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El Mir J, Nasrallah A, Thézé N, Cario M, Fayyad-Kazan H, Thiébaud P, Rezvani HR. Xenopus as a model system for studying pigmentation and pigmentary disorders. Pigment Cell Melanoma Res 2024. [PMID: 38849973 DOI: 10.1111/pcmr.13178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/17/2024] [Accepted: 05/24/2024] [Indexed: 06/09/2024]
Abstract
Human pigmentary disorders encompass a broad spectrum of phenotypic changes arising from disruptions in various stages of melanocyte formation, the melanogenesis process, or the transfer of pigment from melanocytes to keratinocytes. A large number of pigmentation genes associated with pigmentary disorders have been identified, many of them awaiting in vivo confirmation. A more comprehensive understanding of the molecular basis of pigmentary disorders requires a vertebrate animal model where changes in pigmentation are easily observable in vivo and can be combined to genomic modifications and gain/loss-of-function tools. Here we present the amphibian Xenopus with its unique features that fulfill these requirements. Changes in pigmentation are particularly easy to score in Xenopus embryos, allowing whole-organism based phenotypic screening. The development and behavior of Xenopus melanocytes closely mimic those observed in mammals. Interestingly, both Xenopus and mammalian skins exhibit comparable reactions to ultraviolet radiation. This review highlights how Xenopus constitutes an alternative and complementary model to the more commonly used mouse and zebrafish, contributing to the advancement of knowledge in melanocyte cell biology and related diseases.
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Affiliation(s)
- Joudi El Mir
- University of Bordeaux, Inserm, BRIC, UMR 1312, Bordeaux, France
| | - Ali Nasrallah
- University of Bordeaux, Inserm, BRIC, UMR 1312, Bordeaux, France
| | - Nadine Thézé
- University of Bordeaux, Inserm, BRIC, UMR 1312, Bordeaux, France
| | - Muriel Cario
- University of Bordeaux, Inserm, BRIC, UMR 1312, Bordeaux, France
- Aquiderm, University of Bordeaux, Bordeaux, France
| | - Hussein Fayyad-Kazan
- Laboratory of Cancer Biology and Molecular Immunology, Lebanese University, Hadath, Lebanon
| | - Pierre Thiébaud
- University of Bordeaux, Inserm, BRIC, UMR 1312, Bordeaux, France
| | - Hamid-Reza Rezvani
- University of Bordeaux, Inserm, BRIC, UMR 1312, Bordeaux, France
- Aquiderm, University of Bordeaux, Bordeaux, France
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2
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McCluskey KE, Stovell KM, Law K, Kostyanovskaya E, Schmidt J, Exner CRT, Dea J, Brimble E, State MW, Willsey AJ, Willsey HR. Autism gene variants disrupt enteric neuron migration and cause gastrointestinal dysmotility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.593642. [PMID: 38854068 PMCID: PMC11160671 DOI: 10.1101/2024.05.28.593642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The comorbidity of autism spectrum disorders and severe gastrointestinal symptoms is well-established, yet the molecular underpinnings remain unknown. The identification of high-confidence large-effect autism risk genes offers the opportunity to identify convergent, underlying biology by studying these genes in the context of the gastrointestinal system. Here we show that the expression of these genes is enriched in human prenatal gut neurons as well as their migratory progenitors, suggesting that the development and/or function of these neurons may be disrupted by autism-associated pathogenic variants, leading to gastrointestinal dysfunction. Here we document the prevalence of gastrointestinal issues in patients with large-effect variants in sixteen of these genes, highlighting dysmotility, consistent with potential enteric neuron dysfunction. Using the high-throughput diploid frog Xenopus tropicalis , we individually target five of these genes ( SYNGAP1, CHD8, SCN2A, CHD2 , and DYRK1A ) and observe disrupted enteric neuronal progenitor migration for each. More extensive analysis of DYRK1A reveals that perturbation causes gut dysmotility in vivo , which can be ameliorated by treatment with a selective serotonin reuptake inhibitor (escitalopram) or a serotonin receptor 6 agonist, identified by in vivo drug screening. This work suggests that atypical development of enteric neurons contributes to the gastrointestinal distress commonly seen in individuals with autism and that increasing serotonin signaling may be a productive therapeutic avenue.
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Willsey HR, Seaby EG, Godwin A, Ennis S, Guille M, Grainger RM. Modelling human genetic disorders in Xenopus tropicalis. Dis Model Mech 2024; 17:dmm050754. [PMID: 38832520 PMCID: PMC11179720 DOI: 10.1242/dmm.050754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Abstract
Recent progress in human disease genetics is leading to rapid advances in understanding pathobiological mechanisms. However, the sheer number of risk-conveying genetic variants being identified demands in vivo model systems that are amenable to functional analyses at scale. Here we provide a practical guide for using the diploid frog species Xenopus tropicalis to study many genes and variants to uncover conserved mechanisms of pathobiology relevant to human disease. We discuss key considerations in modelling human genetic disorders: genetic architecture, conservation, phenotyping strategy and rigour, as well as more complex topics, such as penetrance, expressivity, sex differences and current challenges in the field. As the patient-driven gene discovery field expands significantly, the cost-effective, rapid and higher throughput nature of Xenopus make it an essential member of the model organism armamentarium for understanding gene function in development and in relation to disease.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94518, USA
| | - Eleanor G Seaby
- Genomic Informatics Group, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Annie Godwin
- European Xenopus Resource Centre (EXRC), School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Sarah Ennis
- Genomic Informatics Group, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Matthew Guille
- European Xenopus Resource Centre (EXRC), School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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Wesselman HM, Arceri L, Nguyen TK, Lara CM, Wingert RA. Genetic mechanisms of multiciliated cell development: from fate choice to differentiation in zebrafish and other models. FEBS J 2023. [PMID: 37997009 DOI: 10.1111/febs.17012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 11/25/2023]
Abstract
Multiciliated cells (MCCS) form bundles of cilia and their activities are essential for the proper development and physiology of many organ systems. Not surprisingly, defects in MCCs have profound consequences and are associated with numerous disease states. Here, we discuss the current understanding of MCC formation, with a special focus on the genetic and molecular mechanisms of MCC fate choice and differentiation. Furthermore, we cast a spotlight on the use of zebrafish to study MCC ontogeny and several recent advances made in understanding MCCs using this vertebrate model to delineate mechanisms of MCC emergence in the developing kidney.
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Affiliation(s)
| | - Liana Arceri
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Thanh Khoa Nguyen
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Caroline M Lara
- Department of Biological Sciences, University of Notre Dame, IN, USA
| | - Rebecca A Wingert
- Department of Biological Sciences, University of Notre Dame, IN, USA
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5
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Edwards NA, Kashyap A, Warren A, Agricola ZN, Kenny AP, Shen Y, Chung WK, Zorn AM. Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in trachea-esophageal morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561909. [PMID: 37873300 PMCID: PMC10592723 DOI: 10.1101/2023.10.11.561909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Disruptions in foregut morphogenesis can result in life-threatening conditions where the trachea and esophagus fail to separate properly, such as esophageal atresia (EA) and tracheoesophageal fistulas (TEF). The developmental basis of these congenital anomalies is poorly understood, but recent genome sequencing reveals that de novo variants in intracellular trafficking genes are enriched in EA/TEF patients. Here we show that mutation of orthologous genes in Xenopus disrupts trachea-esophageal separation similar to EA/TEF patients. We show that the Rab11a recycling endosome pathway is required to localize Vangl-Celsr polarity complexes at the cell surface where opposite sides of the common foregut tube fuse. Partial loss of endosome trafficking or the Vangl/Celsr complex disrupts epithelial polarity and cell division orientation. Mutant cells accumulate at the fusion point, fail to downregulate cadherin, and do not separate into distinct trachea and esophagus. These data provide new insights into the mechanisms of congenital anomalies and general paradigms of tissue fusion during organogenesis.
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Hossain N, Igawa T, Suzuki M, Tazawa I, Nakao Y, Hayashi T, Suzuki N, Ogino H. Phenotype-genotype relationships in Xenopus sox9 crispants provide insights into campomelic dysplasia and vertebrate jaw evolution. Dev Growth Differ 2023; 65:481-497. [PMID: 37505799 DOI: 10.1111/dgd.12884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/29/2023]
Abstract
Since CRISPR-based genome editing technology works effectively in the diploid frog Xenopus tropicalis, a growing number of studies have successfully modeled human genetic diseases in this species. However, most of their targets were limited to non-syndromic diseases that exhibit abnormalities in a small fraction of tissues or organs in the body. This is likely because of the complexity of interpreting the phenotypic variations resulting from somatic mosaic mutations generated in the founder animals (crispants). In this study, we attempted to model the syndromic disease campomelic dysplasia (CD) by generating sox9 crispants in X. tropicalis. The resulting crispants failed to form neural crest cells at neurula stages and exhibited various combinations of jaw, gill, ear, heart, and gut defects at tadpole stages, recapitulating part of the syndromic phenotype of CD patients. Genotyping of the crispants with a variety of allelic series of mutations suggested that the heart and gut defects depend primarily on frame-shift mutations expected to be null, whereas the jaw, gill, and ear defects could be induced not only by such mutations but also by in-frame deletion mutations expected to delete part of the jawed vertebrate-specific domain from the encoded Sox9 protein. These results demonstrate that Xenopus crispants are useful for investigating the phenotype-genotype relationships behind syndromic diseases and examining the tissue-specific role of each functional domain within a single protein, providing novel insights into vertebrate jaw evolution.
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Affiliation(s)
- Nusrat Hossain
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Makoto Suzuki
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Ichiro Tazawa
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Yuta Nakao
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Nanoka Suzuki
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
| | - Hajime Ogino
- Amphibian Research Center, Hiroshima University, Hiroshima, Japan
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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Guille M, Grainger R. Genetics and Gene Editing Methods in Xenopus laevis and Xenopus tropicalis. Cold Spring Harb Protoc 2023; 2023:pdb.top107045. [PMID: 36283837 DOI: 10.1101/pdb.top107045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Our understanding of biological systems has for many years been heavily influenced by experimental approaches that exploit genetic methods. These include gain-of-function experiments that overexpress transgenes or ectopically express injected RNA and loss-of-function experiments that knock out genes or knock down RNAs. Here, we review how these methods have been applied in Xenopus frogs and introduce a variety of protocols for genetic manipulation of Xenopus laevis and Xenopus tropicalis.
