Cilium-Generated Signaling and Cilia-Related Disorders
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Educational Paper Ciliopathies
Eur J Pediatr (2012) 171:1285–1300 DOI 10.1007/s00431-011-1553-z REVIEW Educational paper Ciliopathies Carsten Bergmann Received: 11 June 2011 /Accepted: 3 August 2011 /Published online: 7 September 2011 # The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Cilia are antenna-like organelles found on the (NPHP) . Ivemark syndrome . Meckel syndrome (MKS) . surface of most cells. They transduce molecular signals Joubert syndrome (JBTS) . Bardet–Biedl syndrome (BBS) . and facilitate interactions between cells and their Alstrom syndrome . Short-rib polydactyly syndromes . environment. Ciliary dysfunction has been shown to Jeune syndrome (ATD) . Ellis-van Crefeld syndrome (EVC) . underlie a broad range of overlapping, clinically and Sensenbrenner syndrome . Primary ciliary dyskinesia genetically heterogeneous phenotypes, collectively (Kartagener syndrome) . von Hippel-Lindau (VHL) . termed ciliopathies. Literally, all organs can be affected. Tuberous sclerosis (TSC) . Oligogenic inheritance . Modifier. Frequent cilia-related manifestations are (poly)cystic Mutational load kidney disease, retinal degeneration, situs inversus, cardiac defects, polydactyly, other skeletal abnormalities, and defects of the central and peripheral nervous Introduction system, occurring either isolated or as part of syn- dromes. Characterization of ciliopathies and the decisive Defective cellular organelles such as mitochondria, perox- role of primary cilia in signal transduction and cell isomes, and lysosomes are well-known -
The Emerging Landscape of Dynamic DNA Methylation in Early Childhood
The emerging landscape of dynamic DNA methylation in early childhood Cheng-Jian Xu, Marc Jan Bonder, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, Ulrike Gehring, Soesma Jankipersadsing, Pieter van der Vlies, Cleo van Diemen, Bianca van Rijkom, et al. To cite this version: Cheng-Jian Xu, Marc Jan Bonder, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, et al.. The emerg- ing landscape of dynamic DNA methylation in early childhood. BMC Genomics, BioMed Central, 2017, 18, pp.25. 10.1186/s12864-016-3452-1. hal-01792686 HAL Id: hal-01792686 https://hal.archives-ouvertes.fr/hal-01792686 Submitted on 26 May 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Xu et al. BMC Genomics (2017) 18:25 DOI 10.1186/s12864-016-3452-1 RESEARCHARTICLE Open Access The emerging landscape of dynamic DNA methylation in early childhood Cheng-Jian Xu1,2*, Marc Jan Bonder2, Cilla Söderhäll3,4, Mariona Bustamante5,6,7,8, Nour Baïz9, Ulrike Gehring10, Soesma A. Jankipersadsing1,2, Pieter van der Vlies2, Cleo C. van Diemen2, Bianca van Rijkom2, Jocelyne Just9,11, Inger Kull12, Juha Kere3,13, Josep Maria Antó5,7,8,14, Jean Bousquet15,16,17,18, Alexandra Zhernakova2, Cisca Wijmenga2, Isabella Annesi-Maesano9, Jordi Sunyer5,7,8,14, Erik Melén19, Yang Li2*, Dirkje S. -
Synergistic Genetic Interactions Between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models
BASIC RESEARCH www.jasn.org Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models Rory J. Olson,1 Katharina Hopp ,2 Harrison Wells,3 Jessica M. Smith,3 Jessica Furtado,1,4 Megan M. Constans,3 Diana L. Escobar,3 Aron M. Geurts,5 Vicente E. Torres,3 and Peter C. Harris 1,3 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background Autosomal recessive polycystic kidney disease (ARPKD) and autosomal dominant polycystic kidney disease (ADPKD) are genetically distinct, with ADPKD usually caused by the genes PKD1 or PKD2 (encoding polycystin-1 and polycystin-2, respectively) and ARPKD caused by PKHD1 (encoding fibrocys- tin/polyductin [FPC]). Primary cilia have been considered central to PKD pathogenesis due to protein localization and common cystic phenotypes in syndromic ciliopathies, but their relevance is