1
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Fujii T, Liang L, Nakayama K, Katoh Y. Defects in diffusion barrier function of ciliary transition zone caused by ciliopathy variations of TMEM218. Hum Mol Genet 2024; 33:1442-1453. [PMID: 38751342 DOI: 10.1093/hmg/ddae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 08/09/2024] Open
Abstract
Primary cilia are antenna-like structures protruding from the surface of various eukaryotic cells, and have distinct protein compositions in their membranes. This distinct protein composition is maintained by the presence of the transition zone (TZ) at the ciliary base, which acts as a diffusion barrier between the ciliary and plasma membranes. Defects in cilia and the TZ are known to cause a group of disorders collectively called the ciliopathies, which demonstrate a broad spectrum of clinical features, such as perinatally lethal Meckel syndrome (MKS), relatively mild Joubert syndrome (JBTS), and nonsyndromic nephronophthisis (NPHP). Proteins constituting the TZ can be grouped into the MKS and NPHP modules. The MKS module is composed of several transmembrane proteins and three soluble proteins. TMEM218 was recently reported to be mutated in individuals diagnosed as MKS and JBTS. However, little is known about how TMEM218 mutations found in MKS and JBTS affect the functions of cilia. In this study, we found that ciliary membrane proteins were not localized to cilia in TMEM218-knockout cells, indicating impaired barrier function of the TZ. Furthermore, the exogenous expression of JBTS-associated TMEM218 variants but not MKS-associated variants in TMEM218-knockout cells restored the localization of ciliary membrane proteins. In particular, when expressed in TMEM218-knockout cells, the TMEM218(R115H) variant found in JBTS was able to restore the barrier function of cells, whereas the MKS variant TMEM218(R115C) could not. Thus, the severity of symptoms of MKS and JBTS individuals appears to correlate with the degree of their ciliary defects at the cellular level.
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Affiliation(s)
- Taiju Fujii
- 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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2
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Ewerling A, May-Simera HL. Evolutionary trajectory for nuclear functions of ciliary transport complex proteins. Microbiol Mol Biol Rev 2024:e0000624. [PMID: 38995044 DOI: 10.1128/mmbr.00006-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024] Open
Abstract
SUMMARYCilia and the nucleus were two defining features of the last eukaryotic common ancestor. In early eukaryotic evolution, these structures evolved through the diversification of a common membrane-coating ancestor, the protocoatomer. While in cilia, the descendants of this protein complex evolved into parts of the intraflagellar transport complexes and BBSome, the nucleus gained its selectivity by recruiting protocoatomer-like proteins to the nuclear envelope to form the selective nuclear pore complexes. Recent studies show a growing number of proteins shared between the proteomes of the respective organelles, and it is currently unknown how ciliary transport proteins could acquire nuclear functions and vice versa. The nuclear functions of ciliary proteins are still observable today and remain relevant for the understanding of the disease mechanisms behind ciliopathies. In this work, we review the evolutionary history of cilia and nucleus and their respective defining proteins and integrate current knowledge into theories for early eukaryotic evolution. We postulate a scenario where both compartments co-evolved and that fits current models of eukaryotic evolution, explaining how ciliary proteins and nucleoporins acquired their dual functions.
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Affiliation(s)
- Alexander Ewerling
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Helen Louise May-Simera
- Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
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3
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Wolf MTF, Bonsib SM, Larsen CP, Hildebrandt F. Nephronophthisis: a pathological and genetic perspective. Pediatr Nephrol 2024; 39:1977-2000. [PMID: 37930417 DOI: 10.1007/s00467-023-06174-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 11/07/2023]
Abstract
Nephronophthisis (NPHP) is an autosomal recessive cystic kidney disease and is one of the most frequent genetic causes for kidney failure (KF) in children and adolescents. Over 20 genes cause NPHP and over 90 genes contribute to renal ciliopathies often involving multiple organs. About 15-20% of NPHP patients have additional extrarenal symptoms affecting other organs than the kidneys. The involvement of additional organ systems in syndromic forms of NPHP is explained by shared expression of most NPHP gene products in centrosomes and primary cilia, a sensory organelle present in most mammalian cells. This finding resulted in the classification of NPHP as a ciliopathy. If extrarenal symptoms are present in addition to NPHP, these disorders are defined as NPHP-related ciliopathies (NPHP-RC) and can involve the retina (e.g., with Senior-Løken syndrome), CNS (central nervous system) (e.g., with Joubert syndrome), liver (e.g., Boichis and Arima syndromes), or bone (e.g., Mainzer-Saldino and Sensenbrenner syndromes). This review focuses on the pathological findings and the recent genetic advances in NPHP and NPHP-RC. Different mechanisms and signaling pathways are involved in NPHP ranging from planar cell polarity, sonic hedgehog signaling (Shh), DNA damage response pathway, Hippo, mTOR, and cAMP signaling. A number of therapeutic interventions appear to be promising, ranging from vasopressin receptor 2 antagonists such as tolvaptan, cyclin-dependent kinase inhibitors such as roscovitine, Hh agonists such as purmorphamine, and mTOR inhibitors such as rapamycin.