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Affiliation(s)
- Matthew Guille
- European Xenopus Resource Centre, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2UP, United Kingdom
| | - Robert Grainger
- Department of Biology, University of Virginia, Charlottesville, Virginia 22903, USA
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Douglas AJ, Todd LA, Katzenback BA. The amphibian invitrome: Past, present, and future contributions to our understanding of amphibian immunity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 142:104644. [PMID: 36708792 DOI: 10.1016/j.dci.2023.104644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Many amphibian populations are declining worldwide, and infectious diseases are a leading cause. Given the eminent threat infectious diseases pose to amphibian populations, there is a need to understand the host-pathogen-environment interactions that govern amphibian susceptibility to disease and mortality events. However, using animals in research raises an ethical dilemma, which is magnified by the alarming rates at which many amphibian populations are declining. Thus, in vitro study systems such as cell lines represent valuable tools for furthering our understanding of amphibian immune systems. In this review, we curate a list of the amphibian cell lines established to date (the amphibian invitrome), highlight how research using amphibian cell lines has advanced our understanding of the amphibian immune system, anti-ranaviral defence mechanisms, and Batrachochytrium dendrobatidis replication in host cells, and offer our perspective on how future use of amphibian cell lines can advance the field of amphibian immunology.
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Affiliation(s)
- Alexander J Douglas
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Lauren A Todd
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Barbara A Katzenback
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
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Klämbt V, Buerger F, Wang C, Naert T, Richter K, Nauth T, Weiss AC, Sieckmann T, Lai E, Connaughton DM, Seltzsam S, Mann N, Majmundar AJ, Wu CHW, Onuchic-Whitford AC, Shril S, Schneider S, Schierbaum L, Dai R, Bekheirnia MR, Joosten M, Shlomovitz O, Vivante A, Banne E, Mane S, Lifton RP, Kirschner KM, Kispert A, Rosenberger G, Fischer KD, Lienkamp SS, Zegers MM, Hildebrandt F. Genetic Variants in ARHGEF6 Cause Congenital Anomalies of the Kidneys and Urinary Tract in Humans, Mice, and Frogs. J Am Soc Nephrol 2023; 34:273-290. [PMID: 36414417 PMCID: PMC10103091 DOI: 10.1681/asn.2022010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 09/30/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND About 40 disease genes have been described to date for isolated CAKUT, the most common cause of childhood CKD. However, these genes account for only 20% of cases. ARHGEF6, a guanine nucleotide exchange factor that is implicated in biologic processes such as cell migration and focal adhesion, acts downstream of integrin-linked kinase (ILK) and parvin proteins. A genetic variant of ILK that causes murine renal agenesis abrogates the interaction of ILK with a murine focal adhesion protein encoded by Parva , leading to CAKUT in mice with this variant. METHODS To identify novel genes that, when mutated, result in CAKUT, we performed exome sequencing in an international cohort of 1265 families with CAKUT. We also assessed the effects in vitro of wild-type and mutant ARHGEF6 proteins, and the effects of Arhgef6 deficiency in mouse and frog models. RESULTS We detected six different hemizygous variants in the gene ARHGEF6 (which is located on the X chromosome in humans) in eight individuals from six families with CAKUT. In kidney cells, overexpression of wild-type ARHGEF6 -but not proband-derived mutant ARHGEF6 -increased active levels of CDC42/RAC1, induced lamellipodia formation, and stimulated PARVA-dependent cell spreading. ARHGEF6-mutant proteins showed loss of interaction with PARVA. Three-dimensional Madin-Darby canine kidney cell cultures expressing ARHGEF6-mutant proteins exhibited reduced lumen formation and polarity defects. Arhgef6 deficiency in mouse and frog models recapitulated features of human CAKUT. CONCLUSIONS Deleterious variants in ARHGEF6 may cause dysregulation of integrin-parvin-RAC1/CDC42 signaling, thereby leading to X-linked CAKUT.
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Affiliation(s)
- Verena Klämbt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Florian Buerger
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chunyan Wang
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Nephrology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Thomas Naert
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Karin Richter
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Theresa Nauth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna-Carina Weiss
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Tobias Sieckmann
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Translatationale Physiologie, Berlin, Germany
| | - Ethan Lai
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dervla M. Connaughton
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Steve Seltzsam
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nina Mann
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Amar J. Majmundar
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Chen-Han W. Wu
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Departments of Genetics and Urology, Case Western Reserve University School of Medicine and University Hospitals, Cleveland, Ohio
| | - Ana C. Onuchic-Whitford
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shirlee Shril
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Sophia Schneider
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Luca Schierbaum
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Rufeng Dai
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mir Reza Bekheirnia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Omer Shlomovitz
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Asaf Vivante
- Department of Pediatrics B, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ehud Banne
- The Genetics Institute, Kaplan Medical Center—Rehovot, Hebrew University and Hadassah Medical School, Jerusalem, Israel
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P. Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - Karin M. Kirschner
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institut für Translatationale Physiologie, Berlin, Germany
| | - Andreas Kispert
- Institut für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Georg Rosenberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus-Dieter Fischer
- Institute for Biochemistry and Cell Biology, Medical Faculty, Otto-von-Guericke University, Magdeburg, Germany
| | - Soeren S. Lienkamp
- Institute of Anatomy, Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Mirjam M.P. Zegers
- Department of Cell Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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10
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Corkins ME, Achieng M, DeLay BD, Krneta-Stankic V, Cain MP, Walker BL, Chen J, Lindström NO, Miller RK. A comparative study of cellular diversity between the Xenopus pronephric and mouse metanephric nephron. Kidney Int 2023; 103:77-86. [PMID: 36055600 PMCID: PMC9822858 DOI: 10.1016/j.kint.2022.07.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/30/2022] [Accepted: 07/27/2022] [Indexed: 01/11/2023]
Abstract
The kidney is an essential organ that ensures bodily fluid homeostasis and removes soluble waste products from the organism. Nephrons, the functional units of the kidney, comprise a blood filter, the glomerulus or glomus, and an epithelial tubule that processes the filtrate from the blood or coelom and selectively reabsorbs solutes, such as sugars, proteins, ions, and water, leaving waste products to be eliminated in the urine. Genes coding for transporters are segmentally expressed, enabling the nephron to sequentially process the filtrate. The Xenopus embryonic kidney, the pronephros, which consists of a single large nephron, has served as a valuable model to identify genes involved in nephron formation and patterning. Therefore, the developmental patterning program that generates these segments is of great interest. Prior work has defined the gene expression profiles of Xenopus nephron segments via in situ hybridization strategies, but a comprehensive understanding of the cellular makeup of the pronephric kidney remains incomplete. Here, we carried out single-cell mRNA sequencing of the functional Xenopus pronephric nephron and evaluated its cellular composition through comparative analyses with previous Xenopus studies and single-cell mRNA sequencing of the adult mouse kidney. This study reconstructs the cellular makeup of the pronephric kidney and identifies conserved cells, segments, and associated gene expression profiles. Thus, our data highlight significant conservation in podocytes, proximal and distal tubule cells, and divergence in cellular composition underlying the capacity of each nephron to remove wastes in the form of urine, while emphasizing the Xenopus pronephros as a model for physiology and disease.
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Affiliation(s)
- Mark E Corkins
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA.
| | - MaryAnne Achieng
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Bridget D DeLay
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA
| | - Vanja Krneta-Stankic
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA; Program in Genes and Development, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Margo P Cain
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Brandy L Walker
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Jichao Chen
- Department of Pulmonary Medicine, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Nils O Lindström
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Rachel K Miller
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School, UTHealth Houston, Houston, Texas, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA; Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA; Program in Biochemistry and Cell Biology, MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, Texas, USA.
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11
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Hnf1b renal expression directed by a distal enhancer responsive to Pax8. Sci Rep 2022; 12:19921. [PMID: 36402859 PMCID: PMC9675860 DOI: 10.1038/s41598-022-21171-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022] Open
Abstract
Xenopus provides a simple and efficient model system to study nephrogenesis and explore the mechanisms causing renal developmental defects in human. Hnf1b (hepatocyte nuclear factor 1 homeobox b), a gene whose mutations are the most commonly identified genetic cause of developmental kidney disease, is required for the acquisition of a proximo-intermediate nephron segment in Xenopus as well as in mouse. Genetic networks involved in Hnf1b expression during kidney development remain poorly understood. We decided to explore the transcriptional regulation of Hnf1b in the developing Xenopus pronephros and mammalian renal cells. Using phylogenetic footprinting, we identified an evolutionary conserved sequence (CNS1) located several kilobases (kb) upstream the Hnf1b transcription start and harboring epigenomic marks characteristics of a distal enhancer in embryonic and adult renal cells in mammals. By means of functional expression assays in Xenopus and mammalian renal cell lines we showed that CNS1 displays enhancer activity in renal tissue. Using CRISPR/cas9 editing in Xenopus tropicalis, we demonstrated the in vivo functional relevance of CNS1 in driving hnf1b expression in the pronephros. We further showed the importance of Pax8-CNS1 interaction for CNS1 enhancer activity allowing us to conclude that Hnf1b is a direct target of Pax8. Our work identified for the first time a Hnf1b renal specific enhancer and may open important perspectives into the diagnosis for congenital kidney anomalies in human, as well as modeling HNF1B-related diseases.
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12
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Shiraki T, Hayashi T, Ozue J, Watanabe M. Appropriate Amounts and Activity of the Wilms' Tumor Suppressor Gene, wt1, Are Required for Normal Pronephros Development of Xenopus Embryos. J Dev Biol 2022; 10:jdb10040046. [PMID: 36412640 PMCID: PMC9680428 DOI: 10.3390/jdb10040046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 12/14/2022] Open
Abstract
The Wilms' tumor suppressor gene, wt1, encodes a zinc finger-containing transcription factor that binds to a GC-rich motif and regulates the transcription of target genes. wt1 was first identified as a tumor suppressor gene in Wilms' tumor, a pediatric kidney tumor, and has been implicated in normal kidney development. The WT1 protein has transcriptional activation and repression domains and acts as a transcriptional activator or repressor, depending on the target gene and context. In Xenopus, an ortholog of wt1 has been isolated and shown to be expressed in the developing embryonic pronephros. To investigate the role of wt1 in pronephros development in Xenopus embryos, we mutated wt1 by CRISPR/Cas9 and found that the expression of pronephros marker genes was reduced. In reporter assays in which known WT1 binding sequences were placed upstream of the luciferase gene, WT1 activated transcription of the luciferase gene. The injection of wild-type or artificially altered transcriptional activity of wt1 mRNA disrupted the expression of pronephros marker genes in the embryos. These results suggest that the appropriate amounts and activity of WT1 protein are required for normal pronephros development in Xenopus embryos.
