51
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Meng Y, Zhang W, Zhou J, Liu M, Chen J, Tian S, Zhuo M, Zhang Y, Zhong Y, Du H, Wang X. Genome-wide analysis of positively selected genes in seasonal and non-seasonal breeding species. PLoS One 2015; 10:e0126736. [PMID: 26000771 PMCID: PMC4441472 DOI: 10.1371/journal.pone.0126736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/07/2015] [Indexed: 01/04/2023] Open
Abstract
Some mammals breed throughout the year, while others breed only at certain times of year. These differences in reproductive behavior can be explained by evolution. We identified positively-selected genes in two sets of species with different degrees of relatedness including seasonal and non-seasonal breeding species, using branch-site models. After stringent filtering by sum of pairs scoring, we revealed that more genes underwent positive selection in seasonal compared with non-seasonal breeding species. Positively-selected genes were verified by cDNA mapping of the positive sites with the corresponding cDNA sequences. The design of the evolutionary analysis can effectively lower the false-positive rate and thus identify valid positive genes. Validated, positively-selected genes, including CGA, DNAH1, INVS, and CD151, were related to reproductive behaviors such as spermatogenesis and cell proliferation in non-seasonal breeding species. Genes in seasonal breeding species, including THRAP3, TH1L, and CMTM6, may be related to the evolution of sperm and the circadian rhythm system. Identification of these positively-selected genes might help to identify the molecular mechanisms underlying seasonal and non-seasonal reproductive behaviors.
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Affiliation(s)
- Yuhuan Meng
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Wenlu Zhang
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Jinghui Zhou
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Mingyu Liu
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Junhui Chen
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Shuai Tian
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Min Zhuo
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Yu Zhang
- Guangdong Key Laboratory of Laboratory Animals/Guangdong laboratory animals monitoring institution, Guangzhou, China
| | - Yang Zhong
- School of Life Sciences, Fudan University, Shanghai, China
- Institute of Biodiversity Science, Tibet University, Lhasa, China
| | - Hongli Du
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoning Wang
- School of Bioscience and Bioengineering, Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, China
- Chinese PLA General Hospital, Beijing, China
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52
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Ong ACM, Devuyst O, Knebelmann B, Walz G. Autosomal dominant polycystic kidney disease: the changing face of clinical management. Lancet 2015; 385:1993-2002. [PMID: 26090645 DOI: 10.1016/s0140-6736(15)60907-2] [Citation(s) in RCA: 202] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Autosomal dominant polycystic kidney disease is the most common inherited kidney disease and accounts for 7-10% of all patients on renal replacement therapy worldwide. Although first reported 500 years ago, this disorder is still regarded as untreatable and its pathogenesis is poorly understood despite much study. During the past 40 years, however, remarkable advances have transformed our understanding of how the disease develops and have led to rapid changes in diagnosis, prognosis, and treatment, especially during the past decade. This Review will summarise the key findings, highlight recent developments, and look ahead to the changes in clinical practice that will likely arise from the adoption of a new management framework for this major kidney disease.
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Affiliation(s)
- Albert C M Ong
- Academic Nephrology Unit, University of Sheffield Medical School, Sheffield, UK; Sheffield Kidney Institute, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.
| | - Olivier Devuyst
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland; Division of Nephrology, Université catholique de Louvain, Brussels, Belgium
| | - Bertrand Knebelmann
- Centre de Reference Maladies Rénales Héréditaires MARHEA, AP-HP, Hopital Necker, Université Paris Descartes, Paris, France
| | - Gerd Walz
- Department of Nephrology, University Freiburg Medical Center, Freiburg, Germany
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May-Simera HL, Petralia RS, Montcouquiol M, Wang YX, Szarama KB, Liu Y, Lin W, Deans MR, Pazour GJ, Kelley MW. Ciliary proteins Bbs8 and Ift20 promote planar cell polarity in the cochlea. Development 2015; 142:555-66. [PMID: 25605782 DOI: 10.1242/dev.113696] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Primary cilia have been implicated in the generation of planar cell polarity (PCP). However, variations in the severity of polarity defects in different cilia mutants, coupled with recent demonstrations of non-cilia-related actions of some cilia genes, make it difficult to determine the basis of these polarity defects. To address this issue, we evaluated PCP defects in cochlea from a selection of mice with mutations in cilia-related genes. Results indicated notable PCP defects, including mis-oriented hair cell stereociliary bundles, in Bbs8 and Ift20 single mutants that are more severe than in other cilia gene knockouts. In addition, deletion of either Bbs8 or Ift20 results in disruptions in asymmetric accumulation of the core PCP molecule Vangl2 in cochlear cells, suggesting a role for Bbs8 and/or Ift20, possibly upstream of core PCP asymmetry. Consistent with this, co-immunoprecipitation experiments indicate direct interactions of Bbs8 and Ift20 with Vangl2. We observed localization of Bbs and Ift proteins to filamentous actin as well as microtubules. This could implicate these molecules in selective trafficking of membrane proteins upstream of cytoskeletal reorganization, and identifies new roles for cilia-related proteins in cochlear PCP.
