for the compartmental localization of Nphp3 and Nek8, whereas localization of Inv does not require Nphp3 or Nek8. Nphp1 and Nphp4 also localize at the proximal region of the cilium, but not in Inv compartment. Our results indicate that Inv acts as an anchor for Nphp3 and Nek8 in the Inv compartment, and suggest that Inv compartment is a candidate site for intra-ciliary interaction of Inv, Nphp3 and Nek8.
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Affiliation(s)
- Dai Shiba
- Department of Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Japan
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36
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Smits P, Bolton AD, Funari V, Hong M, Boyden ED, Lu L, Manning DK, Dwyer ND, Moran JL, Prysak M, Merriman B, Nelson SF, Bonafé L, Superti-Furga A, Ikegawa S, Krakow D, Cohn DH, Kirchhausen T, Warman ML, Beier DR. Lethal skeletal dysplasia in mice and humans lacking the golgin GMAP-210. N Engl J Med 2010; 362:206-16. [PMID: 20089971 PMCID: PMC3108191 DOI: 10.1056/nejmoa0900158] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Establishing the genetic basis of phenotypes such as skeletal dysplasia in model organisms can provide insights into biologic processes and their role in human disease. METHODS We screened mutagenized mice and observed a neonatal lethal skeletal dysplasia with an autosomal recessive pattern of inheritance. Through genetic mapping and positional cloning, we identified the causative mutation. RESULTS Affected mice had a nonsense mutation in the thyroid hormone receptor interactor 11 gene (Trip11), which encodes the Golgi microtubule-associated protein 210 (GMAP-210); the affected mice lacked this protein. Golgi architecture was disturbed in multiple tissues, including cartilage. Skeletal development was severely impaired, with chondrocytes showing swelling and stress in the endoplasmic reticulum, abnormal cellular differentiation, and increased cell death. Golgi-mediated glycosylation events were altered in fibroblasts and chondrocytes lacking GMAP-210, and these chondrocytes had intracellular accumulation of perlecan, an extracellular matrix protein, but not of type II collagen or aggrecan, two other extracellular matrix proteins. The similarities between the skeletal and cellular phenotypes in these mice and those in patients with achondrogenesis type 1A, a neonatal lethal form of skeletal dysplasia in humans, suggested that achondrogenesis type 1A may be caused by GMAP-210 deficiency. Sequence analysis revealed loss-of-function mutations in the 10 unrelated patients with achondrogenesis type 1A whom we studied. CONCLUSIONS GMAP-210 is required for the efficient glycosylation and cellular transport of multiple proteins. The identification of a mutation affecting GMAP-210 in mice, and then in humans, as the cause of a lethal skeletal dysplasia underscores the value of screening for abnormal phenotypes in model organisms and identifying the causative mutations.
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Affiliation(s)
- Patrick Smits
- Orthopedic Research Laboratories, Department of Orthopedic Surgery, Children's Hospital, Boston, MA 02115, USA
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37
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Abstract
Transcriptional cofactors are essential to the regulation of transforming growth factor beta (TGFbeta) superfamily signaling and play critical and widespread roles during embryonic development, including craniofacial development. We describe the cleft secondary palate 1 (csp1) N-ethyl-N-nitrosourea-induced mouse model of non-syndromic cleft palate (NSCP) that is caused by an intronic Prdm16 splicing mutation. Prdm16 encodes a transcriptional cofactor that regulates TGFbeta signaling, and its expression pattern is consistent with a role in palate and craniofacial development. The cleft palate (CP) appears to be the result of micrognathia and failed palate shelf elevation due to physical obstruction by the tongue, resembling human Pierre Robin sequence (PRS)-like cleft secondary palate. PRDM16 should be considered a candidate for mutation in human clefting disorders, especially NSCP and PRS-like CP.
