1
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van Karnebeek CDM, Tarailo-Graovac M, Leen R, Meinsma R, Correard S, Jansen-Meijer J, Prykhozhij SV, Pena IA, Ban K, Schock S, Saxena V, Pras-Raves ML, Drögemöller BI, Grootemaat AE, van der Wel NN, Dobritzsch D, Roseboom W, Schomakers BV, Jaspers YRJ, Zoetekouw L, Roelofsen J, Ferreira CR, van der Lee R, Ross CJ, Kochan J, McIntyre RL, van Klinken JB, van Weeghel M, Kramer G, Weschke B, Labrune P, Willemsen MA, Riva D, Garavaglia B, Moeschler JB, Filiano JJ, Ekker M, Berman JN, Dyment D, Vaz FM, Wassermann WW, Houtkooper RH, van Kuilenburg ABP. CIAO1 and MMS19 deficiency: A lethal neurodegenerative phenotype caused by cytosolic Fe-S cluster protein assembly disorders. Genet Med 2024; 26:101104. [PMID: 38411040 DOI: 10.1016/j.gim.2024.101104] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024] Open
Abstract
PURPOSE The functionality of many cellular proteins depends on cofactors; yet, they have only been implicated in a minority of Mendelian diseases. Here, we describe the first 2 inherited disorders of the cytosolic iron-sulfur protein assembly system. METHODS Genetic testing via genome sequencing was applied to identify the underlying disease cause in 3 patients with microcephaly, congenital brain malformations, progressive developmental and neurologic impairments, recurrent infections, and a fatal outcome. Studies in patient-derived skin fibroblasts and zebrafish models were performed to investigate the biochemical and cellular consequences. RESULTS Metabolic analysis showed elevated uracil and thymine levels in body fluids but no pathogenic variants in DPYD, encoding dihydropyrimidine dehydrogenase. Genome sequencing identified compound heterozygosity in 2 patients for missense variants in CIAO1, encoding cytosolic iron-sulfur assembly component 1, and homozygosity for an in-frame 3-nucleotide deletion in MMS19, encoding the MMS19 homolog, cytosolic iron-sulfur assembly component, in the third patient. Profound alterations in the proteome, metabolome, and lipidome were observed in patient-derived fibroblasts. We confirmed the detrimental effect of deficiencies in CIAO1 and MMS19 in zebrafish models. CONCLUSION A general failure of cytosolic and nuclear iron-sulfur protein maturation caused pleiotropic effects. The critical function of the cytosolic iron-sulfur protein assembly machinery for antiviral host defense may well explain the recurrent severe infections occurring in our patients.
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Affiliation(s)
- Clara D M van Karnebeek
- Amsterdam UMC location University of Amsterdam, Departments of Pediatrics and Human Genetics, Emma Center for Personalized Medicine, Amsterdam, The Netherlands; Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; United for Metabolic Diseases, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Maja Tarailo-Graovac
- Departments of Medical Genetics and Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute (ACHRI), Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - René Leen
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Rutger Meinsma
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Solenne Correard
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Judith Jansen-Meijer
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Sergey V Prykhozhij
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Izabella A Pena
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology-MIT, Boston, MA
| | - Kevin Ban
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Sarah Schock
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Vishal Saxena
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Mia L Pras-Raves
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Britt I Drögemöller
- Rady Faculty of Health Sciences, Department of Biochemistry and Medical Genetics, Children's Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anita E Grootemaat
- Amsterdam UMC Location University of Amsterdam, Department of Medical Biology, Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Amsterdam UMC Location University of Amsterdam, Department of Medical Biology, Amsterdam, The Netherlands
| | - Doreen Dobritzsch
- Uppsala University, Department of Chemistry, Biomedical Center, Uppsala, Sweden
| | - Winfried Roseboom
- Swammerdam Institute for Life Sciences, University of Amsterdam, Laboratory for Mass Spectrometry of Biomolecules, Amsterdam, The Netherlands
| | - Bauke V Schomakers
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Yorrick R J Jaspers
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Lida Zoetekouw
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Jeroen Roelofsen
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Robin van der Lee
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Colin J Ross
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Jakub Kochan
- Jagiellonian University, Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biochemistry, Kraków, Poland
| | - Rebecca L McIntyre
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - Jan B van Klinken
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel van Weeghel
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Gertjan Kramer
- Swammerdam Institute for Life Sciences, University of Amsterdam, Laboratory for Mass Spectrometry of Biomolecules, Amsterdam, The Netherlands
| | - Bernhard Weschke
- Department of Neuropediatrics, Charité University Medicine Berlin, Berlin, Germany
| | - Philippe Labrune
- APHP-Université Paris-Saclay, Hôpital Antoine Béclère, Centre de Référence Maladies Héréditaires du Métabolisme Hépatique, Service de Pédiatrie, Clamart, and Paris-Saclay University, and INSERM U 1195, Clamart, France
| | - Michèl A Willemsen
- Department of Pediatric Neurology and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Daria Riva
- Neurogenetic Syndromes and Autism Spectrum Disorders Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan, Italy
| | - Barbara Garavaglia
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico "Carlo Besta," Milan, Italy
| | - John B Moeschler
- Geisel School of Medicine, Dartmouth College and Departments of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH
| | - James J Filiano
- Geisel School of Medicine, Dartmouth College and Departments of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH
| | - Marc Ekker
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Jason N Berman
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - David Dyment
- Faculty of Medicine, CHEO Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - Frédéric M Vaz
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands; Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Wyeth W Wassermann
- Departments of Medical Genetics and Pediatrics, Centre for Molecular Medicine and Therapeutics, Faculty of Pharmaceutical Science, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Riekelt H Houtkooper
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands
| | - André B P van Kuilenburg
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands; Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Amsterdam, The Netherlands.
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Prykhozhij SV, Berman JN. Mutation Knock-in Methods Using Single-Stranded DNA and Gene Editing Tools in Zebrafish. Methods Mol Biol 2024; 2707:279-303. [PMID: 37668920 DOI: 10.1007/978-1-0716-3401-1_19] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Introduction or knock-in of precise genomic modifications remains one of the most important applications of CRISPR/Cas9 in all model systems including zebrafish. The most widely used type of donor template containing the desired modification is single-stranded DNA (ssDNA), either in the form of single-stranded oligodeoxynucleotides (ssODN) (<150 nucleotides (nt)) or as long ssDNA (lssDNA) molecules (up to about 2000 nt). Despite the challenges posed by DNA repair after DNA double-strand breaks, knock-in of precise mutations is relatively straightforward in zebrafish. Knock-in efficiency can be enhanced by careful donor template design, using lssDNA as template or tethering the donor template DNA to the Cas9-guide RNA complex. Other point mutation methods such as base editing and prime editing are starting to be applied in zebrafish and many other model systems. However, these methods may not always be sufficiently accessible or may have limited capacity to perform all desired mutation knock-ins which are possible with ssDNA-based knock-in methods. Thus, it is likely that there will be complementarity in the technologies used for generating precise mutants. Here, we review and describe a suite of CRISPR/Cas9 knock-in procedures utilizing ssDNA as the donor template in zebrafish, point out the potential challenges and suggest possible approaches for their solution ultimately leading to successful generation of precise mutant lines.
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Affiliation(s)
- Sergey V Prykhozhij
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Jason N Berman
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada.
- Departments of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada.