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Affiliation(s)
- Helen L May-Simera
- Section on Developmental Neuroscience, Laboratory of Cochlear Development, National Institute on Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald S Petralia
- Advanced Imaging Core, National Institute on Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mireille Montcouquiol
- Planar Polarity and Plasticity Group, Institut National de la Santé et de la Recherche Médicale U862, Neurocenter Magendie, 33077 Bordeaux, France
| | - Ya-Xian Wang
- Advanced Imaging Core, National Institute on Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine B Szarama
- Section on Developmental Neuroscience, Laboratory of Cochlear Development, National Institute on Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yun Liu
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Weichun Lin
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX 75235, USA
| | - Michael R Deans
- Division of Otolaryngology-Head and Neck Surgery and Department of Neurobiology & Anatomy, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Matthew W Kelley
- Section on Developmental Neuroscience, Laboratory of Cochlear Development, National Institute on Deafness and other Communication Disorders, National Institutes of Health, Bethesda, MD 20892, USA
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54
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Maron JL, Hwang JS, Pathak S, Ruthazer R, Russell RL, Alterovitz G. Computational gene expression modeling identifies salivary biomarker analysis that predict oral feeding readiness in the newborn. J Pediatr 2015; 166:282-8.e5. [PMID: 25620512 PMCID: PMC4306816 DOI: 10.1016/j.jpeds.2014.10.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/05/2014] [Accepted: 10/24/2014] [Indexed: 11/21/2022]
Abstract
OBJECTIVE To combine mathematical modeling of salivary gene expression microarray data and systems biology annotation with reverse-transcription quantitative polymerase chain reaction amplification to identify (phase I) and validate (phase II) salivary biomarker analysis for the prediction of oral feeding readiness in preterm infants. STUDY DESIGN Comparative whole-transcriptome microarray analysis from 12 preterm newborns pre- and postoral feeding success was used for computational modeling and systems biology analysis to identify potential salivary transcripts associated with oral feeding success (phase I). Selected gene expression biomarkers (15 from computational modeling; 6 evidence-based; and 3 reference) were evaluated by reverse-transcription quantitative polymerase chain reaction amplification on 400 salivary samples from successful (n = 200) and unsuccessful (n = 200) oral feeders (phase II). Genes, alone and in combination, were evaluated by a multivariate analysis controlling for sex and postconceptional age (PCA) to determine the probability that newborns achieved successful oral feeding. RESULTS Advancing PCA (P < .001) and female sex (P = .05) positively predicted an infant's ability to feed orally. A combination of 5 genes, neuropeptide Y2 receptor (hunger signaling), adneosine-monophosphate-activated protein kinase (energy homeostasis), plexin A1 (olfactory neurogenesis), nephronophthisis 4 (visual behavior), and wingless-type MMTV integration site family, member 3 (facial development), in addition to PCA and sex, demonstrated good accuracy for determining feeding success (area under the receiver operator characteristic curve = 0.78). CONCLUSIONS We have identified objective and biologically relevant salivary biomarkers that noninvasively assess a newborn's developing brain, sensory, and facial development as they relate to oral feeding success. Understanding the mechanisms that underlie the development of oral feeding readiness through translational and computational methods may improve clinical decision making while decreasing morbidities and health care costs.
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Affiliation(s)
- Jill L Maron
- Division of Newborn Medicine, Mother Infant Research Institute at Tufts Medical Center, Floating Hospital for Children at Tufts Medical Center, Boston, MA.
