1
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Wales-McGrath B, Mercer H, Piontkivska H. Changes in ADAR RNA editing patterns in CMV and ZIKV congenital infections. BMC Genomics 2023; 24:685. [PMID: 37968596 PMCID: PMC10652522 DOI: 10.1186/s12864-023-09778-4] [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: 06/18/2023] [Accepted: 10/31/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND RNA editing is a process that increases transcriptome diversity, often through Adenosine Deaminases Acting on RNA (ADARs) that catalyze the deamination of adenosine to inosine. ADAR editing plays an important role in regulating brain function and immune activation, and is dynamically regulated during brain development. Additionally, the ADAR1 p150 isoform is induced by interferons in viral infection and plays a role in antiviral immune response. However, the question of how virus-induced ADAR expression affects host transcriptome editing remains largely unanswered. This question is particularly relevant in the context of congenital infections, given the dynamic regulation of ADAR editing during brain development, the importance of this editing for brain function, and subsequent neurological symptoms of such infections, including microcephaly, sensory issues, and other neurodevelopmental abnormalities. Here, we begin to address this question, examining ADAR expression in publicly available datasets of congenital infections of human cytomegalovirus (HCMV) microarray expression data, as well as mouse cytomegalovirus (MCMV) and mouse/ human induced pluripotent neuroprogenitor stem cell (hiNPC) Zika virus (ZIKV) RNA-seq data. RESULTS We found that in all three datasets, ADAR1 was overexpressed in infected samples compared to uninfected samples. In the RNA-seq datasets, editing rates were also analyzed. In all mouse infections cases, the number of editing sites was significantly increased in infected samples, albeit this was not the case for hiNPC ZIKV samples. Mouse ZIKV samples showed altered editing of well-established protein-recoding sites such as Gria3, Grik5, and Nova1, as well as editing sites that may impact miRNA binding. CONCLUSIONS Our findings provide evidence for changes in ADAR expression and subsequent dysregulation of ADAR editing of host transcriptomes in congenital infections. These changes in editing patterns of key neural genes have potential significance in the development of neurological symptoms, thus contributing to neurodevelopmental abnormalities. Further experiments should be performed to explore the full range of editing changes that occur in different congenital infections, and to confirm the specific functional consequences of these editing changes.
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Affiliation(s)
- Benjamin Wales-McGrath
- University of Pennsylvania, Perelman School of Medicine, Department of Genetics, Philadelphia, PA, USA
- Children's Hospital of Philadelphia, Division of Cancer Pathobiology, Philadelphia, PA, USA
| | - Heather Mercer
- Department of Biological and Environmental Sciences, University of Mount Union, Alliance, OH, USA
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, USA.
- School of Biomedical Sciences, Kent State University, Kent, OH, USA.
- Brain Health Research Institute, Kent State University, Kent, OH, USA.
- Healthy Communities Research Institute, Kent State University, Kent, OH, USA.
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2
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Abstract
Phosphoinositides (PIs) are phospholipids derived from phosphatidylinositol. PIs are regulated via reversible phosphorylation, which is directed by the opposing actions of PI kinases and phosphatases. PIs constitute a minor fraction of the total cellular lipid pool but play pleiotropic roles in multiple aspects of cell biology. Genetic mutations of PI regulatory enzymes have been identified in rare congenital developmental syndromes, including ciliopathies, and in numerous human diseases, such as cancer and metabolic and neurological disorders. Accordingly, PI regulatory enzymes have been targeted in the design of potential therapeutic interventions for human diseases. Recent advances place PIs as central regulators of membrane dynamics within functionally distinct subcellular compartments. This brief review focuses on the emerging role PIs play in regulating cell signaling within the primary cilium and in directing transfer of molecules at interorganelle membrane contact sites and identifies new roles for PIs in subcellular spaces.
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Affiliation(s)
- Elizabeth Michele Davies
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Christina Anne Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Harald Alfred Stenmark
- Department of Molecular Cell Biology, Institute for Cancer Research. The Norwegian Radium Hospital, Montebello, N-0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, N-0379 Oslo, Norway
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3
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The Role of Primary Cilia-Associated Phosphoinositide Signaling in Development. J Dev Biol 2022; 10:jdb10040051. [PMID: 36547473 PMCID: PMC9785882 DOI: 10.3390/jdb10040051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/07/2022] Open
Abstract
Primary cilia are microtube-based organelles that extend from the cell surface and function as biochemical and mechanical extracellular signal sensors. Primary cilia coordinate a series of signaling pathways during development. Cilia dysfunction leads to a pleiotropic group of developmental disorders, termed ciliopathy. Phosphoinositides (PIs), a group of signaling phospholipids, play a crucial role in development and tissue homeostasis by regulating membrane trafficking, cytoskeleton reorganization, and organelle identity. Accumulating evidence implicates the involvement of PI species in ciliary defects and ciliopathies. The abundance and localization of PIs in the cell are tightly regulated by the opposing actions of kinases and phosphatases, some of which are recently discovered in the context of primary cilia. Here, we review several cilium-associated PI kinases and phosphatases, including their localization along cilia, function in regulating the ciliary biology under normal conditions, as well as the connection of their disease-associated mutations with ciliopathies.
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4
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Hawe JS, Saha A, Waldenberger M, Kunze S, Wahl S, Müller-Nurasyid M, Prokisch H, Grallert H, Herder C, Peters A, Strauch K, Theis FJ, Gieger C, Chambers J, Battle A, Heinig M. Network reconstruction for trans acting genetic loci using multi-omics data and prior information. Genome Med 2022; 14:125. [PMID: 36344995 PMCID: PMC9641770 DOI: 10.1186/s13073-022-01124-9] [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: 06/15/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Molecular measurements of the genome, the transcriptome, and the epigenome, often termed multi-omics data, provide an in-depth view on biological systems and their integration is crucial for gaining insights in complex regulatory processes. These data can be used to explain disease related genetic variants by linking them to intermediate molecular traits (quantitative trait loci, QTL). Molecular networks regulating cellular processes leave footprints in QTL results as so-called trans-QTL hotspots. Reconstructing these networks is a complex endeavor and use of biological prior information can improve network inference. However, previous efforts were limited in the types of priors used or have only been applied to model systems. In this study, we reconstruct the regulatory networks underlying trans-QTL hotspots using human cohort data and data-driven prior information. METHODS We devised a new strategy to integrate QTL with human population scale multi-omics data. State-of-the art network inference methods including BDgraph and glasso were applied to these data. Comprehensive prior information to guide network inference was manually curated from large-scale biological databases. The inference approach was extensively benchmarked using simulated data and cross-cohort replication analyses. Best performing methods were subsequently applied to real-world human cohort data. RESULTS Our benchmarks showed that prior-based strategies outperform methods without prior information in simulated data and show better replication across datasets. Application of our approach to human cohort data highlighted two novel regulatory networks related to schizophrenia and lean body mass for which we generated novel functional hypotheses. CONCLUSIONS We demonstrate that existing biological knowledge can improve the integrative analysis of networks underlying trans associations and generate novel hypotheses about regulatory mechanisms.
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Affiliation(s)
- Johann S Hawe
- Institute of Computational Biology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany.,German Heart Centre Munich, Department of Cardiology, Technical University Munich, Munich, Germany.,Department of Informatics, Technical University of Munich, Garching, Germany
| | - Ashis Saha
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany
| | - Sonja Kunze
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany
| | - Simone Wahl
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany.,IBE, Faculty of Medicine, LMU Munich, 81377, Munich, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany.,Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany.,Institute of Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Christian Herder
- German Center for Diabetes Research (DZD), Neuherberg, Germany.,Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany.,Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Annette Peters
- Institute of Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany.,Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany.,Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Fabian J Theis
- Department of Informatics, Technical University of Munich, Garching, Germany.,Department of Mathematics, Technical University of Munich, Garching, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany.,Institute of Epidemiology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - John Chambers
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Lee Kong Chian School of Medicine, Nanyang Technological University, 308232, Singapore, Singapore
| | - Alexis Battle
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Matthias Heinig
- Institute of Computational Biology, German Research Center for Environmental Health, HelmholtzZentrum München, Neuherberg, Germany. .,Department of Informatics, Technical University of Munich, Garching, Germany. .,Munich Heart Association, Partner Site Munich, DZHK (German Centre for Cardiovascular Research), 10785, Berlin, Germany.
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5
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Cilleros-Rodriguez D, Martin-Morales R, Barbeito P, Deb Roy A, Loukil A, Sierra-Rodero B, Herranz G, Pampliega O, Redrejo-Rodriguez M, Goetz SC, Izquierdo M, Inoue T, Garcia-Gonzalo FR. Multiple ciliary localization signals control INPP5E ciliary targeting. eLife 2022; 11:78383. [PMID: 36063381 PMCID: PMC9444247 DOI: 10.7554/elife.78383] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/21/2022] [Indexed: 12/04/2022] Open
Abstract
Primary cilia are sensory membrane protrusions whose dysfunction causes ciliopathies. INPP5E is a ciliary phosphoinositide phosphatase mutated in ciliopathies like Joubert syndrome. INPP5E regulates numerous ciliary functions, but how it accumulates in cilia remains poorly understood. Herein, we show INPP5E ciliary targeting requires its folded catalytic domain and is controlled by four conserved ciliary localization signals (CLSs): LLxPIR motif (CLS1), W383 (CLS2), FDRxLYL motif (CLS3) and CaaX box (CLS4). We answer two long-standing questions in the field. First, partial CLS1-CLS4 redundancy explains why CLS4 is dispensable for ciliary targeting. Second, the essential need for CLS2 clarifies why CLS3-CLS4 are together insufficient for ciliary accumulation. Furthermore, we reveal that some Joubert syndrome mutations perturb INPP5E ciliary targeting, and clarify how each CLS works: (i) CLS4 recruits PDE6D, RPGR and ARL13B, (ii) CLS2-CLS3 regulate association to TULP3, ARL13B, and CEP164, and (iii) CLS1 and CLS4 cooperate in ATG16L1 binding. Altogether, we shed light on the mechanisms of INPP5E ciliary targeting, revealing a complexity without known parallels among ciliary cargoes.
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Affiliation(s)
- Dario Cilleros-Rodriguez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Raquel Martin-Morales
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pablo Barbeito
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Abhijit Deb Roy
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Abdelhalim Loukil
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, United States
| | - Belen Sierra-Rodero
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Gonzalo Herranz
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Olatz Pampliega
- Department of Neurosciences, University of the Basque Country, Achucarro Basque Center for Neuroscience-UPV/EHU, Leioa, Spain
| | - Modesto Redrejo-Rodriguez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Sarah C Goetz
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, United States
| | - Manuel Izquierdo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Takanari Inoue
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Francesc R Garcia-Gonzalo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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6
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Xie C, Habif JC, Ukhanov K, Uytingco CR, Zhang L, Campbell RJ, Martens JR. Reversal of ciliary mechanisms of disassembly rescues olfactory dysfunction in ciliopathies. JCI Insight 2022; 7:158736. [PMID: 35771640 PMCID: PMC9462494 DOI: 10.1172/jci.insight.158736] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Abstract
Ciliopathies are a class of genetic diseases resulting in cilia dysfunction in multiple organ systems, including the olfactory system. Currently, there are no available curative treatments for olfactory dysfunction and other symptoms in ciliopathies. The loss or shortening of olfactory cilia, as seen in multiple mouse models of the ciliopathy Bardet–Biedl syndrome (BBS), results in olfactory dysfunction. However, the underlying mechanism of the olfactory cilia reduction is unknown, thus limiting the development of therapeutic approaches for BBS and other ciliopathies. Here, we demonstrated that phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2], a phosphoinositide typically excluded from olfactory cilia, aberrantly redistributed into the residual cilia of BBS mouse models, which caused F-actin ciliary infiltration. Importantly, PI(4,5)P2 and F-actin were necessary for olfactory cilia shortening. Using a gene therapeutic approach, the hydrolyzation of PI(4,5)P2 by overexpression of inositol polyphosphate-5-phosphatase E (INPP5E) restored cilia length and rescued odor detection and odor perception in BBS. Together, our data indicate that PI(4,5)P2/F-actin–dependent cilia disassembly is a common mechanism contributing to the loss of olfactory cilia in BBS and provide valuable pan-therapeutic intervention targets for the treatment of ciliopathies.