questioned in the simple PKDs. ARPKD’s mild phenotype in murine models versus in humans has hampered investi- gating its pathogenesis. Methods To study the interaction between Pkhd1 and Pkd1, including dosage effects on the phenotype, we generated digenic mouse and rat models and characterized and compared digenic, monogenic, and wild-type phenotypes. Results The genetic interaction was synergistic in both species, with digenic animals exhibiting pheno- types of rapidly progressive PKD and early lethality resembling classic ARPKD. Genetic interaction be- tween Pkhd1 and Pkd1 depended on dosage in the digenic murine models, with no significant enhancement of the monogenic phenotype until a threshold of reduced expression at the second locus was breached. -
Invited Review: Genetic and Genomic Mouse Models for Livestock Research
Archives Animal Breeding – serving the animal science community for 60 years Arch. Anim. Breed., 61, 87–98, 2018 https://doi.org/10.5194/aab-61-87-2018 Open Access © Author(s) 2018. This work is distributed under the Creative Commons Attribution 4.0 License. Archives Animal Breeding Invited review: Genetic and genomic mouse models for livestock research Danny Arends, Deike Hesse, and Gudrun A. Brockmann Albrecht Daniel Thaer-Institut für Agrar- und Gartenbauwissenschaften, Humboldt-Universität zu Berlin, 10115 Berlin, Germany Correspondence: Danny Arends ([email protected]) and Gudrun A. Brockmann ([email protected]) Received: 7 December 2017 – Revised: 3 January 2018 – Accepted: 8 January 2018 – Published: 13 February 2018 Abstract. Knowledge about the function and functioning of single or multiple interacting genes is of the utmost significance for understanding the organism as a whole and for accurate livestock improvement through genomic selection. This includes, but is not limited to, understanding the ontogenetic and environmentally driven regula- tion of gene action contributing to simple and complex traits. Genetically modified mice, in which the functions of single genes are annotated; mice with reduced genetic complexity; and simplified structured populations are tools to gain fundamental knowledge of inheritance patterns and whole system genetics and genomics. In this re- view, we briefly describe existing mouse resources and discuss their value for fundamental and applied research in livestock. 1 Introduction the generation of targeted mutations found their way from model animals to livestock species. Through this progress, During the last 10 years, tools for genome analyses model organisms attain a new position in fundamental sci- have developed tremendously. -
University of Oklahoma
UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D. -
GENETIC STUDY of RENAL DISEASES (Nephroref Global®) by MASSIVE SEQUENCING (NGS)
Pablo Iglesias, 57 – Polígono Gran Via Sur 08908 L'Hospitalet de Llobregat (Barcelona) Tel. 932 593 700 – Fax. 932 845 000 GENETIC STUDY OF RENAL DISEASES (NephroRef Global®) BY MASSIVE SEQUENCING (NGS) Request No.: 000 Client: - Analysis code: 55580 Patient Name: xxx Date of Birth: N/A Patient Ref.: xxx Gender: Female Sample Type: Blood EDTA Sample Arrival Date: DD/MM/AAAA Date of Result: DD/MM/AAAA Clinical information: A 9-year-old patient with a nephrotic syndrome without response to corticosteroid therapy. She has nephrotic-range proteinuria with microhematuria, hypoalbuminemia with hypercholesterolemia and normal glomerular filtration. Paternal aunt with cortico-resistant nephrotic syndrome with evolution to end-stage renal failure that required renal transplantation at age 13. RESULT AND INTERPRETATION The presence of a heterozygous likely pathogenic variant has been identified. In addition, the presence of a heterozygous variant of uncertain clinical significance (VUS) has been identified.