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Affiliation(s)
- Taisei Shiraki
- Graduate School of Sciences and Technology for Innovation, Tokushima University, 1-1 Minamijosanjima-Cho, Tokushima 770-8054, Japan
| | - Takuma Hayashi
- Graduate School of Sciences and Technology for Innovation, Tokushima University, 1-1 Minamijosanjima-Cho, Tokushima 770-8054, Japan
| | - Jotaro Ozue
- Graduate School of Sciences and Technology for Innovation, Tokushima University, 1-1 Minamijosanjima-Cho, Tokushima 770-8054, Japan
| | - Minoru Watanabe
- Graduate School of Sciences and Technology for Innovation, Tokushima University, 1-1 Minamijosanjima-Cho, Tokushima 770-8054, Japan
- Institute of Liberal Arts and Sciences, Tokushima University, 1-1 Minamijosanjima-Cho, Tokushima 770-8054, Japan
- Correspondence: ; Tel.: +81-088-656-7253
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13
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Adrenergic receptor signaling induced by Klf15, a regulator of regeneration enhancer, promotes kidney reconstruction. Proc Natl Acad Sci U S A 2022; 119:e2204338119. [PMID: 35939709 PMCID: PMC9388080 DOI: 10.1073/pnas.2204338119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite the recent discovery of tissue regeneration enhancers in highly regenerative animals, upstream and downstream genetic programs connected by these enhancers still remain unclear. Here, we performed a genome-wide analysis of enhancers and associated genes in regenerating nephric tubules of Xenopus laevis. Putative enhancers were identified using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) analyses. Their target genes were predicted based on their proximity to enhancers on genomic DNA and consistency of their transcriptome profiles to ATAC-seq/ChIP-seq profiles of the enhancers. Motif enrichment analysis identified the central role of Krüppel-like factors (Klf) in the enhancer. Klf15, a member of the Klf family, directly binds enhancers and stimulates expression of regenerative genes, including adrenoreceptor alpha 1A (adra1a), whereas inhibition of Klf15 activity results in failure of nephric tubule regeneration. Moreover, pharmacological inhibition of Adra1a-signaling suppresses nephric tubule regeneration, while its activation promotes nephric tubule regeneration and restores organ size. These results indicate that Klf15-dependent adrenergic receptor signaling through regeneration enhancers plays a central role in the genetic network for kidney regeneration.
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14
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Shibata Y, Suzuki M, Hirose N, Takayama A, Sanbo C, Inoue T, Umesono Y, Agata K, Ueno N, Suzuki KIT, Mochii M. CRISPR/Cas9-based simple transgenesis in Xenopus laevis. Dev Biol 2022; 489:76-83. [PMID: 35690103 DOI: 10.1016/j.ydbio.2022.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
Transgenic techniques have greatly increased our understanding of the transcriptional regulation of target genes through live reporter imaging, as well as the spatiotemporal function of a gene using loss- and gain-of-function constructs. In Xenopus species, two well-established transgenic methods, restriction enzyme-mediated integration and I-SceI meganuclease-mediated transgenesis, have been used to generate transgenic animals. However, donor plasmids are randomly integrated into the Xenopus genome in both methods. Here, we established a new and simple targeted transgenesis technique based on CRISPR/Cas9 in Xenopus laevis. In this method, Cas9 ribonucleoprotein (RNP) targeting a putative harbor site (the transforming growth factor beta receptor 2-like (tgfbr2l) locus) and a preset donor plasmid DNA were co-injected into the one-cell stage embryos of X. laevis. Approximately 10% of faithful reporter expression was detected in F0 crispants in a promoter/enhancer-specific manner. Importantly, efficient germline transmission and stable transgene expression were observed in the F1 offspring. The simplicity of this method only required preparation of a donor vector containing the tgfbr2l genome fragment and Cas9 RNP targeting this site, which are common experimental procedures used in Xenopus laboratories. Our improved technique allows the simple generation of transgenic X. laevis, so is expected to become a powerful tool for reporter assay and gene function analysis.
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Affiliation(s)
- Yuki Shibata
- Center for the Development of New Model Organisms, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Miyuki Suzuki
- Laboratory for Biothermology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Nao Hirose
- Department of Life Science, Graduate School of Science, University of Hyogo, Akou-gun, Hyogo, Japan
| | - Ayuko Takayama
- Center for the Development of New Model Organisms, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Chiaki Sanbo
- Center for the Development of New Model Organisms, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Takeshi Inoue
- Division of Adaptation Physiology, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Yoshihiko Umesono
- Department of Life Science, Graduate School of Science, University of Hyogo, Akou-gun, Hyogo, Japan
| | - Kiyokazu Agata
- Laboratory of Regeneration Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Naoto Ueno
- Division of Morphogenesis, Department of Developmental Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Ken-Ichi T Suzuki
- Center for the Development of New Model Organisms, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
| | - Makoto Mochii
- Department of Life Science, Graduate School of Science, University of Hyogo, Akou-gun, Hyogo, Japan.
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15
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Ismail V, Zachariassen LG, Godwin A, Sahakian M, Ellard S, Stals KL, Baple E, Brown KT, Foulds N, Wheway G, Parker MO, Lyngby SM, Pedersen MG, Desir J, Bayat A, Musgaard M, Guille M, Kristensen AS, Baralle D. Identification and functional evaluation of GRIA1 missense and truncation variants in individuals with ID: An emerging neurodevelopmental syndrome. Am J Hum Genet 2022; 109:1217-1241. [PMID: 35675825 PMCID: PMC9300760 DOI: 10.1016/j.ajhg.2022.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
GRIA1 encodes the GluA1 subunit of α-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA) receptors, which are ligand-gated ion channels that act as excitatory receptors for the neurotransmitter L-glutamate (Glu). AMPA receptors (AMPARs) are homo- or heteromeric protein complexes with four subunits, each encoded by different genes, GRIA1 to GRIA4. Although GluA1-containing AMPARs have a crucial role in brain function, the human phenotype associated with deleterious GRIA1 sequence variants has not been established. Subjects with de novo missense and nonsense GRIA1 variants were identified through international collaboration. Detailed phenotypic and genetic assessments of the subjects were carried out and the pathogenicity of the variants was evaluated in vitro to characterize changes in AMPAR function and expression. In addition, two Xenopus gria1 CRISPR-Cas9 F0 models were established to characterize the in vivo consequences. Seven unrelated individuals with rare GRIA1 variants were identified. One individual carried a homozygous nonsense variant (p.Arg377Ter), and six had heterozygous missense variations (p.Arg345Gln, p.Ala636Thr, p.Ile627Thr, and p.Gly745Asp), of which the p.Ala636Thr variant was recurrent in three individuals. The cohort revealed subjects to have a recurrent neurodevelopmental disorder mostly affecting cognition and speech. Functional evaluation of major GluA1-containing AMPAR subtypes carrying the GRIA1 variant mutations showed that three of the four missense variants profoundly perturb receptor function. The homozygous stop-gain variant completely destroys the expression of GluA1-containing AMPARs. The Xenopus gria1 models show transient motor deficits, an intermittent seizure phenotype, and a significant impairment to working memory in mutants. These data support a developmental disorder caused by both heterozygous and homozygous variants in GRIA1 affecting AMPAR function.
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Affiliation(s)
- Vardha Ismail
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton SO165YA, UK
| | - Linda G Zachariassen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Annie Godwin
- European Xenopus Resource Centre, School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK
| | - Mane Sahakian
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK
| | - Karen L Stals
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK
| | - Emma Baple
- Exeter Genomics Laboratory, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK; University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter EX2 5DW, UK
| | - Kate Tatton Brown
- South-West Thames Clinical Genetics Service, St George's University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Nicola Foulds
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton SO165YA, UK
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK
| | - Matthew O Parker
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, Old St Michael's Building, White Swan Road, Portsmouth PO1 2DT, UK
| | - Signe M Lyngby
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Miriam G Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Julie Desir
- Département de Génétique Clinique - Institut de Pathologie et de Génétique, Institut de Pathologie et de Génétique, Avenue Georges Lemaître, 25 6041 Gosselies, Belgium
| | - Allan Bayat
- Danish Epilepsy Centre, Department of Epilepsy Genetics and Personalized Medicine, 4293 Dianalund, Denmark; Department of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Maria Musgaard
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 75 Laurier Ave E, Ottawa, ON K1N 6N5, Canada
| | - Matthew Guille
- European Xenopus Resource Centre, School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - Diana Baralle
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton SO165YA, UK; Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton SO16 6YD, UK.
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16
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Tanouchi M, Igawa T, Suzuki N, Suzuki M, Hossain N, Ochi H, Ogino H. Optimization of CRISPR/Cas9-mediated gene disruption in Xenopus laevis using a phenotypic image analysis technique. Dev Growth Differ 2022; 64:219-225. [PMID: 35338712 DOI: 10.1111/dgd.12778] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/25/2021] [Accepted: 01/03/2022] [Indexed: 12/13/2022]
Abstract
The CRISPR/Cas9 method has become popular for gene disruption experiments in Xenopus laevis. However, the experimental conditions that influence the efficiency of CRISPR/Cas9 remain unclear. To that end, we developed an image analysis technique for the semi-quantitative evaluation of the pigment phenotype resulting from the disruption of tyrosinase genes in X. laevis using a CRISPR/Cas9 approach, and then examined the effects of varying five experimental parameters (timing of the CRISPR reagent injection into developing embryos; amount of Cas9 mRNA in the injection reagent; total injection volume per embryo; number of injection sites per embryo; and the culture temperature of the injected embryos) on the gene disruption efficiency. The results of this systematic analysis suggest that the highest possible efficiency of target gene disruption can be achieved by injecting a total of 20 nL of the CRISPR reagent containing 1500 pg of Cas9 mRNA or 4 ng of Cas9 protein into two separate locations (10 nL each) of one-cell stage embryos cultured at 22°C. This study also highlights the importance of balancing the experimental parameters for increasing gene disruption efficiency and provides valuable insights into the optimal conditions for applying the CRISPR/Cas9 system to new experimental organisms.
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Affiliation(s)
- Mikio Tanouchi
- Amphibian Research Center/Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Takeshi Igawa
- Amphibian Research Center/Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Nanoka Suzuki
- Amphibian Research Center/Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Makoto Suzuki
- Amphibian Research Center/Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Nusrat Hossain
- Amphibian Research Center/Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Hajime Ogino
- Amphibian Research Center/Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
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17
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Willsey HR, Guille M, Grainger RM. Modeling Human Genetic Disorders with CRISPR Technologies in Xenopus. Cold Spring Harb Protoc 2022; 2022:pdb.prot106997. [PMID: 34531330 DOI: 10.1101/pdb.prot106997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Combining the power of Xenopus developmental biology with CRISPR-based technologies promises great discoveries in understanding and treating human genetic disorders. Here we provide a practical pipeline for how to go from known disease gene(s) or risk gene(s) of interest to methods for gaining functional insight into the contribution of these genes to disorder etiology in humans.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California 94143, USA;
| | - Matthew Guille
- European Xenopus Resource Centre, School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2UP, United Kingdom
| | - Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
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18
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Corkins ME, DeLay BD, Miller RK. Tissue-Targeted CRISPR-Cas9-Mediated Genome Editing of Multiple Homeologs in F 0-Generation Xenopus laevis Embryos. Cold Spring Harb Protoc 2022; 2022:pdb.prot107037. [PMID: 34911820 PMCID: PMC10829535 DOI: 10.1101/pdb.prot107037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Xenopus laevis frogs are a powerful developmental model that enables studies combining classical embryology and molecular manipulation. Because of the large embryo size, ease of microinjection, and ability to target tissues through established fate maps, X. laevis has become the predominant amphibian research model. Given that their allotetraploid genome has complicated the generation of gene knockouts, strategies need to be established for efficient mutagenesis of multiple homeologs to evaluate gene function. Here we describe a protocol to use CRISPR-Cas9-mediated genome editing to target either single alleles or multiple alloalleles in F0 X. laevis embryos. A single-guide RNA (sgRNA) is designed to target a specific DNA sequence encoding a critical protein domain. To mutagenize a gene with two alloalleles, the sgRNA is designed against a sequence that is common to both homeologs. This sgRNA, along with the Cas9 protein, is microinjected into the zygote to disrupt the genomic sequences in the whole embryo or into a specific blastomere for tissue-targeted effects. Error-prone repair of CRISPR-Cas9-generated DNA double-strand breaks leads to insertions and deletions creating mosaic gene lesions within the embryos. The genomic DNA isolated from each mosaic F0 embryo is sequenced, and software is applied to assess the nature of the mutations generated and degree of mosaicism. This protocol enables the knockout of genes within the whole embryo or in specific tissues in F0 X. laevis embryos to facilitate the evaluation of resulting phenotypes.