| | - Jooyeon S Hwang
- Division of Newborn Medicine, Mother Infant Research Institute at Tufts Medical Center, Floating Hospital for Children at Tufts Medical Center, Boston, MA
| | - Subash Pathak
- Research Design Center/Biostatistics Research Center, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA; Tufts Clinical and Translational Science Institute, Tufts University, Boston, MA
| | - Robin Ruthazer
- Research Design Center/Biostatistics Research Center, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA; Tufts Clinical and Translational Science Institute, Tufts University, Boston, MA
| | - Ruby L Russell
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Gil Alterovitz
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA
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55
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Xiang W, Jiang T, Guo F, Xu T, Gong C, Cheng P, Zhao L, Cheng W, Xu K. Evaluating the role of PTH in promotion of chondrosarcoma cell proliferation and invasion by inhibiting primary cilia expression. Int J Mol Sci 2014; 15:19816-31. [PMID: 25365173 PMCID: PMC4264140 DOI: 10.3390/ijms151119816] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/15/2014] [Accepted: 10/23/2014] [Indexed: 01/28/2023] Open
Abstract
Chondrosarcoma is characterized by secretion of a cartilage-like matrix, with high proliferation ability and metastatic potential. Previous studies have shown that parathyroid hormone-related protein (PTHrP) has a close relationship with various tumor types. The objectives of this study were to research the function played by PTHrP in human chondrosarcoma, especially targeting cell proliferation and invasion, and to search for the potential interaction between PTHrP and primary cilia in tumorigenesis. Surgical resection tissues and the human chondrosarcoma cell line SW1353 were used in the scientific research. Cells were stimulated with an optimum concentration of recombinant PTH (1-84), and siRNA was used to interfere with internal PTHrP. Cell proliferation and invasion assays were applied, including MTS-8 cell proliferation assay, Western blot, RT-PCR, Transwell invasion assay, and immunohistochemistry and immunofluorescence assays. A high level of PTHrP expression was found in human chondrosarcoma tissues, and recombinant PTH exhibited positive promotion in tumor cell proliferation and invasion. In the meantime, PTHrP could inhibit the assembly of primary cilia and regulate downstream gene expression. These findings indicate that PTHrP can regulate tumor cell proliferation and invasion ability, possibly through suppression of primary cilia assembly. Thus, restricting PTHrP over-expression is a feasible potential therapeutic method for chondrosarcoma.
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Affiliation(s)
- Wei Xiang
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Ting Jiang
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Fengjing Guo
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Tao Xu
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Chen Gong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Peng Cheng
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Libo Zhao
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Weiting Cheng
- Department of Oncology, Wuhan Integrated Traditional Chinese Medicine and Western Medicine Hospital, Wuhan No1. Hospital, Wuhan 430030, China.
| | - Kai Xu
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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56
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Nguyen PAT, Liou W, Hall DH, Leroux MR. Ciliopathy proteins establish a bipartite signaling compartment in a C. elegans thermosensory neuron. J Cell Sci 2014; 127:5317-30. [PMID: 25335890 DOI: 10.1242/jcs.157610] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
How signaling domains form is an important, yet largely unexplored question. Here, we show that ciliary proteins help establish two contiguous, yet distinct cyclic GMP (cGMP) signaling compartments in Caenorhabditis elegans thermosensory AFD neurons. One compartment, a bona fide cilium, is delineated by proteins associated with Bardet-Biedl syndrome (BBS), Meckel syndrome and nephronophthisis at its base, and requires NPHP-2 (known as inversin in mammals) to anchor a cGMP-gated ion channel within the proximal ciliary region. The other, a subcompartment with profuse microvilli and a different lipid environment, is separated from the dendrite by a cellular junction and requires BBS-8 and DAF-25 (known as Ankmy2 in mammals) for correct localization of guanylyl cyclases needed for thermosensation. Consistent with a requirement for a membrane diffusion barrier at the subcompartment base, we reveal the unexpected presence of ciliary transition zone proteins where no canonical transition zone ultrastructure exists. We propose that differential compartmentalization of signal transduction components by ciliary proteins is important for the functions of ciliated sensory neurons.
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Affiliation(s)
- Phuong Anh T Nguyen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Willisa Liou
- Department of Anatomy, Chang Gung University, Kwei-san Tao-yuan 333, Taiwan
| | - David H Hall
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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57
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Ke YN, Yang WX. Primary cilium: an elaborate structure that blocks cell division? Gene 2014; 547:175-85. [PMID: 24971504 DOI: 10.1016/j.gene.2014.06.050] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 05/07/2014] [Accepted: 06/23/2014] [Indexed: 11/25/2022]
Abstract
A primary cilium is a microtubule-based membranous protrusion found in almost all cell types. A primary cilium has a "9+0" axoneme that distinguishes this ancient organelle from the canonical motile "9+2" cilium. A primary cilium is the sensory center of the cell that regulates cell proliferation and embryonic development. The primary ciliary pocket is a specialized endocytic membrane domain in the basal region. The basal body of a primary cilium exists as a form of the centriole during interphase of the cell cycle. Although conventional thinking suggests that the cell cycle regulates centrosomal changes, recent studies suggest the opposite, that is, centrosomal changes regulate the cell cycle. In this regard, centrosomal kinase Aurora kinase A (AurA), Polo-like kinase 1 (Plk1), and NIMA related Kinase (Nek or Nrk) propel cell cycle progression by promoting primary cilia disassembly which indicates a non-mitotic function. However, the persistence of primary cilia during spermatocyte division challenges the dominate idea of the incompatibility of primary cilia and cell division. In this review, we demonstrate the detailed structure of primary cilia and discuss the relationship between primary cilia disassembly and cell cycle progression on the background of various mitotic kinases.
