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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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Gregor A, Zweier C. Modelling phenotypes, variants and pathomechanisms of syndromic diseases in different systems. MED GENET-BERLIN 2024; 36:121-131. [PMID: 38854643 PMCID: PMC11154186 DOI: 10.1515/medgen-2024-2020] [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] [Indexed: 06/11/2024]
Abstract
In this review we describe different model organisms and systems that are commonly used to study syndromic disorders. Different use cases in modeling diseases, underlying pathomechanisms and specific effects of certain variants are elucidated. We also highlight advantages and limitations of different systems. Models discussed include budding yeast, the nematode worm, the fruit fly, the frog, zebrafish, mice and human cell-based systems.
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Affiliation(s)
- Anne Gregor
- University of BernDepartment of Human GeneticsInselspital Bern3010BernSwitzerland
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3
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Berger H, Gerstner S, Horstmann MF, Pauli S, Borchers A. Fbrsl1 is required for heart development in Xenopus laevis and de novo variants in FBRSL1 can cause human heart defects. Dis Model Mech 2024; 17:dmm050507. [PMID: 38501224 PMCID: PMC11128277 DOI: 10.1242/dmm.050507] [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: 09/29/2023] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
De novo truncating variants in fibrosin-like 1 (FBRSL1), a member of the AUTS2 gene family, cause a disability syndrome, including organ malformations such as heart defects. Here, we use Xenopus laevis to investigate whether Fbrsl1 plays a role in heart development. Xenopus laevis fbrsl1 is expressed in tissues relevant for heart development, and morpholino-mediated knockdown of Fbrsl1 results in severely hypoplastic hearts. Our data suggest that Fbrsl1 is required for the development of the first heart field, which contributes to the ventricle and the atria, but not for the second heart field, which gives rise to the outflow tract. The morphant heart phenotype could be rescued using a human N-terminal FBRSL1 isoform that contains an alternative exon, but lacks the AUTS2 domain. N-terminal isoforms carrying patient variants failed to rescue. Interestingly, a long human FBRSL1 isoform, harboring the AUTS2 domain, also did not rescue the morphant heart defects. Thus, our data suggest that different FBRSL1 isoforms may have distinct functions and that only the short N-terminal isoform, appears to be critical for heart development.
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Affiliation(s)
- Hanna Berger
- Department of Biology, Molecular Embryology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Sarah Gerstner
- Department of Biology, Molecular Embryology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Marc-Frederik Horstmann
- Department of Biology, Molecular Embryology, Philipps-University Marburg, 35043 Marburg, Germany
| | - Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-University Marburg, 35043 Marburg, Germany
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4
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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Cherry JM, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, dos Santos G, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Gramates LS, Grove CA, Hale P, Harris T, Hayman GT, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Van Auken K, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources central infrastructure. Genetics 2024; 227:iyae049. [PMID: 38552170 PMCID: PMC11075569 DOI: 10.1093/genetics/iyae049] [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: 11/20/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 04/09/2024] Open
Abstract
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).
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Affiliation(s)
| | | | | | - Giulia Antonazzo
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Valerio Arnaboldi
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Helen Attrill
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Andrés Becerra
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Susan M Bello
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Olin Blodgett
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | | | - Carol J Bult
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Scott Cain
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Brian R Calvi
- Department of Biology, Indiana University , Bloomington, IN 47408 , USA
| | - Seth Carbon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Juancarlos Chan
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Wen J Chen
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - J Michael Cherry
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Jaehyoung Cho
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Madeline A Crosby
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Jeffrey L De Pons
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | | | - Stavros Diamantakis
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Mary E Dolan
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gilberto dos Santos
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Sarah Dyer
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Dustin Ebert
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Stacia R Engel
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - David Fashena
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Malcolm Fisher
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University , 5000 Forbes Ave, Pittsburgh, PA 15203
| | - Adam C Gibson
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Varun R Gollapally
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - L Sian Gramates
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Christian A Grove
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Paul Hale
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Todd Harris
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - G Thomas Hayman
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Yanhui Hu
- Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
| | - Christina James-Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Kalpana Karra
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Ranjana Kishore
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Anne E Kwitek