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Affiliation(s)
- Mark E Corkins
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030, USA;
| | - Bridget D DeLay
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030, USA
| | - Rachel K Miller
- Department of Pediatrics, Pediatric Research Center, University of Texas Health Science Center McGovern Medical School, Houston, Texas 77030, USA;
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
- Program in Biochemistry and Cell Biology, The University of Texas MD Anderson Cancer Center University of Texas Health Science Center Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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19
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Hasebe T, Fujimoto K, Ishizuya-Oka A. Essential roles of YAP-TEAD complex in adult stem cell development during thyroid hormone-induced intestinal remodeling of Xenopus laevis. Cell Tissue Res 2022; 388:313-329. [PMID: 35211820 DOI: 10.1007/s00441-022-03600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/16/2022] [Indexed: 11/24/2022]
Abstract
During amphibian metamorphosis which is triggered by thyroid hormone (TH), the small intestine is extensively remodeled from the larval to adult form. In the Xenopus laevis intestine, some of the larval epithelial cells dedifferentiate into adult stem cells, which newly form the adult epithelium similar to the mammalian one. We have previously shown that TH-activated Shh, Wnt and Notch signaling pathways play important roles in adult epithelial development. Here we focus on the Hippo signaling pathway, which is known to interact with these pathways in the mammalian intestine. Our quantitative RT-PCR analysis indicates that the expression of genes involved in this pathway including YAP1, TAZ, TEAD1 and core kinases is differently regulated by TH in the metamorphosing intestine. Additionally, we show by in situ hybridization and immunohistochemistry that the transcriptional co-activator YAP1, a major effector of the Hippo signaling, is expressed in the adult stem cells and connective tissue cells surrounding them and that YAP1 protein is localized in either nucleus or cytoplasm of the stem cells. We further show that YAP1 binds its binding partner TEAD1 (transcription factor) in vivo and that their interaction is inhibited by verteporfin (VP). More importantly, by using VP in organ culture of the tadpole intestine, we experimentally demonstrate that the inhibition of YAP1-TEAD1 interaction decreases both TH-induced stem cells expressing LGR5 and nearby connective tissue cells in number and proliferation, leading to the failure of adult epithelial development. Our results indicate that YAP-TEAD complex is required for stem cell development during intestinal remodeling.
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Affiliation(s)
- Takashi Hasebe
- Department of Biology, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo, 180-0023, Japan.
| | - Kenta Fujimoto
- Department of Biology, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo, 180-0023, Japan
| | - Atsuko Ishizuya-Oka
- Department of Biology, Nippon Medical School, 1-7-1 Kyonan-cho, Musashino, Tokyo, 180-0023, Japan
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20
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CRISPR-SID: Identifying EZH2 as a druggable target for desmoid tumors via in vivo dependency mapping. Proc Natl Acad Sci U S A 2021; 118:2115116118. [PMID: 34789568 DOI: 10.1073/pnas.2115116118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2021] [Indexed: 12/24/2022] Open
Abstract
Cancer precision medicine implies identification of tumor-specific vulnerabilities associated with defined oncogenic pathways. Desmoid tumors are soft-tissue neoplasms strictly driven by Wnt signaling network hyperactivation. Despite this clearly defined genetic etiology and the strict and unique implication of the Wnt/β-catenin pathway, no specific molecular targets for these tumors have been identified. To address this caveat, we developed fast, efficient, and penetrant genetic Xenopus tropicalis desmoid tumor models to identify and characterize drug targets. We used multiplexed CRISPR/Cas9 genome editing in these models to simultaneously target a tumor suppressor gene (apc) and candidate dependency genes. Our methodology CRISPR/Cas9 selection-mediated identification of dependencies (CRISPR-SID) uses calculated deviations between experimentally observed gene editing outcomes and deep-learning-predicted double-strand break repair patterns to identify genes under negative selection during tumorigenesis. This revealed EZH2 and SUZ12, both encoding polycomb repressive complex 2 components, and the transcription factor CREB3L1 as genetic dependencies for desmoid tumors. In vivo EZH2 inhibition by Tazemetostat induced partial regression of established autochthonous tumors. In vitro models of patient desmoid tumor cells revealed a direct effect of Tazemetostat on Wnt pathway activity. CRISPR-SID represents a potent approach for in vivo mapping of tumor vulnerabilities and drug target identification.
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21
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Rosenthal SB, Willsey HR, Xu Y, Mei Y, Dea J, Wang S, Curtis C, Sempou E, Khokha MK, Chi NC, Willsey AJ, Fisch KM, Ideker T. A convergent molecular network underlying autism and congenital heart disease. Cell Syst 2021; 12:1094-1107.e6. [PMID: 34411509 PMCID: PMC8602730 DOI: 10.1016/j.cels.2021.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/10/2021] [Accepted: 07/28/2021] [Indexed: 12/29/2022]
Abstract
Patients with neurodevelopmental disorders, including autism, have an elevated incidence of congenital heart disease, but the extent to which these conditions share molecular mechanisms remains unknown. Here, we use network genetics to identify a convergent molecular network underlying autism and congenital heart disease. This network is impacted by damaging genetic variants from both disorders in multiple independent cohorts of patients, pinpointing 101 genes with shared genetic risk. Network analysis also implicates risk genes for each disorder separately, including 27 previously unidentified genes for autism and 46 for congenital heart disease. For 7 genes with shared risk, we create engineered disruptions in Xenopus tropicalis, confirming both heart and brain developmental abnormalities. The network includes a family of ion channels, such as the sodium transporter SCN2A, linking these functions to early heart and brain development. This study provides a road map for identifying risk genes and pathways involved in co-morbid conditions.
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Affiliation(s)
- Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yuan Mei
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sheng Wang
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA
| | - Charlotte Curtis
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emily Sempou
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Neil C Chi
- Division of Cardiology, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arthur Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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22
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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease. Proc Natl Acad Sci U S A 2021; 118:2106770118. [PMID: 34548398 PMCID: PMC8488674 DOI: 10.1073/pnas.2106770118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic analysis identified ttc30a as a ciliopathy network component, and targeting it replicated skeletal malformations and renal cysts as seen in patients and the amphibian models. A loss of Ttc30a affected cilia by altering posttranslational tubulin modifications. Our findings identify TTC30A/B as a component of ciliary segmentation essential for cartilage differentiation and renal tubulogenesis. These findings may lead to novel therapeutic targets in treating ciliary skeletopathies and cystic kidney disease. Skeletal ciliopathies (e.g., Jeune syndrome, short rib polydactyly syndrome, and Sensenbrenner syndrome) are frequently associated with nephronophthisis-like cystic kidney disease and other organ manifestations. Despite recent progress in genetic mapping of causative loci, a common molecular mechanism of cartilage defects and cystic kidneys has remained elusive. Targeting two ciliary chondrodysplasia loci (ift80 and ift172) by CRISPR/Cas9 mutagenesis, we established models for skeletal ciliopathies in Xenopus tropicalis. Froglets exhibited severe limb deformities, polydactyly, and cystic kidneys, closely matching the phenotype of affected patients. A data mining–based in silico screen found ttc30a to be related to known skeletal ciliopathy genes. CRISPR/Cas9 targeting replicated limb malformations and renal cysts identical to the models of established disease genes. Loss of Ttc30a impaired embryonic renal excretion and ciliogenesis because of altered posttranslational tubulin acetylation, glycylation, and defective axoneme compartmentalization. Ttc30a/b transcripts are enriched in chondrocytes and osteocytes of single-cell RNA-sequenced embryonic mouse limbs. We identify TTC30A/B as an essential node in the network of ciliary chondrodysplasia and nephronophthisis-like disease proteins and suggest that tubulin modifications and cilia segmentation contribute to skeletal and renal ciliopathy manifestations of ciliopathies in a cell type–specific manner. These findings have implications for potential therapeutic strategies.
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Blitz IL, Nakayama T. CRISPR-Cas9 Mutagenesis in Xenopus tropicalis for Phenotypic Analyses in the F 0 Generation and Beyond. Cold Spring Harb Protoc 2021; 2022:pdb.prot106971. [PMID: 34244352 DOI: 10.1101/pdb.prot106971] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
CRISPR-Cas9 mutagenesis is being widely used to create targeted loss-of-function mutations in the diploid frog Xenopus tropicalis Here we describe a simple mutagenesis protocol using microinjection of Cas9 protein or mRNA, together with synthetic guide RNAs (sgRNAs) targeting specific DNA sequences, into the early embryo. Cas9-catalyzed double-strand breaks undergo error-prone repair, resulting in production of short insertions and/or deletions. Thus, careful selection of target sites can lead to mutations that impair normal function of the protein product. CRISPR-Cas9 can be used to create either mosaic loss-of-function Xenopus embryos that display F0 generation phenotypes or mutant lines for downstream analysis. In addition to describing how to mutagenize genes using CRISPR-Cas9, we also discuss a simple method to determine the mutagenesis efficiency, some potential problems that can arise, and possible solutions to overcome them. The protocol described here should be applicable to other amphibians and, in principle, many other organisms.