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Affiliation(s)
- Yi-Ni Ke
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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58
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Powles-Glover N. Cilia and ciliopathies: classic examples linking phenotype and genotype-an overview. Reprod Toxicol 2014; 48:98-105. [PMID: 24859270 DOI: 10.1016/j.reprotox.2014.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 01/22/2023]
Abstract
The importance of the role of cilia in pre and post natal development has been appreciated since the previous century. However, a better understanding of the physiological and, conversely, dysfunctional role that cilia have in developmental disease is still emerging. Dysfunctioning cilia can lead to diseases with a remarkable spectrum of phenotypes ranging from embryofetal lethality, through "classic" organ malformation to severe loss of function that leads to diseases during infancy or more subtle loss of function that may not become apparent until adulthood. Collectively, these diseased are termed ciliopathies. A shift in the focus of research by using tools and models that highlight the similarity between the genetics of mice, zebrafish and human cells, is starting to form an interesting mechanistic picture of how cilia have a role in the developmental pathologies and human diseases. Some of the underlying cellular principles, implicated genes and, where possible, mechanisms will be briefly described in this manuscript and there are several more detailed reviews available [Quinlan et al, 2008; Veland et al, 2009 and Norris and Grimes, 2013].
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Affiliation(s)
- Nicola Powles-Glover
- Astrazeneca, Drug Safety Metabolism, Mereside, Alderley Edge, Cheshire SK10 4TG, UK.
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59
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Oud MM, van Bon BW, Bongers EMHF, Hoischen A, Marcelis CL, de Leeuw N, Mol SJJ, Mortier G, Knoers NVAM, Brunner HG, Roepman R, Arts HH. Early presentation of cystic kidneys in a family with a homozygous INVS mutation. Am J Med Genet A 2014; 164A:1627-34. [PMID: 24677454 DOI: 10.1002/ajmg.a.36501] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 01/27/2014] [Indexed: 11/07/2022]
Abstract
Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease that is the most frequent monogenic cause of end-stage renal disease in children. Infantile NPHP, often in combination with other features like situs inversus, are commonly caused by mutations in the INVS gene. INVS encodes the ciliary protein inversin, and mutations induce dysfunction of the primary cilia. In this article, we present a family with two severely affected fetuses that were aborted after discovery of grossly enlarged cystic kidneys by ultrasonography before 22 weeks gestation. Exome sequencing showed that the fetuses were homozygous for a previously unreported nonsense mutation, resulting in a truncation in the IQ1 domain of inversin. This mutation induces nonsense-mediated RNA decay, as suggested by a reduced RNA level in fibroblasts derived from the fetus. However, a significant amount of mutant INVS RNA was present in these fibroblasts, yielding mutant inversin protein that was mislocalized. In control fibroblasts, inversin was present in the ciliary axoneme as well as at the basal body, whereas in the fibroblasts from the fetus, inversin could only be detected at the basal body. The phenotype of both fetuses is partly characteristic of infantile NPHP and Potter sequence. We also identified that the fetuses had mild skeletal abnormalities, including shortening and bowing of long bones, which may expand the phenotypic spectrum associated with INVS mutations.
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Affiliation(s)
- Machteld M Oud
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Institute for Health Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
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60
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Sung CH, Leroux MR. The roles of evolutionarily conserved functional modules in cilia-related trafficking. Nat Cell Biol 2014; 15:1387-97. [PMID: 24296415 DOI: 10.1038/ncb2888] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cilia are present across most eukaryotic phyla and have diverse sensory and motility roles in animal physiology, cell signalling and development. Their biogenesis and maintenance depend on vesicular and intraciliary (intraflagellar) trafficking pathways that share conserved structural and functional modules. The functional units of the interconnected pathways, which include proteins involved in membrane coating as well as small GTPases and their accessory factors, were first experimentally associated with canonical vesicular trafficking. These components are, however, ancient, having been co-opted by the ancestral eukaryote to establish the ciliary organelle, and their study can inform us about ciliary biology in higher organisms.
