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Bondaruk J, Jaksik R, Wang Z, Cogdell D, Lee S, Chen Y, Dinh KN, Majewski T, Zhang L, Cao S, Tian F, Yao H, Kuś P, Chen H, Weinstein JN, Navai N, Dinney C, Gao J, Theodorescu D, Logothetis C, Guo CC, Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. The origin of bladder cancer from mucosal field effects. iScience 2022; 25:104551. [PMID: 35747385 PMCID: PMC9209726 DOI: 10.1016/j.isci.2022.104551] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/19/2021] [Accepted: 06/02/2022] [Indexed: 12/30/2022] Open
Abstract
Whole-organ mapping was used to study molecular changes in the evolution of bladder cancer from field effects. We identified more than 100 dysregulated pathways, involving immunity, differentiation, and transformation, as initiators of carcinogenesis. Dysregulation of interleukins signified the involvement of inflammation in the incipient phases of the process. An aberrant methylation/expression of multiple HOX genes signified dysregulation of the differentiation program. We identified three types of mutations based on their geographic distribution. The most common were mutations restricted to individual mucosal samples that targeted uroprogenitor cells. Two types of mutations were associated with clonal expansion and involved large areas of mucosa. The α mutations occurred at low frequencies while the β mutations increased in frequency with disease progression. Modeling revealed that bladder carcinogenesis spans 10-15 years and can be divided into dormant and progressive phases. The progressive phase lasted 1-2 years and was driven by β mutations.
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Affiliation(s)
- Jolanta Bondaruk
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roman Jaksik
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Ziqiao Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David Cogdell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sangkyou Lee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yujie Chen
- Systems, Synthetic and Physical Biology Program, Rice University, Houston, TX, USA
| | - Khanh Ngoc Dinh
- Department of Statistics and the Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA
| | - Tadeusz Majewski
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhang
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
| | - Shaolong Cao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Feng Tian
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hui Yao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paweł Kuś
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, Gliwice, Poland
| | - Huiqin Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John N. Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neema Navai
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, TX, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai, Los Angeles, CA, USA
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, TX, USA
| | - Charles C. Guo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenyi Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marek Kimmel
- Department of Statistics, Rice University, Houston, TX, USA
| | - Bogdan Czerniak
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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2
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Wang X, Sun J, Wang Z, Li C, Mao B. EphA7 is required for otic epithelial homeostasis by modulating Claudin6 in Xenopus. Biochem Biophys Res Commun 2020; 526:375-380. [PMID: 32222280 DOI: 10.1016/j.bbrc.2020.03.099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 03/18/2020] [Indexed: 12/20/2022]
Abstract
Receptor tyrosine kinase EphA7 is specifically expressed in otic region in Xenopus early development. However, its role in otocyst development remains unknown. Knockdown of EphA7 by a specific morpholino oligonucleotide (MO) reduced the size of the otocyst and triggered otic epithelial cell extrusion. Interestingly, EphA7 depletion attenuated the membrane level of the tight junction protein Claudin6 (CLDN6). Utilizing the Cldn6 MO, we further confirmed that CLDN6 attenuation also led to otic epithelial cell extrusion. Our work suggested that EphA7 modulates the otic epithelial homeostasis through stabilizing the CLDN6 membrane level.
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Affiliation(s)
- Xiaolei Wang
- Medical College, Qingdao University, Qingdao, 266071, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Jian Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China; Cancer and Developmental Biology Laboratory, National Cancer Institute, National Institute of Health, Frederick, MD, 21702, USA
| | - Zhaobao Wang
- School of Control Science and Engineering, Shandong University, Jinan, 250061, China; Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Chaocui Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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Ringers C, Olstad EW, Jurisch-Yaksi N. The role of motile cilia in the development and physiology of the nervous system. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190156. [PMID: 31884916 DOI: 10.1098/rstb.2019.0156] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Motile cilia are miniature, whip-like organelles whose beating generates a directional fluid flow. The flow generated by ciliated epithelia is a subject of great interest, as defective ciliary motility results in severe human diseases called motile ciliopathies. Despite the abundance of motile cilia in diverse organs including the nervous system, their role in organ development and homeostasis remains poorly understood. Recently, much progress has been made regarding the identity of motile ciliated cells and the role of motile-cilia-mediated flow in the development and physiology of the nervous system. In this review, we will discuss these recent advances from sensory organs, specifically the nose and the ear, to the spinal cord and brain ventricles. This article is part of the Theo Murphy meeting issue 'Unity and diversity of cilia in locomotion and transport'.