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Stanley J F Laulederkind
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Raymond Lee
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Ian Longden
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Manuel Luypaert
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Nicholas Markarian
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Steven J Marygold
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Beverley Matthews
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Monica S McAndrews
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gillian Millburn
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Stuart Miyasato
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Howie Motenko
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Sierra Moxon
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Hans-Michael Muller
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory , Berkeley, CA
| | - Anushya Muruganujan
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Tremayne Mushayahama
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Robert S Nash
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Paulo Nuin
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Holly Paddock
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Troy Pells
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Norbert Perrimon
- Department of Genetics, Howard Hughes Medical Institute , Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115 , USA
| | - Christian Pich
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Mark Quinton-Tulloch
- European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD , UK
| | - Daniela Raciti
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | | | | | - Susan Russo Gelbart
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Leyla Ruzicka
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Gary Schindelman
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - David R Shaw
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Ajay Shrivatsav
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Amy Singer
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Constance M Smith
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Cynthia L Smith
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Jennifer R Smith
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Lincoln Stein
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Paul W Sternberg
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Christopher J Tabone
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Paul D Thomas
- Department of Population and Public Health Sciences, University of Southern California , Los Angeles, CA 90033 , USA
| | - Ketaki Thorat
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Jyothi Thota
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Monika Tomczuk
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Vitor Trovisco
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Marek A Tutaj
- Medical College of Wisconsin—Rat Genome Database, Departments of Physiology and Biomedical Engineering , Medical College of Wisconsin, Milwaukee, WI 53226 , USA
| | - Jose-Maria Urbano
- Department of Physiology, Development and Neuroscience , University of Cambridge, Downing Street, Cambridge CB2 3DY , UK
| | - Kimberly Van Auken
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Ceri E Van Slyke
- Institute of Neuroscience, University of Oregon , Eugene, OR 97403
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary , 507 Campus Dr NW, Calgary, AB T2N 4V8 , Canada
| | - Qinghua Wang
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Shuai Weng
- Department of Genetics, Stanford University , Stanford, CA 94305
| | | | - Laurens G Wilming
- The Jackson Laboratory for Mammalian Genomics, Bar Harbor , ME 04609 , USA
| | - Edith D Wong
- Department of Genetics, Stanford University , Stanford, CA 94305
| | - Adam Wright
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research , Toronto, ON M5G0A3 , Canada
| | - Karen Yook
- Division of Biology and Biological Engineering 140-18, California Institute of Technology , Pasadena, CA 91125 , USA
| | - Pinglei Zhou
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
| | - Aaron Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center , 3333 Burnet Ave, Cincinnati, OH 45229 , USA
| | - Mark Zytkovicz
- The Biological Laboratories, Harvard University , 16 Divinity Avenue, Cambridge, MA 02138 , USA
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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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Pade LR, Lombard-Banek C, Li J, Nemes P. Dilute to Enrich for Deeper Proteomics: A Yolk-Depleted Carrier for Limited Populations of Embryonic (Frog) Cells. J Proteome Res 2024; 23:692-703. [PMID: 37994825 PMCID: PMC10872351 DOI: 10.1021/acs.jproteome.3c00541] [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: 11/24/2023]
Abstract
Abundant proteins challenge deep mass spectrometry (MS) analysis of the proteome. Yolk, the source of food in many developing vertebrate embryos, complicates chemical separation and interferes with detection. We report here a strategy that enhances bottom-up proteomics in yolk-laden specimens by diluting the interferences using a yolk-depleted carrier (YODEC) proteome via isobaric multiplexing quantification. This method was tested on embryos of the South African Clawed Frog (Xenopus laevis), where a >90% yolk proteome content challenges deep proteomics. As a proof of concept, we isolated neural and epidermal fated cell clones from the embryo by dissection or fluorescence-activated cell sorting. Compared with the standard multiplexing carrier approach, YODEC more than doubled the detectable X. laevis proteome, identifying 5,218 proteins from D11 cell clones dissected from the embryo. Ca. ∼80% of the proteins were quantified without dropouts in any of the analytical channels. YODEC with high-pH fractionation quantified 3,133 proteins from ∼8,000 V11 cells that were sorted from ca. 2 embryos (1.5 μg total, or 150 ng yolk-free proteome), marking a 15-fold improvement in proteome coverage vs the standard proteomics approach. About 60% of these proteins were only quantifiable by YODEC, including molecular adaptors, transporters, translation, and transcription factors. While this study was tailored to limited populations of Xenopus cells, we anticipate the approach of "dilute to enrich" using a depleted carrier proteome to be adaptable to other biological models in which abundant proteins challenge deep MS proteomics.