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Affiliation(s)
- Matthias T F Wolf
- Division of Pediatric Nephrology, University of Texas, Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX, 75390, USA.
- Division of Pediatric Nephrology, C.S. Mott Children's Hospital, University of Michigan, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109, USA.
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4
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Hilgendorf KI, Myers BR, Reiter JF. Emerging mechanistic understanding of cilia function in cellular signalling. Nat Rev Mol Cell Biol 2024; 25:555-573. [PMID: 38366037 PMCID: PMC11199107 DOI: 10.1038/s41580-023-00698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2023] [Indexed: 02/18/2024]
Abstract
Primary cilia are solitary, immotile sensory organelles present on most cells in the body that participate broadly in human health, physiology and disease. Cilia generate a unique environment for signal transduction with tight control of protein, lipid and second messenger concentrations within a relatively small compartment, enabling reception, transmission and integration of biological information. In this Review, we discuss how cilia function as signalling hubs in cell-cell communication using three signalling pathways as examples: ciliary G-protein-coupled receptors (GPCRs), the Hedgehog (Hh) pathway and polycystin ion channels. We review how defects in these ciliary signalling pathways lead to a heterogeneous group of conditions known as 'ciliopathies', including metabolic syndromes, birth defects and polycystic kidney disease. Emerging understanding of these pathways' transduction mechanisms reveals common themes between these cilia-based signalling pathways that may apply to other pathways as well. These mechanistic insights reveal how cilia orchestrate normal and pathophysiological signalling outputs broadly throughout human biology.
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Affiliation(s)
- Keren I Hilgendorf
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Benjamin R Myers
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA.
- Department of Bioengineering, University of Utah School of Medicine, Salt Lake City, UT, 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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5
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Rezi CK, Aslanyan MG, Diwan GD, Cheng T, Chamlali M, Junger K, Anvarian Z, Lorentzen E, Pauly KB, Afshar-Bahadori Y, Fernandes EF, Qian F, Tosi S, Christensen ST, Pedersen SF, Strømgaard K, Russell RB, Miner JH, Mahjoub MR, Boldt K, Roepman R, Pedersen LB. DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2. EMBO Rep 2024; 25:3040-3063. [PMID: 38849673 PMCID: PMC11239879 DOI: 10.1038/s44319-024-00170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/08/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney causes ciliary elongation and cystogenesis, and cell-based proximity labeling proteomics and fluorescence microscopy show alterations in the ciliary proteome upon loss of DLG1. Specifically, the retromer-associated protein SDCCAG3, IFT20, and polycystin-2 (PC2) are reduced in the cilia of DLG1-deficient cells compared to control cells. This phenotype is recapitulated in vivo and rescuable by re-expression of wild-type DLG1, but not a Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)-associated DLG1 variant, p.T489R. Finally, biochemical approaches and Alpha Fold modelling suggest that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Our work identifies a key role for DLG1 in regulating ciliary protein composition and suggests that ciliary dysfunction of the p.T489R DLG1 variant may contribute to CAKUT.
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Affiliation(s)
- Csenge K Rezi
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mariam G Aslanyan
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gaurav D Diwan
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Tao Cheng
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Mohamed Chamlali
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Zeinab Anvarian
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Esben Lorentzen
- Department of Molecular Biology and Genetics - Protein Science, Aarhus University, Aarhus, Denmark
| | - Kleo B Pauly
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Eduardo Fa Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sébastien Tosi
- Danish BioImaging Infrastructure Image Analysis Core Facility (DBI-INFRA IACF), University of Copenhagen, Copenhagen, Denmark
| | | | - Stine F Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Robert B Russell
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Jeffrey H Miner
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Moe R Mahjoub
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Ronald Roepman
- Department of Human Genetics, Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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6
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Reddy Palicharla V, Mukhopadhyay S. Molecular and structural perspectives on protein trafficking to the primary cilium membrane. Biochem Soc Trans 2024; 52:1473-1487. [PMID: 38864436 DOI: 10.1042/bst20231403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/13/2024]
Abstract
The primary cilium is a dynamic subcellular compartment templated from the mother centriole or basal body. Cilia are solitary and tiny, but remarkably consequential in cellular pathways regulating proliferation, differentiation, and maintenance. Multiple transmembrane proteins such as G-protein-coupled receptors, channels, enzymes, and membrane-associated lipidated proteins are enriched in the ciliary membrane. The precise regulation of ciliary membrane content is essential for effective signal transduction and maintenance of tissue homeostasis. Surprisingly, a few conserved molecular factors, intraflagellar transport complex A and the tubby family adapter protein TULP3, mediate the transport of most membrane cargoes into cilia. Recent advances in cryogenic electron microscopy provide fundamental insights into these molecular players. Here, we review the molecular players mediating cargo delivery into the ciliary membrane through the lens of structural biology. These mechanistic insights into ciliary transport provide a framework for understanding of disease variants in ciliopathies, enable precise manipulation of cilia-mediated pathways, and provide a platform for the development of targeted therapeutics.