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Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, California 92697, USA
| | - Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
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24
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Krneta-Stankic V, Corkins ME, Paulucci-Holthauzen A, Kloc M, Gladden AB, Miller RK. The Wnt/PCP formin Daam1 drives cell-cell adhesion during nephron development. Cell Rep 2021; 36:109340. [PMID: 34233186 PMCID: PMC8629027 DOI: 10.1016/j.celrep.2021.109340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 03/31/2021] [Accepted: 06/11/2021] [Indexed: 12/02/2022] Open
Abstract
E-cadherin junctions facilitate assembly and disassembly of cell contacts that drive development and homeostasis of epithelial tissues. In this study, using Xenopus embryonic kidney and Madin-Darby canine kidney (MDCK) cells, we investigate the role of the Wnt/planar cell polarity (PCP) formin Daam1 (Dishevelled-associated activator of morphogenesis 1) in regulating E-cadherin-based intercellular adhesion. Using live imaging, we show that Daam1 localizes to newly formed cell contacts in the developing nephron. Furthermore, analyses of junctional filamentous actin (F-actin) upon Daam1 depletion indicate decreased microfilament localization and slowed turnover. We also show that Daam1 is necessary for efficient and timely localization of junctional E-cadherin, mediated by Daam1’s formin homology domain 2 (FH2). Finally, we establish that Daam1 signaling promotes organized movement of renal cells. This study demonstrates that Daam1 formin junctional activity is critical for epithelial tissue organization. How cells remodel their adhesions through cell-surface proteins such as E-cadherin is a central question in epithelial tissue biology. Krneta-Stankic et al. show that the Wnt/PCP formin Daam1 regulates cytoskeletal membrane dynamics and E-cadherin localization within developing nephrons. These findings provide a new framework for studying cell-cell adhesion and nephron morphogenesis.
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Affiliation(s)
- Vanja Krneta-Stankic
- Program in Genes and Development, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA
| | - Mark E Corkins
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA
| | | | - Malgorzata Kloc
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Andrew B Gladden
- Program in Genes and Development, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel K Miller
- Program in Genes and Development, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA; Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Biochemistry and Cell Biology, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
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25
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Abstract
The field of molecular embryology started around 1990 by identifying new genes and analyzing their functions in early vertebrate embryogenesis. Those genes encode transcription factors, signaling molecules, their regulators, etc. Most of those genes are relatively highly expressed in specific regions or exhibit dramatic phenotypes when ectopically expressed or mutated. This review focuses on one of those genes, Lim1/Lhx1, which encodes a transcription factor. Lim1/Lhx1 is a member of the LIM homeodomain (LIM-HD) protein family, and its intimate partner, Ldb1/NLI, binds to two tandem LIM domains of LIM-HDs. The most ancient LIM-HD protein and its partnership with Ldb1 were innovated in the metazoan ancestor by gene fusion combining LIM domains and a homeodomain and by creating the LIM domain-interacting domain (LID) in ancestral Ldb, respectively. The LIM domain has multiple interacting interphases, and Ldb1 has a dimerization domain (DD), the LID, and other interacting domains that bind to Ssbp2/3/4 and the boundary factor, CTCF. By means of these domains, LIM-HD-Ldb1 functions as a hub protein complex, enabling more intricate and elaborate gene regulation. The common, ancestral role of LIM-HD proteins is neuron cell-type specification. Additionally, Lim1/Lhx1 serves crucial roles in the gastrula organizer and in kidney development. Recent studies using Xenopus embryos have revealed Lim1/Lhx1 functions and regulatory mechanisms during development and regeneration, providing insight into evolutionary developmental biology, functional genomics, gene regulatory networks, and regenerative medicine. In this review, we also discuss recent progress at unraveling participation of Ldb1, Ssbp, and CTCF in enhanceosomes, long-distance enhancer-promoter interactions, and trans-interactions between chromosomes.
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Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan.
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26
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Macken WL, Godwin A, Wheway G, Stals K, Nazlamova L, Ellard S, Alfares A, Aloraini T, AlSubaie L, Alfadhel M, Alajaji S, Wai HA, Self J, Douglas AGL, Kao AP, Guille M, Baralle D. Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly. Genome Med 2021; 13:34. [PMID: 33632302 PMCID: PMC7908744 DOI: 10.1186/s13073-021-00850-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as "coatopathies". METHODS Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1's splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2's missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2's mutation. RESULTS We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β'-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. CONCLUSIONS This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.
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Affiliation(s)
- William L Macken
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK
| | - Annie Godwin
- European Xenopus Resource Centre, University of Portsmouth School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK
| | - Gabrielle Wheway
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Karen Stals
- Exeter Genomics Laboratory, Level 3 RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Liliya Nazlamova
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Level 3 RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- University of Exeter Medical School, RILD building, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Ahmed Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Qassim, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Taghrid Aloraini
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Lamia AlSubaie
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Abdullah International Medical Research Centre, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Sulaiman Alajaji
- King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
- Division of Allergy and Clinical Immunology, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | - Htoo A Wai
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Jay Self
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Andrew G L Douglas
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK
| | - Alexander P Kao
- Zeiss Global Centre, School of Mechanical and Design Engineering, University of Portsmouth, Portsmouth, PO1 3DJ, UK
| | - Matthew Guille
- European Xenopus Resource Centre, University of Portsmouth School of Biological Sciences, King Henry Building, King Henry I Street, Portsmouth, PO1 2DY, UK.
| | - Diana Baralle
- Wessex Clinical Genetics Service, Princess Anne Hospital, University Hospital Southampton NHS Foundation Trust, Coxford Rd, Southampton, SO165YA, UK.
- Faculty of Medicine, University of Southampton, Duthie Building, Southampton General Hospital, Tremona Road, Southampton, SO16 6YD, UK.
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27
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Exner CRT, Willsey HR. Xenopus leads the way: Frogs as a pioneering model to understand the human brain. Genesis 2021; 59:e23405. [PMID: 33369095 PMCID: PMC8130472 DOI: 10.1002/dvg.23405] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/12/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022]
Abstract
From its long history in the field of embryology to its recent advances in genetics, Xenopus has been an indispensable model for understanding the human brain. Foundational studies that gave us our first insights into major embryonic patterning events serve as a crucial backdrop for newer avenues of investigation into organogenesis and organ function. The vast array of tools available in Xenopus laevis and Xenopus tropicalis allows interrogation of developmental phenomena at all levels, from the molecular to the behavioral, and the application of CRISPR technology has enabled the investigation of human disorder risk genes in a higher-throughput manner. As the only major tetrapod model in which all developmental stages are easily manipulated and observed, frogs provide the unique opportunity to study organ development from the earliest stages. All of these features make Xenopus a premier model for studying the development of the brain, a notoriously complex process that demands an understanding of all stages from fertilization to organogenesis and beyond. Importantly, core processes of brain development are conserved between Xenopus and human, underlining the advantages of this model. This review begins by summarizing discoveries made in amphibians that form the cornerstones of vertebrate neurodevelopmental biology and goes on to discuss recent advances that have catapulted our understanding of brain development in Xenopus and in relation to human development and disease. As we engage in a new era of patient-driven gene discovery, Xenopus offers exceptional potential to uncover conserved biology underlying human brain disorders and move towards rational drug design.
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Affiliation(s)
- Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, 94143, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, 94143, USA
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28
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Corkins ME, Krneta-Stankic V, Kloc M, Miller RK. Aquatic models of human ciliary diseases. Genesis 2021; 59:e23410. [PMID: 33496382 PMCID: PMC8593908 DOI: 10.1002/dvg.23410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 11/06/2022]
Abstract
Cilia are microtubule-based structures that either transmit information into the cell or move fluid outside of the cell. There are many human diseases that arise from malfunctioning cilia. Although mammalian models provide vital insights into the underlying pathology of these diseases, aquatic organisms such as Xenopus and zebrafish provide valuable tools to help screen and dissect out the underlying causes of these diseases. In this review we focus on recent studies that identify or describe different types of human ciliopathies and outline how aquatic organisms have aided our understanding of these diseases.
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Affiliation(s)
- Mark E. Corkins
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston Texas 77030
| | - Vanja Krneta-Stankic
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston Texas 77030
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genes & Development, Houston Texas 77030
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas 77030
| | - Malgorzata Kloc
- Houston Methodist, Research Institute, Houston Texas 77030
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston Texas 77030
| | - Rachel K. Miller
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston Texas 77030
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas 77030
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston Texas 77030
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Biochemistry & Cell Biology, Houston Texas 77030
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29
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Wyatt BH, Raymond TO, Lansdon LA, Darbro BW, Murray JC, Manak JR, Dickinson AJG. Using an aquatic model, Xenopus laevis, to uncover the role of chromodomain 1 in craniofacial disorders. Genesis 2021; 59:e23394. [PMID: 32918369 PMCID: PMC10701884 DOI: 10.1002/dvg.23394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
The chromodomain family member chromodomain 1 (CHD1) has been shown to have numerous critical molecular functions including transcriptional regulation, splicing, and DNA repair. Complete loss of function of this gene is not compatible with life. On the other hand, missense and copy number variants of CHD1 can result in intellectual disabilities and craniofacial malformations in human patients including cleft palate and Pilarowski-Bjornsson Syndrome. We have used the aquatic developmental model organism Xenopus laevis, to determine a specific role for Chd1 in such cranioafcial disorders. Protein and gene knockdown techniques in Xenopus, including antisense oligos and mosaic Crispr/Cas9-mediated mutagenesis, recapitulated the craniofacial defects observed in humans. Further analysis indicated that embryos deficient in Chd1 had defects in cranial neural crest development and jaw cartilage morphology. Additionally, flow cytometry and immunohistochemistry revealed that decreased Chd1 resulted in increased in apoptosis in the developing head. Together, these experiments demonstrate that Chd1 is critical for fundamental processes and cell survival in craniofacial development. We also presented evidence that Chd1 is regulated by retinoic acid signaling during craniofacial development. Expression levels of chd1 mRNA, specifically in the head, were increased by RAR agonist exposure and decreased upon antagonist treatment. Subphenotypic levels of an RAR antagonist and Chd1 morpholinos synergized to result in orofacial defects. Further, RAR DNA binding sequences (RAREs) were detected in chd1 regulatory regions by bioinformatic analysis. In summary, by combining human genetics and experiments in an aquatic model we now have a better understanding of the role of CHD1 in craniofacial disorders.