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Affiliation(s)
- Christa Ringers
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Emilie W Olstad
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Nathalie Jurisch-Yaksi
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway.,Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway.,Department of Neurology and Clinical Neurophysiology, St Olavs University Hospital, Edvard Griegs Gate 8, 7030 Trondheim, Norway
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4
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Garas FN, Kormann E, Shah RS, Vinciati F, Smith Y, Magill PJ, Sharott A. Structural and molecular heterogeneity of calretinin-expressing interneurons in the rodent and primate striatum. J Comp Neurol 2017; 526:877-898. [PMID: 29218729 PMCID: PMC5814860 DOI: 10.1002/cne.24373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 12/25/2022]
Abstract
Calretinin‐expressing (CR+) interneurons are the most common type of striatal interneuron in primates. However, because CR+ interneurons are relatively scarce in rodent striatum, little is known about their molecular and other properties, and they are typically excluded from models of striatal circuitry. Moreover, CR+ interneurons are often treated in models as a single homogenous population, despite previous descriptions of their heterogeneous structures and spatial distributions in rodents and primates. Here, we demonstrate that, in rodents, the combinatorial expression of secretagogin (Scgn), specificity protein 8 (SP8) and/or LIM homeobox protein 7 (Lhx7) separates striatal CR+ interneurons into three structurally and topographically distinct cell populations. The CR+/Scgn+/SP8+/Lhx7− interneurons are small‐sized (typically 7–11 µm in somatic diameter), possess tortuous, partially spiny dendrites, and are rostrally biased in their positioning within striatum. The CR+/Scgn−/SP8−/Lhx7− interneurons are medium‐sized (typically 12–15 µm), have bipolar dendrites, and are homogenously distributed throughout striatum. The CR+/Scgn−/SP8−/Lhx7+ interneurons are relatively large‐sized (typically 12–20 µm), and have thick, infrequently branching dendrites. Furthermore, we provide the first in vivo electrophysiological recordings of identified CR+ interneurons, all of which were the CR+/Scgn−/SP8−/Lhx7− cell type. In the primate striatum, Scgn co‐expression also identified a topographically distinct CR+ interneuron population with a rostral bias similar to that seen in both rats and mice. Taken together, these results suggest that striatal CR+ interneurons comprise at least three molecularly, structurally, and topographically distinct cell populations in rodents. These properties are partially conserved in primates, in which the relative abundance of CR+ interneurons suggests that they play a critical role in striatal microcircuits.
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Affiliation(s)
- Farid N Garas
- Medical Research Council Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Eszter Kormann
- Medical Research Council Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Rahul S Shah
- Medical Research Council Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Federica Vinciati
- Medical Research Council Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Yoland Smith
- Yerkes National Primate Research Center, Department of Neurology and Udall Center of Excellence for Parkinson's Disease Research, Emory University, Atlanta, Georgia
| | - Peter J Magill
- Medical Research Council Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford, Oxford, United Kingdom
| | - Andrew Sharott
- Medical Research Council Brain Network Dynamics Unit, Department of Pharmacology, University of Oxford, Oxford, United Kingdom
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5
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Expression and function of the zinc finger transcription factor Sp6-9 in the spider Parasteatoda tepidariorum. Dev Genes Evol 2017; 227:389-400. [PMID: 29116381 DOI: 10.1007/s00427-017-0595-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/17/2017] [Indexed: 12/22/2022]
Abstract
Zinc finger transcription factors of the Sp6-9 group are evolutionarily conserved in all metazoans and have important functions in, e.g., limb formation and heart development. The function of Sp6-9-related genes has been studied in a number of vertebrates and invertebrates, but data from chelicerates (spiders and allies) was lacking so far. We have isolated the ortholog of Sp6-9 from the common house spider Parasteatoda tepidariorum and the cellar spider Pholcus phalangioides. We show that the Sp6-9 gene in these spider species is expressed in the developing appendages thus suggesting a conserved role in limb formation. Indeed, RNAi with Sp6-9 in P. tepidariorum leads not only to strong limb defects, but also to the loss of body segments and head defects in more strongly affected animals. Together with a new expression domain in the early embryo, these data suggest that Sp6-9 has a dual role P. tepidariorum. The early role in head and body segment formation is not known from other arthropods, but the role in limb formation is evolutionarily highly conserved.