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Affiliation(s)
- Ching-Hwa Sung
- Margaret M. Dyson Vision Research Institute, Department of Ophthalmology, Weill Medical College of Cornell University, 1300 York Avenue, New York, New York 10065, USA
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61
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Surface topography regulates wnt signaling through control of primary cilia structure in mesenchymal stem cells. Sci Rep 2013; 3:3545. [PMID: 24346024 PMCID: PMC3866595 DOI: 10.1038/srep03545] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 12/03/2013] [Indexed: 12/22/2022] Open
Abstract
The primary cilium regulates cellular signalling including influencing wnt sensitivity by sequestering β-catenin within the ciliary compartment. Topographic regulation of intracellular actin-myosin tension can control stem cell fate of which wnt is an important mediator. We hypothesized that topography influences mesenchymal stem cell (MSC) wnt signaling through the regulation of primary cilia structure and function. MSCs cultured on grooves expressed elongated primary cilia, through reduced actin organization. siRNA inhibition of anterograde intraflagellar transport (IFT88) reduced cilia length and increased active nuclear β-catenin. Conversely, increased primary cilia assembly in MSCs cultured on the grooves was associated with decreased levels of nuclear active β-catenin, axin-2 induction and proliferation, in response to wnt3a. This negative regulation, on grooved topography, was reversed by siRNA to IFT88. This indicates that subtle regulation of IFT and associated cilia structure, tunes the wnt response controlling stem cell differentiation.
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62
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Koefoed K, Veland IR, Pedersen LB, Larsen LA, Christensen ST. Cilia and coordination of signaling networks during heart development. Organogenesis 2013; 10:108-25. [PMID: 24345806 DOI: 10.4161/org.27483] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Primary cilia are unique sensory organelles that coordinate a wide variety of different signaling pathways to control cellular processes during development and in tissue homeostasis. Defects in function or assembly of these antenna-like structures are therefore associated with a broad range of developmental disorders and diseases called ciliopathies. Recent studies have indicated a major role of different populations of cilia, including nodal and cardiac primary cilia, in coordinating heart development, and defects in these cilia are associated with congenital heart disease. Here, we present an overview of the role of nodal and cardiac primary cilia in heart development.
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Affiliation(s)
- Karen Koefoed
- Department of Biology; University of Copenhagen; Copenhagen, Denmark; Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen, Denmark
| | - Iben Rønn Veland
- Department of Biology; University of Copenhagen; Copenhagen, Denmark
| | | | - Lars Allan Larsen
- Wilhelm Johannsen Centre for Functional Genome Research; Department of Cellular and Molecular Medicine; University of Copenhagen; Copenhagen, Denmark
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63
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Abstract
Primary cilia are generally solitary organelles that emanate from the surface of almost all vertebrate cell types. Until recently, details regarding the function of these structures were lacking; however, extensive evidence now suggests that primary cilia have critical roles in sensing the extracellular environment, and in coordinating developmental and homeostatic signalling pathways. Furthermore, disruption of these functions seems to underlie a diverse spectrum of disorders, known as primary ciliopathies. These disorders are characterized by wide-ranging clinical and genetic heterogeneity, but with substantial overlap among distinct conditions. Indeed, ciliopathies are associated with a large variety of manifestations that often include distinctive neurological findings. Herein, we review neurological features associated with primary ciliopathies, highlight genotype-phenotype correlations, and discuss potential mechanisms underlying these findings.
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64
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Seeger-Nukpezah T, Little JL, Serzhanova V, Golemis EA. Cilia and cilia-associated proteins in cancer. ACTA ACUST UNITED AC 2013; 10:e135-e142. [PMID: 24982684 DOI: 10.1016/j.ddmec.2013.03.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The primary cilium is a well-established target in the pathogenesis of numerous developmental and chronic disorders, and more recently is attracting interest as a structure relevant to cancer. Here we discuss mechanisms by which changes in cilia can contribute to the formation and growth of tumors. We emphasize the cancer-relevance of cilia-dependent signaling pathways and proteins including mTOR, VHL, TSC, WNT, Aurora-A, NEDD9, and Hedgehog, and highlight the emerging role of ciliary dysfunction in renal cell carcinoma, medulloblastoma, and breast cancer.