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Affiliation(s)
- Leena R. Pade
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
| | - Camille Lombard-Banek
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
| | - Jie Li
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD, 20742
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7
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Virk SM, Trujillo-Provencio C, Serrano EE. Transcriptomic Analysis Identifies Candidate Genes for Differential Expression during Xenopus laevis Inner Ear Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.29.573599. [PMID: 38260420 PMCID: PMC10802236 DOI: 10.1101/2023.12.29.573599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background The genes involved in inner ear development and maintenance of the adult organ have yet to be fully characterized. Previous genetic analysis has emphasized the early development that gives rise to the otic vesicle. This study aimed to bridge the knowledge gap and identify candidate genes that are expressed as the auditory and vestibular sensory organs continue to grow and develop until the systems reach postmetamorphic maturity. Methods Affymetrix microarrays were used to assess inner ear transcriptome profiles from three Xenopus laevis developmental ages where all eight endorgans comprise mechanosensory hair cells: larval stages 50 and 56, and the post-metamorphic juvenile. Pairwise comparisons were made between the three developmental stages and the resulting differentially expressed X. laevis Probe Set IDs (Xl-PSIDs) were assigned to four groups based on differential expression patterns. DAVID analysis was undertaken to impart functional annotation to the differentially regulated Xl-PSIDs. Results Analysis identified 1510 candidate genes for differential gene expression in one or more pairwise comparison. Annotated genes not previously associated with inner ear development emerged from this analysis, as well as annotated genes with established inner ear function, such as oncomodulin, neurod1, and sp7. Notably, 36% of differentially expressed Xl-PSIDs were unannotated. Conclusions Results draw attention to the complex gene regulatory patterns that characterize Xenopus inner ear development, and underscore the need for improved annotation of the X. laevis genome. Outcomes can be utilized to select candidate inner ear genes for functional analysis, and to promote Xenopus as a model organism for biomedical studies of hearing and balance.
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Affiliation(s)
- Selene M Virk
- Biology Department, New Mexico State University, Las Cruces NM USA 88003
| | | | - Elba E Serrano
- Biology Department, New Mexico State University, Las Cruces NM USA 88003
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Aleksander SA, Anagnostopoulos AV, Antonazzo G, Arnaboldi V, Attrill H, Becerra A, Bello SM, Blodgett O, Bradford YM, Bult CJ, Cain S, Calvi BR, Carbon S, Chan J, Chen WJ, Michael Cherry J, Cho J, Crosby MA, De Pons JL, D’Eustachio P, Diamantakis S, Dolan ME, Santos GD, Dyer S, Ebert D, Engel SR, Fashena D, Fisher M, Foley S, Gibson AC, Gollapally VR, Sian Gramates L, Grove CA, Hale P, Harris T, Thomas Hayman G, Hu Y, James-Zorn C, Karimi K, Karra K, Kishore R, Kwitek AE, Laulederkind SJF, Lee R, Longden I, Luypaert M, Markarian N, Marygold SJ, Matthews B, McAndrews MS, Millburn G, Miyasato S, Motenko H, Moxon S, Muller HM, Mungall CJ, Muruganujan A, Mushayahama T, Nash RS, Nuin P, Paddock H, Pells T, Perrimon N, Pich C, Quinton-Tulloch M, Raciti D, Ramachandran S, Richardson JE, Gelbart SR, Ruzicka L, Schindelman G, Shaw DR, Sherlock G, Shrivatsav A, Singer A, Smith CM, Smith CL, Smith JR, Stein L, Sternberg PW, Tabone CJ, Thomas PD, Thorat K, Thota J, Tomczuk M, Trovisco V, Tutaj MA, Urbano JM, Auken KV, Van Slyke CE, Vize PD, Wang Q, Weng S, Westerfield M, Wilming LG, Wong ED, Wright A, Yook K, Zhou P, Zorn A, Zytkovicz M. Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567935. [PMID: 38045425 PMCID: PMC10690154 DOI: 10.1101/2023.11.20.567935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and APIs. Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific "landing pages" and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).