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no privacy, a Xenopus tropicalis mutant, is a model of human Hermansky-Pudlak Syndrome and allows visualization of internal organogenesis during tadpole development. Dev Biol 2017; 426:472-486. [DOI: 10.1016/j.ydbio.2016.08.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/17/2016] [Accepted: 08/17/2016] [Indexed: 11/19/2022]
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7
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Sculpting the labyrinth: Morphogenesis of the developing inner ear. Semin Cell Dev Biol 2017; 65:47-59. [DOI: 10.1016/j.semcdb.2016.09.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/26/2016] [Accepted: 09/25/2016] [Indexed: 01/23/2023]
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8
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Pearl E, Morrow S, Noble A, Lerebours A, Horb M, Guille M. An optimized method for cryogenic storage of Xenopus sperm to maximise the effectiveness of research using genetically altered frogs. Theriogenology 2017; 92:149-155. [PMID: 28237331 PMCID: PMC5340284 DOI: 10.1016/j.theriogenology.2017.01.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/26/2016] [Accepted: 01/04/2017] [Indexed: 02/06/2023]
Abstract
Cryogenic storage of sperm from genetically altered Xenopus improves cost effectiveness and animal welfare associated with their use in research; currently it is routine for X. tropicalis but not reliable for X. laevis. Here we compare directly the three published protocols for Xenopus sperm freeze-thaw and determine whether sperm storage temperature, method of testes maceration and delays in the freezing protocols affect successful fertilisation and embryo development in X. laevis. We conclude that the protocol is robust and that the variability observed in fertilisation rates is due to differences between individuals. We show that the embryos made from the frozen-thawed sperm are normal and that the adults they develop into are reproductively indistinguishable from others in the colony. This opens the way for using cryopreserved sperm to distribute dominant genetically altered (GA) lines, potentially saving travel-induced stress to the male frogs, reducing their numbers used and making Xenopus experiments more cost effective. Xenopus cryopreservation is robust using an optimized method. Success is dependent on the quality of animals from which the sperm are taken. Frozen sperm may now be used to distribute lines and wild-type male gametes around the world.
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Affiliation(s)
- Esther Pearl
- National Xenopus Resource, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Sean Morrow
- European Xenopus Resource Centre, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, UK
| | - Anna Noble
- European Xenopus Resource Centre, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, UK
| | - Adelaide Lerebours
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Marko Horb
- National Xenopus Resource, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Matthew Guille
- European Xenopus Resource Centre, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, PO1 2DT, UK; School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2DY, UK.
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9
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Walentek P, Quigley IK. What we can learn from a tadpole about ciliopathies and airway diseases: Using systems biology in Xenopus to study cilia and mucociliary epithelia. Genesis 2017; 55:10.1002/dvg.23001. [PMID: 28095645 PMCID: PMC5276738 DOI: 10.1002/dvg.23001] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 12/11/2022]
Abstract
Over the past years, the Xenopus embryo has emerged as an incredibly useful model organism for studying the formation and function of cilia and ciliated epithelia in vivo. This has led to a variety of findings elucidating the molecular mechanisms of ciliated cell specification, basal body biogenesis, cilia assembly, and ciliary motility. These findings also revealed the deep functional conservation of signaling, transcriptional, post-transcriptional, and protein networks employed in the formation and function of vertebrate ciliated cells. Therefore, Xenopus research can contribute crucial insights not only into developmental and cell biology, but also into the molecular mechanisms underlying cilia related diseases (ciliopathies) as well as diseases affecting the ciliated epithelium of the respiratory tract in humans (e.g., chronic lung diseases). Additionally, systems biology approaches including transcriptomics, genomics, and proteomics have been rapidly adapted for use in Xenopus, and broaden the applications for current and future translational biomedical research. This review aims to present the advantages of using Xenopus for cilia research, highlight some of the evolutionarily conserved key concepts and mechanisms of ciliated cell biology that were elucidated using the Xenopus model, and describe the potential for Xenopus research to address unresolved questions regarding the molecular mechanisms of ciliopathies and airway diseases.