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3
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Rajan V, Prykhozhij SV, Pandey A, Cohen AM, Rainey JK, Berman JN. KIT D816V is dimerization-independent and activates downstream pathways frequently perturbed in mastocytosis. Br J Haematol 2023; 202:960-970. [PMID: 35245395 DOI: 10.1111/bjh.18116] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 11/30/2022]
Abstract
KIT, a type III tyrosine kinase receptor, plays a crucial role in haematopoietic development. The KIT receptor forms a dimer after ligand binding; this activates tyrosine kinase activity leading to downstream signal transduction. The D816V KIT mutation is extensively implicated in haematological malignancies, including mastocytosis and leukaemia. KIT D816V is constitutively active, but the molecular nuances that lead to constitutive tyrosine kinase activity are unclear. For the first time, we present experimental evidence that the KIT D816V mutant does not dimerize like KIT wild type. We further show evidence of decreased stabilization of the tyrosine kinase domain in the KIT D816V mutant, a phenomenon that might contribute to its constitutive activity. Since the mechanism of KIT D816V activation varies from that of the wild type, we explored downstream signal transduction events and found that even though KIT D816V targets similar signalling moieties, the signalling is amplified in the mutant compared to stem cell factor-activated wild type receptor. Uniquely, KIT D816V induces infection-related pathways and the spliceosome pathway, providing alternate options for selective as well as combinatorial therapeutic targeting.
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Affiliation(s)
- Vinothkumar Rajan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | - Sergey V Prykhozhij
- Children's Hospital of Eastern Ontario (CHEO) Research Institute and University of Ottawa, Ottawa, ON, Canada
| | - Aditya Pandey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Alejandro M Cohen
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada
- School of Biomedical Engineering, Dalhousie University, Halifax, NS, Canada
| | - Jason N Berman
- Children's Hospital of Eastern Ontario (CHEO) Research Institute and University of Ottawa, Ottawa, ON, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
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4
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MacLean JE, Wertman JN, Prykhozhij SV, Chedrawe E, Langley S, Steele SL, Ban K, Blake K, Berman JN. phox2ba: The Potential Genetic Link behind the Overlap in the Symptomatology between CHARGE and Central Congenital Hypoventilation Syndromes. Genes (Basel) 2023; 14:genes14051086. [PMID: 37239446 DOI: 10.3390/genes14051086] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
CHARGE syndrome typically results from mutations in the gene encoding chromodomain helicase DNA-binding protein 7 (CHD7). CHD7 is involved in regulating neural crest development, which gives rise to tissues of the skull/face and the autonomic nervous system (ANS). Individuals with CHARGE syndrome are frequently born with anomalies requiring multiple surgeries and often experience adverse events post-anesthesia, including oxygen desaturations, decreased respiratory rates, and heart rate abnormalities. Central congenital hypoventilation syndrome (CCHS) affects ANS components that regulate breathing. Its hallmark feature is hypoventilation during sleep, clinically resembling observations in anesthetized CHARGE patients. Loss of PHOX2B (paired-like homeobox 2b) underlies CCHS. Employing a chd7-null zebrafish model, we investigated physiologic responses to anesthesia and compared these to loss of phox2b. Heart rates were lower in chd7 mutants compared to the wild-type. Exposure to tricaine, a zebrafish anesthetic/muscle relaxant, revealed that chd7 mutants took longer to become anesthetized, with higher respiratory rates during recovery. chd7 mutant larvae demonstrated unique phox2ba expression patterns. The knockdown of phox2ba reduced larval heart rates similar to chd7 mutants. chd7 mutant fish are a valuable preclinical model to investigate anesthesia in CHARGE syndrome and reveal a novel functional link between CHARGE syndrome and CCHS.
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Affiliation(s)
- Jessica E MacLean
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Jaime N Wertman
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Sergey V Prykhozhij
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Emily Chedrawe
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Stewart Langley
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Kevin Ban
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Kim Blake
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Jason N Berman
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Departments of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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5
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Prykhozhij SV, Caceres L, Ban K, Cordeiro-Santanach A, Nagaraju K, Hoffman EP, Berman JN. Loss of calpain3b in Zebrafish, a Model of Limb-Girdle Muscular Dystrophy, Increases Susceptibility to Muscle Defects Due to Elevated Muscle Activity. Genes (Basel) 2023; 14:492. [PMID: 36833417 PMCID: PMC9957097 DOI: 10.3390/genes14020492] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/06/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Limb-Girdle Muscular Dystrophy Type R1 (LGMDR1; formerly LGMD2A), characterized by progressive hip and shoulder muscle weakness, is caused by mutations in CAPN3. In zebrafish, capn3b mediates Def-dependent degradation of p53 in the liver and intestines. We show that capn3b is expressed in the muscle. To model LGMDR1 in zebrafish, we generated three deletion mutants in capn3b and a positive-control dmd mutant (Duchenne muscular dystrophy). Two partial deletion mutants showed transcript-level reduction, whereas the RNA-less mutant lacked capn3b mRNA. All capn3b homozygous mutants were developmentally-normal adult-viable animals. Mutants in dmd were homozygous-lethal. Bathing wild-type and capn3b mutants in 0.8% methylcellulose (MC) for 3 days beginning 2 days post-fertilization resulted in significantly pronounced (20-30%) birefringence-detectable muscle abnormalities in capn3b mutant embryos. Evans Blue staining for sarcolemma integrity loss was strongly positive in dmd homozygotes, negative in wild-type embryos, and negative in MC-treated capn3b mutants, suggesting membrane instability is not a primary muscle pathology determinant. Increased birefringence-detected muscle abnormalities in capn3b mutants compared to wild-type animals were observed following induced hypertonia by exposure to cholinesterase inhibitor, azinphos-methyl, reinforcing the MC results. These mutant fish represent a novel tractable model for studying the mechanisms underlying muscle repair and remodeling, and as a preclinical tool for whole-animal therapeutics and behavioral screening in LGMDR1.
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Affiliation(s)
- Sergey V. Prykhozhij
- Children’s Hospital of Eastern Ontario (CHEO) Research Institute & University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Lucia Caceres
- Department of Psychology & Neuroscience, Dalhousie University, Halifax, NS B3H 4J1, Canada
- AGADA BioSciences, Halifax, NS B3H 0A8, Canada
| | - Kevin Ban
- Children’s Hospital of Eastern Ontario (CHEO) Research Institute & University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | | | - Kanneboyina Nagaraju
- AGADA BioSciences, Halifax, NS B3H 0A8, Canada
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University—State University of New York, Binghamton, NY 13902, USA
| | - Eric P. Hoffman
- AGADA BioSciences, Halifax, NS B3H 0A8, Canada
- School of Pharmacy and Pharmaceutical Sciences, Binghamton University—State University of New York, Binghamton, NY 13902, USA
| | - Jason N. Berman
- Children’s Hospital of Eastern Ontario (CHEO) Research Institute & University of Ottawa, Ottawa, ON K1H 8L1, Canada
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6
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Biggs CM, Cordeiro-Santanach A, Prykhozhij SV, Deveau AP, Lin Y, Del Bel KL, Orben F, Ragotte RJ, Saferali A, Mostafavi S, Dinh L, Dai D, Weinacht KG, Dobbs K, Ott de Bruin L, Sharma M, Tsai K, Priatel JJ, Schreiber RA, Rozmus J, Hosking MC, Shopsowitz KE, McKinnon ML, Vercauteren S, Seear M, Notarangelo LD, Lynn FC, Berman JN, Turvey SE. Human JAK1 gain of function causes dysregulated myelopoeisis and severe allergic inflammation. JCI Insight 2022; 7:e150849. [PMID: 36546480 PMCID: PMC9869972 DOI: 10.1172/jci.insight.150849] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
Primary atopic disorders are a group of inborn errors of immunity that skew the immune system toward severe allergic disease. Defining the biology underlying these extreme monogenic phenotypes reveals shared mechanisms underlying common polygenic allergic disease and identifies potential drug targets. Germline gain-of-function (GOF) variants in JAK1 are a cause of severe atopy and eosinophilia. Modeling the JAK1GOF (p.A634D) variant in both zebrafish and human induced pluripotent stem cells (iPSCs) revealed enhanced myelopoiesis. RNA-Seq of JAK1GOF human whole blood, iPSCs, and transgenic zebrafish revealed a shared core set of dysregulated genes involved in IL-4, IL-13, and IFN signaling. Immunophenotypic and transcriptomic analysis of patients carrying a JAK1GOF variant revealed marked Th cell skewing. Moreover, long-term ruxolitinib treatment of 2 children carrying the JAK1GOF (p.A634D) variant remarkably improved their growth, eosinophilia, and clinical features of allergic inflammation. This work highlights the role of JAK1 signaling in atopic immune dysregulation and the clinical impact of JAK1/2 inhibition in treating eosinophilic and allergic disease.