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Affiliation(s)
- Vivek Reddy Palicharla
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, U.S.A
| | - Saikat Mukhopadhyay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, U.S.A
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7
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Arai Y, Ito H, Shimizu T, Shimoda Y, Song D, Matsuo-Takasaki M, Hayata T, Hayashi Y. Patient-derived and gene-edited pluripotent stem cells lacking NPHP1 recapitulate juvenile nephronophthisis in abnormalities of primary cilia and renal cyst formation. Front Cell Dev Biol 2024; 12:1370723. [PMID: 38989059 PMCID: PMC11233770 DOI: 10.3389/fcell.2024.1370723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/21/2024] [Indexed: 07/12/2024] Open
Abstract
Juvenile nephronophthisis is an inherited renal ciliopathy with cystic kidney disease, renal fibrosis, and end-stage renal failure in children and young adults. Mutations in the NPHP1 gene encoding nephrocystin-1 protein have been identified as the most frequently responsible gene and cause the formation of cysts in the renal medulla. The molecular pathogenesis of juvenile nephronophthisis remains elusive, and no effective medicines to prevent end-stage renal failure exist even today. No human cellular models have been available yet. Here, we report a first disease model of juvenile nephronophthisis using patient-derived and gene-edited human induced pluripotent stem cells (hiPSCs) and kidney organoids derived from these hiPSCs. We established NPHP1-overexpressing hiPSCs from patient-derived hiPSCs and NPHP1-deficient hiPSCs from healthy donor hiPSCs. Comparing these series of hiPSCs, we found abnormalities in primary cilia associated with NPHP1 deficiency in hiPSCs. Kidney organoids generated from the hiPSCs lacking NPHP1 formed renal cysts frequently in suspension culture with constant rotation. This cyst formation in patient-derived kidney organoids was rescued by overexpression of NPHP1. Transcriptome analysis on these kidney organoids revealed that loss of NPHP1 caused lower expression of genes related to primary cilia in epithelial cells and higher expression of genes related to the cell cycle. These findings suggested the relationship between abnormality in primary cilia induced by NPHP1 loss and abnormal proliferative characteristics in the formation of renal cysts. These findings demonstrated that hiPSC-based systematic disease modeling of juvenile nephronophthisis contributed to elucidating the molecular pathogenesis and developing new therapies.
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Affiliation(s)
- Yutaka Arai
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Hidenori Ito
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Tomoya Shimizu
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yuzuno Shimoda
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Dan Song
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Mami Matsuo-Takasaki
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
| | - Tadayoshi Hayata
- Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences and Faculty of Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yohei Hayashi
- iPS Cell Advanced Characterization and Development Team, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Ibaraki, Japan
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8
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Mercey O, Mukherjee S, Guichard P, Hamel V. The molecular architecture of the ciliary transition zones. Curr Opin Cell Biol 2024; 88:102361. [PMID: 38648677 DOI: 10.1016/j.ceb.2024.102361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 04/25/2024]
Abstract
Cilia and flagella are specialized eukaryotic organelles projecting from the surface of eukaryotic cells that play a central role in various physiological processes, including cell motility, sensory perception, and signal transduction. At the base of these structures lies the ciliary transition zone, a pivotal region that functions as a gatekeeper and communication hub for ciliary activities. Despite its crucial role, the intricacies of its architecture remain poorly understood, especially given the variations in its organization across different cell types and species. In this review, we explore the molecular architecture of the ciliary transition zone, with a particular focus on recent findings obtained using cryotomography and super-resolution imaging techniques.
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Affiliation(s)
- Olivier Mercey
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Souradip Mukherjee
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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9
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Tingey M, Ruba A, Jiang Z, Yang W. Deciphering vesicle-assisted transport mechanisms in cytoplasm to cilium trafficking. Front Cell Neurosci 2024; 18:1379976. [PMID: 38860265 PMCID: PMC11163138 DOI: 10.3389/fncel.2024.1379976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 06/12/2024] Open
Abstract
The cilium, a pivotal organelle crucial for cell signaling and proper cell function, relies on meticulous macromolecular transport from the cytoplasm for its formation and maintenance. While the intraflagellar transport (IFT) pathway has traditionally been the focus of extensive study concerning ciliogenesis and ciliary maintenance, recent research highlights a complementary and alternative mechanism-vesicle-assisted transport (VAT) in cytoplasm to cilium trafficking. Despite its potential significance, the VAT pathway remains largely uncharacterized. This review explores recent studies providing evidence for the dynamics of vesicle-related diffusion and transport within the live primary cilium, employing high-speed super-resolution light microscopy. Additionally, we analyze the spatial distribution of vesicles in the cilium, mainly relying on electron microscopy data. By scrutinizing the VAT pathways that facilitate cargo transport into the cilium, with a specific emphasis on recent advancements and imaging data, our objective is to synthesize a comprehensive model of ciliary transport through the integration of IFT-VAT mechanisms.