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Affiliation(s)
- Peter Walentek
- Department of Molecular and Cell Biology; Genetics, Genomics and Development Division; Developmental and Regenerative Biology Group; University of California, Berkeley, CA 94720, USA
| | - Ian K. Quigley
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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10
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Young JJ, Kjolby RAS, Wu G, Wong D, Hsu SW, Harland RM. Noggin is required for first pharyngeal arch differentiation in the frog Xenopus tropicalis. Dev Biol 2016; 426:245-254. [PMID: 27364468 DOI: 10.1016/j.ydbio.2016.06.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/18/2016] [Accepted: 06/24/2016] [Indexed: 02/02/2023]
Abstract
The dorsal ventral axis of vertebrates requires high BMP activity for ventral development and inhibition of BMP activity for dorsal development. Presumptive dorsal regions of the embryo are protected from the ventralizing activity of BMPs by the secretion of BMP antagonists from the mesoderm. Noggin, one such antagonist, binds BMP ligands and prevents them from binding their receptors, however, a unique role for Noggin in amphibian development has remained unclear. Previously, we used zinc-finger nucleases to mutagenize the noggin locus in Xenopus tropicalis. Here, we report on the phenotype of noggin mutant frogs as a result of breeding null mutations to homozygosity. Early homozygous noggin mutant embryos are indistinguishable from wildtype siblings, with normal neural induction and neural tube closure. However, in late tadpole stages mutants present severe ventral craniofacial defects, notably a fusion of Meckel's cartilage to the palatoquadrate cartilage. Consistent with a noggin loss-of-function, mutants show expansions of BMP target gene expression and the mutant phenotype can be rescued with transient BMP inhibition. These results demonstrate that in amphibians, Noggin is dispensable for early embryonic patterning but is critical for cranial skeletogenesis.
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Affiliation(s)
- John J Young
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Rachel A S Kjolby
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Gloria Wu
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Daniel Wong
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Shu-Wei Hsu
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Richard M Harland
- Department of Molecular Cell Biology, University of California, Berkeley, Berkeley, CA 94720, United States
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11
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Van Otterloo E, Williams T, Artinger KB. The old and new face of craniofacial research: How animal models inform human craniofacial genetic and clinical data. Dev Biol 2016; 415:171-187. [PMID: 26808208 DOI: 10.1016/j.ydbio.2016.01.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 01/16/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
The craniofacial skeletal structures that comprise the human head develop from multiple tissues that converge to form the bones and cartilage of the face. Because of their complex development and morphogenesis, many human birth defects arise due to disruptions in these cellular populations. Thus, determining how these structures normally develop is vital if we are to gain a deeper understanding of craniofacial birth defects and devise treatment and prevention options. In this review, we will focus on how animal model systems have been used historically and in an ongoing context to enhance our understanding of human craniofacial development. We do this by first highlighting "animal to man" approaches; that is, how animal models are being utilized to understand fundamental mechanisms of craniofacial development. We discuss emerging technologies, including high throughput sequencing and genome editing, and new animal repository resources, and how their application can revolutionize the future of animal models in craniofacial research. Secondly, we highlight "man to animal" approaches, including the current use of animal models to test the function of candidate human disease variants. Specifically, we outline a common workflow deployed after discovery of a potentially disease causing variant based on a select set of recent examples in which human mutations are investigated in vivo using animal models. Collectively, these topics will provide a pipeline for the use of animal models in understanding human craniofacial development and disease for clinical geneticist and basic researchers alike.