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Affiliation(s)
- Chao Xie
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, United States of America
| | - Julien C Habif
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, United States of America
| | - Kirill Ukhanov
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, United States of America
| | - Cedric R Uytingco
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, United States of America
| | - Lian Zhang
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, United States of America
| | - Robert J Campbell
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, United States of America
| | - Jeffrey R Martens
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, Gainesville, United States of America
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7
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Rusterholz TDS, Hofmann C, Bachmann-Gagescu R. Insights Gained From Zebrafish Models for the Ciliopathy Joubert Syndrome. Front Genet 2022; 13:939527. [PMID: 35846153 PMCID: PMC9280682 DOI: 10.3389/fgene.2022.939527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/26/2022] [Indexed: 12/04/2022] Open
Abstract
Cilia are quasi-ubiquitous microtubule-based sensory organelles, which play vital roles in signal transduction during development and cell homeostasis. Dysfunction of cilia leads to a group of Mendelian disorders called ciliopathies, divided into different diagnoses according to clinical phenotype constellation and genetic causes. Joubert syndrome (JBTS) is a prototypical ciliopathy defined by a diagnostic cerebellar and brain stem malformation termed the “Molar Tooth Sign” (MTS), in addition to which patients display variable combinations of typical ciliopathy phenotypes such as retinal dystrophy, fibrocystic renal disease, polydactyly or skeletal dystrophy. Like most ciliopathies, JBTS is genetically highly heterogeneous with ∼40 associated genes. Zebrafish are widely used to model ciliopathies given the high conservation of ciliary genes and the variety of specialized cilia types similar to humans. In this review, we compare different existing JBTS zebrafish models with each other and describe their contributions to our understanding of JBTS pathomechanism. We find that retinal dystrophy, which is the most investigated ciliopathy phenotype in zebrafish ciliopathy models, is caused by distinct mechanisms according to the affected gene. Beyond this, differences in phenotypes in other organs observed between different JBTS-mutant models suggest tissue-specific roles for proteins implicated in JBTS. Unfortunately, the lack of systematic assessment of ciliopathy phenotypes in the mutants described in the literature currently limits the conclusions that can be drawn from these comparisons. In the future, the numerous existing JBTS zebrafish models represent a valuable resource that can be leveraged in order to gain further insights into ciliary function, pathomechanisms underlying ciliopathy phenotypes and to develop treatment strategies using small molecules.
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Affiliation(s)
- Tamara D. S. Rusterholz
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Claudia Hofmann
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- *Correspondence: Ruxandra Bachmann-Gagescu,
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8
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Van De Weghe JC, Gomez A, Doherty D. The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies. Annu Rev Genomics Hum Genet 2022; 23:301-329. [PMID: 35655331 DOI: 10.1146/annurev-genom-121321-093528] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Joubert syndrome (JS), Meckel syndrome (MKS), and nephronophthisis (NPH) ciliopathy spectrum could be the poster child for advances and challenges in Mendelian human genetics over the past half century. Progress in understanding these conditions illustrates many core concepts of human genetics. The JS phenotype alone is caused by pathogenic variants in more than 40 genes; remarkably, all of the associated proteins function in and around the primary cilium. Primary cilia are near-ubiquitous, microtubule-based organelles that play crucial roles in development and homeostasis. Protruding from the cell, these cellular antennae sense diverse signals and mediate Hedgehog and other critical signaling pathways. Ciliary dysfunction causes many human conditions termed ciliopathies, which range from multiple congenital malformations to adult-onset single-organ failure. Research on the genetics of the JS-MKS-NPH spectrum has spurred extensive functional work exploring the broadly important role of primary cilia in health and disease. This functional work promises to illuminate the mechanisms underlying JS-MKS-NPH in humans, identify therapeutic targets across genetic causes, and generate future precision treatments. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
| | - Arianna Gomez
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Molecular Medicine and Mechanisms of Disease Program, Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA;
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA; .,Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA;
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9
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Cilia and their role in neural tube development and defects. REPRODUCTIVE AND DEVELOPMENTAL MEDICINE 2022. [DOI: 10.1097/rd9.0000000000000014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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10
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Devane J, Ott E, Olinger EG, Epting D, Decker E, Friedrich A, Bachmann N, Renschler G, Eisenberger T, Briem-Richter A, Grabhorn EF, Powell L, Wilson IJ, Rice SJ, Miles CG, Wood K, Trivedi P, Hirschfield G, Pietrobattista A, Wohler E, Mezina A, Sobreira N, Agolini E, Maggiore G, Dahmer-Heath M, Yilmaz A, Boerries M, Metzger P, Schell C, Grünewald I, Konrad M, König J, Schlevogt B, Sayer JA, Bergmann C. Progressive liver, kidney, and heart degeneration in children and adults affected by TULP3 mutations. Am J Hum Genet 2022; 109:928-943. [PMID: 35397207 PMCID: PMC9118107 DOI: 10.1016/j.ajhg.2022.03.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/22/2022] [Indexed: 12/31/2022] Open
Abstract
Organ fibrosis is a shared endpoint of many diseases, yet underlying mechanisms are not well understood. Several pathways governed by the primary cilium, a sensory antenna present on most vertebrate cells, have been linked with fibrosis. Ciliopathies usually start early in life and represent a considerable disease burden. We performed massively parallel sequencing by using cohorts of genetically unsolved individuals with unexplained liver and kidney failure and correlated this with clinical, imaging, and histopathological analyses. Mechanistic studies were conducted with a vertebrate model and primary cells. We detected bi-allelic deleterious variants in TULP3, encoding a critical adaptor protein for ciliary trafficking, in a total of 15 mostly adult individuals, originating from eight unrelated families, with progressive degenerative liver fibrosis, fibrocystic kidney disease, and hypertrophic cardiomyopathy with atypical fibrotic patterns on histopathology. We recapitulated the human phenotype in adult zebrafish and confirmed disruption of critical ciliary cargo composition in several primary cell lines derived from affected individuals. Further, we show interaction between TULP3 and the nuclear deacetylase SIRT1, with roles in DNA damage repair and fibrosis, and report increased DNA damage ex vivo. Transcriptomic studies demonstrated upregulation of profibrotic pathways with gene clusters for hypertrophic cardiomyopathy and WNT and TGF-β signaling. These findings identify variants in TULP3 as a monogenic cause for progressive degenerative disease of major organs in which affected individuals benefit from early detection and improved clinical management. Elucidation of mechanisms crucial for DNA damage repair and tissue maintenance will guide novel therapeutic avenues for this and similar genetic and non-genomic diseases.
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Affiliation(s)
- John Devane
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Elisabeth Ott
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Eric G Olinger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Daniel Epting
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany
| | - Eva Decker
- Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany
| | - Anja Friedrich
- Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany
| | - Nadine Bachmann
- Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany
| | - Gina Renschler
- Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany
| | | | - Andrea Briem-Richter
- University Medical Center Hamburg-Eppendorf, Department of Pediatrics, 20251 Hamburg, Germany
| | - Enke Freya Grabhorn
- University Medical Center Hamburg-Eppendorf, Department of Pediatrics, 20251 Hamburg, Germany
| | - Laura Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Ian J Wilson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Sarah J Rice
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Colin G Miles
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Katrina Wood
- Histopathology Department, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Palak Trivedi
- NIHR Birmingham BRC, Centre for Liver and Gastrointestinal Research, University of Birmingham, Birmingham B15 2TT, UK; Liver Unit, University Hospitals Birmingham, Birmingham B15 2GW, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK; Institute of Applied Health Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Gideon Hirschfield
- Toronto Centre for Liver Disease, University Health Network, Toronto, ON M6H 3M1, Canada
| | - Andrea Pietrobattista
- Hepatogastroenterology and Liver Transplant Unit and Medical Genetics Laboratory, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anya Mezina
- Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emanuele Agolini
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Giuseppe Maggiore
- Hepatogastroenterology and Liver Transplant Unit and Medical Genetics Laboratory, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Mareike Dahmer-Heath
- Department of General Pediatrics, University Hospital Münster, 48149 Münster, Germany
| | - Ali Yilmaz
- Department of Cardiology I, University Hospital Münster, 48149 Münster, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine Medical Center - University of Freiburg, Medical Faculty, University of Freiburg, 79110 Freiburg, Germany; The German Cancer Consortium, Partner Site Freiburg and Cancer Research Center, 69120 Heidelberg, Germany
| | - Patrick Metzger
- Institute of Medical Bioinformatics and Systems Medicine Medical Center - University of Freiburg, Medical Faculty, University of Freiburg, 79110 Freiburg, Germany
| | - Christoph Schell
- Institute for Pathology, Medical Center - University of Freiburg, Medical Faculty, University of Freiburg, 79002 Freiburg, Germany
| | - Inga Grünewald
- Institute for Pathology, University Hospital Münster, 48149 Münster, Germany
| | - Martin Konrad
- Department of General Pediatrics, University Hospital Münster, 48149 Münster, Germany
| | - Jens König
- Department of General Pediatrics, University Hospital Münster, 48149 Münster, Germany
| | - Bernhard Schlevogt
- Department of Internal Medicine B, Gastroenterology, University Hospital Münster, 48149 Münster, Germany
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK; Renal Services, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK; Newcastle Biomedical Research Centre, NIHR, Newcastle upon Tyne NE4 5PL, UK.
| | - Carsten Bergmann
- Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, 79106 Freiburg, Germany; Medizinische Genetik Mainz, Limbach Genetics, 55128 Mainz, Germany.
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11
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Lin T, Ma Y, Zhou D, Sun L, Chen K, Xiang Y, Tong K, Jia C, Jiang K, Liu D, Huang G. Case Report: Preimplantation Genetic Testing for Meckel Syndrome Induced by Novel Compound Heterozygous Mutations of MKS1. Front Genet 2022; 13:843931. [PMID: 35360848 PMCID: PMC8963843 DOI: 10.3389/fgene.2022.843931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/02/2022] [Indexed: 11/13/2022] Open
Abstract
Meckel syndrome (MKS), also known as the Meckel–Gruber syndrome, is a severe pleiotropic autosomal recessive developmental disorder caused by dysfunction of the primary cilia during early embryogenesis. The diagnostic criteria are based on clinical variability and genetic heterogeneity. Mutations in the MKS1 gene constitute approximately 7% of all MKS cases. Herein, we present a non-consanguineous couple with three abnormal pregnancies as the fetuses showed MKS-related phenotypes of the central nervous system malformation and postaxial polydactyly. Whole-exome sequencing identified two novel heterozygous mutations of MKS1: c.350C>A and c.1408-14A>G. The nonsense mutation c.350C>A produced a premature stop codon and induced the truncation of the MKS1 protein (p.S117*). Reverse-transcription polymerase chain reaction (RT-PCR) showed that c.1408-14A>G skipped exon 16 and encoded the mutant MKS1 p.E471Lfs*92. Functional studies showed that these two mutations disrupted the B9–C2 domain of the MKS1 protein and attenuated the interactions with B9D2, the essential component of the ciliary transition zone. The couple finally got a healthy baby through preimplantation genetic testing for monogenic disorder (PGT-M) with haplotype linkage analysis. Thus, this study expanded the mutation spectrum of MKS1 and elucidated the genetic heterogeneity of MKS1 in clinical cases.