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Affiliation(s)
- Catherine M. Biggs
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | | | | | - Adam P. Deveau
- Department of Internal Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Yi Lin
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Kate L. Del Bel
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Felix Orben
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Robert J. Ragotte
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Aabida Saferali
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara Mostafavi
- Department of Medical Genetics and
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Louie Dinh
- Department of Medical Genetics and
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Darlene Dai
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Katja G. Weinacht
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford, California, USA
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Lisa Ott de Bruin
- Division of Immunology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mehul Sharma
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Kevin Tsai
- BC Children’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine and
| | - John J. Priatel
- BC Children’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine and
| | - Richard A. Schreiber
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Jacob Rozmus
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Martin C.K. Hosking
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Kevin E. Shopsowitz
- BC Children’s Hospital, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine and
| | | | | | - Michael Seear
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Francis C. Lynn
- BC Children’s Hospital, Vancouver, British Columbia, Canada
- Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jason N. Berman
- CHEO Research Institute, University of Ottawa, Ottawa, Ontario, Canada
- Departments of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Stuart E. Turvey
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children’s Hospital, Vancouver, British Columbia, Canada
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7
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Ketharnathan S, Rajan V, Prykhozhij SV, Berman JN. Zebrafish models of inflammation in hematopoietic development and disease. Front Cell Dev Biol 2022; 10:955658. [PMID: 35923854 PMCID: PMC9340492 DOI: 10.3389/fcell.2022.955658] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Zebrafish offer an excellent tool for studying the vertebrate hematopoietic system thanks to a highly conserved and rapidly developing hematopoietic program, genetic amenability, optical transparency, and experimental accessibility. Zebrafish studies have contributed to our understanding of hematopoiesis, a complex process regulated by signaling cues, inflammation being crucial among them. Hematopoietic stem cells (HSCs) are multipotent cells producing all the functional blood cells, including immune cells. HSCs respond to inflammation during infection and malignancy by proliferating and producing the blood cells in demand for a specific scenario. We first focus on how inflammation plays a crucial part in steady-state HSC development and describe the critical role of the inflammasome complex in regulating HSC expansion and balanced lineage production. Next, we review zebrafish studies of inflammatory innate immune mechanisms focusing on interferon signaling and the downstream JAK-STAT pathway. We also highlight insights gained from zebrafish models harbouring genetic perturbations in the role of inflammation in hematopoietic disorders such as bone marrow failure, myelodysplastic syndrome, and myeloid leukemia. Indeed, inflammation has been recently identified as a potential driver of clonal hematopoiesis and leukemogenesis, where cells acquire somatic mutations that provide a proliferative advantage in the presence of inflammation. Important insights in this area come from mutant zebrafish studies showing that hematopoietic differentiation can be compromised by epigenetic dysregulation and the aberrant induction of signaling pathways.
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Affiliation(s)
- Sarada Ketharnathan
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Vinothkumar Rajan
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, ON, Canada
| | | | - Jason N. Berman
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Departments of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- *Correspondence: Jason N. Berman,
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8
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Abstract
Cancer predisposition syndromes are rare, typically monogenic disorders that result from germline mutations that increase the likelihood of developing cancer. Although these disorders are individually rare, resulting cancers collectively represent 5-10% of all malignancies. In addition to a greater incidence of cancer, affected individuals have an earlier tumor onset and are frequently subjected to long-term multi-modal cancer screening protocols for earlier detection and initiation of treatment. In vivo models are needed to better understand tumor-driving mechanisms, tailor patient screening approaches and develop targeted therapies to improve patient care and disease prognosis. The zebrafish (Danio rerio) has emerged as a robust model for cancer research due to its high fecundity, time- and cost-efficient genetic manipulation and real-time high-resolution imaging. Tumors developing in zebrafish cancer models are histologically and molecularly similar to their human counterparts, confirming the validity of these models. The zebrafish platform supports both large-scale random mutagenesis screens to identify potential candidate/modifier genes and recently optimized genome editing strategies. These techniques have greatly increased our ability to investigate the impact of certain mutations and how these lesions impact tumorigenesis and disease phenotype. These unique characteristics position the zebrafish as a powerful in vivo tool to model cancer predisposition syndromes and as such, several have already been created, including those recapitulating Li-Fraumeni syndrome, familial adenomatous polyposis, RASopathies, inherited bone marrow failure syndromes, and several other pathogenic mutations in cancer predisposition genes. In addition, the zebrafish platform supports medium- to high-throughput preclinical drug screening to identify compounds that may represent novel treatment paradigms or even prevent cancer evolution. This review will highlight and synthesize the findings from zebrafish cancer predisposition models created to date. We will discuss emerging trends in how these zebrafish cancer models can improve our understanding of the genetic mechanisms driving cancer predisposition and their potential to discover therapeutic and/or preventative compounds that change the natural history of disease for these vulnerable children, youth and adults.
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Affiliation(s)
- Kim Kobar
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Keon Collett
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | | | - Jason N. Berman
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
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9
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Prykhozhij SV, Cordeiro-Santanach A, Caceres L, Berman JN. Genome Editing in Zebrafish Using High-Fidelity Cas9 Nucleases: Choosing the Right Nuclease for the Task. Methods Mol Biol 2020; 2115:385-405. [PMID: 32006412 DOI: 10.1007/978-1-0716-0290-4_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Shortly after the development of the CRISPR/Cas9 system, it was recognized that it is prone to induce off-target mutations at significant frequencies. Therefore, there is a strong motivation to develop Cas9 enzymes with reduced off-target activity. Multiple rational design or selection approaches have been applied to develop several Cas9 versions with reduced off-target activities (high fidelity). To make these high-fidelity Cas9s available for model systems other than human cells and bacterial strains, as, for example, in zebrafish, new specialized expression vectors need to be developed. In this chapter, we focused on the HypaCas9 and HiFi Cas9 high-fidelity enzymes and incorporated the mutations of these Cas9 versions into a codon-optimized zebrafish Cas9 vector. This optimized vector was further improved by introducing an artificial polyadenine insert (A71) since polyadenylation is known to enhance mRNA translational efficiency. The Hypa-nCas9n and HiFi-nCas9n vectors were produced by single-site mutagenesis from pT3TS-nCas9n-A71 vector. We then tested the polyadenylated mRNAs for nCas9n, Hypa-nCas9n, HiFi-nCas9n, and HiFi-Cas9 protein for editing efficiency in five genome editing strategies and found that these high-fidelity Cas9 versions had different performances ranging from activity at 2-4 sites, where the wild-type nCas9n is active, indicating that these Cas9 versions have different sgRNA preferences. In summary, the developed new high-fidelity Cas9 vectors will enable researchers to perform much more accurate genome editing.
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10
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Caceres L, Prykhozhij SV, Cairns E, Gjerde H, Duff NM, Collett K, Ngo M, Nasrallah GK, McMaster CR, Litvak M, Robitaille JM, Berman JN. Frizzled 4 regulates ventral blood vessel remodeling in the zebrafish retina. Dev Dyn 2019; 248:1243-1256. [PMID: 31566834 DOI: 10.1002/dvdy.117] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Familial exudative vitreoretinopathy (FEVR) is a rare congenital disorder characterized by a lack of blood vessel growth to the periphery of the retina with secondary fibrovascular proliferation at the vascular-avascular junction. These structurally abnormal vessels cause leakage and hemorrhage, while the fibroproliferative scarring results in retinal dragging, detachment and blindness. Mutations in the FZD4 gene represent one of the most common causes of FEVR. METHODS A loss of function mutation resulting from a 10-nucleotide insertion into exon 1 of the zebrafish fzd4 gene was generated using transcription activator-like effector nucleases (TALENs). Structural and functional integrity of the retinal vasculature was examined by fluorescent microscopy and optokinetic responses. RESULTS Zebrafish retinal vasculature is asymmetrically distributed along the dorsoventral axis, with active vascular remodeling on the ventral surface of the retina throughout development. fzd4 mutants exhibit disorganized ventral retinal vasculature with discernable tubular fusion by week 8 of development. Furthermore, fzd4 mutants have impaired optokinetic responses requiring increased illumination. CONCLUSION We have generated a visually impaired zebrafish FEVR model exhibiting abnormal retinal vasculature. These fish provide a tractable system for studying vascular biology in retinovascular disorders, and demonstrate the feasibility of using zebrafish for evaluating future FEVR genes identified in humans.