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Affiliation(s)
| | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA, United States
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10
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Rezi CK, Aslanyan MG, Diwan GD, Cheng T, Chamlali M, Junger K, Anvarian Z, Lorentzen E, Pauly KB, Afshar-Bahadori Y, Fernandes EFA, Qian F, Tosi S, Christensen ST, Pedersen SF, Strømgaard K, Russell RB, Miner JH, Mahjoub MR, Boldt K, Roepman R, Pedersen LB. DLG1 functions upstream of SDCCAG3 and IFT20 to control ciliary targeting of polycystin-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.10.566524. [PMID: 37987012 PMCID: PMC10659422 DOI: 10.1101/2023.11.10.566524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Polarized vesicular trafficking directs specific receptors and ion channels to cilia, but the underlying mechanisms are poorly understood. Here we describe a role for DLG1, a core component of the Scribble polarity complex, in regulating ciliary protein trafficking in kidney epithelial cells. Conditional knockout of Dlg1 in mouse kidney caused ciliary elongation and cystogenesis, and cell-based proximity labelling proteomics and fluorescence microscopy showed alterations in the ciliary proteome upon loss of DLG1. Specifically, the retromer-associated protein SDCCAG3, IFT20 and polycystin-2 (PC2) were reduced in cilia of DLG1 deficient cells compared to control cells. This phenotype was recapitulated in vivo and rescuable by re-expression of wildtype DLG1, but not a Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)-associated DLG1 variant, p.T489R. Finally, biochemical approaches and Alpha Fold modelling suggested that SDCCAG3 and IFT20 form a complex that associates, at least indirectly, with DLG1. Our work identifies a key role for DLG1 in regulating ciliary protein composition and suggests that ciliary dysfunction of the p.T489R DLG1 variant may contribute to CAKUT.
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Affiliation(s)
- Csenge K. Rezi
- Department of Biology, University of Copenhagen, Denmark
| | - Mariam G. Aslanyan
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Gaurav D. Diwan
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Tao Cheng
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | | | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | | | - Esben Lorentzen
- Department of Molecular Biology and Genetics - Protein Science, Aarhus University, Denmark
| | - Kleo B. Pauly
- Department of Biology, University of Copenhagen, Denmark
| | | | - Eduardo F. A. Fernandes
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Feng Qian
- Division of Nephrology, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sébastien Tosi
- Danish BioImaging Infrastructure Image Analysis Core Facility (DBI-INFRA IACF), University of Copenhagen, Denmark
| | | | | | - Kristian Strømgaard
- Center for Biopharmaceuticals, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Robert B. Russell
- BioQuant, Heidelberg University, Heidelberg, Germany
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Jeffrey H. Miner
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Moe R. Mahjoub
- Department of Medicine (Nephrology Division) and Department of Cell Biology and Physiology, Washington University, St Louis, MO, USA
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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11
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Wang Y, Yao H, Zhang Y, Mu N, Lu T, Du Z, Wu Y, Li X, Su M, Shao M, Sun X, Su L, Liu X. TMEM216 promotes primary ciliogenesis and Hedgehog signaling through the SUFU-GLI2/GLI3 axis. Sci Signal 2024; 17:eabo0465. [PMID: 38261656 DOI: 10.1126/scisignal.abo0465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/04/2024] [Indexed: 01/25/2024]
Abstract
Primary cilia are enriched in signaling receptors, and defects in their formation or function can induce conditions such as polycystic kidney disease, postaxial hexadactyly, and microphthalmia. Mammalian Hedgehog (Hh) signaling is important in the development of primary cilia, and TMEM216, a transmembrane protein that localizes to the base of cilia, is also implicated in ciliogenesis in zebrafish. Here, we found that Tmem216-deficient mice had impaired Hh signaling and displayed typical ciliopathic phenotypes. These phenomena were also observed in cells deficient in TMEM216. Furthermore, TMEM216 interacted with core Hh signaling proteins, including SUFU, a negative regulator of Hh, and GLI2/GLI3, transcription factors downstream of Hh. The competition between TMEM216 and SUFU for binding to GLI2/GLI3 inhibited the cleavage of GLI2/GLI3 into their repressor forms, which resulted in the nuclear accumulation of full-length GLI2 and the decreased nuclear localization of cleaved GLI3, ultimately leading to the activation of Hh signaling. Together, these data suggest that the TMEM216-SUFU-GLI2/GLI3 axis plays a role in TMEM216 deficiency-induced ciliopathies and Hh signaling abnormalities.