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Affiliation(s)
| | - Joy L Little
- Program in Developmental Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Victoria Serzhanova
- Program in Developmental Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Erica A Golemis
- Program in Developmental Therapeutics, Fox Chase Cancer Center, Philadelphia, PA 19111
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65
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Mitchell KAP. Isolation of primary cilia by shear force. CURRENT PROTOCOLS IN CELL BIOLOGY 2013; Chapter 3:3.42.1-3.42.9. [PMID: 23728745 DOI: 10.1002/0471143030.cb0342s59] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The cell's primary cilium is both a mechanical and chemical sensor involved in many signaling pathways. In order to ascertain protein enrichment in the primary cilium or study sub-ciliary localization of various proteins, it is advantageous to remove the primary cilium from the cell body. The protocol described here gives detailed instructions on purifying primary cilia by separating them from the cell body using shear force. This simple technique avoids using harsh purification conditions that may affect signaling proteins in the cilium or cause the ciliary membrane to disintegrate. In addition, as the cell body remains mostly intact, contamination of the isolated cilia by proteins from the cell body is minimized. This protocol is ideally suited for isolating cilia from renal cell lines, as primary cilia in these cells grow to greater lengths than in other cell types (up to 50-µm long in Xenopus A6 toad kidney cells as opposed to 1 to 5 µm in NIH3T3 fibroblast cells).
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Clement C, Ajbro K, Koefoed K, Vestergaard M, Veland I, Henriques de Jesus M, Pedersen L, Benmerah A, Andersen C, Larsen L, Christensen S. TGF-β Signaling Is Associated with Endocytosis at the Pocket Region of the Primary Cilium. Cell Rep 2013; 3:1806-14. [DOI: 10.1016/j.celrep.2013.05.020] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 03/21/2013] [Accepted: 05/13/2013] [Indexed: 12/28/2022] Open
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Veland IR, Montjean R, Eley L, Pedersen LB, Schwab A, Goodship J, Kristiansen K, Pedersen SF, Saunier S, Christensen ST. Inversin/Nephrocystin-2 is required for fibroblast polarity and directional cell migration. PLoS One 2013; 8:e60193. [PMID: 23593172 PMCID: PMC3620528 DOI: 10.1371/journal.pone.0060193] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/22/2013] [Indexed: 12/30/2022] Open
Abstract
Inversin is a ciliary protein that critically regulates developmental processes and tissue homeostasis in vertebrates, partly through the degradation of Dishevelled (Dvl) proteins to coordinate Wnt signaling in planar cell polarity (PCP). Here, we investigated the role of Inversin in coordinating cell migration, which highly depends on polarity processes at the single-cell level, including the spatial and temporal organization of the cytoskeleton as well as expression and cellular localization of proteins in leading edge formation of migrating cells. Using cultures of mouse embryonic fibroblasts (MEFs) derived from inv(-/-) and inv(+/+) animals, we confirmed that both inv(-/-) and inv(+/+) MEFs form primary cilia, and that Inversin localizes to the primary cilium in inv(+/+) MEFs. In wound healing assays, inv(-/-) MEFs were severely compromised in their migratory ability and exhibited cytoskeletal rearrangements, including distorted lamellipodia formation and cilia orientation. Transcriptome analysis revealed dysregulation of Wnt signaling and of pathways regulating actin organization and focal adhesions in inv(-/-) MEFs as compared to inv(+/+) MEFs. Further, Dvl-1 and Dvl-3 localized to MEF primary cilia, and β-catenin/Wnt signaling was elevated in inv(-/-) MEFs, which moreover showed reduced ciliary localization of Dvl-3. Finally, inv(-/-) MEFs displayed dramatically altered activity and localization of RhoA, Rac1, and Cdc42 GTPases, and aberrant expression and targeting of the Na(+)/H(+) exchanger NHE1 and ezrin/radixin/moesin (ERM) proteins to the edge of cells facing the wound. Phosphorylation of β-catenin at the ciliary base and formation of well-defined lamellipodia with localization and activation of ERM to the leading edge of migrating cells were restored in inv(-/-) MEFs expressing Inv-GFP. Collectively, our findings point to the significance of Inversin in controlling cell migration processes, at least in part through transcriptional regulation of genes involved in Wnt signaling and pathways that control cytoskeletal organization and ion transport.