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Affiliation(s)
- Bryan C Bjork
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, New Research Building, Boston, MA 02115, USA
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38
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Heydemann A, Ceco E, Lim JE, Hadhazy M, Ryder P, Moran JL, Beier DR, Palmer AA, McNally EM. Latent TGF-beta-binding protein 4 modifies muscular dystrophy in mice. J Clin Invest 2009; 119:3703-12. [PMID: 19884661 DOI: 10.1172/jci39845] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Accepted: 09/09/2009] [Indexed: 11/17/2022] Open
Abstract
Most single-gene diseases, including muscular dystrophy, display a nonuniform phenotype. Phenotypic variability arises, in part, due to the presence of genetic modifiers that enhance or suppress the disease process. We employed an unbiased mapping approach to search for genes that modify muscular dystrophy in mice. In a genome-wide scan, we identified a single strong locus on chromosome 7 that influenced two pathological features of muscular dystrophy, muscle membrane permeability and muscle fibrosis. Within this genomic interval, an insertion/deletion polymorphism of 36 bp in the coding region of the latent TGF-beta-binding protein 4 gene (Ltbp4) was found. Ltbp4 encodes a latent TGF-beta-binding protein that sequesters TGF-beta and regulates its availability for binding to the TGF-beta receptor. Insertion of 12 amino acids into the proline-rich region of LTBP4 reduced proteolytic cleavage and was associated with reduced TGF-beta signaling, decreased fibrosis, and improved muscle pathology in a mouse model of muscular dystrophy. In contrast, a 12-amino-acid deletion in LTBP4 was associated with increased proteolysis, SMAD signaling, and fibrosis. These data identify Ltbp4 as a target gene to regulate TGF-beta signaling and modify outcomes in muscular dystrophy.
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Affiliation(s)
- Ahlke Heydemann
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, Illinois, USA
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39
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Stottmann RW, Tran PV, Turbe-Doan A, Beier DR. Ttc21b is required to restrict sonic hedgehog activity in the developing mouse forebrain. Dev Biol 2009; 335:166-78. [PMID: 19732765 DOI: 10.1016/j.ydbio.2009.08.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Revised: 08/24/2009] [Accepted: 08/24/2009] [Indexed: 10/20/2022]
Abstract
Organizing centers in the developing brain provide an assortment of instructive patterning cues, including Sonic hedgehog (Shh). Here we characterize the forebrain phenotype caused by loss of Ttc21b, a gene we identified in an ENU mutagenesis screen as a novel ciliary gene required for retrograde intraflagellar transport. The Ttc21b mutant has defects in limb, eye and, most dramatically, brain development. We show that Shh signaling is elevated in the rostral portion of the mutant embryo, including in a domain in or near the zona limitans intrathalamica. We demonstrate here that ciliary defects seen in the Ttc21b mutant extend to the embryonic brain, adding forebrain development to the spectrum of tissues affected by defects in ciliary physiology. We show that development of the Ttc21b brain phenotype is modified by lowering levels of the Shh ligand, supporting our hypothesis that the abnormal patterning is a consequence of elevated Shh signaling. Finally, we evaluate Wnt signaling but do not find evidence that this plays a role in causing the perturbed neurodevelopmental phenotype we describe.
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Affiliation(s)
- R W Stottmann
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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40
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Trapp ML, Galtseva A, Manning DK, Beier DR, Rosenblum ND, Quarmby LM. Defects in ciliary localization of Nek8 is associated with cystogenesis. Pediatr Nephrol 2008; 23:377-87. [PMID: 18189147 PMCID: PMC6890203 DOI: 10.1007/s00467-007-0692-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2007] [Revised: 10/08/2007] [Accepted: 10/10/2007] [Indexed: 01/01/2023]
Abstract
Mutations in the human NIMA (Never in Mitosis gene A)-related kinase 8 (Nek8) are associated with a rare form of the juvenile renal cystic disease, nephronophthisis type 9, and mutations in murine Nek8 cause renal cysts in jck mice. Cystogenesis involves dysfunctional ciliary signaling, and we have previously reported that Nek8 localizes to the primary cilium in mouse kidney epithelial cells. We now report that in developing mouse kidney, Nek8 is detected in the cilia of a subset of ureteric-bud-derived tubules at embryonic day (E)15.5. An increasing proportion of ureteric-bud-derived tubules express ciliary Nek8 until E18.5. Postnatal day 1 and 7 Nek8 is observed with equal frequency in both ureteric-bud and non-ureteric-bud-derived tubules. To investigate the cell biological consequences of kinase-deficient and jck mutant forms of Nek8, we transiently expressed green fluorescent protein (GFP)-tagged constructs in vitro. Mutations in the kinase and C-terminal domains of Nek8 adversely affected ciliary targeting but did not affect ciliogenesis or ciliary length. Consistent with these in vitro observations, kidneys from homozygous jck mice revealed reduced ciliary expression of Nek8 compared with kidneys from heterozygous (unaffected) mice. These data indicate that the ciliary localization of Nek8 in a subset of ureteric-bud-derived kidney tubules is essential for maintaining the integrity of those tubules in the mammalian kidney.