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Affiliation(s)
- Yingying Wang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Huili Yao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Yu Zhang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Ning Mu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Tong Lu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Zhiyuan Du
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Yingdi Wu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaopeng Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Min Su
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Ming Shao
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaoyang Sun
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Ling Su
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiangguo Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong University, Jinan, China
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12
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Kalot R, Sentell Z, Kitzler TM, Torban E. Primary cilia and actin regulatory pathways in renal ciliopathies. FRONTIERS IN NEPHROLOGY 2024; 3:1331847. [PMID: 38292052 PMCID: PMC10824913 DOI: 10.3389/fneph.2023.1331847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/20/2023] [Indexed: 02/01/2024]
Abstract
Ciliopathies are a group of rare genetic disorders caused by defects to the structure or function of the primary cilium. They often affect multiple organs, leading to brain malformations, congenital heart defects, and anomalies of the retina or skeletal system. Kidney abnormalities are among the most frequent ciliopathic phenotypes manifesting as smaller, dysplastic, and cystic kidneys that are often accompanied by renal fibrosis. Many renal ciliopathies cause chronic kidney disease and often progress to end-stage renal disease, necessitating replacing therapies. There are more than 35 known ciliopathies; each is a rare hereditary condition, yet collectively they account for a significant proportion of chronic kidney disease worldwide. The primary cilium is a tiny microtubule-based organelle at the apex of almost all vertebrate cells. It serves as a "cellular antenna" surveying environment outside the cell and transducing this information inside the cell to trigger multiple signaling responses crucial for tissue morphogenesis and homeostasis. Hundreds of proteins and unique cellular mechanisms are involved in cilia formation. Recent evidence suggests that actin remodeling and regulation at the base of the primary cilium strongly impacts ciliogenesis. In this review, we provide an overview of the structure and function of the primary cilium, focusing on the role of actin cytoskeleton and its regulators in ciliogenesis. We then describe the key clinical, genetic, and molecular aspects of renal ciliopathies. We highlight what is known about actin regulation in the pathogenesis of these diseases with the aim to consider these recent molecular findings as potential therapeutic targets for renal ciliopathies.
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Affiliation(s)
- Rita Kalot
- Department of Medicine and Department of Physiology, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Zachary Sentell
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Thomas M. Kitzler
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Health Center, Montreal, QC, Canada
| | - Elena Torban
- Department of Medicine and Department of Physiology, McGill University, Montreal, QC, Canada
- The Research Institute of the McGill University Health Center, Montreal, QC, Canada
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13
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Shaikh Qureshi WM, Hentges KE. Functions of cilia in cardiac development and disease. Ann Hum Genet 2024; 88:4-26. [PMID: 37872827 PMCID: PMC10952336 DOI: 10.1111/ahg.12534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/08/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023]
Abstract
Errors in embryonic cardiac development are a leading cause of congenital heart defects (CHDs), including morphological abnormalities of the heart that are often detected after birth. In the past few decades, an emerging role for cilia in the pathogenesis of CHD has been identified, but this topic still largely remains an unexplored area. Mouse forward genetic screens and whole exome sequencing analysis of CHD patients have identified enrichment for de novo mutations in ciliary genes or non-ciliary genes, which regulate cilia-related pathways, linking cilia function to aberrant cardiac development. Key events in cardiac morphogenesis, including left-right asymmetric development of the heart, are dependent upon cilia function. Cilia dysfunction during left-right axis formation contributes to CHD as evidenced by the substantial proportion of heterotaxy patients displaying complex CHD. Cilia-transduced signaling also regulates later events during heart development such as cardiac valve formation, outflow tract septation, ventricle development, and atrioventricular septa formation. In this review, we summarize the role of motile and non-motile (primary cilia) in cardiac asymmetry establishment and later events during heart development.
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Affiliation(s)
- Wasay Mohiuddin Shaikh Qureshi
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science CentreUniversity of ManchesterManchesterUK
| | - Kathryn E. Hentges
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine, and Health, Manchester Academic Health Science CentreUniversity of ManchesterManchesterUK
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14
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Bhat S, Dietz A, Senf K, Nietzsche S, Hirabayashi Y, Westermann M, Neuhaus EM. GPRC5C regulates the composition of cilia in the olfactory system. BMC Biol 2023; 21:292. [PMID: 38110903 PMCID: PMC10729543 DOI: 10.1186/s12915-023-01790-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Olfactory sensory neurons detect odourants via multiple long cilia that protrude from their dendritic endings. The G protein-coupled receptor GPRC5C was identified as part of the olfactory ciliary membrane proteome, but its function and localization is unknown. RESULTS High-resolution confocal and electron microscopy revealed that GPRC5C is located at the base of sensory cilia in olfactory neurons, but not in primary cilia of immature neurons or stem cells. Additionally, GPRC5C localization in sensory cilia parallels cilia formation and follows the formation of the basal body. In closer examination, GPRC5C was found in the ciliary transition zone. GPRC5C deficiency altered the structure of sensory cilia and increased ciliary layer thickness. However, primary cilia were unaffected. Olfactory sensory neurons from Gprc5c-deficient mice exhibited altered localization of olfactory signalling cascade proteins, and of ciliary phosphatidylinositol-4,5-bisphosphat. Sensory neurons also exhibited increased neuronal activity as well as altered mitochondrial morphology, and knockout mice had an improved ability to detect food pellets based on smell. CONCLUSIONS Our study shows that GPRC5C regulates olfactory cilia composition and length, thereby controlling odour perception.