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Affiliation(s)
- Iben R. Veland
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rodrick Montjean
- Inserm U-983, Imagine Institut, Paris Descartes-Sorbonne Paris Cité University, Necker Hospital, Paris, France
| | - Lorraine Eley
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lotte B. Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albrecht Schwab
- Institute of Physiology II, Münster University, Münster, Germany
| | - Judith Goodship
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Stine F. Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sophie Saunier
- Inserm U-983, Imagine Institut, Paris Descartes-Sorbonne Paris Cité University, Necker Hospital, Paris, France
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Abstract
The centrosome is the main microtubule-organizing center in animal cells, and helps to influence the morphology of the microtubule cytoskeleton in interphase and mitosis. The centrosome also templates the assembly of the primary cilium, and together they serve as a nexus of cell signaling that provide cells with diverse organization, motility, and sensory functions. The majority of cells in the human body contain a solitary centrosome and cilium, and cells have evolved regulatory mechanisms to precisely control the numbers of these essential organelles. Defects in the structure and function of cilia lead to a variety of complex disease phenotypes termed ciliopathies, while dysregulation of centrosome number has long been proposed to induce genome instability and tumor formation. Here, we review recent findings that link centrosome amplification to changes in cilium number and signaling capacity, and discuss how supernumerary centrosomes may be an important aspect of a set of cilia-related disease phenotypes.
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Affiliation(s)
- Moe R Mahjoub
- Department of Medicine, Washington University, St Louis, MO, USA.
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Yu H, Ye X, Guo N, Nathans J. Frizzled 2 and frizzled 7 function redundantly in convergent extension and closure of the ventricular septum and palate: evidence for a network of interacting genes. Development 2012; 139:4383-94. [PMID: 23095888 DOI: 10.1242/dev.083352] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Frizzled (Fz) 2 and Fz7, together with Fz1, form a distinct subfamily within the Frizzled family of Wnt receptors. Using targeted gene deletion, we show that: Fz7(-/-) mice exhibit tail truncation and kinking with 100% penetrance and ventricular septal defects (VSDs) with ~15% penetrance; Fz2(+/-);Fz7(-/-) mice exhibit VSDs with ~50% penetrance and cleft palate with less than 10% penetrance; and Fz2(-/-);Fz7(-/-) mice exhibit convergent extension defects and mid-gestational lethality with 100% penetrance. When Fz2 and/or Fz7 mutations are combined with mutations in Vangl2, Dvl3, Wnt3a, Wnt5a or Wnt11, an increased frequency of VSDs is observed with Dvl3, Wnt3a and Wnt11; an increased frequency of palate closure defects is observed with Vangl2; and early lethality and enhanced tail shortening are observed with Wnt5a. To assess the signaling pathways that underlie these and other Frizzled-mediated genetic interactions, we used transfected mammalian cells to analyze (1) canonical Wnt signaling induced by all pairwise combinations of the ten mouse Frizzleds and the 19 mouse Wnts and (2) localization of each Frizzled at cell-cell junctional complexes formed by mouse Celsr1, a likely indicator of competence for planar cell polarity signaling. These in vitro experiments indicate that Fz2 and Fz7 are competent to signal via the canonical pathway. Taken together, the data suggest that genetic interactions between Fz2, Fz7 and Vangl2, Dvl3 and Wnt genes reflect interactions among different signaling pathways in developmental processes that are highly sensitive to perturbations in Frizzled signaling.
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Affiliation(s)
- Huimin Yu
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MA 21205, USA
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Rao S, Ge S, Shelly M. Centrosome positioning and primary cilia assembly orchestrate neuronal development. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s11515-012-1231-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ronquillo CC, Bernstein PS, Baehr W. Senior-Løken syndrome: a syndromic form of retinal dystrophy associated with nephronophthisis. Vision Res 2012; 75:88-97. [PMID: 22819833 DOI: 10.1016/j.visres.2012.07.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 07/06/2012] [Accepted: 07/09/2012] [Indexed: 02/06/2023]
Abstract
Senior-Løken syndrome (SLS) is an autosomal recessive disease characterized by development of a retinitis pigmentosa (RP)- or Leber congenital amaurosis (LCA)-like retinal dystrophy and a medullary cystic kidney disease, nephronophthisis. Mutations in several genes (called nephrocystins) have been shown to cause SLS. The proteins encoded by these genes are localized in the connecting cilium of photoreceptor cells and in the primary cilium of kidney cells. Nephrocystins are thought to have a role in regulating transport of proteins bound to the outer segment/primary cilium; however, the precise molecular mechanisms are largely undetermined. This review will survey the biochemistry, cell biology and existing animal models for each of the nephrocystins as it relates to photoreceptor biology and pathogenesis of retinal degeneration.