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Affiliation(s)
- Lucia Caceres
- Department of Pediatrics, IWK Health Centre/Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sergey V Prykhozhij
- Department of Pediatrics, IWK Health Centre/Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elizabeth Cairns
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Harald Gjerde
- Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Nicole M Duff
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Keon Collett
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mike Ngo
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | - Matthew Litvak
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Johane M Robitaille
- Department of Pediatrics, IWK Health Centre/Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason N Berman
- Department of Pediatrics, IWK Health Centre/Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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11
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Prykhozhij SV, Fuller C, Steele SL, Veinotte CJ, Razaghi B, Robitaille JM, McMaster CR, Shlien A, Malkin D, Berman JN. Optimized knock-in of point mutations in zebrafish using CRISPR/Cas9. Nucleic Acids Res 2019; 46:e102. [PMID: 29905858 PMCID: PMC6158492 DOI: 10.1093/nar/gky512] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 01/11/2018] [Accepted: 05/23/2018] [Indexed: 12/21/2022] Open
Abstract
We have optimized point mutation knock-ins into zebrafish genomic sites using clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 reagents and single-stranded oligodeoxynucleotides. The efficiency of knock-ins was assessed by a novel application of allele-specific polymerase chain reaction and confirmed by high-throughput sequencing. Anti-sense asymmetric oligo design was found to be the most successful optimization strategy. However, cut site proximity to the mutation and phosphorothioate oligo modifications also greatly improved knock-in efficiency. A previously unrecognized risk of off-target trans knock-ins was identified that we obviated through the development of a workflow for correct knock-in detection. Together these strategies greatly facilitate the study of human genetic diseases in zebrafish, with additional applicability to enhance CRISPR-based approaches in other animal model systems.
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Affiliation(s)
- Sergey V Prykhozhij
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Charlotte Fuller
- Michael G. DeGroote School of Medicine, McMaster University,Hamilton, ON, L8S4L8, Canada
| | | | - Chansey J Veinotte
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Babak Razaghi
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Johane M Robitaille
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Christopher R McMaster
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Adam Shlien
- Departments of Pediatrics and Medical Biophysics, University of Toronto, Toronto, ON, M5G 1X8, Canada
| | - David Malkin
- Departments of Pediatrics and Medical Biophysics, University of Toronto, Toronto, ON, M5G 1X8, Canada
| | - Jason N Berman
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
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12
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Prykhozhij SV, Caceres L, Berman JN. New Developments in CRISPR/Cas-based Functional Genomics and their Implications for Research Using Zebrafish. Curr Gene Ther 2019; 17:286-300. [PMID: 29173171 DOI: 10.2174/1566523217666171121164132] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 03/11/2017] [Accepted: 11/15/2017] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Genome editing using CRISPR/Cas9 has advanced very rapidly in its scope, versatility and ease of use. Zebrafish (Danio rerio) has been one of the vertebrate model species where CRISPR/Cas9 has been applied very extensively for many different purposes and with great success. In particular, disease modeling in zebrafish is useful for testing specific gene variants for pathogenicity in a preclinical setting. Here we describe multiple advances in diverse species and systems that can improve genome editing in zebrafish. OBJECTIVE To achieve temporal and spatial precision of genome editing, many new technologies can be applied in zebrafish such as artificial transcription factors, drug-inducible or optogenetically-driven expression of Cas9, or chemically-inducible activation of Cas9. Moreover, chemically- or optogenetically- inducible reconstitution of dead Cas9 (catalytically inactive, dCas9) can enable spatiotemporal control of gene regulation. In addition to controlling where and when genome editing occurs, using oligonucleotides allows for the introduction (knock-in) of precise modifications of the genome. CONCLUSION We review recent trends to improve the precision and efficiency of oligo-based point mutation knock-ins and discuss how these improvements can apply to work in zebrafish. Similarly to how chemical mutagenesis enabled the first genetic screens in zebrafish, multiplexed sgRNA libraries and Cas9 can enable the next revolutionary transition in how genetic screens are performed in this species. We discuss the first examples and prospects of approaches using sgRNAs as specific and effective mutagens. Moreover, we have reviewed methods aimed at measuring the phenotypes of single cells after their mutagenic perturbation with vectors encoding individual sgRNAs. These methods can range from different cell-based reporters to single-cell RNA sequencing and can serve as great tools for high-throughput genetic screens.
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Affiliation(s)
- Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lucia Caceres
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
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13
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Kopton RA, Baillie JS, Rafferty SA, Moss R, Zgierski-Johnston CM, Prykhozhij SV, Stoyek MR, Smith FM, Kohl P, Quinn TA, Schneider-Warme F. Cardiac Electrophysiological Effects of Light-Activated Chloride Channels. Front Physiol 2018; 9:1806. [PMID: 30618818 PMCID: PMC6304430 DOI: 10.3389/fphys.2018.01806] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/30/2018] [Indexed: 12/17/2022] Open
Abstract
During the last decade, optogenetics has emerged as a paradigm-shifting technique to monitor and steer the behavior of specific cell types in excitable tissues, including the heart. Activation of cation-conducting channelrhodopsins (ChR) leads to membrane depolarization, allowing one to effectively trigger action potentials (AP) in cardiomyocytes. In contrast, the quest for optogenetic tools for hyperpolarization-induced inhibition of AP generation has remained challenging. The green-light activated ChR from Guillardia theta (GtACR1) mediates Cl--driven photocurrents that have been shown to silence AP generation in different types of neurons. It has been suggested, therefore, to be a suitable tool for inhibition of cardiomyocyte activity. Using single-cell electrophysiological recordings and contraction tracking, as well as intracellular microelectrode recordings and in vivo optical recordings of whole hearts, we find that GtACR1 activation by prolonged illumination arrests cardiac cells in a depolarized state, thus inhibiting re-excitation. In line with this, GtACR1 activation by transient light pulses elicits AP in rabbit isolated cardiomyocytes and in spontaneously beating intact hearts of zebrafish. Our results show that GtACR1 inhibition of AP generation is caused by cell depolarization. While this does not address the need for optogenetic silencing through physiological means (i.e., hyperpolarization), GtACR1 is a potentially attractive tool for activating cardiomyocytes by transient light-induced depolarization.