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Affiliation(s)
- Brent H. Wyatt
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Thomas O. Raymond
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Lisa A. Lansdon
- Department of Biology, University of Iowa, Iowa City, Iowa
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, Missouri
| | | | | | - John Robert Manak
- Department of Biology, University of Iowa, Iowa City, Iowa
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
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30
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Willsey HR, Exner CRT, Xu Y, Everitt A, Sun N, Wang B, Dea J, Schmunk G, Zaltsman Y, Teerikorpi N, Kim A, Anderson AS, Shin D, Seyler M, Nowakowski TJ, Harland RM, Willsey AJ, State MW. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron 2021; 109:788-804.e8. [PMID: 33497602 DOI: 10.1016/j.neuron.2021.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022]
Abstract
Gene Ontology analyses of autism spectrum disorders (ASD) risk genes have repeatedly highlighted synaptic function and transcriptional regulation as key points of convergence. However, these analyses rely on incomplete knowledge of gene function across brain development. Here we leverage Xenopus tropicalis to study in vivo ten genes with the strongest statistical evidence for association with ASD. All genes are expressed in developing telencephalon at time points mapping to human mid-prenatal development, and mutations lead to an increase in the ratio of neural progenitor cells to maturing neurons, supporting previous in silico systems biological findings implicating cortical neurons in ASD vulnerability, but expanding the range of convergent functions to include neurogenesis. Systematic chemical screening identifies that estrogen, via Sonic hedgehog signaling, rescues this convergent phenotype in Xenopus and human models of brain development, suggesting a resilience factor that may mitigate a range of ASD genetic risks.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amanda Everitt
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Galina Schmunk
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yefim Zaltsman
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nia Teerikorpi
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Albert Kim
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aoife S Anderson
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Shin
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Meghan Seyler
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
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31
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Le L, Escobar IE, Ho T, Lefkovith AJ, Latteri E, Haltaufderhyde KD, Dennis MK, Plowright L, Sviderskaya EV, Bennett DC, Oancea E, Marks MS. SLC45A2 protein stability and regulation of melanosome pH determine melanocyte pigmentation. Mol Biol Cell 2020; 31:2687-2702. [PMID: 32966160 PMCID: PMC7927184 DOI: 10.1091/mbc.e20-03-0200] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
SLC45A2 encodes a putative transporter expressed primarily in pigment cells. SLC45A2 mutations cause oculocutaneous albinism type 4 (OCA4) and polymorphisms are associated with pigmentation variation, but the localization, function, and regulation of SLC45A2 and its variants remain unknown. We show that SLC45A2 localizes to a cohort of mature melanosomes that only partially overlaps with the cohort expressing the chloride channel OCA2. SLC45A2 expressed ectopically in HeLa cells localizes to lysosomes and raises lysosomal pH, suggesting that in melanocytes SLC45A2 expression, like OCA2 expression, results in the deacidification of maturing melanosomes to support melanin synthesis. Interestingly, OCA2 overexpression compensates for loss of SLC45A2 expression in pigmentation. Analyses of SLC45A2- and OCA2-deficient mouse melanocytes show that SLC45A2 likely functions later during melanosome maturation than OCA2. Moreover, the light skin-associated SLC45A2 allelic F374 variant restores only moderate pigmentation to SLC45A2-deficient melanocytes due to rapid proteasome-dependent degradation resulting in lower protein expression levels in melanosomes than the dark skin-associated allelic L374 variant. Our data suggest that SLC45A2 maintains melanosome neutralization that is initially orchestrated by transient OCA2 activity to support melanization at late stages of melanosome maturation, and that a common allelic variant imparts reduced activity due to protein instability.
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Affiliation(s)
- Linh Le
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Iliana E Escobar
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Tina Ho
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ariel J Lefkovith
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Emily Latteri
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and
| | - Kirk D Haltaufderhyde
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Megan K Dennis
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and.,Biology Department, Marist College, Poughkeepsie, NY 12601
| | - Lynn Plowright
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Elena V Sviderskaya
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Dorothy C Bennett
- Molecular & Clinical Sciences Research Institute, St George's, University of London, London SW17 0RE, UK
| | - Elena Oancea
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912
| | - Michael S Marks
- Department of Pathology & Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104.,Department of Pathology and Laboratory Medicine and Department of Physiology and
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Naert T, Tulkens D, Edwards NA, Carron M, Shaidani NI, Wlizla M, Boel A, Demuynck S, Horb ME, Coucke P, Willaert A, Zorn AM, Vleminckx K. Maximizing CRISPR/Cas9 phenotype penetrance applying predictive modeling of editing outcomes in Xenopus and zebrafish embryos. Sci Rep 2020; 10:14662. [PMID: 32887910 PMCID: PMC7473854 DOI: 10.1038/s41598-020-71412-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/13/2020] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9 genome editing has revolutionized functional genomics in vertebrates. However, CRISPR/Cas9 edited F0 animals too often demonstrate variable phenotypic penetrance due to the mosaic nature of editing outcomes after double strand break (DSB) repair. Even with high efficiency levels of genome editing, phenotypes may be obscured by proportional presence of in-frame mutations that still produce functional protein. Recently, studies in cell culture systems have shown that the nature of CRISPR/Cas9-mediated mutations can be dependent on local sequence context and can be predicted by computational methods. Here, we demonstrate that similar approaches can be used to forecast CRISPR/Cas9 gene editing outcomes in Xenopus tropicalis, Xenopus laevis, and zebrafish. We show that a publicly available neural network previously trained in mouse embryonic stem cell cultures (InDelphi-mESC) is able to accurately predict CRISPR/Cas9 gene editing outcomes in early vertebrate embryos. Our observations can have direct implications for experiment design, allowing the selection of guide RNAs with predicted repair outcome signatures enriched towards frameshift mutations, allowing maximization of CRISPR/Cas9 phenotype penetrance in the F0 generation.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Dieter Tulkens
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Nicole A Edwards
- Division of Developmental Biology, Perinatal Institute, and Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital, Cincinnati, USA
| | - Marjolein Carron
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nikko-Ideen Shaidani
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Marcin Wlizla
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Annekatrien Boel
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Suzan Demuynck
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Marko E Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Paul Coucke
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Andy Willaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Aaron M Zorn
- Division of Developmental Biology, Perinatal Institute, and Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital, Cincinnati, USA
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark 71, 9052, Ghent (Zwijnaarde), Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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Willsey HR, Xu Y, Everitt A, Dea J, Exner CRT, Willsey AJ, State MW, Harland RM. The neurodevelopmental disorder risk gene DYRK1A is required for ciliogenesis and control of brain size in Xenopus embryos. Development 2020; 147:dev189290. [PMID: 32467234 PMCID: PMC10755402 DOI: 10.1242/dev.189290] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/11/2020] [Indexed: 12/30/2023]
Abstract
DYRK1A [dual specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A] is a high-confidence autism risk gene that encodes a conserved kinase. In addition to autism, individuals with putative loss-of-function variants in DYRK1A exhibit microcephaly, intellectual disability, developmental delay and/or congenital anomalies of the kidney and urinary tract. DYRK1A is also located within the critical region for Down syndrome; therefore, understanding the role of DYRK1A in brain development is crucial for understanding the pathobiology of multiple developmental disorders. To characterize the function of this gene, we used the diploid frog Xenopus tropicalis We discover that Dyrk1a is expressed in ciliated tissues, localizes to ciliary axonemes and basal bodies, and is required for ciliogenesis. We also demonstrate that Dyrk1a localizes to mitotic spindles and that its inhibition leads to decreased forebrain size, abnormal cell cycle progression and cell death during brain development. These findings provide hypotheses about potential mechanisms of pathobiology and underscore the utility of X. tropicalis as a model system for understanding neurodevelopmental disorders.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
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34
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Nakayama T, Grainger RM, Cha SW. Simple embryo injection of long single-stranded donor templates with the CRISPR/Cas9 system leads to homology-directed repair in Xenopus tropicalis and Xenopus laevis. Genesis 2020; 58:e23366. [PMID: 32277804 DOI: 10.1002/dvg.23366] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/24/2020] [Accepted: 03/27/2020] [Indexed: 01/05/2023]
Abstract
We report model experiments in which simple microinjection of fertilized eggs has been used to effectively perform homology-directed repair (HDR)-mediated gene editing in the two Xenopus species used most frequently for research: X. tropicalis and X. laevis. We have used long single-stranded DNAs having phosphorothioate modifications as donor templates for HDR at targeted genomic sites using the Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. First, X. tropicalis tyr mutant (i.e., albino) embryos were successfully rescued: partially pigmented tadpoles were seen in up to 35% of injected embryos, demonstrating the potential for efficient insertion of targeted point mutations. Second, in order to demonstrate the ability to tag genes with fluorescent proteins (FPs), we targeted the melanocyte-specific gene slc45a2.L of X. laevis to label it with the Superfolder green FP (sfGFP), seeing mosaic expression of sfGFP in melanophores in up to 20% of injected tadpoles. Tadpoles generated by these two approaches were raised to sexual maturity, and shown to successfully transmit HDR constructs through the germline with precise targeting and seamless recombination. F1 embryos showed rescue of the tyr mutation (X. tropicalis) and tagging in the appropriate pigment cell-specific manner of slc45a2.L with sfGFP (X. laevis).
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Affiliation(s)
- Takuya Nakayama
- Department of Biology, University of Virginia, Charlottesville, Virginia
| | - Robert M Grainger
- Department of Biology, University of Virginia, Charlottesville, Virginia
| | - Sang-Wook Cha
- School of Natural Sciences, University of Central Missouri, Warrensburg, Missouri
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35
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Martin A, Wolcott NS, O'Connell LA. Bringing immersive science to undergraduate laboratory courses using CRISPR gene knockouts in frogs and butterflies. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb208793. [PMID: 32034043 DOI: 10.1242/jeb.208793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The use of CRISPR/Cas9 for gene editing offers new opportunities for biology students to perform genuine research exploring the gene-to-phenotype relationship. It is important to introduce the next generation of scientists, health practitioners and other members of society to the technical and ethical aspects of gene editing. Here, we share our experience leading hands-on undergraduate laboratory classes, where students formulate hypotheses regarding the roles of candidate genes involved in development, perform loss-of-function experiments using programmable nucleases and analyze the phenotypic effects of mosaic mutant animals. This is enabled by the use of the amphibian Xenopus laevis and the butterfly Vanessa cardui, two organisms that reliably yield hundreds of large and freshly fertilized eggs in a scalable manner. Frogs and butterflies also present opportunities to teach key biological concepts about gene regulation and development. To complement these practical aspects, we describe learning activities aimed at equipping students with a broad understanding of genome editing techniques, their application in fundamental and translational research, and the bioethical challenges they raise. Overall, our work supports the introduction of CRISPR technology into undergraduate classrooms and, when coupled with classroom undergraduate research experiences, enables hypothesis-driven research by undergraduates.
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Affiliation(s)
- Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Nora S Wolcott
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
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36
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Mullen RD, Ontiveros AE, Moses MM, Behringer RR. AMH and AMHR2 mutations: A spectrum of reproductive phenotypes across vertebrate species. Dev Biol 2019; 455:1-9. [PMID: 31301298 PMCID: PMC6754765 DOI: 10.1016/j.ydbio.2019.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/04/2019] [Accepted: 07/09/2019] [Indexed: 01/02/2023]
Abstract
Anti-Müllerian hormone (AMH) is a member of the Transforming Growth Factor-β family of secreted signaling proteins. AMH is expressed in Sertoli cells of the fetal and adult testes and granulosa cells of the postnatal ovary. AMH is required for the regression of the Müllerian ducts in mammalian fetuses during male differentiation. AMH signals through its Type II receptor, AMHR2. AMHR2 is expressed in mesenchyme adjacent to the Müllerian ducts, and in Sertoli, Leydig, and granulosa cells. Although AMH and AMHR2 genes have been identified in numerous vertebrate species, spontaneous or engineered mutations or variants have been found or created in only a few mammals and teleost fishes. AMH or AMHR2 mutations in mammals lead to the development of Persistent Müllerian Duct Syndrome (PMDS), a recessive condition in which affected males are fully virilized but retain Müllerian duct-derived tissues, including a uterus and oviducts, and in human and dog, undescended testes. Amh mutant female mice had accelerated ovarian primordial follicle recruitment, suggesting a role for AMH in regulating germ cells. amh and amhr2 mutations have also been experimentally generated in various teleost fishes. Depending on the fish species, loss of AMH signaling results in infertility, germ cell tumors, or male-to-female sex reversal. Here we compare the spectrum of phenotypes caused by AMH and AMHR2 mutations in a variety of vertebrate species. There are both common and unique phenotypes between species, highlighting the range of biological processes regulated by AMH signaling.