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Affiliation(s)
- Tingting Lin
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yongyi Ma
- The Southwest Hospital of Army Medical University, Chongqing, China
| | - Danni Zhou
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
| | - Liwei Sun
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
| | - Ke Chen
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
| | - Yezhou Xiang
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
| | - Keya Tong
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
| | - Chaoli Jia
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
| | - Kean Jiang
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
| | - Dongyun Liu
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
- *Correspondence: Dongyun Liu, ; Guoning Huang,
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing, China
- Reproductive and Genetic Institute, Chongqing Health Center for Women and Children, Chongqing, China
- *Correspondence: Dongyun Liu, ; Guoning Huang,
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12
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Gana S, Serpieri V, Valente EM. Genotype-phenotype correlates in Joubert syndrome: A review. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:72-88. [PMID: 35238134 PMCID: PMC9314610 DOI: 10.1002/ajmg.c.31963] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 01/20/2023]
Abstract
Joubert syndrome (JS) is a genetically heterogeneous primary ciliopathy characterized by a pathognomonic cerebellar and brainstem malformation, the “molar tooth sign,” and variable organ involvement. Over 40 causative genes have been identified to date, explaining up to 94% of cases. To date, gene‐phenotype correlates have been delineated only for a handful of genes, directly translating into improved counseling and clinical care. For instance, JS individuals harboring pathogenic variants in TMEM67 have a significantly higher risk of liver fibrosis, while pathogenic variants in NPHP1, RPGRIP1L, and TMEM237 are frequently associated to JS with renal involvement, requiring a closer monitoring of liver parameters, or renal functioning. On the other hand, individuals with causal variants in the CEP290 or AHI1 need a closer surveillance for retinal dystrophy and, in case of CEP290, also for chronic kidney disease. These examples highlight how an accurate description of the range of clinical symptoms associated with defects in each causative gene, including the rare ones, would better address prognosis and help guiding a personalized management. This review proposes to address this issue by assessing the available literature, to confirm known, as well as to propose rare gene‐phenotype correlates in JS.
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Affiliation(s)
- Simone Gana
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Enza Maria Valente
- Neurogenetics Research Center, IRCCS Mondino Foundation, Pavia, Italy.,Department of Molecular Medicine, University of Pavia, Pavia, Italy
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13
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Yang Y, Paivinen P, Xie C, Krup AL, Makela TP, Mostov KE, Reiter JF. Ciliary Hedgehog signaling patterns the digestive system to generate mechanical forces driving elongation. Nat Commun 2021; 12:7186. [PMID: 34893605 PMCID: PMC8664829 DOI: 10.1038/s41467-021-27319-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/08/2021] [Indexed: 11/24/2022] Open
Abstract
How tubular organs elongate is poorly understood. We found that attenuated ciliary Hedgehog signaling in the gut wall impaired patterning of the circumferential smooth muscle and inhibited proliferation and elongation of developing intestine and esophagus. Similarly, ablation of gut-wall smooth muscle cells reduced lengthening. Disruption of ciliary Hedgehog signaling or removal of smooth muscle reduced residual stress within the gut wall and decreased activity of the mechanotransductive effector YAP. Removing YAP in the mesenchyme also reduced proliferation and elongation, but without affecting smooth muscle formation, suggesting that YAP interprets the smooth muscle-generated force to promote longitudinal growth. Additionally, we developed an intestinal culture system that recapitulates the requirements for cilia and mechanical forces in elongation. Pharmacologically activating YAP in this system restored elongation of cilia-deficient intestines. Thus, our results reveal that ciliary Hedgehog signaling patterns the circumferential smooth muscle to generate radial mechanical forces that activate YAP and elongate the gut.
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Affiliation(s)
- Ying Yang
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Pekka Paivinen
- iCAN Digital Precision Cancer Medicine Flagship, Research Programs Unit, Faculty of Medicine and HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Chang Xie
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Alexis Leigh Krup
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Tomi P Makela
- iCAN Digital Precision Cancer Medicine Flagship, Research Programs Unit, Faculty of Medicine and HiLIFE-Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Keith E Mostov
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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14
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Abrams SR, Reiter JF. Ciliary Hedgehog signaling regulates cell survival to build the facial midline. eLife 2021; 10:e68558. [PMID: 34672258 PMCID: PMC8592574 DOI: 10.7554/elife.68558] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/20/2021] [Indexed: 01/03/2023] Open
Abstract
Craniofacial defects are among the most common phenotypes caused by ciliopathies, yet the developmental and molecular etiology of these defects is poorly understood. We investigated multiple mouse models of human ciliopathies (including Tctn2, Cc2d2a, and Tmem231 mutants) and discovered that each displays hypotelorism, a narrowing of the midface. As early in development as the end of gastrulation, Tctn2 mutants displayed reduced activation of the Hedgehog (HH) pathway in the prechordal plate, the head organizer. This prechordal plate defect preceded a reduction of HH pathway activation and Shh expression in the adjacent neurectoderm. Concomitant with the reduction of HH pathway activity, Tctn2 mutants exhibited increased cell death in the neurectoderm and facial ectoderm, culminating in a collapse of the facial midline. Enhancing HH signaling by decreasing the gene dosage of a negative regulator of the pathway, Ptch1, decreased cell death and rescued the midface defect in both Tctn2 and Cc2d2a mutants. These results reveal that ciliary HH signaling mediates communication between the prechordal plate and the neurectoderm to provide cellular survival cues essential for development of the facial midline.
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Affiliation(s)
- Shaun R Abrams
- Department of Biochemistry and Biophysics, Cardiovascular Research InstituteSan FranciscoUnited States
- Oral and Craniofacial Sciences Program, School of DentistrySan FranciscoUnited States
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research InstituteSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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15
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Petsouki E, Gerakopoulos V, Szeto N, Chang W, Humphrey MB, Tsiokas L. FBW7 couples structural integrity with functional output of primary cilia. Commun Biol 2021; 4:1066. [PMID: 34518642 PMCID: PMC8438042 DOI: 10.1038/s42003-021-02504-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/30/2021] [Indexed: 11/26/2022] Open
Abstract
Structural defects in primary cilia have robust effects in diverse tissues and systems. However, how disorders of ciliary length lead to functional outcomes are unknown. We examined the functional role of a ciliary length control mechanism of FBW7-mediated destruction of NDE1, in mesenchymal stem cell (MSC) differentiation. We show that FBW7 functions as a master regulator of both negative (NDE1) and positive (TALPID3) regulators of ciliogenesis, with an overall positive net effect on primary cilia formation, MSC differentiation to osteoblasts, and bone architecture. Deletion of Fbxw7 suppresses ciliation, Hedgehog activity, and differentiation, which are partially rescued in Fbxw7/Nde1-null cells. We also show that NDE1, despite suppressing ciliogenesis, promotes MSC differentiation by increasing the activity of the Hedgehog pathway by direct binding and enhancing GLI2 activity in a cilia-independent manner. We propose that FBW7 controls a protein-protein interaction network coupling ciliary structure and function, which is essential for stem cell differentiation. Petsouki et al. dissect the importance of FBW7-mediated regulation of NDE1 and TALPID3 in mesenchymal stem cells (MSCs). They find that by modulating the abundance of negative (NDE1) and positive (TALPID3) cilia regulators, FBW7 contributes to both the assembly and signaling functions of primary cilia that are necessary for osteoblast differentiation.
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Affiliation(s)
- Eleni Petsouki
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Vasileios Gerakopoulos
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Nicholas Szeto
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Francisco, San Francisco, CA, USA
| | - Wenhan Chang
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Francisco, San Francisco, CA, USA
| | - Mary Beth Humphrey
- Department of Internal Medicine, Division of Rheumatology, Immunology, and Allergy, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.,Department of Medicine, Oklahoma City Veteran's Affairs Medical Center, Oklahoma City, OK, USA
| | - Leonidas Tsiokas
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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16
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Roopasree OJ, Adivitiya, Chakraborty S, Kateriya S, Veleri S. Centriole is the pivot coordinating dynamic signaling for cell proliferation and organization during early development in the vertebrates. Cell Biol Int 2021; 45:2178-2197. [PMID: 34288241 DOI: 10.1002/cbin.11667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/12/2021] [Indexed: 11/07/2022]
Abstract
Vertebrates have an elaborate and functionally segmented body. It evolves from a single cell by systematic cell proliferation but attains a complex body structure with exquisite precision. This development requires two cellular events: cell cycle and ciliogenesis. For these events, the dynamic molecular signaling is converged at the centriole. The cell cycle helps in cell proliferation and growth of the body and is a highly regulated and integrated process. Its errors cause malignancies and developmental disorders. The cells newly proliferated are organized during organogenesis. For a cellular organization, dedicated signaling hubs are developed in the cells, and most often cilia are utilized. The cilium is generated from one of the centrioles involved in cell proliferation. The developmental signaling pathways hosted in cilia are essential for the elaboration of the body plan. The cilium's compartmental seclusion is ideal for noise-free molecular signaling and is essential for the precision of the body layout. The dysfunctional centrioles and primary cilia distort the development of body layout that manifest as serious developmental disorders. Thus, centriole has a dual role in the growth and cellular organization. It organizes dynamically expressed molecules of cell cycle and ciliogenesis and plays a balancing act to generate new cells and organize them during development. A putative master molecule may regulate and coordinate the dynamic gene expression at the centrioles. The convergence of many critical signaling components at the centriole reiterates the idea that centriole is a major molecular workstation involved in elaborating the structural design and complexity in vertebrates. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- O J Roopasree
- Agroprocessing Technology Division, CSIR-National Institute of Interdisciplinary Science and Technology, Thiruvananthapuram, Kerala 695019 and Academy of CSIR, Uttar Pradesh - 201002, India
| | - Adivitiya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Soura Chakraborty
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Suneel Kateriya
- Laboratory of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Shobi Veleri
- Drug Safety Division, ICMR-National Institute of Nutrition, Hyderabad, 500007, India
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17
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Suciu SK, Long AB, Caspary T. Smoothened and ARL13B are critical in mouse for superior cerebellar peduncle targeting. Genetics 2021; 218:6300527. [PMID: 34132778 PMCID: PMC8864748 DOI: 10.1093/genetics/iyab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023] Open
Abstract
Patients with the ciliopathy Joubert syndrome present with physical anomalies, intellectual disability, and a hindbrain malformation described as the "molar tooth sign" due to its appearance on an MRI. This radiological abnormality results from a combination of hypoplasia of the cerebellar vermis and inappropriate targeting of the white matter tracts of the superior cerebellar peduncles. ARL13B is a cilia-enriched regulatory GTPase established to regulate cell fate, cell proliferation, and axon guidance through vertebrate Hedgehog signaling. In patients, mutations in ARL13B cause Joubert syndrome. To understand the etiology of the molar tooth sign, we used mouse models to investigate the role of ARL13B during cerebellar development. We found that ARL13B regulates superior cerebellar peduncle targeting and these fiber tracts require Hedgehog signaling for proper guidance. However, in mouse, the Joubert-causing R79Q mutation in ARL13B does not disrupt Hedgehog signaling nor does it impact tract targeting. We found a small cerebellar vermis in mice lacking ARL13B function but no cerebellar vermis hypoplasia in mice expressing the Joubert-causing R79Q mutation. In addition, mice expressing a cilia-excluded variant of ARL13B that transduces Hedgehog normally showed normal tract targeting and vermis width. Taken together, our data indicate that ARL13B is critical for the control of cerebellar vermis width as well as superior cerebellar peduncle axon guidance, likely via Hedgehog signaling. Thus, our work highlights the complexity of ARL13B in molar tooth sign etiology.
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Affiliation(s)
- Sarah K Suciu
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA,Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Alyssa B Long
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Tamara Caspary
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA,Corresponding author: Department of Human Genetics, 615 Michael Street, Suite 301, Atlanta, GA 30322.