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Bocquet B, Borday C, Erkilic N, Mamaeva D, Donval A, Masson C, Parain K, Kaminska K, Quinodoz M, Perea-Romero I, Garcia-Garcia G, Jimenez-Medina C, Boukhaddaoui H, Coget A, Leboucq N, Calzetti G, Gandolfi S, Percesepe A, Barili V, Uliana V, Delsante M, Bozzetti F, Scholl HP, Corton M, Ayuso C, Millan JM, Rivolta C, Meunier I, Perron M, Kalatzis V. TBC1D32 variants disrupt retinal ciliogenesis and cause retinitis pigmentosa. JCI Insight 2023; 8:e169426. [PMID: 37768732 PMCID: PMC10721274 DOI: 10.1172/jci.insight.169426] [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: 02/07/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4 patients presenting with RP from 3 unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human induced pluripotent stem cell-derived (iPSC-derived) retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition-like phenotype. Last, our results suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data highlight a critical role for TBC1D32 in the retina and demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD-causative gene.
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Affiliation(s)
- Béatrice Bocquet
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Caroline Borday
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Nejla Erkilic
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Daria Mamaeva
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Alicia Donval
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Christel Masson
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karine Parain
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Garcia-Garcia
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carla Jimenez-Medina
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Hassan Boukhaddaoui
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Arthur Coget
- Department of Neuroradiology and
- Institute for Human Functional Imaging (I2FH), University of Montpellier, CHU, Montpellier, France
| | | | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Medicine and Surgery
| | | | | | | | | | | | - Francesca Bozzetti
- Neuroradiology Unit, Diagnostic Department, University Hospital of Parma, Parma, Italy
| | - Hendrik P.N. Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Marta Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose M. Millan
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Muriel Perron
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
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Lange S, Inal JM. Animal Models of Human Disease. Int J Mol Sci 2023; 24:15821. [PMID: 37958801 PMCID: PMC10650829 DOI: 10.3390/ijms242115821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
The use of animal models of human disease is critical for furthering our understanding of disease mechanisms, for the discovery of novel targets for treatment, and for translational research. This Special Topic entitled "Animal Models of Human Disease" aimed to collect state-of-the-art primary research studies and review articles from international experts and leading groups using animal models to study human diseases. Submissions were welcomed on a wide range of animal models and pathologies, including infectious disease, acute injury, regeneration, cancer, autoimmunity, degenerative and chronic disease. Seven participating MDPI journals supported the Special Topic, namely: Biomedicines, Cells, Current Issues in Molecular Biology, Diagnostics, Genes, the International Journal of Molecular Sciences, and the International Journal of Translational Medicine. In total, 46 papers were published in this Special Topic, with 37 full length original research papers, 2 research communications and 7 reviews. These contributions cover a wide range of clinically relevant, translatable, and comparative animal models, as well as furthering understanding of fundamental sciences, covering topics on physiological processes, on degenerative, inflammatory, infectious, autoimmune, neurological, metabolic, heamatological, hormonal and mitochondrial disorders, developmental processes and diseases, cardiology, cancer, trauma, stress, and ageing.
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Affiliation(s)
- Sigrun Lange
- Tissue Architecture and Regeneration Research Group, Department of Biomedical Sciences, University of Westminster, London W1W 6UW, UK
- Pathobiology and Extracellular Vesicles Research Group, Department of Biomedical Sciences, University of Westminster, London W1W 6UW, UK
| | - Jameel M. Inal
- Cell Communication in Disease Pathology, School of Human Sciences, London Metropolitan University, London N7 8DB, UK;
- Biosciences Research Group, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9EU, UK
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11
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Horr B, Kurtz R, Pandey A, Hoffstrom BG, Schock E, LaBonne C, Alfandari D. Production and characterization of monoclonal antibodies to Xenopus proteins. Development 2023; 150:dev201309. [PMID: 36789951 PMCID: PMC10112901 DOI: 10.1242/dev.201309] [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: 09/22/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
Monoclonal antibodies are powerful and versatile tools that enable the study of proteins in diverse contexts. They are often utilized to assist with identification of subcellular localization and characterization of the function of target proteins of interest. However, because there can be considerable sequence diversity between orthologous proteins in Xenopus and mammals, antibodies produced against mouse or human proteins often do not recognize Xenopus counterparts. To address this issue, we refined existing mouse monoclonal antibody production protocols to generate antibodies against Xenopus proteins of interest. Here, we describe several approaches for the generation of useful mouse anti-Xenopus antibodies to multiple Xenopus proteins and their validation in various experimental approaches. These novel antibodies are now available to the research community through the Developmental Study Hybridoma Bank (DSHB).