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Affiliation(s)
- Sneha Bhat
- Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Str. 1, 07747, Jena, Germany
| | - André Dietz
- Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Str. 1, 07747, Jena, Germany
| | - Katja Senf
- Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Str. 1, 07747, Jena, Germany
| | - Sandor Nietzsche
- Centre for Electron Microscopy, Jena University Hospital, Friedrich Schiller University Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Yoshio Hirabayashi
- Institute for Environmental and Gender-Specific Medicine, Juntendo University Graduate School of Medicine, Chiba, 279-0021, Japan
- RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, 351-0198, Japan
| | - Martin Westermann
- Centre for Electron Microscopy, Jena University Hospital, Friedrich Schiller University Jena, Ziegelmühlenweg 1, 07743, Jena, Germany
| | - Eva Maria Neuhaus
- Pharmacology and Toxicology, Jena University Hospital, Friedrich Schiller University Jena, Drackendorfer Str. 1, 07747, Jena, Germany.
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15
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Cideciyan AV, Jacobson SG, Ho AC, Swider M, Sumaroka A, Roman AJ, Wu V, Russell RC, Viarbitskaya I, Garafalo AV, Schwartz MR, Girach A. Durable vision improvement after a single intravitreal treatment with antisense oligonucleotide in CEP290-LCA: Replication in two eyes. Am J Ophthalmol Case Rep 2023; 32:101873. [PMID: 37388818 PMCID: PMC10302566 DOI: 10.1016/j.ajoc.2023.101873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/15/2023] [Accepted: 06/11/2023] [Indexed: 07/01/2023] Open
Abstract
Purpose An intravitreally injected antisense oligonucleotide, sepofarsen, was designed to modulate splicing within retinas of patients with severe vision loss due to deep intronic c.2991 + 1655A > G variant in the CEP290 gene. A previous report showed vision improvements following a single injection in one eye with unexpected durability lasting at least 15 months. The current study evaluated durability of efficacy beyond 15 months in the previously treated left eye. In addition, peak efficacy and durability were evaluated in the treatment-naive right eye, and re-injection of the left eye 4 years after the first injection. Observations Visual function was evaluated with best corrected standard and low-luminance visual acuities, microperimetry, dark-adapted chromatic perimetry, and full-field sensitivity testing. Retinal structure was evaluated with OCT imaging. At the fovea, all visual function measures and IS/OS intensity of the OCT showed transient improvements peaking at 3-6 months, remaining better than baseline at ∼2 years, and returning to baseline by 3-4 years after each single injection. Conclusions and Importance These results suggest that sepofarsen reinjection intervals may need to be longer than 2 years.
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Affiliation(s)
- Artur V. Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel G. Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allen C. Ho
- Wills Eye Hospital, Thomas Jefferson University, Philadelphia, USA
| | - Malgorzata Swider
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander Sumaroka
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alejandro J. Roman
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Vivian Wu
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert C. Russell
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iryna Viarbitskaya
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandra V. Garafalo
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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16
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Deretic J, Odabasi E, Firat-Karalar EN. The multifaceted roles of microtubule-associated proteins in the primary cilium and ciliopathies. J Cell Sci 2023; 136:jcs261148. [PMID: 38095645 DOI: 10.1242/jcs.261148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023] Open
Abstract
The primary cilium is a conserved microtubule-based organelle that is critical for transducing developmental, sensory and homeostatic signaling pathways. It comprises an axoneme with nine parallel doublet microtubules extending from the basal body, surrounded by the ciliary membrane. The axoneme exhibits remarkable stability, serving as the skeleton of the cilium in order to maintain its shape and provide tracks to ciliary trafficking complexes. Although ciliary trafficking and signaling have been exhaustively characterized over the years, less is known about the unique structural and functional complexities of the axoneme. Recent work has yielded new insights into the mechanisms by which the axoneme is built with its proper length and architecture, particularly regarding the activity of microtubule-associated proteins (MAPs). In this Review, we first summarize current knowledge about the architecture, composition and specialized compartments of the primary cilium. Next, we discuss the mechanistic underpinnings of how a functional cilium is assembled, maintained and disassembled through the regulation of its axonemal microtubules. We conclude by examining the diverse localizations and functions of ciliary MAPs for the pathobiology of ciliary diseases.