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18
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Conduit SE, Davies EM, Fulcher AJ, Oorschot V, Mitchell CA. Superresolution Microscopy Reveals Distinct Phosphoinositide Subdomains Within the Cilia Transition Zone. Front Cell Dev Biol 2021; 9:634649. [PMID: 33996795 PMCID: PMC8120242 DOI: 10.3389/fcell.2021.634649] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 04/06/2021] [Indexed: 11/30/2022] Open
Abstract
Primary cilia are evolutionary conserved microtubule-based organelles that protrude from the surface of most mammalian cells. Phosphoinositides (PI) are membrane-associated signaling lipids that regulate numerous cellular events via the recruitment of lipid-binding effectors. The temporal and spatial membrane distribution of phosphoinositides is regulated by phosphoinositide kinases and phosphatases. Recently phosphoinositide signaling and turnover has been observed at primary cilia. However, the precise localization of the phosphoinositides to specific ciliary subdomains remains undefined. Here we use superresolution microscopy (2D stimulated emission depletion microscopy) to map phosphoinositide distribution at the cilia transition zone. PI(3,4,5)P3 and PI(4,5)P2 localized to distinct subregions of the transition zone in a ring-shape at the inner transition zone membrane. Interestingly, the PI(3,4,5)P3 subdomain was more distal within the transition zone relative to PtdIns(4,5)P2. The phosphoinositide effector kinase pAKT(S473) localized in close proximity to these phosphoinositides. The inositol polyphosphate 5-phosphatase, INPP5E, degrades transition zone phosphoinositides, however, studies of fixed cells have reported recombinant INPP5E localizes to the ciliary axoneme, distant from its substrates. Notably, here using live cell imaging and optimized fixation/permeabilization protocols INPP5E was found concentrated at the cilia base, in a distribution characteristic of the transition zone in a ring-shaped domain of similar dimensions to the phosphoinositides. Collectively, this superresolution map places the phosphoinositides in situ with the transition zone proteins and reveals that INPP5E also likely localizes to a subdomain of the transition zone membrane, where it is optimally situated to control local phosphoinositide metabolism.
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Affiliation(s)
- Sarah E Conduit
- Cancer Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Elizabeth M Davies
- Cancer Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Alex J Fulcher
- Monash Micro Imaging, Monash University, Clayton, VIC, Australia
| | - Viola Oorschot
- Monash Ramaciotti Centre for Structural Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Christina A Mitchell
- Cancer Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
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19
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Hazime KS, Zhou Z, Joachimiak E, Bulgakova NA, Wloga D, Malicki JJ. STORM imaging reveals the spatial arrangement of transition zone components and IFT particles at the ciliary base in Tetrahymena. Sci Rep 2021; 11:7899. [PMID: 33846423 PMCID: PMC8041816 DOI: 10.1038/s41598-021-86909-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/22/2021] [Indexed: 11/17/2022] Open
Abstract
The base of the cilium comprising the transition zone (TZ) and transition fibers (TF) acts as a selecting gate to regulate the intraflagellar transport (IFT)-dependent trafficking of proteins to and from cilia. Before entering the ciliary compartment, IFT complexes and transported cargoes accumulate at or near the base of the cilium. The spatial organization of IFT proteins at the cilia base is key for understanding cilia formation and function. Using stochastic optical reconstruction microscopy (STORM) and computational averaging, we show that seven TZ, nine IFT, three Bardet–Biedl syndrome (BBS), and one centrosomal protein, form 9-clustered rings at the cilium base of a ciliate Tetrahymena thermophila. In the axial dimension, analyzed TZ proteins localize to a narrow region of about 30 nm while IFT proteins dock approximately 80 nm proximal to TZ. Moreover, the IFT-A subcomplex is positioned peripheral to the IFT-B subcomplex and the investigated BBS proteins localize near the ciliary membrane. The positioning of the HA-tagged N- and C-termini of the selected proteins enabled the prediction of the spatial orientation of protein particles and likely cargo interaction sites. Based on the obtained data, we built a comprehensive 3D-model showing the arrangement of the investigated ciliary proteins.
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Affiliation(s)
- Khodor S Hazime
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Zhu Zhou
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, 3 Pasteur Street, 02-093, Warsaw, Poland
| | - Natalia A Bulgakova
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, 3 Pasteur Street, 02-093, Warsaw, Poland.
| | - Jarema J Malicki
- Bateson Centre and the Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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20
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The Transition Zone Protein AHI1 Regulates Neuronal Ciliary Trafficking of MCHR1 and Its Downstream Signaling Pathway. J Neurosci 2021; 41:3932-3943. [PMID: 33741721 DOI: 10.1523/jneurosci.2993-20.2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 11/21/2022] Open
Abstract
The Abelson-helper integration site 1 (AHI1) gene encodes for a ciliary transition zone localizing protein that when mutated causes the human ciliopathy, Joubert syndrome. We prepared and examined neuronal cultures derived from male and female embryonic Ahi1 +/+ and Ahi1 -/- mice (littermates) and found that the distribution of ciliary melanin-concentrating hormone receptor-1 (MchR1) was significantly reduced in Ahi1 -/- neurons; however, the total and surface expression of MchR1 on Ahi1 -/- neurons was similar to controls (Ahi1 +/+). This indicates that a pathway for MchR1 trafficking to the surface plasma membrane is intact, but the process of targeting MchR1 into cilia is impaired in Ahi1-deficient mouse neurons, indicating a role for Ahi1 in localizing MchR1 to the cilium. Mouse Ahi1 -/- neurons that fail to accumulate MchR1 in the ciliary membrane have significant decreases in two downstream MchR1 signaling pathways [cAMP and extracellular signal-regulated kinase (Erk)] on MCH stimulation. These results suggest that the ciliary localization of MchR1 is necessary and critical for MchR1 signaling, with Ahi1 participating in regulating MchR1 localization to cilia, and further supporting cilia as critical signaling centers in neurons.SIGNIFICANCE STATEMENT Our work here demonstrates that neuronal primary cilia are powerful and focused signaling centers for the G-protein-coupled receptor (GPCR), melanin-concentrating hormone receptor-1 (MCHR1), with a role for the ciliary transition zone protein, Abelson-helper integration site 1 (AHI1), in mediating ciliary trafficking of MCHR1. Moreover, our manuscript further expands the repertoire of cilia functions on neurons, a cell type that has not received significant attention in the cilia field. Lastly, our work demonstrates the significant influence of ciliary GPCR signaling in the overall signaling of neurons.
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21
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Lange KI, Tsiropoulou S, Kucharska K, Blacque OE. Interpreting the pathogenicity of Joubert syndrome missense variants in Caenorhabditis elegans. Dis Model Mech 2021; 14:dmm.046631. [PMID: 33234550 PMCID: PMC7859701 DOI: 10.1242/dmm.046631] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/13/2020] [Indexed: 12/26/2022] Open
Abstract
Ciliopathies are inherited disorders caused by defects in motile and non-motile (primary) cilia. Ciliopathy syndromes and associated gene variants are often highly pleiotropic and represent exemplars for interrogating genotype-phenotype correlations. Towards understanding disease mechanisms in the context of ciliopathy mutations, we have used a leading model organism for cilia and ciliopathy research, Caenorhabditis elegans, together with gene editing, to characterise two missense variants (P74S and G155S) in mksr-2/B9D2 associated with Joubert syndrome (JBTS). B9D2 functions within the Meckel syndrome (MKS) module at the ciliary base transition zone (TZ) compartment and regulates the molecular composition and sensory/signalling functions of the cilium. Quantitative assays of cilium/TZ structure and function, together with knock-in reporters, confirm that both variant alleles are pathogenic in worms. G155S causes a more severe overall phenotype and disrupts endogenous MKSR-2 organisation at the TZ. Recapitulation of the patient biallelic genotype shows that compound heterozygous worms phenocopy worms homozygous for P74S. The P74S and G155S alleles also reveal evidence of a very close functional association between the B9D2-associated B9 complex and MKS-2/TMEM216. Together, these data establish C. elegans as a model for interpreting JBTS mutations and provide further insight into MKS module organisation. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Karen I Lange
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Sofia Tsiropoulou
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Katarzyna Kucharska
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
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22
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Wang T, Liu YX, Luo FM, Dong Y, Li YL, Fan LL. A Novel Homozygous Variant of TMEM231 in a Case With Hypoplasia of the Cerebellar Vermis and Polydactyly. Front Pediatr 2021; 9:774575. [PMID: 34912761 PMCID: PMC8666876 DOI: 10.3389/fped.2021.774575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 10/22/2021] [Indexed: 12/25/2022] Open
Abstract
Background: Transmembrane protein 231 (TMEM231) is a component of the B9 complex that participates in the formation of the diffusion barrier between the cilia and plasma membrane. Mutations in TMEM231 gene may contribute to the Joubert syndrome (JBTS) or Meckel-Gruber syndrome (MKS). However, reports on JBTS or MKS caused by TMEM231 mutations are comparatively rare. Method: We describe a Chinese fetus with unexplained hypoplasia of the cerebellar vermis and polydactyly, detected by ultrasound imaging. The fetus was primarily diagnosed with JBTS/MKS. The parents of this fetus were non-consanguineous and healthy. Whole-exome sequencing (WES) and bioinformatics strategies were employed to explore the genetic lesion of this family. Results: An unknown missense variant (c.19C>T;p.R7W) of TMEM231 gene was detected. The variant was predicted as pathogenic and was absent in our 200 healthy controls. Conclusion: WES was employed to explore the genetic lesion of a fetus with unexplained hypoplasia of the cerebellar vermis and polydactyly. A novel variant in TMEM231 gene was identified. Our study not only provided data for genetic counseling and prenatal diagnosis to this family but also broadened the spectrum of TMEM231 mutations.
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Affiliation(s)
- Tao Wang
- Departments of Reproductive Genetics, HeBei General Hospital, ShiJiaZhuang, China
| | - Yu-Xing Liu
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Fang-Mei Luo
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Yi Dong
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China
| | - Ya-Li Li
- Departments of Reproductive Genetics, HeBei General Hospital, ShiJiaZhuang, China
| | - Liang-Liang Fan
- Departments of Reproductive Genetics, HeBei General Hospital, ShiJiaZhuang, China.,Department of Cell Biology, School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Disease, School of Life Sciences, Central South University, Changsha, China
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23
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Luo M, He R, Lin Z, Shen Y, Zhang G, Cao Z, Lu C, Meng D, Zhang J, Ma X, Cao M. Novel Compound Heterozygous Variants in MKS1 Leading to Joubert Syndrome. Front Genet 2020; 11:576235. [PMID: 33193692 PMCID: PMC7592398 DOI: 10.3389/fgene.2020.576235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/14/2020] [Indexed: 11/13/2022] Open
Abstract
Joubert syndrome (JBTS) and Meckel-Gruber syndrome (MKS) are rare recessive disorders caused by defects of cilia, and they share overlapping clinical features and allelic loci. Mutations of MKS1 contribute approximately 7% to all MKS cases and are found in some JBTS patients. Here, we describe a JBTS patient with two novel mutations of MKS1. Whole exome sequencing (WES) revealed c.191-1G > A and c.1058delG compound heterozygous variants. The patient presented with typical cerebellar vermis hypoplasia, hypotonia, and developmental delay, but without other renal/hepatic involvement or polydactyly. Functional studies showed that the c.1058delG mutation disrupts the B9 domain of MKS1, attenuates the interactions with B9D2, and impairs its ciliary localization at the transition zone (TZ), indicating that the B9 domain of MKS1 is essential for the integrity of the B9 protein complex and localization of MKS1 at the TZ. This work expands the mutation spectrum of MKS1 and elucidates the clinical heterogeneity of MKS1-related ciliopathies.
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Affiliation(s)
- Minna Luo
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Ruida He
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zaisheng Lin
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue Shen
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Guangyu Zhang
- Department of Children Rehabilitation, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zongfu Cao
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Chao Lu
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Dan Meng
- Tianjin Key Laboratory of Food and Biotechnology, School of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Jing Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Muqing Cao
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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24
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Conduit SE, Vanhaesebroeck B. Phosphoinositide lipids in primary cilia biology. Biochem J 2020; 477:3541-3565. [PMID: 32970140 PMCID: PMC7518857 DOI: 10.1042/bcj20200277] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/30/2020] [Accepted: 08/27/2020] [Indexed: 12/11/2022]
Abstract
Primary cilia are solitary signalling organelles projecting from the surface of most cell types. Although the ciliary membrane is continuous with the plasma membrane it exhibits a unique phospholipid composition, a feature essential for normal cilia formation and function. Recent studies have illustrated that distinct phosphoinositide lipid species localise to specific cilia subdomains, and have begun to build a 'phosphoinositide map' of the cilium. The abundance and localisation of phosphoinositides are tightly regulated by the opposing actions of lipid kinases and lipid phosphatases that have also been recently discovered at cilia. The critical role of phosphoinositides in cilia biology is highlighted by the devastating consequences of genetic defects in cilia-associated phosphoinositide regulatory enzymes leading to ciliopathy phenotypes in humans and experimental mouse and zebrafish models. Here we provide a general introduction to primary cilia and the roles phosphoinositides play in cilia biology. In addition to increasing our understanding of fundamental cilia biology, this rapidly expanding field may inform novel approaches to treat ciliopathy syndromes caused by deregulated phosphoinositide metabolism.