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Affiliation(s)
- Eric Van Otterloo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kristin Bruk Artinger
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Ramírez-Gordillo D, Powers TR, van Velkinburgh JC, Trujillo-Provencio C, Schilkey F, Serrano EE. RNA-Seq and microarray analysis of the Xenopus inner ear transcriptome discloses orthologous OMIM(®) genes for hereditary disorders of hearing and balance. BMC Res Notes 2015; 8:691. [PMID: 26582541 PMCID: PMC4652436 DOI: 10.1186/s13104-015-1485-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 09/21/2015] [Indexed: 12/14/2022] Open
Abstract
Background Auditory and vestibular disorders are prevalent sensory disabilities caused by genetic and environmental (noise, trauma, chemicals) factors that often damage mechanosensory hair cells of the inner ear. Development of treatments for inner ear disorders of hearing and balance relies on the use of animal models such as fish, amphibians, reptiles, birds, and non-human mammals. Here, we aimed to augment the utility of the genus Xenopus for uncovering genetic mechanisms essential for the maintenance of inner ear structure and function. Results Using Affymetrix GeneChip®X. laevis Genome 2.0 Arrays and Illumina-Solexa sequencing methods, we determined that the transcriptional profile of the Xenopuslaevis inner ear comprises hundreds of genes that are orthologous to OMIM® genes implicated in deafness and vestibular disorders in humans. Analysis of genes that mapped to both technologies demonstrated that, with our methods, a combination of microarray and RNA-Seq detected expression of more genes than either platform alone. Conclusions As part of this study we identified candidate scaffold regions of the Xenopus tropicalis genome that can be used to investigate hearing and balance using genetic and informatics procedures that are available through the National Xenopus Resource (NXR), and the open access data repository, Xenbase. The results and approaches presented here expand the viability of Xenopus as an animal model for inner ear research. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1485-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - TuShun R Powers
- Biology Department, New Mexico State University (NMSU), Las Cruces, NM, 88003, USA.
| | | | | | - Faye Schilkey
- National Center for Genome Resources (NCGR), Santa Fe, NM, 87505, USA.
| | - Elba E Serrano
- Biology Department, New Mexico State University (NMSU), Las Cruces, NM, 88003, USA.
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13
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Identifying Regulators of Morphogenesis Common to Vertebrate Neural Tube Closure and Caenorhabditis elegans Gastrulation. Genetics 2015; 202:123-39. [PMID: 26434722 DOI: 10.1534/genetics.115.183137] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 09/29/2015] [Indexed: 12/18/2022] Open
Abstract
Neural tube defects including spina bifida are common and severe congenital disorders. In mice, mutations in more than 200 genes can result in neural tube defects. We hypothesized that this large gene set might include genes whose homologs contribute to morphogenesis in diverse animals. To test this hypothesis, we screened a set of Caenorhabditis elegans homologs for roles in gastrulation, a topologically similar process to vertebrate neural tube closure. Both C. elegans gastrulation and vertebrate neural tube closure involve the internalization of surface cells, requiring tissue-specific gene regulation, actomyosin-driven apical constriction, and establishment and maintenance of adhesions between specific cells. Our screen identified several neural tube defect gene homologs that are required for gastrulation in C. elegans, including the transcription factor sptf-3. Disruption of sptf-3 in C. elegans reduced the expression of early endodermally expressed genes as well as genes expressed in other early cell lineages, establishing sptf-3 as a key contributor to multiple well-studied C. elegans cell fate specification pathways. We also identified members of the actin regulatory WAVE complex (wve-1, gex-2, gex-3, abi-1, and nuo-3a). Disruption of WAVE complex members reduced the narrowing of endodermal cells' apical surfaces. Although WAVE complex members are expressed broadly in C. elegans, we found that expression of a vertebrate WAVE complex member, nckap1, is enriched in the developing neural tube of Xenopus. We show that nckap1 contributes to neural tube closure in Xenopus. This work identifies in vivo roles for homologs of mammalian neural tube defect genes in two manipulable genetic model systems.
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