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Affiliation(s)
- Melissa L Trapp
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Dr., Burnaby, BC V5A1S6, Canada
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Sohara E, Luo Y, Zhang J, Manning DK, Beier DR, Zhou J. Nek8 regulates the expression and localization of polycystin-1 and polycystin-2. J Am Soc Nephrol 2008; 19:469-76. [PMID: 18235101 DOI: 10.1681/asn.2006090985] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Nek8 is a serine/threonine kinase that is mutated in the jck (juvenile cystic kidneys) mouse, a model of autosomal recessive juvenile polycystic kidney disease, but its function is poorly understood. We used the jck mouse to study the functional relationship between Nek8 and other proteins that have been implicated in polycystic kidney diseases. In the collecting tubules and collecting ducts of wild-type mice, we found that Nek8 was localized to the proximal portion of primary cilia and was weakly detected in the cytosol. In the jck mutant, however, Nek8 was found along the entire length of cilia. Coimmunoprecipitation experiments demonstrated that Nek8 interacted with polycystin-2, but not with polycystin-1, and that the jck mutation did not affect this interaction. Western blot analysis and real-time reverse transcriptase PCR revealed that the protein and mRNA expression of polycystin-1 (PC1) and polycystin-2 (PC2) were increased in jck mouse kidneys. The jck mutation also led to abnormal phosphorylatin of PC2, and this was associated with longer cilia and ciliary accumulation of PC1 and PC2. Our data suggests that Nek8 interacts with the signal transduction pathways of the polycystins and may control the targeting of these ciliary proteins. Dysfunction Nek8 may lead to cystogenesis by altering the structure and function of cilia in the distal nephron.
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Affiliation(s)
- Eisei Sohara
- Harvard Institutes of Medicine, Room 522, Brigham and Women's Hospital and Harvard Medical School, 4 Blackfan Circle, Boston, MA 02115, USA
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Kubo E, Fatma N, Akagi Y, Beier DR, Singh SP, Singh DP. TAT-mediated PRDX6 protein transduction protects against eye lens epithelial cell death and delays lens opacity. Am J Physiol Cell Physiol 2008; 294:C842-55. [PMID: 18184874 DOI: 10.1152/ajpcell.00540.2007] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A diminished level of endogenous antioxidant in cells/tissues is associated with reduced resistance to oxidative stress. Peroxiredoxin 6 (PRDX6), a protective molecule, regulates gene expression/function by controlling reactive oxygen species (ROS) levels. Using PRDX6 protein linked to TAT, the transduction domain from human immunodeficiency virus type 1 TAT protein, we demonstrated that PRDX6 was transduced into lens epithelial cells derived from rat or mouse lenses. The protein was biologically active, negatively regulating apoptosis and delaying progression of cataractogenesis by attenuating deleterious signaling. Lens epithelial cells from cataractous lenses bore elevated levels of ROS and were susceptible to oxidative stress. These cells harbored increased levels of active transforming growth factor (TGF)-beta 1 and of alpha-smooth muscle actin and beta ig-h3, markers for cataractogenesis. Importantly, cataractous lenses showed a 10-fold reduction in PRDX6 expression, whereas TGF-beta1 mRNA and protein levels were elevated. The changes were reversed, and cataractogenesis was delayed when PRDX6 was supplied. Results suggest that delivery of PRDX6 can postpone cataractogenesis, and this should be an effective approach to delaying cataracts and other degenerative diseases that are associated with increased ROS.