(See Interpretation and recommendations) The complete list of studied genes is available in Annex 1. (Methodology) The list of reported genes and coverage details is available in Table 1. (Methodology) Gene Variant* Zygosity Inheritance pattern Classification^ NPHS2 NM_014625.3: c.842A>C Heterozygosis Autosomal Recessive Likely Patogénica p.(Glu281Ala) INF2 NM_022489.3: c.67T>A Heterozygosis Autosomal Recessive VUS p.(Ser23Thr) * Nomenclature according to HGVS v15.11 ^ Based on the recommendations of the American College of Medical Genetics and Genomics (ACMG) Physician, technical specialist responsible for Clinical Analysis: Jaime Torrents Pont. The results relate to samples received and analysed. This report may not be reproduced in part without permission. This document is addressed to the addressee and contains confidential information. -
SDCCAG8 Interacts with RAB Effector Proteins RABEP2 and ERC1 and Is Required for Hedgehog Signaling
SDCCAG8 Interacts with RAB Effector Proteins RABEP2 and ERC1 and Is Required for Hedgehog Signaling Airik, Rannar; Schueler, Markus; Airik, Merlin; Cho, Jang; Ulanowicz, Kelsey A; Porath, Jonathan D; Hurd, Toby W; Bekker-Jensen, Simon; Schrøder, Jacob Morville; Andersen, Jens S.; Hildebrandt, Friedhelm Published in: P L o S One DOI: 10.1371/journal.pone.0156081 Publication date: 2016 Document version Publisher's PDF, also known as Version of record Document license: CC BY Citation for published version (APA): Airik, R., Schueler, M., Airik, M., Cho, J., Ulanowicz, K. A., Porath, J. D., Hurd, T. W., Bekker-Jensen, S., Schrøder, J. M., Andersen, J. S., & Hildebrandt, F. (2016). SDCCAG8 Interacts with RAB Effector Proteins RABEP2 and ERC1 and Is Required for Hedgehog Signaling. P L o S One, 11(5), [e0156081]. https://doi.org/10.1371/journal.pone.0156081 Download date: 04. Oct. 2021 RESEARCH ARTICLE SDCCAG8 Interacts with RAB Effector Proteins RABEP2 and ERC1 and Is Required for Hedgehog Signaling Rannar Airik1¤‡*, Markus Schueler1, Merlin Airik1, Jang Cho1, Kelsey A. Ulanowicz2, Jonathan D. Porath1, Toby W. Hurd3, Simon Bekker-Jensen4, Jacob M. Schrøder5, Jens S. Andersen5, Friedhelm Hildebrandt1,6‡* 1 Department of Medicine, Division of Nephrology, Boston Children’s Hospital, Boston, Massachusetts, United States of America, 2 Department of Pediatrics, Division of Nephrology, Children’s Hospital of a11111 Pittsburgh of UPMC, Pittsburgh, Pennsylvania, United States of America, 3 Medical Research Council Human Genetics Unit, Institute of -
Inhibition of Hedgehog Signaling Suppresses Proliferation And
www.nature.com/scientificreports OPEN Inhibition of Hedgehog signaling suppresses proliferation and microcyst formation of human Received: 21 August 2017 Accepted: 9 March 2018 Autosomal Dominant Polycystic Published: xx xx xxxx Kidney Disease cells Luciane M. Silva1,5, Damon T. Jacobs1,5, Bailey A. Allard1,5, Timothy A. Fields2,5, Madhulika Sharma4,5, Darren P. Wallace3,4,5 & Pamela V. Tran 1,5 Autosomal Dominant Polycystic Kidney Disease (ADPKD) is caused by mutation of PKD1 or PKD2, which encode polycystin 1 and 2, respectively. The polycystins localize to primary cilia and the functional loss of the polycystin complex leads to the formation and progressive growth of fuid-flled cysts in the kidney. The pathogenesis of ADPKD is complex and molecular mechanisms connecting ciliary dysfunction to renal cystogenesis are unclear. Primary cilia mediate Hedgehog signaling, which modulates cell proliferation and diferentiation in a tissue-dependent manner. Previously, we showed that Hedgehog signaling was increased in cystic kidneys of several PKD mouse models and that Hedgehog inhibition prevented cyst formation in embryonic PKD mouse kidneys treated with cAMP. Here, we show that in human ADPKD tissue, Hedgehog target and activator, Glioma 1, was elevated and localized to cyst-lining epithelial cells and to interstitial cells, suggesting increased autocrine and paracrine Hedgehog signaling in ADPKD, respectively. Further, Hedgehog inhibitors reduced basal and cAMP-induced proliferation of ADPKD cells and cyst formation in vitro. These data suggest that Hedgehog signaling is increased in human ADPKD and that suppression of Hedgehog signaling can counter cellular processes that promote cyst growth in vitro. Autosomal Dominant Polycystic Kidney Disease (ADPKD) is among the most commonly inherited, life-threatening diseases, afecting 1:500 adults worldwide. -