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Affiliation(s)
- Sarah E. Conduit
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, U.K
| | - Bart Vanhaesebroeck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, U.K
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25
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Okazaki M, Kobayashi T, Chiba S, Takei R, Liang L, Nakayama K, Katoh Y. Formation of the B9-domain protein complex MKS1-B9D2-B9D1 is essential as a diffusion barrier for ciliary membrane proteins. Mol Biol Cell 2020; 31:2259-2268. [PMID: 32726168 PMCID: PMC7550698 DOI: 10.1091/mbc.e20-03-0208] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 01/20/2023] Open
Abstract
Cilia are plasma membrane protrusions that act as cellular antennae and propellers in eukaryotes. To achieve their sensory and motile functions, cilia maintain protein and lipid compositions that are distinct from those of the cell body. The transition zone (TZ) is a specialized region located at the ciliary base, which functions as a barrier separating the interior and exterior of cilia. The TZ comprises a number of transmembrane and soluble proteins. Meckel syndrome (MKS)1, B9 domain (B9D)1/MKS9, and B9D2/MKS10 are soluble TZ proteins that are encoded by causative genes of MKS and have a B9D in common. We here demonstrate the interaction mode of these B9D proteins to be MKS1-B9D2-B9D1 and demonstrate their interdependent localization to the TZ. Phenotypic analyses of MKS1-knockout (KO) and B9D2-KO cells show that the B9D proteins are involved in, although not essential for, normal cilia biogenesis. Rescue experiments of these KO cells show that formation of the B9D protein complex is crucial for creating a diffusion barrier for ciliary membrane proteins.
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Affiliation(s)
- Misato Okazaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuhei Chiba
- Department of Genetic Disease Research, Graduate School of Medicine, Osaka City University, Abeno-ku, Osaka 545-8585, Japan
| | - Ryota Takei
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Luxiaoxue Liang
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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26
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Zhang M, Chang Z, Tian Y, Wang L, Lu Y. Two novel TCTN2 mutations cause Meckel-Gruber syndrome. J Hum Genet 2020; 65:1039-1043. [PMID: 32655147 DOI: 10.1038/s10038-020-0804-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/26/2020] [Indexed: 11/09/2022]
Abstract
Meckel-Gruber syndrome (MKS) is a clinically and genetically heterogeneous ciliopathy characterized by a triad of occipital encephalocele, polycystic kidneys, and postaxial polydactyly. Pathogenesis of MKS is related to dysfunction of primary cilia. However, reports on MKS caused by Tectonic2 (TCTN2) mutations are scanty whilst. There is no direct evidence of ciliogenesis in such MKS patients. Here, we identified two novel nonsense variants of TCTN2 (c.343G > T, p.E115*; c.1540C > T, p.Q514*) in a Chinese MKS fetus. Compared to reported TCTN2-causing MKS patients, our case represented an endocardial pad defect, which was not reported previously. We also found primary cilia protruded normally from the surface of epithelial cells in the affected fetal kidney tubules compared to controls, indicating TCTN2 is not necessary for ciliogenesis in the kidney. To our knowledge, this is the first case of MKS fetus caused by TCTN2 mutations from China.
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Affiliation(s)
- Manli Zhang
- Translational Medicine Center, Chinese PLA General Hospital, 28 Fuxing Road, 100853, Beijing, People's Republic of China
| | - Zhijie Chang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Medicine, School of Life Sciences, Tsinghua University, 30 Shuangqing Road, 100084, Beijing, People's Republic of China
| | - Yaping Tian
- Translational Medicine Center, Chinese PLA General Hospital, 28 Fuxing Road, 100853, Beijing, People's Republic of China
| | - Longxia Wang
- Department of Ultrasound, Chinese PLA General Hospital, 28 Fuxing Road, 100853, Beijing, People's Republic of China.
| | - Yanping Lu
- Department of Gynaecology and Obstetrics, Chinese PLA General Hospital, 28 Fuxing Road, 100853, Beijing, People's Republic of China.
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27
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Katiyar D, Anderson N, Bommireddipalli S, Bournazos A, Cooper S, Goel H. Two novel B9D1 variants causing Joubert syndrome: Utility of mRNA and splicing studies. Eur J Med Genet 2020; 63:104000. [PMID: 32622957 DOI: 10.1016/j.ejmg.2020.104000] [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: 04/08/2020] [Revised: 05/28/2020] [Accepted: 06/28/2020] [Indexed: 11/26/2022]
Abstract
The primary cilium is an organelle which plays an important role in the transduction of signals in the Wnt and Sonic hedgehog pathways. Abnormal or absent primary cilia result in various neurodevelopmental, retinal, renal, hepatic and musculoskeletal abnormalities. Joubert syndrome (JS) is a ciliopathy with a prevalence estimated to be between 1:80 000 and 1:100 000. JS occurs due to bi-allelic mutations in one of the 34 identified genes, all of which encode for protein components of the primary cilia. The presentation of JS is highly variable, however a clinical diagnosis can be established by the presence of the molar tooth sign on axial brain MRI, hypotonia in infancy, and developmental delay. JS is less severe than Meckel syndrome (MKS), which is another recessive, and often lethal, ciliopathy. This report outlines an interesting case of JS, in which two novel mutations in B9D1 were identified. This gene is not commonly associated with JS, and is often implicated in MKS. Functional mRNA study was helpful in delineating the pathogenic role of novel variants in this case.
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Affiliation(s)
- Disha Katiyar
- University of New England, Armidale, NSW, 2351, Australia; University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Neil Anderson
- John Hunter Children's Hospital, Hunter New England Local Health District (HNELHD), New Lambton Heights, NSW, Australia
| | | | - Adam Bournazos
- Kids Neuroscience Centre, The Children's Hospital at Westmead Sydney, Australia
| | - Sandra Cooper
- Kids Neuroscience Centre, The Children's Hospital at Westmead Sydney, Australia
| | - Himanshu Goel
- University of Newcastle, Callaghan, NSW, 2308, Australia; Hunter Genetics, Hunter New England Local Health District (HNELHD), Waratah, NSW, 2298, Australia.
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28
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Nakayama K, Katoh Y. Architecture of the IFT ciliary trafficking machinery and interplay between its components. Crit Rev Biochem Mol Biol 2020; 55:179-196. [PMID: 32456460 DOI: 10.1080/10409238.2020.1768206] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cilia and flagella serve as cellular antennae and propellers in various eukaryotic cells, and contain specific receptors and ion channels as well as components of axonemal microtubules and molecular motors to achieve their sensory and motile functions. Not only the bidirectional trafficking of specific proteins within cilia but also their selective entry and exit across the ciliary gate is mediated by the intraflagellar transport (IFT) machinery with the aid of motor proteins. The IFT-B complex, which is powered by the kinesin-2 motor, mediates anterograde protein trafficking from the base to the tip of cilia, whereas the IFT-A complex together with the dynein-2 complex mediates retrograde protein trafficking. The BBSome complex connects ciliary membrane proteins to the IFT machinery. Defects in any component of this trafficking machinery lead to abnormal ciliogenesis and ciliary functions, and results in a broad spectrum of disorders, collectively called the ciliopathies. In this review article, we provide an overview of the architectures of the components of the IFT machinery and their functional interplay in ciliary protein trafficking.
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Affiliation(s)
- Kazuhisa Nakayama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Katoh
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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29
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Shylo NA, Emmanouil E, Ramrattan D, Weatherbee SD. Loss of ciliary transition zone protein TMEM107 leads to heterotaxy in mice. Dev Biol 2019; 460:187-199. [PMID: 31887266 DOI: 10.1016/j.ydbio.2019.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 11/15/2022]
Abstract
Cilia in most vertebrate left-right organizers are involved in the original break in left-right (L-R) symmetry, however, less is known about their roles in subsequent steps of the cascade - relaying the signaling and maintaining the established asymmetry. Here we describe the L-R patterning cascades in two mutants of a ciliary transition zone protein TMEM107, revealing that near-complete loss of cilia in Tmem107null leads to left pulmonary isomerism due to the failure of the midline barrier. Contrary, partially retained cilia in the node and the midline of a hypomorphic Tmem107schlei mutant appear sufficient for the formation of the midline barrier and establishment and maintenance of the L-R asymmetry. Despite misregulation of Shh signaling in both mutants, the presence of normal Lefty1 expression and midline barrier formation in Tmem107schlei mutants, suggests a requirement for cilia, but not necessarily Shh signaling for Lefty1 expression and midline barrier formation.
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Affiliation(s)
- Natalia A Shylo
- Yale University, Genetics Department, 333 Cedar Street, New Haven, CT, 06510, USA.
| | - Elli Emmanouil
- Yale University, Genetics Department, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Dylan Ramrattan
- Yale University, Genetics Department, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Scott D Weatherbee
- Yale University, Genetics Department, 333 Cedar Street, New Haven, CT, 06510, USA
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30
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Garcia G, Raleigh DR, Reiter JF. How the Ciliary Membrane Is Organized Inside-Out to Communicate Outside-In. Curr Biol 2019; 28:R421-R434. [PMID: 29689227 DOI: 10.1016/j.cub.2018.03.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cilia, organelles that move to execute functions like fertilization and signal to execute functions like photoreception and embryonic patterning, are composed of a core of nine-fold doublet microtubules overlain by a membrane. Distinct types of cilia display distinct membrane morphologies, ranging from simple domed cylinders to the highly ornate invaginations and membrane disks of photoreceptor outer segments. Critical for the ability of cilia to signal, both the protein and the lipid compositions of ciliary membranes are different from those of other cellular membranes. This specialization presents a unique challenge for the cell as, unlike membrane-bounded organelles, the ciliary membrane is contiguous with the surrounding plasma membrane. This distinct ciliary membrane is generated in concert with multiple membrane remodeling events that comprise the process of ciliogenesis. Once the cilium is formed, control of ciliary membrane composition relies on discrete molecular machines, including a barrier to membrane proteins entering the cilium at a specialized region of the base of the cilium called the transition zone and a trafficking adaptor that controls G protein-coupled receptor (GPCR) localization to the cilium called the BBSome. The ciliary membrane can be further remodeled by the removal of membrane proteins by the release of ciliary extracellular vesicles that may function in intercellular communication, removal of unneeded proteins or ciliary disassembly. Here, we review the structures and transport mechanisms that control ciliary membrane composition, and discuss how membrane specialization enables the cilium to function as the antenna of the cell.
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Affiliation(s)
- Galo Garcia
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - David R Raleigh
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Department of Radiation Oncology, University of California, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA.