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Affiliation(s)
- Ramona A Kopton
- Institute for Experimental Cardiovascular Medicine, University Heart Centre Freiburg-Bad Krozingen Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine University of Freiburg, Freiburg, Germany.,Faculty of Biology University of Freiburg, Freiburg, Germany
| | - Jonathan S Baillie
- Department of Physiology and Biophysics, Dalhousie University Halifax, NS, Canada
| | - Sara A Rafferty
- Department of Physiology and Biophysics, Dalhousie University Halifax, NS, Canada
| | - Robin Moss
- Institute for Experimental Cardiovascular Medicine, University Heart Centre Freiburg-Bad Krozingen Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine University of Freiburg, Freiburg, Germany
| | - Callum M Zgierski-Johnston
- Institute for Experimental Cardiovascular Medicine, University Heart Centre Freiburg-Bad Krozingen Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine University of Freiburg, Freiburg, Germany
| | | | - Matthew R Stoyek
- Department of Physiology and Biophysics, Dalhousie University Halifax, NS, Canada
| | - Frank M Smith
- Department of Medical Neuroscience, Dalhousie University Halifax, NS, Canada
| | - Peter Kohl
- Institute for Experimental Cardiovascular Medicine, University Heart Centre Freiburg-Bad Krozingen Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine University of Freiburg, Freiburg, Germany
| | - T Alexander Quinn
- Department of Physiology and Biophysics, Dalhousie University Halifax, NS, Canada.,School of Biomedical Engineering, Dalhousie University Halifax, NS, Canada
| | - Franziska Schneider-Warme
- Institute for Experimental Cardiovascular Medicine, University Heart Centre Freiburg-Bad Krozingen Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine University of Freiburg, Freiburg, Germany
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14
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Abstract
The zebrafish is an increasingly popular model organism for human genetic disease research. CRISPR/Cas9-based approaches are currently used for multiple gene-editing purposes in zebrafish, but few studies have developed reliable ways to introduce precise mutations. Point mutation knock-in using CRISPR/Cas9 and single-stranded oligodeoxynucleotides (ssODNs) is currently the most promising technology for this purpose. Despite some progress in applying this technique to zebrafish, there is still a great need for improvements in terms of its efficiency, optimal design of sgRNA and ssODNs and broader applicability. The papers discussed in this Editorial provide excellent case studies on identifying problems inherent in the mutation knock-in technique, quantifying these issues and proposing strategies to overcome them. These reports also illustrate how the procedures for introducing specific mutations can be straightforward, such that ssODNs with only the target mutation are sufficient for generating the intended knock-in animals. Two of the studies also develop interesting point mutant knock-in models for cardiac diseases, validating the translational relevance of generating knock-in mutations and opening the door to many possibilities for their further study.
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Affiliation(s)
- Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada .,Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada.,Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
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15
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Prykhozhij SV, Fuller C, Steele SL, Veinotte CJ, Razaghi B, Robitaille JM, McMaster CR, Shlien A, Malkin D, Berman JN. Optimized knock-in of point mutations in zebrafish using CRISPR/Cas9. Nucleic Acids Res 2018; 46:e102. [PMID: 29905858 PMCID: PMC6158492 DOI: 10.1093/nar/gky512 10.1093/nar/gky674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/28/2018] [Accepted: 05/23/2018] [Indexed: 01/19/2024] Open
Abstract
We have optimized point mutation knock-ins into zebrafish genomic sites using clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 reagents and single-stranded oligodeoxynucleotides. The efficiency of knock-ins was assessed by a novel application of allele-specific polymerase chain reaction and confirmed by high-throughput sequencing. Anti-sense asymmetric oligo design was found to be the most successful optimization strategy. However, cut site proximity to the mutation and phosphorothioate oligo modifications also greatly improved knock-in efficiency. A previously unrecognized risk of off-target trans knock-ins was identified that we obviated through the development of a workflow for correct knock-in detection. Together these strategies greatly facilitate the study of human genetic diseases in zebrafish, with additional applicability to enhance CRISPR-based approaches in other animal model systems.
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Affiliation(s)
- Sergey V Prykhozhij
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Charlotte Fuller
- Michael G. DeGroote School of Medicine, McMaster University,Hamilton, ON, L8S4L8, Canada
| | | | - Chansey J Veinotte
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Babak Razaghi
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Johane M Robitaille
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Christopher R McMaster
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Adam Shlien
- Departments of Pediatrics and Medical Biophysics, University of Toronto, Toronto, ON, M5G 1X8, Canada
| | - David Malkin
- Departments of Pediatrics and Medical Biophysics, University of Toronto, Toronto, ON, M5G 1X8, Canada
| | - Jason N Berman
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
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16
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Prykhozhij SV, Fuller C, Steele SL, Veinotte CJ, Razaghi B, Robitaille JM, McMaster CR, Shlien A, Malkin D, Berman JN. Optimized knock-in of point mutations in zebrafish using CRISPR/Cas9. Nucleic Acids Res 2018; 46:9252. [PMID: 30053067 PMCID: PMC6158599 DOI: 10.1093/nar/gky674] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Sergey V Prykhozhij
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Charlotte Fuller
- Michael G. DeGroote School of Medicine, McMaster University,Hamilton, ON, L8S4L8, Canada
| | | | - Chansey J Veinotte
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Babak Razaghi
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Johane M Robitaille
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Christopher R McMaster
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Adam Shlien
- Departments of Pediatrics and Medical Biophysics, University of Toronto, Toronto, ON, M5G 1X8, Canada
| | - David Malkin
- Departments of Pediatrics and Medical Biophysics, University of Toronto, Toronto, ON, M5G 1X8, Canada
| | - Jason N Berman
- Departments of Pediatrics, Microbiology & Immunology, and Pathology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
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17
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Cloney K, Steele SL, Stoyek MR, Croll RP, Smith FM, Prykhozhij SV, Brown MM, Midgen C, Blake K, Berman JN. Etiology and functional validation of gastrointestinal motility dysfunction in a zebrafish model of CHARGE syndrome. FEBS J 2018; 285:2125-2140. [PMID: 29660852 DOI: 10.1111/febs.14473] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 03/17/2018] [Accepted: 04/09/2018] [Indexed: 12/21/2022]
Abstract
CHARGE syndrome is linked to autosomal-dominant mutations in the CHD7 gene and results in a number of physiological and structural abnormalities, including heart defects, hearing and vision loss, and gastrointestinal (GI) problems. Of these challenges, GI problems have a profound impact throughout an individual's life, resulting in increased morbidity and mortality. A homolog of CHD7 has been identified in the zebrafish, the loss of which recapitulates many of the features of the human disease. Using a morpholino chd7 knockdown model complemented by a chd7 null mutant zebrafish line, we examined GI structure, innervation, and motility in larval zebrafish. Loss of chd7 resulted in physically smaller GI tracts with normal epithelial and muscular histology, but decreased and disorganized vagal projections, particularly in the foregut. chd7 morphant larvae had significantly less ability to empty their GI tract of gavaged fluorescent beads, and this condition was only minimally improved by the prokinetic agents, domperidone and erythromycin, in keeping with mixed responses to these agents in patients with CHARGE syndrome. The conserved genetics and transparency of the zebrafish have provided new insights into the consequences of chd7 gene dysfunction on the GI system and cranial nerve patterning. These findings highlight the opportunity of the zebrafish to serve as a preclinical model for studying compounds that may improve GI motility in individuals with CHARGE syndrome.