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Affiliation(s)
- Brett Horr
- The University of Massachusetts Amherst, Department of Veterinary and Animal Sciences, Amherst, MA 01003, USA
| | - Ryan Kurtz
- The University of Massachusetts Amherst, Department of Veterinary and Animal Sciences, Amherst, MA 01003, USA
| | - Ankit Pandey
- The University of Massachusetts Amherst, Department of Veterinary and Animal Sciences, Amherst, MA 01003, USA
| | - Benjamin G. Hoffstrom
- Antibody Technology Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Elizabeth Schock
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Dominique Alfandari
- The University of Massachusetts Amherst, Department of Veterinary and Animal Sciences, Amherst, MA 01003, USA
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12
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Shan Z, Li S, Yu C, Bai S, Zhang J, Tang Y, Wang Y, Irwin DM, Li J, Wang Z. Embryonic and skeletal development of the albino African clawed frog (Xenopus laevis). J Anat 2023; 242:1051-1066. [PMID: 36708289 PMCID: PMC10184547 DOI: 10.1111/joa.13835] [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: 08/26/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/29/2023] Open
Abstract
The normal stages of embryonic development for wild-type Xenopus laevis were established by Nieuwkoop and Faber in 1956, a milestone in the history of understanding embryonic development. However, this work lacked photographic images and staining for skeleton structures from the corresponding stages. Here, we provide high-quality images of embryonic morphology and skeleton development to facilitate studies on amphibian development. On the basis of the classical work, we selected the albino mutant of X. laevis as the observation material to restudy embryonic development in this species. The lower level of pigmentation makes it easier to interpret histochemical experiments. At 23°C, albino embryos develop at the same rate as wild-type embryos, which can be divided into 66 stages as they develop into adults in about 58 days. We described the complete embryonic development system for X. laevis, supplemented with pictures of limb and skeleton development that are missing from previous studies, and summarized the characteristics and laws of limb and skeleton development. Our study should aid research into the development of X. laevis and the evolution of amphibians.
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Affiliation(s)
- Zhixin Shan
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Shanshan Li
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Chenghua Yu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shibin Bai
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Junpeng Zhang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yining Tang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yutong Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jun Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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13
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Niziolek M, Bicka M, Osinka A, Samsel Z, Sekretarska J, Poprzeczko M, Bazan R, Fabczak H, Joachimiak E, Wloga D. PCD Genes-From Patients to Model Organisms and Back to Humans. Int J Mol Sci 2022; 23:ijms23031749. [PMID: 35163666 PMCID: PMC8836003 DOI: 10.3390/ijms23031749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a hereditary genetic disorder caused by the lack of motile cilia or the assembxly of dysfunctional ones. This rare human disease affects 1 out of 10,000-20,000 individuals and is caused by mutations in at least 50 genes. The past twenty years brought significant progress in the identification of PCD-causative genes and in our understanding of the connections between causative mutations and ciliary defects observed in affected individuals. These scientific advances have been achieved, among others, due to the extensive motile cilia-related research conducted using several model organisms, ranging from protists to mammals. These are unicellular organisms such as the green alga Chlamydomonas, the parasitic protist Trypanosoma, and free-living ciliates, Tetrahymena and Paramecium, the invertebrate Schmidtea, and vertebrates such as zebrafish, Xenopus, and mouse. Establishing such evolutionarily distant experimental models with different levels of cell or body complexity was possible because both basic motile cilia ultrastructure and protein composition are highly conserved throughout evolution. Here, we characterize model organisms commonly used to study PCD-related genes, highlight their pros and cons, and summarize experimental data collected using these models.
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Affiliation(s)
- Michal Niziolek
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Marta Bicka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Faculty of Chemistry, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Anna Osinka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Zuzanna Samsel
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Justyna Sekretarska
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Martyna Poprzeczko
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Rafal Bazan
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Hanna Fabczak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Correspondence: (E.J.); (D.W.); Tel.: +48-22-58-92-338 (E.J. & D.W.)
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Correspondence: (E.J.); (D.W.); Tel.: +48-22-58-92-338 (E.J. & D.W.)
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