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31
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Muñoz-Estrada J, Ferland RJ. Ahi1 promotes Arl13b ciliary recruitment, regulates Arl13b stability and is required for normal cell migration. J Cell Sci 2019; 132:jcs.230680. [PMID: 31391239 DOI: 10.1242/jcs.230680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/24/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in the Abelson-helper integration site 1 (AHI1) gene are associated with neurological/neuropsychiatric disorders, and cause the neurodevelopmental ciliopathy Joubert syndrome (JBTS). Here, we show that deletion of the transition zone (TZ) protein Ahi1 in mouse embryonic fibroblasts (MEFs) has a small effect on cilia formation. However, Ahi1 loss in these cells results in: (1) reduced localization of the JBTS-associated protein Arl13b to the ciliary membrane, (2) decreased sonic hedgehog signaling, (3) and an abnormally elongated ciliary axoneme accompanied by an increase in ciliary IFT88 concentrations. While no changes in Arl13b levels are detected in crude cell membrane extracts, loss of Ahi1 significantly reduced the level of non-membrane-associated Arl13b and its stability via the proteasome pathway. Exogenous expression of Ahi1-GFP in Ahi1-/- MEFs restored ciliary length, increased ciliary recruitment of Arl13b and augmented Arl13b stability. Finally, Ahi1-/- MEFs displayed defects in cell motility and Pdgfr-α-dependent migration. Overall, our findings support molecular mechanisms underlying JBTS etiology that involve: (1) disruptions at the TZ resulting in defects of membrane- and non-membrane-associated proteins to localize to primary cilia, and (2) defective cell migration.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Jesús Muñoz-Estrada
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208, USA
| | - Russell J Ferland
- Department of Neuroscience and Experimental Therapeutics, Albany Medical College, Albany, NY 12208, USA .,Department of Neurology, Albany Medical College, Albany, NY 12208, USA
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32
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Radhakrishnan P, Nayak SS, Shukla A, Lindstrand A, Girisha KM. Meckel syndrome: Clinical and mutation profile in six fetuses. Clin Genet 2019; 96:560-565. [PMID: 31411728 DOI: 10.1111/cge.13623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 11/30/2022]
Abstract
Meckel syndrome (MKS) is a perinatally lethal, genetically heterogeneous, autosomal recessive condition caused by defective primary cilium formation leading to polydactyly, multiple cysts in kidneys and malformations of nervous system. We performed exome sequencing in six fetuses from six unrelated families with MKS. We identified seven novel variants in B9D2, TNXDC15, CC2D2A, CEP290 and TMEM67. We describe the second family with MKS due to a homozygous variant in B9D2 and fifth family with bi-allelic variant in TXNDC15. Our data validates the causation of MKS by pathogenic variation in B9D2 and TXNDC15 and also adds novel variants in CC2D2A, CEP290 and TMEM67 to the literature.
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Affiliation(s)
- Periyasamy Radhakrishnan
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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33
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Kim A, Savary C, Dubourg C, Carré W, Mouden C, Hamdi-Rozé H, Guyodo H, Douce JL, Pasquier L, Flori E, Gonzales M, Bénéteau C, Boute O, Attié-Bitach T, Roume J, Goujon L, Akloul L, Odent S, Watrin E, Dupé V, de Tayrac M, David V. Integrated clinical and omics approach to rare diseases: novel genes and oligogenic inheritance in holoprosencephaly. Brain 2019; 142:35-49. [PMID: 30508070 DOI: 10.1093/brain/awy290] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 09/28/2018] [Indexed: 12/27/2022] Open
Abstract
Holoprosencephaly is a pathology of forebrain development characterized by high phenotypic heterogeneity. The disease presents with various clinical manifestations at the cerebral or facial levels. Several genes have been implicated in holoprosencephaly but its genetic basis remains unclear: different transmission patterns have been described including autosomal dominant, recessive and digenic inheritance. Conventional molecular testing approaches result in a very low diagnostic yield and most cases remain unsolved. In our study, we address the possibility that genetically unsolved cases of holoprosencephaly present an oligogenic origin and result from combined inherited mutations in several genes. Twenty-six unrelated families, for whom no genetic cause of holoprosencephaly could be identified in clinical settings [whole exome sequencing and comparative genomic hybridization (CGH)-array analyses], were reanalysed under the hypothesis of oligogenic inheritance. Standard variant analysis was improved with a gene prioritization strategy based on clinical ontologies and gene co-expression networks. Clinical phenotyping and exploration of cross-species similarities were further performed on a family-by-family basis. Statistical validation was performed on 248 ancestrally similar control trios provided by the Genome of the Netherlands project and on 574 ancestrally matched controls provided by the French Exome Project. Variants of clinical interest were identified in 180 genes significantly associated with key pathways of forebrain development including sonic hedgehog (SHH) and primary cilia. Oligogenic events were observed in 10 families and involved both known and novel holoprosencephaly genes including recurrently mutated FAT1, NDST1, COL2A1 and SCUBE2. The incidence of oligogenic combinations was significantly higher in holoprosencephaly patients compared to two control populations (P < 10-9). We also show that depending on the affected genes, patients present with particular clinical features. This study reports novel disease genes and supports oligogenicity as clinically relevant model in holoprosencephaly. It also highlights key roles of SHH signalling and primary cilia in forebrain development. We hypothesize that distinction between different clinical manifestations of holoprosencephaly lies in the degree of overall functional impact on SHH signalling. Finally, we underline that integrating clinical phenotyping in genetic studies is a powerful tool to specify the clinical relevance of certain mutations.
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Affiliation(s)
- Artem Kim
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France
| | - Clara Savary
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France
| | - Christèle Dubourg
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Wilfrid Carré
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Charlotte Mouden
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France
| | - Houda Hamdi-Rozé
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Hélène Guyodo
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France
| | - Jerome Le Douce
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France
| | | | | | | | - Elisabeth Flori
- Laboratoire de Cytogénétique, Cytologie et Histologie Quantitative, Hôpital de Hautepierre, HUS, Strasbourg, France
| | - Marie Gonzales
- Service de Génétique et Embryologie Médicales, Hôpital Armand Trousseau, Paris, France
| | | | | | - Tania Attié-Bitach
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants-Malades, Université Paris Descartes, 149, rue de Sèvres, Paris, France
| | - Joelle Roume
- Department of Clinical Genetics, Centre de Référence “AnDDI Rares”, Poissy Hospital GHU PIFO, Poissy, France
| | | | - Linda Akloul
- Service de Génétique Clinique, CHU, Rennes, France
| | - Sylvie Odent
- Service de Génétique Clinique, CHU, Rennes, France
| | - Erwan Watrin
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France
| | - Valérie Dupé
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France
| | - Marie de Tayrac
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
| | - Véronique David
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France.,Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
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The complexity of the cilium: spatiotemporal diversity of an ancient organelle. Curr Opin Cell Biol 2018; 55:139-149. [PMID: 30138887 DOI: 10.1016/j.ceb.2018.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 02/06/2023]
Abstract
Cilia are microtubule-based appendages present on almost all vertebrate cell types where they mediate a myriad of cellular processes critical for development and homeostasis. In humans, impaired ciliary function is associated with an ever-expanding repertoire of phenotypically-overlapping yet highly variable genetic disorders, the ciliopathies. Extensive work to elucidate the structure, function, and composition of the cilium is offering hints that the `static' representation of the cilium is a gross oversimplification of a highly dynamic organelle whose functions are choreographed dynamically across cell types, developmental, and homeostatic contexts. Understanding this diversity will require discerning ciliary versus non-ciliary roles for classically-defined `ciliary' proteins; defining ciliary protein-protein interaction networks within and beyond the cilium; and resolving the spatiotemporal diversity of ciliary structure and function. Here, focusing on one evolutionarily conserved ciliary module, the intraflagellar transport system, we explore these ideas and propose potential future studies that will improve our knowledge gaps of the oversimplified cilium and, by extension, inform the reasons that underscore the striking range of clinical pathologies associated with ciliary dysfunction.
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35
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Weng RR, Yang TT, Huang CE, Chang CW, Wang WJ, Liao JC. Super-Resolution Imaging Reveals TCTN2 Depletion-Induced IFT88 Lumen Leakage and Ciliary Weakening. Biophys J 2018; 115:263-275. [PMID: 29866362 DOI: 10.1016/j.bpj.2018.04.051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/07/2018] [Accepted: 04/23/2018] [Indexed: 11/28/2022] Open
Abstract
The primary cilium is an essential organelle mediating key signaling activities, such as sonic hedgehog signaling. The molecular composition of the ciliary compartment is distinct from that of the cytosol, with the transition zone (TZ) gated the ciliary base. The TZ is a packed and organized protein complex containing multiple ciliopathy-associated protein species. Tectonic 2 (TCTN2) is one of the TZ proteins in the vicinity of the ciliary membrane, and its mutation is associated with Meckel syndrome. Despite its importance in ciliopathies, the role of TCTN2 in ciliary structure and molecules remains unclear. Here, we created a CRISPR/Cas9 TCTN2 knockout human retinal pigment epithelial cell line and conducted quantitative analysis of geometric localization using both wide-field and super-resolution microscopy techniques. We found that TCTN2 depletion resulted in partial TZ damage, loss of ciliary membrane proteins, leakage of intraflagellar transport protein IFT88 toward the basal body lumen, and cilium shortening and curving. The basal body lumen occupancy of IFT88 was also observed in si-RPGRIP1L cells and cytochalasin-D-treated wild-type cells, suggesting varying lumen accessibility for intraflagellar transport proteins under different perturbed conditions. Our findings support two possible models for the lumen leakage of IFT88, i.e., a tip leakage model and a misregulation model. Together, our quantitative image analysis augmented by super-resolution microscopy facilitates the observation of structural destruction and molecular redistribution in TCTN2-/- cilia, shedding light on mechanistic understanding of TZ-protein-associated ciliopathies.
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Affiliation(s)
- Rueyhung Roc Weng
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - T Tony Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Chia-En Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Chih-Wei Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Won-Jing Wang
- Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei, Taiwan
| | - Jung-Chi Liao
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan.
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36
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Wiegering A, Dildrop R, Kalfhues L, Spychala A, Kuschel S, Lier JM, Zobel T, Dahmen S, Leu T, Struchtrup A, Legendre F, Vesque C, Schneider-Maunoury S, Saunier S, Rüther U, Gerhardt C. Cell type-specific regulation of ciliary transition zone assembly in vertebrates. EMBO J 2018; 37:embj.201797791. [PMID: 29650680 PMCID: PMC5978567 DOI: 10.15252/embj.201797791] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 03/12/2018] [Accepted: 03/15/2018] [Indexed: 01/07/2023] Open
Abstract
Ciliopathies are life-threatening human diseases caused by defective cilia. They can often be traced back to mutations of genes encoding transition zone (TZ) proteins demonstrating that the understanding of TZ organisation is of paramount importance. The TZ consists of multimeric protein modules that are subject to a stringent assembly hierarchy. Previous reports place Rpgrip1l at the top of the TZ assembly hierarchy in Caenorhabditis elegans By performing quantitative immunofluorescence studies in RPGRIP1L-/- mouse embryos and human embryonic cells, we recognise a different situation in vertebrates in which Rpgrip1l deficiency affects TZ assembly in a cell type-specific manner. In cell types in which the loss of Rpgrip1l alone does not affect all modules, additional truncation or removal of vertebrate-specific Rpgrip1 results in an impairment of all modules. Consequently, Rpgrip1l and Rpgrip1 synergistically ensure the TZ composition in several vertebrate cell types, revealing a higher complexity of TZ assembly in vertebrates than in invertebrates.
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Affiliation(s)
- Antonia Wiegering
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Renate Dildrop
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Lisa Kalfhues
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - André Spychala
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Stefanie Kuschel
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Johanna Maria Lier
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Thomas Zobel
- Center for Advanced Imaging (CAi), Heinrich Heine University, Düsseldorf, Germany
| | - Stefanie Dahmen
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Tristan Leu
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Andreas Struchtrup
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Flora Legendre
- INSERM, U983, Hôpital Necker-Enfants Malades, Paris, France.,Sorbonne Paris Cité, Faculté de Médecine, Université Paris-Descartes, Paris, France
| | - Christine Vesque
- Paris-Seine (IBPS) - Developmental Biology Laboratory, Institut de Biologie, CNRS, UMR7622, INSERM U1156, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Sylvie Schneider-Maunoury
- Paris-Seine (IBPS) - Developmental Biology Laboratory, Institut de Biologie, CNRS, UMR7622, INSERM U1156, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | - Sophie Saunier
- INSERM, U983, Hôpital Necker-Enfants Malades, Paris, France.,Sorbonne Paris Cité, Faculté de Médecine, Université Paris-Descartes, Paris, France
| | - Ulrich Rüther
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Christoph Gerhardt
- Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, Düsseldorf, Germany
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37
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Li H, Zhang J, Chen S, Wang F, Zhang T, Niswander L. Genetic contribution of retinoid-related genes to neural tube defects. Hum Mutat 2018; 39:550-562. [PMID: 29297599 PMCID: PMC5839987 DOI: 10.1002/humu.23397] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/27/2017] [Accepted: 12/28/2017] [Indexed: 12/21/2022]
Abstract
Rare variants are considered underlying causes of complex diseases. The complex and severe group of disorders called neural tube defects (NTDs) results from failure of the neural tube to close during early embryogenesis. Neural tube closure requires the coordination of numerous signaling pathways, including the precise regulation of retinoic acid (RA) concentration, which is controlled by enzymes involved in RA synthesis and degradation. Here, we used a case-control mutation screen study to reveal rare variants in retinoid-related genes in a Han Chinese NTD population by sequencing six genes in 355 NTD cases and 225 controls. More specific rare variants were found in exonic and upstream regions in NTD cases. The RA-responsive genes CYP26A1, CRABP1, and ALDH1A2 harbored NTD-specific rare variants in their upstream regions. Unexpectedly, the majority of missense variants in NTD cases were found in CYP26B1, which encodes a RA degradation enzyme, whereas no missense variants in this gene were found in controls. Functional analysis indicated that the CYP26B1 NTD variants were inefficient in the degradation of RA using assays of RA-induced transcription and RA-initiated neuronal differentiation. Our study supports the contribution of rare variants in RA-related genes to the etiology of human NTDs.