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Affiliation(s)
- Jovana Deretic
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Ezgi Odabasi
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul 34450, Turkey
- School of Medicine, Koç University, Istanbul 34450, Turkey
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17
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Freke GM, Martins T, Davies RJ, Beyer T, Seda M, Peskett E, Haq N, Prasai A, Otto G, Jeyabalan Srikaran J, Hernandez V, Diwan GD, Russell RB, Ueffing M, Huranova M, Boldt K, Beales PL, Jenkins D. De-Suppression of Mesenchymal Cell Identities and Variable Phenotypic Outcomes Associated with Knockout of Bbs1. Cells 2023; 12:2662. [PMID: 37998397 PMCID: PMC10670506 DOI: 10.3390/cells12222662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is an archetypal ciliopathy caused by dysfunction of primary cilia. BBS affects multiple tissues, including the kidney, eye and hypothalamic satiety response. Understanding pan-tissue mechanisms of pathogenesis versus those which are tissue-specific, as well as gauging their associated inter-individual variation owing to genetic background and stochastic processes, is of paramount importance in syndromology. The BBSome is a membrane-trafficking and intraflagellar transport (IFT) adaptor protein complex formed by eight BBS proteins, including BBS1, which is the most commonly mutated gene in BBS. To investigate disease pathogenesis, we generated a series of clonal renal collecting duct IMCD3 cell lines carrying defined biallelic nonsense or frameshift mutations in Bbs1, as well as a panel of matching wild-type CRISPR control clones. Using a phenotypic screen and an unbiased multi-omics approach, we note significant clonal variability for all assays, emphasising the importance of analysing panels of genetically defined clones. Our results suggest that BBS1 is required for the suppression of mesenchymal cell identities as the IMCD3 cell passage number increases. This was associated with a failure to express epithelial cell markers and tight junction formation, which was variable amongst clones. Transcriptomic analysis of hypothalamic preparations from BBS mutant mice, as well as BBS patient fibroblasts, suggested that dysregulation of epithelial-to-mesenchymal transition (EMT) genes is a general predisposing feature of BBS across tissues. Collectively, this work suggests that the dynamic stability of the BBSome is essential for the suppression of mesenchymal cell identities as epithelial cells differentiate.
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Affiliation(s)
- Grace Mercedes Freke
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Tiago Martins
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Rosalind Jane Davies
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Tina Beyer
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Marian Seda
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Emma Peskett
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Naila Haq
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Avishek Prasai
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic (M.H.)
| | - Georg Otto
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Jeshmi Jeyabalan Srikaran
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Victor Hernandez
- Life Sciences Department, CHMLS, Brunel University London, Kingston Lane, Uxbridge UB8 3PH, UK;
| | - Gaurav D. Diwan
- BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (G.D.D.); (R.B.R.)
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Robert B. Russell
- BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; (G.D.D.); (R.B.R.)
- Biochemistry Center (BZH), University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, 14220 Prague, Czech Republic (M.H.)
| | - Karsten Boldt
- Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Elfriede-Aulhorn-Strasse 7, 72076 Tübingen, Germany; (T.B.); (M.U.); (K.B.)
| | - Philip L. Beales
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
| | - Dagan Jenkins
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (G.M.F.); (T.M.); (M.S.); (E.P.); (N.H.); (G.O.); (J.J.S.); (P.L.B.)
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18
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Chatzifrangkeskou M, Kouis P, Skourides PA. JNK regulates ciliogenesis through the interflagellar transport complex and actin networks. J Cell Biol 2023; 222:e202303052. [PMID: 37851005 PMCID: PMC10585068 DOI: 10.1083/jcb.202303052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/16/2023] [Accepted: 08/29/2023] [Indexed: 10/19/2023] Open
Abstract
The c-Jun N-terminal kinase (JNK) regulates various important physiological processes. Although the JNK pathway has been under intense investigation for over 20 yr, its complexity is still perplexing, with multiple protein partners underlying the diversity of its activity. We show that JNK is associated with the basal bodies in both primary and motile cilia. Loss of JNK disrupts basal body migration and docking and leads to severe ciliogenesis defects. JNK's involvement in ciliogenesis stems from a dual role in the regulation of the actin networks of multiciliated cells (MCCs) and the establishment of the intraflagellar transport-B core complex. JNK signaling is also critical for the maintenance of the actin networks and ciliary function in mature MCCs. JNK is implicated in the development of diabetes, neurodegeneration, and liver disease, all of which have been linked to ciliary dysfunction. Our work uncovers a novel role of JNK in ciliogenesis and ciliary function that could have important implications for JNK's role in the disease.