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Affiliation(s)
- Eri Kubo
- Department of Ophthalmology, University of Fukui, Fukui, Japan
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Leder A, McMenamin J, Zhou F, Moran JL, Beier DR, Leder P. Genome-wide SNP analysis of Tg.AC transgenic mice reveals an oncogenic collaboration between v-Ha-ras and Ink4a, which is absent in p53 deficiency. Oncogene 2007; 27:2456-65. [DOI: 10.1038/sj.onc.1210866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Matera I, Cockroft JL, Moran JL, Beier DR, Goldowitz D, Pavan WJ. A mouse model of Waardenburg syndrome type IV resulting from an ENU-induced mutation in endothelin 3. ACTA ACUST UNITED AC 2007; 20:210-5. [PMID: 17516928 DOI: 10.1111/j.1600-0749.2007.00371.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A line of mutant mice (114-CH19) exhibiting white spotting and preweaning lethality was identified during an N-ethyl-N-nitrosourea (ENU) mutagenesis screen. The trait segregated as a semidominant bellyspot with reduced penetrance. Homozygous mutant mice showed preweaning lethality, and exhibited white spotting over the majority of the body surface, with pigmented patches remaining around the pinnae, eyes and tail. Linkage analysis localized 114-CH19 on mouse chromosome 2, suggesting endothelin 3 (Edn3) as a candidate gene. Sequence analysis of Edn3 identified a G > A transversion that encodes an arginine to histidine substitution (R96H). This mutation is predicted to disrupt furin-mediated proteolytic cleavage of pro-endothelin that is necessary to form biologically active EDN3. This mutation is novel among human and mouse EDN3 mutants, is the first reported EDN3 ENU mutant, and is the second reported EDN3 point mutation. This study demonstrates the power of using ENU mutagenesis screens to generate new animal models of human disease, and expands the spectrum of EDN3 mutant alleles.
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Affiliation(s)
- Ivana Matera
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20855, USA
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Poirier C, Moran JL, Kovanci E, Petit DC, Beier DR, Bishop CE. Three loci on mouse chromosome 5 and 10 modulate sex determination in XX Ods/+ mice. Genesis 2007; 45:452-5. [PMID: 17607692 DOI: 10.1002/dvg.20312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In mouse, XY embryos are committed to the male sex determination pathway after the transient expression of the Y-linked Sry gene in the Sertoli cell lineage between 10.5 and 12.5 dpc. In the C57BL/6J strain, male sex determination program can be modulated by some autosomal genes. The C57BL/6J alleles at these autosomal loci can antagonize male sex determination in combination with specific Sry alleles. In this report, the authors have identified an effect of these C57BL/6J specific alleles in combination with a mutated Sox9 allele, Sox9(Ods). Authors report the mapping of three of these genetic loci on mouse chromosome 5 and 10 in a backcross of the Ods mutation to the C57BL/6J background. Our study confirms the importance of the strain C57BL/6J for the investigation of the genetic mechanisms that control sex determination.
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Moran JL, Qiu H, Turbe-Doan A, Yun Y, Boeglin WE, Brash AR, Beier DR. A mouse mutation in the 12R-lipoxygenase, Alox12b, disrupts formation of the epidermal permeability barrier. J Invest Dermatol 2007; 127:1893-7. [PMID: 17429434 DOI: 10.1038/sj.jid.5700825] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nonbullous congenital ichthyosiform erythroderma (NCIE) is a nonsyndromic form of autosomal recessive congenital ichthyosis characterized by hyperkeratosis and a disruption in the epidermal permeability barrier. Identification of mutations in two lipoxygenases (LOXs), ALOX12B (12R-LOX) and ALOXE3 (eLOX3), and further functional studies implicate ALOX12B and ALOXE3 in the etiology of NCIE. Here, we report a mutation in Alox12b in the recessive ethylnitrosurea-induced mouse mutant, mummy (Alox12b(mmy-Bei)). mummy mutants have red, scaly skin and die perinatally. Histologically, mummy mutants display defects in the epidermis. We mapped mummy to a 1.9 Mb interval on Chr. 11 containing Alox12b (12R-LOX), Aloxe3 (eLOX3) and Alox15b (8-LOX). Sequencing of all three genes identified a nonsense mutation in the catalytic domain of Alox12b. We demonstrate that mummy mutants have a disrupted epidermal permeability barrier and that the nonsense mutation in mummy abolishes the enzyme activity of 12R-LOX. The mummy mutant provides a mouse model for LOX-mediated NCIE and is the first described mouse mutant affecting epidermal barrier formation identified by forward genetics.
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Affiliation(s)
- Jennifer L Moran
- Genetics Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Abstract
Mutations of Fog2 in mice result in a phenotype that includes pulmonary lobar defects. To determine whether formation of the accessory lobe bronchus is mediated by a Gata family cofactor, we evaluated embryonic lungs from mice carrying missense mutations that cause loss of FOG-GATA protein interaction. Lungs from embryos carrying a missense mutation in Gata6 were structurally normal, while lungs from embryos carrying mutations of either Gata4 or of both Gata4 and Gata6 had a structural phenotype that matched the Fog2 mutant phenotype. Expression analysis showed that Gata4 and Fog2 are expressed in the ventral and medial pulmonary mesenchyme during secondary budding. Although Gata4 has not previously been suspected as playing a role in lung development, we have found that a Fog2-Gata4 interaction is critical for the development of normal pulmonary lobar structure, and this phenotype is not influenced by the additional loss of Gata6 interaction. Fog2 and Gata4 in the early pulmonary mesenchyme participate in patterning the secondary bronchus of the accessory lobe.