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Affiliation(s)
- Kellie Cloney
- Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, Canada
| | - Matthew R Stoyek
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Canada
| | - Roger P Croll
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Canada
| | - Frank M Smith
- Department of Medical Neuroscience, Dalhousie University, Halifax, Canada
| | | | - Mary M Brown
- Departments of Pediatrics and Obstetrics and Gynaecology, Dalhousie University, Halifax, Canada
| | - Craig Midgen
- Department of Pathology, Dalhousie University, Halifax, Canada
| | - Kim Blake
- Faculty of Medicine, Dalhousie University, Halifax, Canada.,Department of Pediatrics, Dalhousie University, Halifax, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, Canada.,Department of Pathology, Dalhousie University, Halifax, Canada.,Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
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18
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Razaghi B, Steele SL, Prykhozhij SV, Stoyek MR, Hill JA, Cooper MD, McDonald L, Lin W, Daugaard M, Crapoulet N, Chacko S, Lewis SM, Scott IC, Sorensen PHB, Berman JN. hace1 Influences zebrafish cardiac development via ROS-dependent mechanisms. Dev Dyn 2017; 247:289-303. [PMID: 29024245 DOI: 10.1002/dvdy.24600] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/23/2017] [Accepted: 09/15/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In this study, we reveal a previously undescribed role of the HACE1 (HECT domain and Ankyrin repeat Containing E3 ubiquitin-protein ligase 1) tumor suppressor protein in normal vertebrate heart development using the zebrafish (Danio rerio) model. We examined the link between the cardiac phenotypes associated with hace1 loss of function to the expression of the Rho small family GTPase, rac1, which is a known target of HACE1 and promotes ROS production via its interaction with NADPH oxidase holoenzymes. RESULTS We demonstrate that loss of hace1 in zebrafish via morpholino knockdown results in cardiac deformities, specifically a looping defect, where the heart is either tubular or "inverted". Whole-mount in situ hybridization of cardiac markers shows distinct abnormalities in ventricular morphology and atrioventricular valve formation in the hearts of these morphants, as well as increased expression of rac1. Importantly, this phenotype appears to be directly related to Nox enzyme-dependent ROS production, as both genetic inhibition by nox1 and nox2 morpholinos or pharmacologic rescue using ROS scavenging agents restores normal cardiac structure. CONCLUSIONS Our study demonstrates that HACE1 is critical in the normal development and proper function of the vertebrate heart via a ROS-dependent mechanism. Developmental Dynamics 247:289-303, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Babak Razaghi
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew R Stoyek
- Department of Physiology & Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jessica A Hill
- Department of Marine Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew D Cooper
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lindsay McDonald
- Department of Emergency Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - William Lin
- Undergraduate Program, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mads Daugaard
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.,Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Simi Chacko
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Ian C Scott
- Department of Molecular Genetics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Poul H B Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada.,IWK Health Centre, Halifax, Nova Scotia, Canada
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Prykhozhij SV, Steele SL, Razaghi B, Berman JN. A rapid and effective method for screening, sequencing and reporter verification of engineered frameshift mutations in zebrafish. Dis Model Mech 2017; 10:811-822. [PMID: 28280001 PMCID: PMC5483001 DOI: 10.1242/dmm.026765] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 03/03/2017] [Indexed: 12/30/2022] Open
Abstract
Clustered regularly interspaced palindromic repeats (CRISPR)/Cas-based adaptive immunity against pathogens in bacteria has been adapted for genome editing and applied in zebrafish (Danio rerio) to generate frameshift mutations in protein-coding genes. Although there are methods to detect, quantify and sequence CRISPR/Cas9-induced mutations, identifying mutations in F1 heterozygous fish remains challenging. Additionally, sequencing a mutation and assuming that it causes a frameshift does not prove causality because of possible alternative translation start sites and potential effects of mutations on splicing. This problem is compounded by the relatively few antibodies available for zebrafish proteins, limiting validation at the protein level. To address these issues, we developed a detailed protocol to screen F1 mutation carriers, and clone and sequence identified mutations. In order to verify that mutations actually cause frameshifts, we created a fluorescent reporter system that can detect frameshift efficiency based on the cloning of wild-type and mutant cDNA fragments and their expression levels. As proof of principle, we applied this strategy to three CRISPR/Cas9-induced mutations in pycr1a, chd7 and hace1 genes. An insertion of seven nucleotides in pycr1a resulted in the first reported observation of exon skipping by CRISPR/Cas9-induced mutations in zebrafish. However, of these three mutant genes, the fluorescent reporter revealed effective frameshifting exclusively in the case of a two-nucleotide deletion in chd7, suggesting activity of alternative translation sites in the other two mutants even though pycr1a exon-skipping deletion is likely to be deleterious. This article provides a protocol for characterizing frameshift mutations in zebrafish, and highlights the importance of checking mutations at the mRNA level and verifying their effects on translation by fluorescent reporters when antibody detection of protein loss is not possible.
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Affiliation(s)
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8
| | - Babak Razaghi
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada B3K 6R8 .,Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada B3H 4R2.,Department of Pathology, Dalhousie University, Halifax, NS, Canada B3H4R2
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Ceasar SA, Rajan V, Prykhozhij SV, Berman JN, Ignacimuthu S. Insert, remove or replace: A highly advanced genome editing system using CRISPR/Cas9. Biochim Biophys Acta 2016; 1863:2333-44. [PMID: 27350235 DOI: 10.1016/j.bbamcr.2016.06.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 12/26/2022]
Abstract
The clustered, regularly interspaced, short palindromic repeat (CRISPR) and CRISPR associated protein 9 (Cas9) system discovered as an adaptive immunity mechanism in prokaryotes has emerged as the most popular tool for the precise alterations of the genomes of diverse species. CRISPR/Cas9 system has taken the world of genome editing by storm in recent years. Its popularity as a tool for altering genomes is due to the ability of Cas9 protein to cause double-stranded breaks in DNA after binding with short guide RNA molecules, which can be produced with dramatically less effort and expense than required for production of transcription-activator like effector nucleases (TALEN) and zinc-finger nucleases (ZFN). This system has been exploited in many species from prokaryotes to higher animals including human cells as evidenced by the literature showing increasing sophistication and ease of CRISPR/Cas9 as well as increasing species variety where it is applicable. This technology is poised to solve several complex molecular biology problems faced in life science research including cancer research. In this review, we highlight the recent advancements in CRISPR/Cas9 system in editing genomes of prokaryotes, fungi, plants and animals and provide details on software tools available for convenient design of CRISPR/Cas9 targeting plasmids. We also discuss the future prospects of this advanced molecular technology.
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Affiliation(s)
- S Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India; Centre for Plant Sciences and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Vinothkumar Rajan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason N Berman
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada; Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - S Ignacimuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India; International Scientific Partnership Program, Deanship of Scientific Research, College of Science, King Saud University, Riyadh, Saudi Arabia.
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21
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Telorac J, Prykhozhij SV, Schöne S, Meierhofer D, Sauer S, Thomas-Chollier M, Meijsing SH. Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements. Nucleic Acids Res 2016; 44:6142-56. [PMID: 27016732 PMCID: PMC5291246 DOI: 10.1093/nar/gkw203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 11/06/2015] [Accepted: 03/16/2016] [Indexed: 01/13/2023] Open
Abstract
Out of the myriad of potential DNA binding sites of the glucocorticoid receptor (GR) found in the human genome, only a cell-type specific minority is actually bound, indicating that the presence of a recognition sequence alone is insufficient to specify where GR binds. Cooperative interactions with other transcription factors (TFs) are known to contribute to binding specificity. Here, we reasoned that sequence signals preventing GR recruitment to certain loci provide an alternative means to confer specificity. Motif analyses uncovered candidate Negative Regulatory Sequences (NRSs) that interfere with genomic GR binding. Subsequent functional analyses demonstrated that NRSs indeed prevent GR binding to nearby response elements. We show that NRS activity is conserved across species, found in most tissues and that they also interfere with the genomic binding of other TFs. Interestingly, the effects of NRSs appear not to be a simple consequence of changes in chromatin accessibility. Instead, we find that NRSs interact with proteins found at sub-nuclear structures called paraspeckles and that these proteins might mediate the repressive effects of NRSs. Together, our studies suggest that the joint influence of positive and negative sequence signals partition the genome into regions where GR can bind and those where it cannot.