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Affiliation(s)
- Rachel D Mullen
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alejandra E Ontiveros
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Malcolm M Moses
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, 77030, USA; Program in Genetics and Epigenetics, MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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37
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Corkins ME, Krneta-Stankic V, Kloc M, McCrea PD, Gladden AB, Miller RK. Divergent roles of the Wnt/PCP Formin Daam1 in renal ciliogenesis. PLoS One 2019; 14:e0221698. [PMID: 31469868 PMCID: PMC6716777 DOI: 10.1371/journal.pone.0221698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/13/2019] [Indexed: 12/16/2022] Open
Abstract
Kidneys are composed of numerous ciliated epithelial tubules called nephrons. Each nephron functions to reabsorb nutrients and concentrate waste products into urine. Defects in primary cilia are associated with abnormal formation of nephrons and cyst formation in a wide range of kidney disorders. Previous work in Xenopus laevis and zebrafish embryos established that loss of components that make up the Wnt/PCP pathway, Daam1 and ArhGEF19 (wGEF) perturb kidney tubulogenesis. Dishevelled, which activates both the canonical and non-canonical Wnt/PCP pathway, affect cilia formation in multiciliated cells. In this study, we investigated the role of the noncanoncial Wnt/PCP components Daam1 and ArhGEF19 (wGEF) in renal ciliogenesis utilizing polarized mammalian kidney epithelia cells (MDCKII and IMCD3) and Xenopus laevis embryonic kidney. We demonstrate that knockdown of Daam1 and ArhGEF19 in MDCKII and IMCD3 cells leads to loss of cilia, and Daam1's effect on ciliogenesis is mediated by the formin-activity of Daam1. Moreover, Daam1 co-localizes with the ciliary transport protein Ift88 and is present in cilia. Interestingly, knocking down Daam1 in Xenopus kidney does not lead to loss of cilia. These data suggests a new role for Daam1 in the formation of primary cilia.
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Affiliation(s)
- Mark E. Corkins
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, Texas, United States of America
| | - Vanja Krneta-Stankic
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genes and Development, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas, United States of America
| | - Malgorzata Kloc
- Houston Methodist, Research Institute, Houston, Texas, United States of America
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Pierre D. McCrea
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas, United States of America
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Andrew B. Gladden
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas, United States of America
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Rachel K. Miller
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics & Epigenetics, Houston, Texas, United States of America
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Biochemistry & Cell Biology, Houston, Texas, United States of America
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38
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Hwang WY, Marquez J, Khokha MK. Xenopus: Driving the Discovery of Novel Genes in Patient Disease and Their Underlying Pathological Mechanisms Relevant for Organogenesis. Front Physiol 2019; 10:953. [PMID: 31417417 PMCID: PMC6682594 DOI: 10.3389/fphys.2019.00953] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 07/09/2019] [Indexed: 12/16/2022] Open
Abstract
Frog model organisms have been appreciated for their utility in exploring physiological phenomena for nearly a century. Now, a vibrant community of biologists that utilize this model organism has poised Xenopus to serve as a high throughput vertebrate organism to model patient-driven genetic diseases. This has facilitated the investigation of effects of patient mutations on specific organs and signaling pathways. This approach promises a rapid investigation into novel mechanisms that disrupt normal organ morphology and function. Considering that many disease states are still interrogated in vitro to determine relevant biological processes for further study, the prospect of interrogating genetic disease in Xenopus in vivo is an attractive alternative. This model may more closely capture important aspects of the pathology under investigation such as cellular micro environments and local forces relevant to a specific organ's development and homeostasis. This review aims to highlight recent methodological advances that allow investigation of genetic disease in organ-specific contexts in Xenopus as well as provide examples of how these methods have led to the identification of novel mechanisms and pathways important for understanding human disease.
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Affiliation(s)
| | | | - Mustafa K. Khokha
- Department of Pediatrics and Genetics, The Pediatric Genomics Discovery Program, Yale University School of Medicine, New Haven, CT, United States
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39
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Horb M, Wlizla M, Abu-Daya A, McNamara S, Gajdasik D, Igawa T, Suzuki A, Ogino H, Noble A, Robert J, James-Zorn C, Guille M. Xenopus Resources: Transgenic, Inbred and Mutant Animals, Training Opportunities, and Web-Based Support. Front Physiol 2019; 10:387. [PMID: 31073289 PMCID: PMC6497014 DOI: 10.3389/fphys.2019.00387] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 03/21/2019] [Indexed: 02/06/2023] Open
Abstract
Two species of the clawed frog family, Xenopus laevis and X. tropicalis, are widely used as tools to investigate both normal and disease-state biochemistry, genetics, cell biology, and developmental biology. To support both frog specialist and non-specialist scientists needing access to these models for their research, a number of centralized resources exist around the world. These include centers that hold live and frozen stocks of transgenic, inbred and mutant animals and centers that hold molecular resources. This infrastructure is supported by a model organism database. Here, we describe much of this infrastructure and encourage the community to make the best use of it and to guide the resource centers in developing new lines and libraries.
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Affiliation(s)
- Marko Horb
- National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Marcin Wlizla
- National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Anita Abu-Daya
- European Xenopus Resource Centre, Portsmouth, United Kingdom
| | - Sean McNamara
- National Xenopus Resource, Marine Biological Laboratory, Woods Hole, MA, United States
| | - Dominika Gajdasik
- School of Biological Sciences, King Henry Building, Portsmouth, United Kingdom
| | - Takeshi Igawa
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
| | - Atsushi Suzuki
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
| | - Hajime Ogino
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Japan
| | - Anna Noble
- European Xenopus Resource Centre, Portsmouth, United Kingdom
| | | | - Jacques Robert
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Christina James-Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, United States
| | - Matthew Guille
- European Xenopus Resource Centre, Portsmouth, United Kingdom.,School of Biological Sciences, King Henry Building, Portsmouth, United Kingdom
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40
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Blackburn ATM, Miller RK. Modeling congenital kidney diseases in Xenopus laevis. Dis Model Mech 2019; 12:12/4/dmm038604. [PMID: 30967415 PMCID: PMC6505484 DOI: 10.1242/dmm.038604] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Congenital anomalies of the kidney and urinary tract (CAKUT) occur in ∼1/500 live births and are a leading cause of pediatric kidney failure. With an average wait time of 3-5 years for a kidney transplant, the need is high for the development of new strategies aimed at reducing the incidence of CAKUT and preserving renal function. Next-generation sequencing has uncovered a significant number of putative causal genes, but a simple and efficient model system to examine the function of CAKUT genes is needed. Xenopus laevis (frog) embryos are well-suited to model congenital kidney diseases and to explore the mechanisms that cause these developmental defects. Xenopus has many advantages for studying the kidney: the embryos develop externally and are easily manipulated with microinjections, they have a functional kidney in ∼2 days, and 79% of identified human disease genes have a verified ortholog in Xenopus. This facilitates high-throughput screening of candidate CAKUT-causing genes. In this Review, we present the similarities between Xenopus and mammalian kidneys, highlight studies of CAKUT-causing genes in Xenopus and describe how common kidney diseases have been modeled successfully in this model organism. Additionally, we discuss several molecular pathways associated with kidney disease that have been studied in Xenopus and demonstrate why it is a useful model for studying human kidney diseases. Summary: Understanding how congenital kidney diseases arise is imperative to their treatment. Using Xenopus as a model will aid in elucidating kidney development and congenital kidney diseases.
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Affiliation(s)
- Alexandria T M Blackburn
- Pediatric Research Center, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics and Epigenetics, Houston, TX 77030, USA
| | - Rachel K Miller
- Pediatric Research Center, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center, Houston, TX 77030, USA .,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Genetics and Epigenetics, Houston, TX 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Program in Biochemistry and Cell Biology Houston, Houston, TX 77030, USA.,Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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41
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Zarei A, Razban V, Hosseini SE, Tabei SMB. Creating cell and animal models of human disease by genome editing using CRISPR/Cas9. J Gene Med 2019; 21:e3082. [DOI: 10.1002/jgm.3082] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/02/2019] [Accepted: 02/02/2019] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ali Zarei
- Department of Molecular Genetics, Marvdasht BranchIslamic Azad University Marvdasht Iran
- Department of Molecular Genetics, Science and Research BranchIslamic Azad University Fars Iran
| | - Vahid Razban
- Department of Molecular medicine, School of Advanced Medical Sciences and Technologies Shiraz Iran
- Stem Cell and Transgenic Technology Research CenterShiraz University of Medical Sciences Shiraz Iran
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42
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DeLay BD, Baldwin TA, Miller RK. Dynamin Binding Protein Is Required for Xenopus laevis Kidney Development. Front Physiol 2019; 10:143. [PMID: 30863317 PMCID: PMC6399408 DOI: 10.3389/fphys.2019.00143] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/07/2019] [Indexed: 12/13/2022] Open
Abstract
The adult human kidney contains over one million nephrons, with each nephron consisting of a tube containing segments that have specialized functions in nutrient and water absorption and waste excretion. The embryonic kidney of Xenopus laevis consists of a single functional nephron composed of regions that are analogous to those found in the human nephron, making it a simple model for the study of nephrogenesis. The exocyst complex, which traffics proteins to the cell membrane in vesicles via CDC42, is essential for normal kidney development. Here, we show that the CDC42-GEF, dynamin binding protein (Dnmbp/Tuba), is essential for nephrogenesis in Xenopus. dnmbp is expressed in Xenopus embryo kidneys during development, and knockdown of Dnmbp using two separate morpholino antisense oligonucleotides results in reduced expression of late pronephric markers, whereas the expression of early markers of nephrogenesis remains unchanged. A greater reduction in expression of markers of differentiated distal and connecting tubules was seen in comparison to proximal tubule markers, indicating that Dnmbp reduction may have a greater impact on distal and connecting tubule differentiation. Additionally, Dnmbp reduction results in glomus and ciliary defects. dnmbp knockout using CRISPR results in a similar reduction of late markers of pronephric tubulogenesis and also results in edema formation in later stage embryos. Overexpression of dnmbp in the kidney also resulted in disrupted pronephric tubules, suggesting that dnmbp levels in the developing kidney are tightly regulated, with either increased or decreased levels leading to developmental defects. Together, these data suggest that Dnmbp is required for nephrogenesis.