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Affiliation(s)
- Kate G Ackerman
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School New Research Building 458, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
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Abstract
The novel neurological mutant Cincinatti arose by genomic duplication of exon 5 in the glycine receptor gene Glra1. The mutant transcript results in premature protein truncation. A direct repeat of the pentamer GGGGC is present adjacent to the breakpoints and may have mediated the duplication event by a replication slippage mechanism.
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Affiliation(s)
- Katherine D Holland
- Division of Neurology, Cincinnati Children's Hospital Medical Center, OH 45229-3039, and Department of Human Genetics, University of Michigan, Ann Arbor 48109-0618, USA
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Lehoczky JA, Cai WW, Douglas JA, Moran JL, Beier DR, Innis JW. Description and genetic mapping of Polypodia: an X-linked dominant mouse mutant with ectopic caudal limbs and other malformations. Mamm Genome 2006; 17:903-13. [PMID: 16964440 DOI: 10.1007/s00335-006-0041-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Accepted: 05/04/2006] [Indexed: 11/25/2022]
Abstract
In this report we present a spontaneous mouse mutant, named Polypodia (Ppd), that primarily exhibits ectopic, ventral/caudal limbs and associated pelvic girdle malformation or duplication. Less penetrant features include diphallia, microphthalmia, small kidney, curled or kinked tail, forelimb anomaly, and skin papillae. Ppd mice have a normal karyotype and no large-scale genomic deletions or insertions by BAC-based array comparative genomic hybridization (CGH). Ppd is X-linked dominant with approximately 20% penetrance on the C3H background and maps to X:61.6 Mb-X:71.24 Mb. The limb and a subset of the nonlimb anomalies are similar to those in offspring from retinoic acid-treated dams at E4.5-5.5 and feature overlap with the Disorganization mouse mutant and human patients with ectopic legs. We hypothesize that Ppd affects very early steps in the formation of caudal structures including limb and appendage number. The existence of noncaudal anomalies implies the involvement of Ppd in a broad array of cell fate decisions.
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Affiliation(s)
- Jessica A Lehoczky
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109-0618, USA
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Smith LA, Bukanov NO, Husson H, Russo RJ, Barry TC, Taylor AL, Beier DR, Ibraghimov-Beskrovnaya O. Development of polycystic kidney disease in juvenile cystic kidney mice: insights into pathogenesis, ciliary abnormalities, and common features with human disease. J Am Soc Nephrol 2006; 17:2821-31. [PMID: 16928806 DOI: 10.1681/asn.2006020136] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Significant progress in understanding the molecular mechanisms of polycystic kidney disease (PKD) has been made in recent years. Translating this understanding into effective therapeutics will require testing in animal models that closely resemble human PKD by multiple parameters. Similar to autosomal dominant PKD, juvenile cystic kidney (jck) mice develop cysts in multiple nephron segments, including cortical collecting ducts, distal tubules, and loop of Henle. The jck mice display gender dimorphism in kidney disease progression with more aggressive disease in male mice. Gonadectomy experiments show that testosterone aggravates the severity of the disease in jck male mice, while female gonadal hormones have protective effects. EGF receptor is overexpressed and mislocalized in jck cystic epithelia, a hallmark of human disease. Increased cAMP levels in jck kidneys and activation of the B-Raf/extracellular signal-regulated kinase pathway are demonstrated. The effect of jck mutation on the expression of Nek8, a NIMA-related (never in mitosis A) kinase, and polycystins in jck cilia is shown for the first time. Nek8 overexpression and loss of ciliary localization in jck epithelia are accompanied by enhanced expression of polycystins along the cilia. The primary cilia in jck kidneys are significantly more lengthened than the cilia in wild-type mice, suggesting a role for Nek8 in controlling ciliary length. Collectively, these data demonstrate that the jck mice should be useful for testing potential therapies and for studying the molecular mechanisms that link ciliary structure/function and cystogenesis.
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Affiliation(s)
- Laurie A Smith
- Genzyme Corporation, 5 Mountain Road, Framingham, MA 01701-9322, USA
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