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Affiliation(s)
- Huili Li
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado 80045
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Jing Zhang
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado 80045
| | - Shuyuan Chen
- Department of Pediatrics, XiangYa Hospital of Central South University, Changsha 410008, China
| | - Fang Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Lee Niswander
- Department of Pediatrics, University of Colorado Anschutz Medical Campus, Children’s Hospital Colorado, Aurora, Colorado 80045
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38
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Wang C, Li J, Takemaru KI, Jiang X, Xu G, Wang B. Centrosomal protein Dzip1l binds Cby, promotes ciliary bud formation, and acts redundantly with Bromi to regulate ciliogenesis in the mouse. Development 2018; 145:dev.164236. [PMID: 29487109 DOI: 10.1242/dev.164236] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 02/16/2018] [Indexed: 12/14/2022]
Abstract
The primary cilium is a microtubule-based organelle required for Hedgehog (Hh) signaling and consists of a basal body, a ciliary axoneme and a compartment between the first two structures, called the transition zone (TZ). The TZ serves as a gatekeeper to control protein composition in cilia, but less is known about its role in ciliary bud formation. Here, we show that centrosomal protein Dzip1l is required for Hh signaling between Smoothened and Sufu. Dzip1l colocalizes with basal body appendage proteins and Rpgrip1l, a TZ protein. Loss of Dzip1l results in reduced ciliogenesis and dysmorphic cilia in vivo Dzip1l interacts with, and acts upstream of, Cby, an appendage protein, in ciliogenesis. Dzip1l also has overlapping functions with Bromi (Tbc1d32) in ciliogenesis, cilia morphogenesis and neural tube patterning. Loss of Dzip1l arrests ciliogenesis at the stage of ciliary bud formation from the TZ. Consistent with this, Dzip1l mutant cells fail to remove the capping protein Cp110 (Ccp110) from the distal end of mother centrioles and to recruit Rpgrip1l to the TZ. Therefore, Dzip1l promotes ciliary bud formation and is required for the integrity of the TZ.
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Affiliation(s)
- Chengbing Wang
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA
| | - Jia Li
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA
| | - Ken-Ichi Takemaru
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Xiaogang Jiang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Baolin Wang
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA .,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA
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Abstract
PURPOSE OF REVIEW To review disorders that are associated with renal cystic disease during prenatal life and to highlight the strong association between renal cystic disease and ciliopathies. RECENT FINDINGS There are numerous causative genes for ciliopathies that can present with cystic kidney disease. In the group of single gene ciliopathies, autosomal dominant polycystic kidney disease is by far the most prevalent one. Other examples are autosomal recessive polycystic kidney disease, nephronophthisis, Bardet-Biedl syndrome, Meckel-Gruber syndrome, Joubert syndrome and related disorders as well as X-linked orofaciodigital syndrome type 1, respectively. The prevalence of these inherited disorders sums up to about in 1 : 2000 people. These disorders with their hepatorenal fibrocystic character should be classified as multisystem diseases. SUMMARY Understanding of the origin of renal cystic disease and associated disorders is important to make the appropriate prenatal diagnosis and for counseling affected parents. In the future, understanding of the pathophysiology may help to develop new treatment strategies.
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40
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Seo S, Datta P. Photoreceptor outer segment as a sink for membrane proteins: hypothesis and implications in retinal ciliopathies. Hum Mol Genet 2017; 26:R75-R82. [PMID: 28453661 DOI: 10.1093/hmg/ddx163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 04/24/2017] [Indexed: 12/28/2022] Open
Abstract
The photoreceptor outer segment (OS) is a unique modification of the primary cilium, specialized for light perception. Being homologous organelles, the primary cilium and the OS share common building blocks and molecular machinery to construct and maintain them. The OS, however, has several unique structural features that are not seen in primary cilia. Although these unique features of the OS have been well documented, their implications in protein localization have been under-appreciated. In this review, we compare the structural properties of the primary cilium and the OS, and propose a hypothesis that the OS can act as a sink for membrane proteins. We further discuss the implications of this hypothesis in polarized protein localization in photoreceptors and mechanisms of photoreceptor degeneration in retinal ciliopathies.
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Affiliation(s)
- Seongjin Seo
- Department of Ophthalmology and Visual Sciences, Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Poppy Datta
- Department of Ophthalmology and Visual Sciences, Wynn Institute for Vision Research, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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41
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Youn YH, Han YG. Primary Cilia in Brain Development and Diseases. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:11-22. [PMID: 29030052 DOI: 10.1016/j.ajpath.2017.08.031] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Revised: 08/02/2017] [Accepted: 08/17/2017] [Indexed: 01/20/2023]
Abstract
The primary cilium, a sensory appendage that is present in most mammalian cells, plays critical roles in signaling pathways and cell cycle progression. Mutations that affect the structure or function of primary cilia result in ciliopathies, a group of developmental and degenerative diseases that affect almost all organs and tissues. Our understanding of the constituents, development, and function of primary cilia has advanced considerably in recent years, revealing pathogenic mechanisms that potentially underlie ciliopathies. In the brain, the primary cilia are crucial for early patterning, neurogenesis, neuronal maturation and survival, and tumorigenesis, mostly through regulating cell cycle progression, Hedgehog signaling, and WNT signaling. We review these advances in our knowledge of primary cilia, focusing on brain development, and discuss the mechanisms that may underlie brain abnormalities in ciliopathies.
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Affiliation(s)
- Yong Ha Youn
- Department of Developmental Neurobiology, Neurobiology and Brain Tumor Program, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Young-Goo Han
- Department of Developmental Neurobiology, Neurobiology and Brain Tumor Program, St. Jude Children's Research Hospital, Memphis, Tennessee.
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42
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Bujakowska KM, Liu Q, Pierce EA. Photoreceptor Cilia and Retinal Ciliopathies. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028274. [PMID: 28289063 DOI: 10.1101/cshperspect.a028274] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Photoreceptors are sensory neurons designed to convert light stimuli into neurological responses. This process, called phototransduction, takes place in the outer segments (OS) of rod and cone photoreceptors. OS are specialized sensory cilia, with analogous structures to those present in other nonmotile cilia. Deficient morphogenesis and/or dysfunction of photoreceptor sensory cilia (PSC) caused by mutations in a variety of photoreceptor-specific and common cilia genes can lead to inherited retinal degenerations (IRDs). IRDs can manifest as isolated retinal diseases or syndromic diseases. In this review, we describe the structure and composition of PSC and different forms of ciliopathies with retinal involvement. We review the genetics of the IRDs, which are monogenic disorders but genetically diverse with regard to causality.
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Affiliation(s)
- Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114
| | - Qin Liu
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114
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43
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Shi X, Garcia G, Van De Weghe JC, McGorty R, Pazour GJ, Doherty D, Huang B, Reiter JF. Super-resolution microscopy reveals that disruption of ciliary transition-zone architecture causes Joubert syndrome. Nat Cell Biol 2017; 19:1178-1188. [PMID: 28846093 DOI: 10.1038/ncb3599] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022]
Abstract
Ciliopathies, including nephronophthisis (NPHP), Meckel syndrome (MKS) and Joubert syndrome (JBTS), can be caused by mutations affecting components of the transition zone, a domain near the base of the cilium that controls the protein composition of its membrane. We defined the three-dimensional arrangement of key proteins in the transition zone using two-colour stochastic optical reconstruction microscopy (STORM). NPHP and MKS complex components form nested rings comprised of nine-fold doublets. JBTS-associated mutations in RPGRIP1L or TCTN2 displace certain transition-zone proteins. Diverse ciliary proteins accumulate at the transition zone in wild-type cells, suggesting that the transition zone is a waypoint for proteins entering and exiting the cilium. JBTS-associated mutations in RPGRIP1L disrupt SMO accumulation at the transition zone and the ciliary localization of SMO. We propose that the disruption of transition-zone architecture in JBTS leads to a failure of SMO to accumulate at the transition zone and cilium, disrupting developmental signalling in JBTS.
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Affiliation(s)
- Xiaoyu Shi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, USA
| | - Galo Garcia
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94143, USA.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, USA
| | - Julie C Van De Weghe
- Department of Pediatrics, University of Washington Medical Center, Seattle, Washington 98195, USA
| | - Ryan McGorty
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Biotech II, Suite 213, 373 Plantation Street, Worcester, Massachusetts 01605, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington Medical Center, Seattle, Washington 98195, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94143, USA.,Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California 94143, USA.,Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143, USA
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Meder B, Haas J, Sedaghat-Hamedani F, Kayvanpour E, Frese K, Lai A, Nietsch R, Scheiner C, Mester S, Bordalo DM, Amr A, Dietrich C, Pils D, Siede D, Hund H, Bauer A, Holzer DB, Ruhparwar A, Mueller-Hennessen M, Weichenhan D, Plass C, Weis T, Backs J, Wuerstle M, Keller A, Katus HA, Posch AE. Epigenome-Wide Association Study Identifies Cardiac Gene Patterning and a Novel Class of Biomarkers for Heart Failure. Circulation 2017; 136:1528-1544. [PMID: 28838933 DOI: 10.1161/circulationaha.117.027355] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/08/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND Biochemical DNA modification resembles a crucial regulatory layer among genetic information, environmental factors, and the transcriptome. To identify epigenetic susceptibility regions and novel biomarkers linked to myocardial dysfunction and heart failure, we performed the first multi-omics study in myocardial tissue and blood of patients with dilated cardiomyopathy and controls. METHODS Infinium human methylation 450 was used for high-density epigenome-wide mapping of DNA methylation in left-ventricular biopsies and whole peripheral blood of living probands. RNA deep sequencing was performed on the same samples in parallel. Whole-genome sequencing of all patients allowed exclusion of promiscuous genotype-induced methylation calls. RESULTS In the screening stage, we detected 59 epigenetic loci that are significantly associated with dilated cardiomyopathy (false discovery corrected P≤0.05), with 3 of them reaching epigenome-wide significance at P≤5×10-8. Twenty-seven (46%) of these loci could be replicated in independent cohorts, underlining the role of epigenetic regulation of key cardiac transcription regulators. Using a staged multi-omics study design, we link a subset of 517 epigenetic loci with dilated cardiomyopathy and cardiac gene expression. Furthermore, we identified distinct epigenetic methylation patterns that are conserved across tissues, rendering these CpGs novel epigenetic biomarkers for heart failure. CONCLUSIONS The present study provides to our knowledge the first epigenome-wide association study in living patients with heart failure using a multi-omics approach.