Ciliopathies Gene Panel
Ciliopathies Gene Panel Contact details Introduction Regional Genetics Service The ciliopathies are a heterogeneous group of conditions with considerable phenotypic overlap. Levels 4-6, Barclay House These inherited diseases are caused by defects in cilia; hair-like projections present on most 37 Queen Square cells, with roles in key human developmental processes via their motility and signalling functions. Ciliopathies are often lethal and multiple organ systems are affected. Ciliopathies are London, WC1N 3BH united in being genetically heterogeneous conditions and the different subtypes can share T +44 (0) 20 7762 6888 many clinical features, predominantly cystic kidney disease, but also retinal, respiratory, F +44 (0) 20 7813 8578 skeletal, hepatic and neurological defects in addition to metabolic defects, laterality defects and polydactyly. Their clinical variability can make ciliopathies hard to recognise, reflecting the ubiquity of cilia. Gene panels currently offer the best solution to tackling analysis of genetically Samples required heterogeneous conditions such as the ciliopathies. Ciliopathies affect approximately 1:2,000 5ml venous blood in plastic EDTA births. bottles (>1ml from neonates) Ciliopathies are generally inherited in an autosomal recessive manner, with some autosomal Prenatal testing must be arranged dominant and X-linked exceptions. in advance, through a Clinical Genetics department if possible. Referrals Amniotic fluid or CV samples Patients presenting with a ciliopathy; due to the phenotypic variability this could be a diverse set should be sent to Cytogenetics for of features. For guidance contact the laboratory or Dr Hannah Mitchison dissecting and culturing, with ([email protected]) / Prof Phil Beales ([email protected]) instructions to forward the sample to the Regional Molecular Genetics Referrals will be accepted from clinical geneticists and consultants in nephrology, metabolic, laboratory for analysis respiratory and retinal diseases. -
Diagnostic Test: OBESITÀ GENETICHE MENDELIANE
Diagnostic test: OBESITÀ GENETICHE MENDELIANE MENDELIAN OBESITY Panel / Illumina Custom panel, Nextera Enrichment Technology / Coding exons and flanking regions of genes List of gene(s) and disease(s) tested: ALMS1, ARL6, BBIP1, BBS1, BBS10, BBS12, BBS2, BBS4, BBS5, BBS7, BBS9, C8orf37, CARTPT, CEP19, CEP290, DYRK1B, GNAS, HDAC8, IFT172, IFT27, INPP5E, INSR, KSR2, LEP, LEPR, LZTFL1, MC3R, MC4R, MCHR1, MEGF8, MKKS, MKS1, NR0B2, PCSK1, PHF6, POMC, PPARG, PPP1R3A, RAB23, SDCCAG8, SH2B1, SIM1, TRIM32, TTC8, UCP3, VPS13B, WDPCP ORPHA:98267 Obesità non sindromica genetica Obesità sindromica Tabella Elenco delle forme di OBESITÀ GENETICHE MENDELIANE e la loro eziologia genetica Phenotype OMIM# Gene OMIM# Phenotype Gene Alstrom syndrome 203800 ALMS1 606844 Bardet-Biedl syndrome 3 600151 ARL6 608845 Bardet-Biedl syndrome 18 615995 BBIP1 613605 Bardet-Biedl syndrome 1 209900 BBS1 209901 Bardet-Biedl syndrome 10 615987 BBS10 610148 Bardet-Biedl syndrome 12 615989 BBS12 610683 Bardet-Biedl syndrome 2 615981 BBS2 606151 Bardet-Biedl syndrome 4 615982 BBS4 600374 Bardet-Biedl syndrome 5 615983 BBS5 603650 Bardet-Biedl syndrome 7 615984 BBS7 607590 Bardet-Biedl syndrome 21 617406 C8orf37 614477 Obesity, severe HGMD CARTPT 602606 Morbid obesity and spermatogenic failure; Bardet-Biedl syndrome; Morbid obesity 615703; HGMD CEP19 615586 Bardet-Biedl syndrome 14 615991 CEP290 610142 Abdominal obesity-metabolic syndrome 3 615812 DYRK1B 604556 Pseudohypoparathyroidism Ia; Pseudohypoparathyroidism Ic 103580; 612462 GNAS 139320 Cornelia de Lange syndrome 5 300882 -