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Affiliation(s)
- Jonas Telorac
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - Sergey V Prykhozhij
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - Sascha Sauer
- CU Systems Medicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Morgane Thomas-Chollier
- Computational Systems Biology, Institut de Biologie de l'Ecole Normale, Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
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Prykhozhij SV, Rajan V, Berman JN. A Guide to Computational Tools and Design Strategies for Genome Editing Experiments in Zebrafish Using CRISPR/Cas9. Zebrafish 2016; 13:70-3. [DOI: 10.1089/zeb.2015.1158] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
| | - Vinothkumar Rajan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason N. Berman
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
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Fernández-Murray JP, Prykhozhij SV, Dufay JN, Steele SL, Gaston D, Nasrallah GK, Coombs AJ, Liwski RS, Fernandez CV, Berman JN, McMaster CR. Glycine and Folate Ameliorate Models of Congenital Sideroblastic Anemia. PLoS Genet 2016; 12:e1005783. [PMID: 26821380 PMCID: PMC4731144 DOI: 10.1371/journal.pgen.1005783] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/11/2015] [Indexed: 01/25/2023] Open
Abstract
Sideroblastic anemias are acquired or inherited anemias that result in a decreased ability to synthesize hemoglobin in red blood cells and result in the presence of iron deposits in the mitochondria of red blood cell precursors. A common subtype of congenital sideroblastic anemia is due to autosomal recessive mutations in the SLC25A38 gene. The current treatment for SLC25A38 congenital sideroblastic anemia is chronic blood transfusion coupled with iron chelation. The function of SLC25A38 is not known. Here we report that the SLC25A38 protein, and its yeast homolog Hem25, are mitochondrial glycine transporters required for the initiation of heme synthesis. To do so, we took advantage of the fact that mitochondrial glycine has several roles beyond the synthesis of heme, including the synthesis of folate derivatives through the glycine cleavage system. The data were consistent with Hem25 not being the sole mitochondrial glycine importer, and we identify a second SLC25 family member Ymc1, as a potential secondary mitochondrial glycine importer. Based on these findings, we observed that high levels of exogenous glycine, or 5-aminolevulinic acid (5-Ala) a metabolite downstream of Hem25 in heme biosynthetic pathway, were able to restore heme levels to normal in yeast cells lacking Hem25 function. While neither glycine nor 5-Ala could ameliorate SLC25A38 congenital sideroblastic anemia in a zebrafish model, we determined that the addition of folate with glycine was able to restore hemoglobin levels. This difference is likely due to the fact that yeast can synthesize folate, whereas in zebrafish folate is an essential vitamin that must be obtained exogenously. Given the tolerability of glycine and folate in humans, this study points to a potential novel treatment for SLC25A38 congenital sideroblastic anemia. Mutations in the SLC25A38 gene cause an inherited anemia. In this study we determine that the function of SLC25A38, and its yeast homolgue Hem25, is to act as mitochondrial glycine importers providing a molecular explanation for why patients with SLC25A38 mutations have low hemoglobin levels and become anemic. Using this new knowledge, we go on to determine that supplementation with glycine and folate restore hemoglobin levels in a zebrafish model of the disease pointing to a potentially new, safe, and cost effective treatment for SLC25A38 congenital sideroblastic anemia.
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Affiliation(s)
| | - Sergey V. Prykhozhij
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Canada
| | - J. Noelia Dufay
- Department of Pharmacology, Dalhousie University, Halifax, Canada
| | - Shelby L. Steele
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Canada
| | - Daniel Gaston
- Department of Pathology, Dalhousie University, Halifax, Canada
| | | | - Andrew J. Coombs
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Canada
| | | | - Conrad V. Fernandez
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Canada
| | - Jason N. Berman
- Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Canada
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24
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Prykhozhij SV, Rajan V, Gaston D, Berman JN. CRISPR multitargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences. PLoS One 2015; 10:e0119372. [PMID: 25742428 PMCID: PMC4351176 DOI: 10.1371/journal.pone.0119372] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/30/2015] [Indexed: 01/16/2023] Open
Abstract
Genome engineering has been revolutionized by the discovery of clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated system genes (Cas) in bacteria. The type IIB Streptococcus pyogenes CRISPR/Cas9 system functions in many species and additional types of CRISPR/Cas systems are under development. In the type II system, expression of CRISPR single guide RNA (sgRNA) targeting a defined sequence and Cas9 generates a sequence-specific nuclease inducing small deletions or insertions. Moreover, knock-in of large DNA inserts has been shown at the sites targeted by sgRNAs and Cas9. Several tools are available for designing sgRNAs that target unique locations in the genome. However, the ability to find sgRNA targets common to several similar sequences or, by contrast, unique to each of these sequences, would also be advantageous. To provide such a tool for several types of CRISPR/Cas system and many species, we developed the CRISPR MultiTargeter software. Similar DNA sequences in question are duplicated genes and sets of exons of different transcripts of a gene. Thus, we implemented a basic sgRNA target search of input sequences for single-sgRNA and two-sgRNA/Cas9 nickase targeting, as well as common and unique sgRNA target searches in 1) a set of input sequences; 2) a set of similar genes or transcripts; or 3) transcripts a single gene. We demonstrate potential uses of the program by identifying unique isoform-specific sgRNA sites in 71% of zebrafish alternative transcripts and common sgRNA target sites in approximately 40% of zebrafish duplicated gene pairs. The design of unique targets in alternative exons is helpful because it will facilitate functional genomic studies of transcript isoforms. Similarly, its application to duplicated genes may simplify multi-gene mutational targeting experiments. Overall, this program provides a unique interface that will enhance use of CRISPR/Cas technology.
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Affiliation(s)
| | - Vinothkumar Rajan
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel Gaston
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jason N. Berman
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
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Prykhozhij SV, Berman JN. The progress and promise of zebrafish as a model to study mast cells. Dev Comp Immunol 2014; 46:74-83. [PMID: 24508982 DOI: 10.1016/j.dci.2014.01.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/29/2014] [Accepted: 01/29/2014] [Indexed: 06/03/2023]
Abstract
Immunological and hematological research using the zebrafish (Danio rerio) has significantly advanced our understanding of blood lineage ontology, cellular functions and mechanisms, and provided opportunities for disease modeling. Mast cells are an immunological cell type involved in innate and adaptive immune systems, hypersensitivity reactions and cancer progression. The application of zebrafish to study mast cell biology exploits the developmental and imaging opportunities inherent in this model system to enable detailed genetic and molecular studies of this lineage outside of traditional mammalian models. In this review, we first place the importance of mast cell research in zebrafish into the context of comparative studies of mast cells in other fish species and highlight its advantages due to superior experimental tractability and direct visualization in transparent embryos. We discuss current and future tools for mast cell research in zebrafish and the notable results of using zebrafish for understanding mast cell fate determination and our development of a systemic mastocytosis model.
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Affiliation(s)
- Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, NS B3K 6R8, Canada.
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26
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Balci TB, Prykhozhij SV, Teh EM, Da'as SI, McBride E, Liwski R, Chute IC, Leger D, Lewis SM, Berman JN. A transgenic zebrafish model expressing KIT-D816V recapitulates features of aggressive systemic mastocytosis. Br J Haematol 2014; 167:48-61. [PMID: 24989799 DOI: 10.1111/bjh.12999] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/20/2014] [Indexed: 12/12/2022]
Abstract
Systemic mastocytosis (SM) is a rare myeloproliferative disease without curative therapy. Despite clinical variability, the majority of patients harbour a KIT-D816V mutation, but efforts to inhibit mutant KIT with tyrosine kinase inhibitors have been unsatisfactory, indicating a need for new preclinical approaches to identify alternative targets and novel therapies in this disease. Murine models to date have been limited and do not fully recapitulate the most aggressive forms of SM. We describe the generation of a transgenic zebrafish model expressing the human KIT-D816V mutation. Adult fish demonstrate a myeloproliferative disease phenotype, including features of aggressive SM in haematopoeitic tissues and high expression levels of endopeptidases, consistent with SM patients. Transgenic embryos demonstrate a cell-cycle phenotype with corresponding expression changes in genes associated with DNA maintenance and repair, such as reduced dnmt1. In addition, epcam was consistently downregulated in both transgenic adults and embryos. Decreased embryonic epcam expression was associated with reduced neuromast numbers, providing a robust in vivo phenotypic readout for chemical screening in KIT-D816V-induced disease. This study represents the first zebrafish model of a mast cell disease with an aggressive adult phenotype and embryonic markers that could be exploited to screen for novel agents in SM.