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Affiliation(s)
- Benjamin Meder
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Jan Haas
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Farbod Sedaghat-Hamedani
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Elham Kayvanpour
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Karen Frese
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Alan Lai
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Rouven Nietsch
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Christina Scheiner
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Stefan Mester
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Diana Martins Bordalo
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Ali Amr
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Carsten Dietrich
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Dietmar Pils
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Dominik Siede
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Hauke Hund
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Andrea Bauer
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Daniel Benjamin Holzer
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Arjang Ruhparwar
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Matthias Mueller-Hennessen
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Dieter Weichenhan
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Christoph Plass
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Tanja Weis
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Johannes Backs
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Maximilian Wuerstle
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Andreas Keller
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
| | - Hugo A Katus
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.).
| | - Andreas E Posch
- From Department of Internal Medicine III, Institute for Cardiomyopathies, University of Heidelberg, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., R.N., C.S., S.M., D.M.-B., A.A., H.H., D.B.H., M.M.-H., T.W., H.A.K.); Siemens Healthcare GmbH, Strategy and Innovation, Erlangen, Germany (C.D., M.W., A.E.P.); Department of Bioinformatics, University of Saarland, Saarbrücken, Germany (A.K.); German Centre for Cardiovascular Research, Berlin, Germany (B.M., J.H., F.S.-H., E.K., K.F., A.L., D.S., M.M.-H., T.W., J.B., H.A.K.); Institute for Molecular Cardiology and Epigenetics, University of Heidelberg, Germany (D.S., J.B.); Funktionelle Genomanalyse, Deutsches Krebsforschungszentrum, Heidelberg, Germany (A.B.); Department of Cardiac Surgery, University of Heidelberg, Germany (A.R.); Siemens AG, Corporate Technology, Vienna, Austria (D.P.); Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Austria (D.P.); and Division of Epigenomics and Cancer Risk Factors, Deutsches Krebsforschungszentrum, Heidelberg, Germany (D.W., C.P.)
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45
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Takao D, Wang L, Boss A, Verhey KJ. Protein Interaction Analysis Provides a Map of the Spatial and Temporal Organization of the Ciliary Gating Zone. Curr Biol 2017; 27:2296-2306.e3. [PMID: 28736169 DOI: 10.1016/j.cub.2017.06.044] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/09/2017] [Accepted: 06/16/2017] [Indexed: 11/19/2022]
Abstract
The motility and signaling functions of the primary cilium require a unique protein and lipid composition that is determined by gating mechanisms localized at the base of the cilium. Several protein complexes localize to the gating zone and may regulate ciliary protein composition; however, the mechanisms of ciliary gating and the dynamics of the gating components are largely unknown. Here, we used the BiFC (bimolecular fluorescence complementation) assay and report for the first time on the protein-protein interactions that occur between ciliary gating components and transiting cargoes during ciliary entry. We find that the nucleoporin Nup62 and the C termini of the nephronophthisis (NPHP) proteins NPHP4 and NPHP5 interact with the axoneme-associated kinesin-2 motor KIF17 and thus spatially map to the inner region of the ciliary gating zone. Nup62 and NPHP4 exhibit rapid turnover at the transition zone and thus define dynamic components of the gate. We find that B9D1, AHI1, and the N termini of NPHP4 and NPHP5 interact with the transmembrane protein SSTR3 and thus spatially map to the outer region of the ciliary gating zone. B9D1, AHI1, and NPHP5 exhibit little to no turnover at the transition zone and thus define components of a stable gating structure. These data provide the first comprehensive map of the molecular orientations of gating zone components along the inner-to-outer axis of the ciliary gating zone. These results advance our understanding of the functional roles of gating zone components in regulating ciliary protein composition.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Liang Wang
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, 101 Shanghai Road, Tongshan District, Xuzhou 221116, China
| | - Allison Boss
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
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46
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Tian H, Feng J, Li J, Ho TV, Yuan Y, Liu Y, Brindopke F, Figueiredo JC, Magee W, Sanchez-Lara PA, Chai Y. Intraflagellar transport 88 (IFT88) is crucial for craniofacial development in mice and is a candidate gene for human cleft lip and palate. Hum Mol Genet 2017; 26:860-872. [PMID: 28069795 DOI: 10.1093/hmg/ddx002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 01/03/2016] [Indexed: 01/08/2023] Open
Abstract
Ciliopathies are pleiotropic human diseases resulting from defects of the primary cilium, and these patients often have cleft lip and palate. IFT88 is required for the assembly and function of the primary cilia, which mediate the activity of key developmental signaling pathways. Through whole exome sequencing of a family of three affected siblings with isolated cleft lip and palate, we discovered that they share a novel missense mutation in IFT88 (c.915G > C, p.E305D), suggesting this gene should be considered a candidate for isolated orofacial clefting. In order to evaluate the function of IFT88 in regulating craniofacial development, we generated Wnt1-Cre;Ift88fl/fl mice to eliminate Ift88 specifically in cranial neural crest (CNC) cells. Wnt1-Cre;Ift88fl/flpups died at birth due to severe craniofacial defects including bilateral cleft lip and palate and tongue agenesis, following the loss of the primary cilia in the CNC-derived palatal mesenchyme. Loss of Ift88 also resulted in a decrease in neural crest cell proliferation during early stages of palatogenesis as well as a downregulation of the Shh signaling pathway in the palatal mesenchyme. Importantly, Osr2KI-Cre;Ift88fl/flmice, in which Ift88 is lost specifically in the palatal mesenchyme, exhibit isolated cleft palate. Taken together, our results demonstrate that IFT88 has a highly conserved function within the primary cilia of the CNC-derived mesenchyme in the lip and palate region in mice and is a strong candidate as an orofacial clefting gene in humans.
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Affiliation(s)
- Hua Tian
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Department of Cariology and Endodontology, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Jingyuan Li
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing 100050, China
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Yuan Yuan
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Liu
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - Frederick Brindopke
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - William Magee
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Pedro A Sanchez-Lara
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA.,Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.,Department of Pathology & Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033, USA
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47
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Stayner C, Poole CA, McGlashan SR, Pilanthananond M, Brauning R, Markie D, Lett B, Slobbe L, Chae A, Johnstone AC, Jensen CG, McEwan JC, Dittmer K, Parker K, Wiles A, Blackburne W, Leichter A, Leask M, Pinnapureddy A, Jennings M, Horsfield JA, Walker RJ, Eccles MR. An ovine hepatorenal fibrocystic model of a Meckel-like syndrome associated with dysmorphic primary cilia and TMEM67 mutations. Sci Rep 2017; 7:1601. [PMID: 28487520 PMCID: PMC5431643 DOI: 10.1038/s41598-017-01519-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 03/29/2017] [Indexed: 01/20/2023] Open
Abstract
Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, caused by mutations in TMEM67, characterized by occipital encephalocoele, renal cysts, hepatic fibrosis, and polydactyly. Here we describe an ovine model of MKS, with kidney and liver abnormalities, without polydactyly or occipital encephalocoele. Homozygous missense p.(Ile681Asn; Ile687Ser) mutations identified in ovine TMEM67 were pathogenic in zebrafish phenotype rescue assays. Meckelin protein was expressed in affected and unaffected kidney epithelial cells by immunoblotting, and in primary cilia of lamb kidney cyst epithelial cells by immunofluorescence. In contrast to primary cilia of relatively consistent length and morphology in unaffected kidney cells, those of affected cyst-lining cells displayed a range of short and extremely long cilia, as well as abnormal morphologies, such as bulbous regions along the axoneme. Putative cilia fragments were also consistently located within the cyst luminal contents. The abnormal ciliary phenotype was further confirmed in cultured interstitial fibroblasts from affected kidneys. These primary cilia dysmorphologies and length control defects were significantly greater in affected cells compared to unaffected controls. In conclusion, we describe abnormalities involving primary cilia length and morphology in the first reported example of a large animal model of MKS, in which we have identified TMEM67 mutations.
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Affiliation(s)
- C Stayner
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - C A Poole
- Department of Medicine, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand.,150 Warren Street, Wanaka, 9305, New Zealand
| | - S R McGlashan
- Department of Anatomy and Medical Imaging, The University of Auckland 1142, Private Bag, 92019, Auckland, New Zealand
| | - M Pilanthananond
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - R Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel, 9053, New Zealand
| | - D Markie
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - B Lett
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - L Slobbe
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Chae
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A C Johnstone
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Tennant Drive, Palmerston North, 4472, New Zealand
| | - C G Jensen
- Department of Anatomy and Medical Imaging, The University of Auckland 1142, Private Bag, 92019, Auckland, New Zealand
| | - J C McEwan
- AgResearch Invermay Agricultural Centre, Mosgiel, 9053, New Zealand
| | - K Dittmer
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Tennant Drive, Palmerston North, 4472, New Zealand
| | - K Parker
- Department of Medicine, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Wiles
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - W Blackburne
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Leichter
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - M Leask
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - A Pinnapureddy
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - M Jennings
- Department of Medicine, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - J A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - R J Walker
- Department of Medicine, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - M R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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48
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Trempus CS, Song W, Lazrak A, Yu Z, Creighton JR, Young BM, Heise RL, Yu YR, Ingram JL, Tighe RM, Matalon S, Garantziotis S. A novel role for primary cilia in airway remodeling. Am J Physiol Lung Cell Mol Physiol 2017; 313:L328-L338. [PMID: 28473325 DOI: 10.1152/ajplung.00284.2016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 04/21/2017] [Accepted: 05/01/2017] [Indexed: 01/26/2023] Open
Abstract
Primary cilia (PC) are solitary cellular organelles that play critical roles in development, homeostasis, and disease pathogenesis by modulating key signaling pathways such as Sonic Hedgehog and calcium flux. The antenna-like shape of PC enables them also to facilitate sensing of extracellular and mechanical stimuli into the cell, and a critical role for PC has been described for mesenchymal cells such as chondrocytes. However, nothing is known about the role of PC in airway smooth muscle cells (ASMCs) in the context of airway remodeling. We hypothesized that PC on ASMCs mediate cell contraction and are thus integral in the remodeling process. We found that PC are expressed on ASMCs in asthmatic lungs. Using pharmacological and genetic methods, we demonstrated that PC are necessary for ASMC contraction in a collagen gel three-dimensional model both in the absence of external stimulus and in response to the extracellular component hyaluronan. Mechanistically, we demonstrate that the effect of PC on ASMC contraction is, to a small extent, due to their effect on Sonic Hedgehog signaling and, to a larger extent, due to their effect on calcium influx and membrane depolarization. In conclusion, PC are necessary for the development of airway remodeling by mediating calcium flux and Sonic Hedgehog signaling.
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Affiliation(s)
- Carol S Trempus
- Matrix Biology Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Weifeng Song
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, and Pulmonary Injury and Repair Center, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Ahmed Lazrak
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, and Pulmonary Injury and Repair Center, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhihong Yu
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, and Pulmonary Injury and Repair Center, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Judy R Creighton
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, and Pulmonary Injury and Repair Center, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Bethany M Young
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia; and
| | - Rebecca L Heise
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia; and
| | - Yen Rei Yu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Jennifer L Ingram
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Robert M Tighe
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Sadis Matalon
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, and Pulmonary Injury and Repair Center, School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Stavros Garantziotis
- Matrix Biology Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina;
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49
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A nonsense mutation inCEP55defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy. Clin Genet 2017; 92:510-516. [DOI: 10.1111/cge.13012] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/09/2017] [Accepted: 03/03/2017] [Indexed: 01/05/2023]
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50
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Gonçalves J, Pelletier L. The Ciliary Transition Zone: Finding the Pieces and Assembling the Gate. Mol Cells 2017; 40:243-253. [PMID: 28401750 PMCID: PMC5424270 DOI: 10.14348/molcells.2017.0054] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 12/23/2022] Open
Abstract
Eukaryotic cilia are organelles that project from the surface of cells to fulfill motility and sensory functions. In vertebrates, the functions of both motile and immotile cilia are critical for embryonic development and adult tissue homeostasis. Importantly, a multitude of human diseases is caused by abnormal cilia biogenesis and functions which rely on the compartmentalization of the cilium and the maintenance of its protein composition. The transition zone (TZ) is a specialized ciliary domain present at the base of the cilium and is part of a gate that controls protein entry and exit from this organelle. The relevance of the TZ is highlighted by the fact that several of its components are coded by ciliopathy genes. Here we review recent developments in the study of TZ proteomes, the mapping of individual components to the TZ structure and the establishment of the TZ as a lipid gate.
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Affiliation(s)
- João Gonçalves
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5,
Canada
| | - Laurence Pelletier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5,
Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8,
Canada
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