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Affiliation(s)
- C C Ronquillo
- Program in Neuroscience, University of Utah Health Science Center, Salt Lake City, UT 84132, USA
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Borgal L, Habbig S, Hatzold J, Liebau MC, Dafinger C, Sacarea I, Hammerschmidt M, Benzing T, Schermer B. The ciliary protein nephrocystin-4 translocates the canonical Wnt regulator Jade-1 to the nucleus to negatively regulate β-catenin signaling. J Biol Chem 2012; 287:25370-80. [PMID: 22654112 DOI: 10.1074/jbc.m112.385658] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nephronophthisis (NPH) is an autosomal-recessive cystic kidney disease and represents the most common genetic cause for end-stage renal disease in children and adolescents. It can be caused by the mutation of genes encoding for the nephrocystin proteins (NPHPs). All NPHPs localize to primary cilia, classifying this disease as a "ciliopathy." The primary cilium is a critical regulator of several cell signaling pathways. Cystogenesis in the kidney is thought to involve overactivation of canonical Wnt signaling, which is negatively regulated by the primary cilium and several NPH proteins, although the mechanism remains unclear. Jade-1 has recently been identified as a novel ubiquitin ligase targeting the canonical Wnt downstream effector β-catenin for proteasomal degradation. Here, we identify Jade-1 as a novel component of the NPHP protein complex. Jade-1 colocalizes with NPHP1 at the transition zone of primary cilia and interacts with NPHP4. Furthermore, NPHP4 stabilizes protein levels of Jade-1 and promotes the translocation of Jade-1 to the nucleus. Finally, NPHP4 and Jade-1 additively inhibit canonical Wnt signaling, and this genetic interaction is conserved in zebrafish. The stabilization and nuclear translocation of Jade-1 by NPHP4 enhances the ability of Jade-1 to negatively regulate canonical Wnt signaling. Loss of this repressor function in nephronophthisis might be an important factor promoting Wnt activation and contributing to cyst formation.
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Affiliation(s)
- Lori Borgal
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany
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May-Simera HL, Kelley MW. Cilia, Wnt signaling, and the cytoskeleton. Cilia 2012; 1:7. [PMID: 23351924 PMCID: PMC3555707 DOI: 10.1186/2046-2530-1-7] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Accepted: 05/02/2012] [Indexed: 12/14/2022] Open
Abstract
Primary cilia have recently been highlighted as key regulators in development and disease. This review focuses on current work demonstrating the broad role of cilia-related proteins in developmental signaling systems. Of particular consideration is the importance of the basal body region, located at the base of the cilium, in its role as a focal point for many signaling pathways and as a microtubule organizing center. As the cilium is effectively a microtubular extension of the cytoskeleton, investigating connections between the cilium and the cytoskeleton provides greater insight into signaling and cell function. Of the many signaling pathways associated with primary cilia, the most extensively studied in association with the cytoskeleton and cytoskeletal rearrangements are both canonical and non-canonical Wnt pathways. One of the key concepts currently emerging is a possible additional role for the traditionally 'cilia-related' proteins in other aspects of cellular processes. In many cases, disruption of such processes manifests at the level of the cilium. While the involvement of cilia and cilia-related proteins in signaling pathways is currently being unraveled, there is a growing body of evidence to support the notion that ciliary proteins are required not only for regulation of Wnt signaling, but also as downstream effectors of Wnt signaling. This review summarizes recent advances in our understanding of the involvement of cilia and basal body proteins in Wnt signaling pathways.
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Affiliation(s)
- Helen L May-Simera
- Laboratory of Cochlear Development, National Institute on Deafness and Other Communication Disorders, NIH, 35 Convent Drive, Bethesda, MD 20892, USA.
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Abstract
The inner ears of vertebrates represent one of the most striking examples of planar cell polarity (PCP). Populations of directionally sensitive mechanosensory hair cells develop actin-based stereociliary bundles that are uniformly oriented. Analysis of perturbations in bundle polarity in mice with mutations in Vangl2 formed the basis for the initial demonstration of conservation of the PCP signaling pathway in vertebrates. Subsequent studies have demonstrated roles for other "core" PCP genes, such as Frizzled, Disheveled, and Celsr, and for identifying novel PCP molecules such as Scribble and Ptk7. In addition, the demonstration of hearing deficits in humans with mutations in cilia genes combined with analysis of PCP defects in mice with ciliary deletion has implicated the cilia as an important modulator of hair cell polarization. Finally, the presence of shortened cochleae in many PCP mouse mutants has revealed an additional role for the PCP pathway in the development of the auditory system.
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Affiliation(s)
- Helen May-Simera
- Laboratory of Cochlear Development, NIDCD, NIH, Bethesda, Maryland, USA
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