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Affiliation(s)
- Tugce B Balci
- Department of Pediatrics, IWK Health Centre, Halifax, NS, Canada; Department of Medical Genetics, University of Ottawa, Ottawa, ON, Canada
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Steele SL, Prykhozhij SV, Berman JN. Zebrafish as a model system for mitochondrial biology and diseases. Transl Res 2014; 163:79-98. [PMID: 24055494 DOI: 10.1016/j.trsl.2013.08.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/21/2013] [Accepted: 08/25/2013] [Indexed: 12/19/2022]
Abstract
Animal models for studying human disease are essential to the continuing evolution of medicine. Rodent models are attractive for the obvious similarities in development and genetic makeup compared with humans, but have cost and technical limitations. The zebrafish (Danio rerio) represents an ideal alternative vertebrate model of human disease because of its high conservation of genetic information and physiological processes, inexpensive maintenance, and optical clarity facilitating direct observation. This review highlights recent advances in understanding genetic disease states associated with the dynamic organelle, the mitochondrion, using the zebrafish. Mitochondrial diseases that have been replicated in the zebrafish include those affecting the nervous and cardiovascular systems, as well as red blood cell function. Gene silencing techniques, including morpholino knockdown and transcription activator-like (TAL)-effector endonucleases, have been exploited to demonstrate how loss of function can induce human disease-like states in zebrafish. Moreover, modeling mitochondrial diseases has been facilitated greatly by the creation of transgenic fish with fluorescently labeled mitochondria for in vivo visualization of these structures. In addition, behavioral assays have been developed to examine changes in motor activity and sensory responses, particularly in larval stages. Zebrafish are poised to advance our understanding of the pathogenesis of human mitochondrial diseases beyond the current state of knowledge and provide a key tool in the development of novel therapeutic approaches to treat these conditions.
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Affiliation(s)
- Shelby L Steele
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, Nova Scotia, Canada
| | - Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, Nova Scotia, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, IWK Health Centre, Halifax, Nova Scotia, Canada.
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Prykhozhij SV, Marsico A, Meijsing SH. Zebrafish Expression Ontology of Gene Sets (ZEOGS): a tool to analyze enrichment of zebrafish anatomical terms in large gene sets. Zebrafish 2013; 10:303-15. [PMID: 23656298 DOI: 10.1089/zeb.2012.0865] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The zebrafish (Danio rerio) is an established model organism for developmental and biomedical research. It is frequently used for high-throughput functional genomics experiments, such as genome-wide gene expression measurements, to systematically analyze molecular mechanisms. However, the use of whole embryos or larvae in such experiments leads to a loss of the spatial information. To address this problem, we have developed a tool called Zebrafish Expression Ontology of Gene Sets (ZEOGS) to assess the enrichment of anatomical terms in large gene sets. ZEOGS uses gene expression pattern data from several sources: first, in situ hybridization experiments from the Zebrafish Model Organism Database (ZFIN); second, it uses the Zebrafish Anatomical Ontology, a controlled vocabulary that describes connected anatomical structures; and third, the available connections between expression patterns and anatomical terms contained in ZFIN. Upon input of a gene set, ZEOGS determines which anatomical structures are overrepresented in the input gene set. ZEOGS allows one for the first time to look at groups of genes and to describe them in terms of shared anatomical structures. To establish ZEOGS, we first tested it on random gene selections and on two public microarray datasets with known tissue-specific gene expression changes. These tests showed that ZEOGS could reliably identify the tissues affected, whereas only very few enriched terms to none were found in the random gene sets. Next we applied ZEOGS to microarray datasets of 24 and 72 h postfertilization zebrafish embryos treated with beclomethasone, a potent glucocorticoid. This analysis resulted in the identification of several anatomical terms related to glucocorticoid-responsive tissues, some of which were stage-specific. Our studies highlight the ability of ZEOGS to extract spatial information from datasets derived from whole embryos, indicating that ZEOGS could be a useful tool to automatically analyze gene expression pattern features of any large zebrafish gene set.
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Prykhozhij SV. In the absence of Sonic hedgehog, p53 induces apoptosis and inhibits retinal cell proliferation, cell-cycle exit and differentiation in zebrafish. PLoS One 2010; 5:e13549. [PMID: 21042410 PMCID: PMC2958845 DOI: 10.1371/journal.pone.0013549] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Accepted: 09/30/2010] [Indexed: 11/25/2022] Open
Abstract
Background Sonic hedgehog (Shh) signaling regulates cell proliferation during vertebrate development via induction of cell-cycle regulator gene expression or activation of other signalling pathways, prevents cell death by an as yet unclear mechanism and is required for differentiation of retinal cell types. Thus, an unsolved question is how the same signalling molecule can regulate such distinct cell processes as proliferation, cell survival and differentiation. Methodology/Principal Findings Analysis of the zebrafish shh−/− mutant revealed that in this context p53 mediates elevated apoptosis during nervous system and retina development and interferes with retinal proliferation and differentiation. While in shh−/− mutants there is activation of p53 target genes and p53-mediated apoptosis, an increase in Hedgehog (Hh) signalling by over-expression of dominant-negative Protein Kinase A strongly decreased p53 target gene expression and apoptosis levels in shh−/− mutants. Using a novel p53 reporter transgene, I confirm that p53 is active in tissues that require Shh for cell survival. Proliferation assays revealed that loss of p53 can rescue normal cell-cycle exit and the mitotic indices in the shh−/− mutant retina at 24, 36 and 48 hpf. Moreover, generation of amacrine cells and photoreceptors was strongly enhanced in the double p53−/−shh−/− mutant retina suggesting the effect of p53 on retinal differentiation. Conclusions Loss of Shh signalling leads to the p53-dependent apoptosis in the developing nervous system and retina. Moreover, Shh-mediated control of p53 activity is required for proliferation and cell cycle exit of retinal cells as well as differentiation of amacrine cells and photoreceptors.
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Affiliation(s)
- Sergey V Prykhozhij
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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Prykhozhij SV, Neumann CJ. Distinct roles of Shh and Fgf signaling in regulating cell proliferation during zebrafish pectoral fin development. BMC Dev Biol 2008; 8:91. [PMID: 18811955 PMCID: PMC2562996 DOI: 10.1186/1471-213x-8-91] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 09/23/2008] [Indexed: 11/13/2022]
Abstract
Background Cell proliferation in multicellular organisms must be coordinated with pattern formation. The major signaling pathways directing pattern formation in the vertebrate limb are well characterized, and we have therefore chosen this organ to examine the interaction between proliferation and patterning. Two important signals for limb development are members of the Hedgehog (Hh) and Fibroblast Growth Factor (Fgf) families of secreted signaling proteins. Sonic hedgehog (Shh) directs pattern formation along the anterior/posterior axis of the limb, whereas several Fgfs in combination direct pattern formation along the proximal/distal axis of the limb. Results We used the genetic and pharmacological amenability of the zebrafish model system to dissect the relative importance of Shh and Fgf signaling in regulating proliferation during development of the pectoral fin buds. In zebrafish mutants disrupting the shh gene, proliferation in the pectoral fin buds is initially normal, but later is strongly reduced. Correlating with this reduction, Fgf signaling is normal at early stages, but is later lost in shh mutants. Furthermore, pharmacological inhibition of Hh signaling for short periods has little effect on either Fgf signaling, or on expression of G1- and S-phase cell-cycle genes, whereas long periods of inhibition lead to the downregulation of both. In contrast, even short periods of pharmacological inhibition of Fgf signaling lead to strong disruption of proliferation in the fin buds, without affecting Shh signaling. To directly test the ability of Fgf signaling to regulate proliferation in the absence of Shh signaling, we implanted beads soaked with Fgf protein into shh mutant fin buds. We find that Fgf-soaked beads rescue proliferation in the pectoral find buds of shh mutants, indicating that Fgf signaling is sufficient to direct proliferation in zebrafish fin buds in the absence of Shh. Conclusion Previous studies have shown that both Shh and Fgf signaling are crucial for outgrowth of the vertebrate limb. The results presented here show that the role of Shh in this process is indirect, and is mediated by its effect on Fgf signaling. By contrast, the activity of the Fgf pathway affects proliferation directly and independently of its effect on Shh. These results show that Fgf signaling is of primary importance in directing outgrowth of the limb bud, and clarify the role of the Shh-Fgf feedback loop in regulating proliferation.
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Affiliation(s)
- Sergey V Prykhozhij
- Developmental Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany.
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