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Affiliation(s)
- Bridget D. DeLay
- Department of Pediatrics, McGovern Medical School, Pediatric Research Center, University of Texas Health Science Center, Houston, TX, United States
| | - Tanya A. Baldwin
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
- Program in Biochemistry and Cell Biology, Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, University of Texas Health Science Center, Houston, TX, United States
| | - Rachel K. Miller
- Department of Pediatrics, McGovern Medical School, Pediatric Research Center, University of Texas Health Science Center, Houston, TX, United States
- Program in Biochemistry and Cell Biology, Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, University of Texas Health Science Center, Houston, TX, United States
- Program in Genetics and Epigenetics, Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, University of Texas Health Science Center, Houston, TX, United States
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, United States
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43
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Suzuki N, Hirano K, Ogino H, Ochi H. Arid3a regulates nephric tubule regeneration via evolutionarily conserved regeneration signal-response enhancers. eLife 2019; 8:43186. [PMID: 30616715 PMCID: PMC6324879 DOI: 10.7554/elife.43186] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/18/2018] [Indexed: 12/15/2022] Open
Abstract
Amphibians and fish have the ability to regenerate numerous tissues, whereas mammals have a limited regenerative capacity. Despite numerous developmental genes becoming reactivated during regeneration, an extensive analysis is yet to be performed on whether highly regenerative animals utilize unique cis-regulatory elements for the reactivation of genes during regeneration and how such cis-regulatory elements become activated. Here, we screened regeneration signal-response enhancers at the lhx1 locus using Xenopus and found that the noncoding elements conserved from fish to human function as enhancers in the regenerating nephric tubules. A DNA-binding motif of Arid3a, a component of H3K9me3 demethylases, was commonly found in RSREs. Arid3a binds to RSREs and reduces the H3K9me3 levels. It promotes cell cycle progression and causes the outgrowth of nephric tubules, whereas the conditional knockdown of arid3a using photo-morpholino inhibits regeneration. These results suggest that Arid3a contributes to the regeneration of nephric tubules by decreasing H3K9me3 on RSREs.
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Affiliation(s)
- Nanoka Suzuki
- Institute for Promotion of Medical Science Research, Yamagata University, Faculty of Medicine, Yamagata, Japan
| | - Kodai Hirano
- Institute for Promotion of Medical Science Research, Yamagata University, Faculty of Medicine, Yamagata, Japan
| | - Hajime Ogino
- Amphibian Research Center, Hiroshima University, Higashi-hiroshima, Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Yamagata University, Faculty of Medicine, Yamagata, Japan
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Espiritu EB, Crunk AE, Bais A, Hochbaum D, Cervino AS, Phua YL, Butterworth MB, Goto T, Ho J, Hukriede NA, Cirio MC. The Lhx1-Ldb1 complex interacts with Furry to regulate microRNA expression during pronephric kidney development. Sci Rep 2018; 8:16029. [PMID: 30375416 PMCID: PMC6207768 DOI: 10.1038/s41598-018-34038-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022] Open
Abstract
The molecular events driving specification of the kidney have been well characterized. However, how the initial kidney field size is established, patterned, and proportioned is not well characterized. Lhx1 is a transcription factor expressed in pronephric progenitors and is required for specification of the kidney, but few Lhx1 interacting proteins or downstream targets have been identified. By tandem-affinity purification, we isolated FRY like transcriptional coactivator (Fryl), one of two paralogous genes, fryl and furry (fry), have been described in vertebrates. Both proteins were found to interact with the Ldb1-Lhx1 complex, but our studies focused on Lhx1/Fry functional roles, as they are expressed in overlapping domains. We found that Xenopus embryos depleted of fry exhibit loss of pronephric mesoderm, phenocopying the Lhx1-depleted animals. In addition, we demonstrated a synergism between Fry and Lhx1, identified candidate microRNAs regulated by the pair, and confirmed these microRNA clusters influence specification of the kidney. Therefore, our data shows that a constitutively-active Ldb1-Lhx1 complex interacts with a broadly expressed microRNA repressor, Fry, to establish the kidney field.
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Affiliation(s)
- Eugenel B Espiritu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amanda E Crunk
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Abha Bais
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel Hochbaum
- Universidad de Buenos Aires, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
| | - Ailen S Cervino
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina.,CONICET- Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Yu Leng Phua
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Toshiyasu Goto
- Department of Molecular Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neil A Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Cecilia Cirio
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina. .,CONICET- Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
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45
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Naert T, Vleminckx K. CRISPR/Cas9 disease models in zebrafish and Xenopus: The genetic renaissance of fish and frogs. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 28:41-52. [PMID: 30205880 DOI: 10.1016/j.ddtec.2018.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/29/2018] [Accepted: 07/13/2018] [Indexed: 12/11/2022]
Abstract
The speed by which clinical genomics is currently identifying novel potentially pathogenic variants is outperforming the speed by which these can be functionally (genotype-phenotype) annotated in animal disease models. However, over the past few years the emergence of CRISPR/Cas9 as a straight-forward genome editing technology has revolutionized disease modeling in vertebrate non-mammalian model organisms such as zebrafish, medaka and Xenopus. It is now finally possible, by CRISPR/Cas9, to rapidly establish clinically relevant disease models in these organisms. Interestingly, these can provide both cost-effective genotype-phenotype correlations for gene-(variants) and genomic rearrangements obtained from clinical practice, as well as be exploited to perform translational research to improve prospects of disease afflicted patients. In this review, we show an extensive overview of these new CRISPR/Cas9-mediated disease models and provide future prospects that will allow increasingly accurate modeling of human disease in zebrafish, medaka and Xenopus.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Belgium; Cancer Research Institute Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Belgium; Center for Medical Genetics, Ghent University, Belgium; Cancer Research Institute Ghent, Belgium.
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Corkins ME, Hanania HL, Krneta-Stankic V, DeLay BD, Pearl EJ, Lee M, Ji H, Davidson AJ, Horb ME, Miller RK. Transgenic Xenopus laevis Line for In Vivo Labeling of Nephrons within the Kidney. Genes (Basel) 2018; 9:E197. [PMID: 29642376 PMCID: PMC5924539 DOI: 10.3390/genes9040197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/29/2018] [Accepted: 04/04/2018] [Indexed: 12/21/2022] Open
Abstract
Xenopus laevis embryos are an established model for studying kidney development. The nephron structure and genetic pathways that regulate nephrogenesis are conserved between Xenopus and humans, allowing for the study of human disease-causing genes. Xenopus embryos are also amenable to large-scale screening, but studies of kidney disease-related genes have been impeded because assessment of kidney development has largely been limited to examining fixed embryos. To overcome this problem, we have generated a transgenic line that labels the kidney. We characterize this cdh17:eGFP line, showing green fluorescent protein (GFP) expression in the pronephric and mesonephric kidneys and colocalization with known kidney markers. We also demonstrate the feasibility of live imaging of embryonic kidney development and the use of cdh17:eGFP as a kidney marker for secretion assays. Additionally, we develop a new methodology to isolate and identify kidney cells for primary culture. We also use morpholino knockdown of essential kidney development genes to establish that GFP expression enables observation of phenotypes, previously only described in fixed embryos. Taken together, this transgenic line will enable primary kidney cell culture and live imaging of pronephric and mesonephric kidney development. It will also provide a simple means for high-throughput screening of putative human kidney disease-causing genes.
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Affiliation(s)
- Mark E. Corkins
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA; (M.E.C.); (H.L.H.); (V.K.-S.); (B.D.D.)
| | - Hannah L. Hanania
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA; (M.E.C.); (H.L.H.); (V.K.-S.); (B.D.D.)
- Program in Biochemistry and Cell Biology, Rice University, Houston, TX 77005, USA
| | - Vanja Krneta-Stankic
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA; (M.E.C.); (H.L.H.); (V.K.-S.); (B.D.D.)
- Program in Genes and Development, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
| | - Bridget D. DeLay
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA; (M.E.C.); (H.L.H.); (V.K.-S.); (B.D.D.)
| | - Esther J. Pearl
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA; (E.J.P.); (M.E.H.)
| | - Moonsup Lee
- Program in Genes and Development, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA;
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Hong Ji
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Alan J. Davidson
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland 1010, New Zealand;
| | - Marko E. Horb
- National Xenopus Resource and Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, Woods Hole, MA 02543, USA; (E.J.P.); (M.E.H.)
| | - Rachel K. Miller
- Department of Pediatrics, Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX 77030, USA; (M.E.C.); (H.L.H.); (V.K.-S.); (B.D.D.)
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Program in Genetics and Epigenetics, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Program in Biochemistry and Cell Biology, MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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47
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Abstract
The targeted nuclease revolution (ZFN, TALEN, and CRISPR/Cas9) has led to a myriad of reports describing genotyping methodologies for genome edited founders (F0-crispants) and their offspring (F1). As such, choosing a specific genotyping methodology for your Xenopus CRISPR/Cas9 experiments can be challenging. In this chapter we will discuss, with emphasis on Xenopus tropicalis (X. tropicalis), different methods for assessing genome editing efficiencies within F0 CRISPR/Cas9 founders and for identification of their hetero-, compound hetero-, and homozygous mutant F1 offspring. For F0 crispants, we will provide the protocols and the respective (dis)advantages of genotyping with heteroduplex mobility assay (HMA), subclone Sanger sequencing, and sequence trace decomposition. Furthermore, we provide a previously unpublished pipe-line for rapid genotyping of F1 offspring-high resolution melting analysis (HRMA) and sequence trace decomposition-procured from breeding with F0 crispants. As such, we report here the current state-of-the-art cost- and time-effective approaches to perform genotyping of CRISPR/Cas9 experiments for the Xenopus tropicalis researcher.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
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48
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Naert T, Vleminckx K. Methods for CRISPR/Cas9 Xenopus tropicalis Tissue-Specific Multiplex Genome Engineering. Methods Mol Biol 2018; 1865:33-54. [PMID: 30151757 DOI: 10.1007/978-1-4939-8784-9_3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this chapter, we convey a state-of-the art update to the 2014 Nakayama protocol for CRISPR/Cas9 genome engineering in Xenopus tropicalis (X. tropicalis). We discuss in depth, gRNA design software and rules, gRNA synthesis, and procedures for tissue- and tissue-specific CRISPR/Cas9 genome editing by targeted microinjection in X. tropicalis embryos. We demonstrate the methodology by which any standard equipped Xenopus researcher with microinjection experience can generate F0 CRISPR/Cas9 mediated mosaic mutants (crispants) within one to two work-week(s). The described methodology allows CRISPR/Cas9 efficiencies to be high enough to read out phenotypic consequences, and thus perform gene function analysis, in the F0 crispant. Additionally, we provide the framework for performing multiplex tissue-specific CRISPR/Cas9 experiments generating crispants mosaic mutant in up to four genes simultaneously, which can be of importance for Laevis researchers aiming to target by CRISPR/Cas9 both the S and L homeolog of a gene simultaneously. Finally, we discuss off-target concerns, how to minimize these and ways to rapidly bypass reviewer off-target critique by exploiting the advantages of X. tropicalis.
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Affiliation(s)
- Thomas Naert
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Kris Vleminckx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
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