The Role of Primary Cilia in the Crosstalk Between the Ubiquitin–Proteasome System and Autophagy
cells Review The Role of Primary Cilia in the Crosstalk between the Ubiquitin–Proteasome System and Autophagy Antonia Wiegering, Ulrich Rüther and Christoph Gerhardt * Institute for Animal Developmental and Molecular Biology, Heinrich Heine University, 40225 Düsseldorf, Germany; [email protected] (A.W.); [email protected] (U.R.) * Correspondence: [email protected]; Tel.: +49-(0)211-81-12236 Received: 29 December 2018; Accepted: 11 March 2019; Published: 14 March 2019 Abstract: Protein degradation is a pivotal process for eukaryotic development and homeostasis. The majority of proteins are degraded by the ubiquitin–proteasome system and by autophagy. Recent studies describe a crosstalk between these two main eukaryotic degradation systems which allows for establishing a kind of safety mechanism. If one of these degradation systems is hampered, the other compensates for this defect. The mechanism behind this crosstalk is poorly understood. Novel studies suggest that primary cilia, little cellular protrusions, are involved in the regulation of the crosstalk between the two degradation systems. In this review article, we summarise the current knowledge about the association between cilia, the ubiquitin–proteasome system and autophagy. Keywords: protein aggregation; neurodegenerative diseases; OFD1; BBS4; RPGRIP1L; hedgehog; mTOR; IFT; GLI 1. Introduction Protein aggregates are huge protein accumulations that develop as a consequence of misfolded proteins. The occurrence of protein aggregates is associated with the development of neurodegenerative diseases, such as Huntington’s disease, prion disorders, Alzheimer’s disease and Parkinson’s disease [1–3], demonstrating that the degradation of incorrectly folded proteins is of eminent importance for human health. In addition to the destruction of useless and dangerous proteins (protein quality control), protein degradation is an important process to regulate the cell cycle, to govern transcription and also to control intra- and intercellular signal transduction [4–6]. -
Intraflagellar Transport Proteins Are Essential for Cilia Formation and for Planar Cell Polarity
BASIC RESEARCH www.jasn.org Intraflagellar Transport Proteins Are Essential for Cilia Formation and for Planar Cell Polarity Ying Cao, Alice Park, and Zhaoxia Sun Department of Genetics, Yale University School of Medicine, New Haven, Connecticut ABSTRACT The highly conserved intraflagellar transport (IFT) proteins are essential for cilia formation in multiple organisms, but surprisingly, cilia form in multiple zebrafish ift mutants. Here, we detected maternal deposition of ift gene products in zebrafish and found that ciliary assembly occurs only during early developmental stages, supporting the idea that maternal contribution of ift gene products masks the function of IFT proteins during initial development. In addition, the basal bodies in multiciliated cells of the pronephric duct in ift mutants were disorganized, with a pattern suggestive of defective planar cell polarity (PCP). Depletion of pk1, a core PCP component, similarly led to kidney cyst formation and basal body disorganization. Furthermore, we found that multiple ift genes genetically interact with pk1. Taken together, these data suggest that IFT proteins play a conserved role in cilia formation and planar cell polarity in zebrafish. J Am Soc Nephrol 21: 1326–1333, 2010. doi: 10.1681/ASN.2009091001 The cilium is a cell surface organelle that is almost In zebrafish, mutants of ift57, ift81, ift88, and ubiquitously present on vertebrate cells. Pro- ift172 have numerous defects commonly associated truding from the cell into its environment, the with ciliary abnormalities.13,14