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Affiliation(s)
| | - Panayiotis Kouis
- Respiratory Physiology Laboratory, Medical School, University of Cyprus, Nicosia, Cyprus
| | - Paris A. Skourides
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
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19
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Masek M, Bachmann-Gagescu R. Control of protein and lipid composition of photoreceptor outer segments-Implications for retinal disease. Curr Top Dev Biol 2023; 155:165-225. [PMID: 38043951 DOI: 10.1016/bs.ctdb.2023.09.001] [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] [Indexed: 12/05/2023]
Abstract
Vision is arguably our most important sense, and its loss brings substantial limitations to daily life for affected individuals. Light is perceived in retinal photoreceptors (PRs), which are highly specialized neurons subdivided into several compartments with distinct functions. The outer segments (OSs) of photoreceptors represent highly specialized primary ciliary compartments hosting the phototransduction cascade, which transforms incoming light into a neuronal signal. Retinal disease can result from various pathomechanisms originating in distinct subcompartments of the PR cell, or in the retinal pigment epithelium which supports the PRs. Dysfunction of primary cilia causes human disorders known as "ciliopathies", in which retinal disease is a common feature. This chapter focuses on PR OSs, discussing the mechanisms controlling their complex structure and composition. A sequence of tightly regulated sorting and trafficking events, both upstream of and within this ciliary compartment, ensures the establishment and maintenance of the adequate proteome and lipidome required for signaling in response to light. We discuss in particular our current understanding of the role of ciliopathy proteins involved in multi-protein complexes at the ciliary transition zone (CC2D2A) or BBSome (BBS1) and how their dysfunction causes retinal disease. While the loss of CC2D2A prevents the fusion of vesicles and delivery of the photopigment rhodopsin to the ciliary base, leading to early OS ultrastructural defects, BBS1 deficiency results in precocious accumulation of cholesterol in mutant OSs and decreased visual function preceding morphological changes. These distinct pathomechanisms underscore the central role of ciliary proteins involved in multiple processes controlling OS protein and lipid composition.
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Affiliation(s)
- Markus Masek
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; University Research Priority Program AdaBD, University of Zurich, Zurich, Switzerland.
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20
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Lee KH. Primary cilia: a novel research approach to overcome anticancer drug resistance. Front Mol Biosci 2023; 10:1270639. [PMID: 37900915 PMCID: PMC10602908 DOI: 10.3389/fmolb.2023.1270639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/11/2023] [Indexed: 10/31/2023] Open
Abstract
Primary cilia are cellular organelles that consist of a microtubule skeleton surrounded by a membrane filled with cell signaling receptors. Many studies have shown that primary cilia are cellular antennas, which serve as signaling hubs and their assembly and disassembly are dynamically regulated throughout the cell cycle, playing an important role in regulating cellular homeostasis. Aberrant control of primary cilia dynamics causes a number of genetic disorders known as ciliopathies and is closely associated with tumorigenesis. Anticancer drug resistance is a primary cause of chemotherapy failure, although there is no apparent remedy. The recent identification of a relationship between anticancer drug resistance and primary ciliary dynamics has made primary cilia an important target subcellular organelle for overcoming anticancer drug resistance. Therefore, the research on primary ciliary dynamics may provide new strategies to overcome anticancer drug resistance, which is urgently needed. This review aims to summarize research on the relevance of primary cilia and anticancer drug resistance, as well as future possibilities for research on overcoming anticancer drug resistance utilizing primary cilia dynamics.
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Affiliation(s)
- Kyung Ho Lee
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Ochang-eup, Republic of Korea
- Department of Bio-Molecular Science, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
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21
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Fang L, Wang L, Yang L, Xu X, Pei S, Wu D. Novel variants identified in five Chinese families with Joubert Syndrome: a case report. BMC Med Genomics 2023; 16:221. [PMID: 37735380 PMCID: PMC10512497 DOI: 10.1186/s12920-023-01669-7] [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: 01/17/2023] [Accepted: 09/20/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Joubert syndrome (JS) is a group of rare ciliopathies, mainly characterized by cerebellar dysplasia representing the "molar tooth sign (MTS)" on neuroimaging, hypotonia, and developmental delay. Having a complicated genotype-phenotype correlation due to its rich genetic heterogeneity, JS is usually combined with other organic defects affecting the retina, kidney, and liver. This report aimed to present new cases and novel variants of JS. CASE PRESENTATION Five unrelated patients who were diagnosed with JS, with or without typical clinical characteristics, received integrated examinations, including whole-exome sequencing (WES) and Sanger sequencing. We identified nine pathogenic variants in the TCTN2, CPLANE1, INPP5E, NPHP1, and CC2D2A genes. CONCLUSION Four novel pathogenic mutations in the TCTN2, CPLANE1, and INPP5E genes were reported. The findings broadened the genotypic spectrum of JS and contributed to a better understanding of genotype-phenotype correlation.
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Affiliation(s)
- Liwei Fang
- Pediatric Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China
| | - Lulu Wang
- Pediatric Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China
| | - Li Yang
- Pediatric Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China
| | - Xiaoyan Xu
- Pediatric Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China
| | - Shanai Pei
- Pediatric Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China
| | - De Wu
- Pediatric Neurorehabilitation Center, Pediatric Department, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China.
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22
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Truong HM, Cruz-Colón KO, Martínez-Márquez JY, Willer JR, Travis AM, Biswas SK, Lo WK, Bolz HJ, Pearring JN. The tectonic complex regulates membrane protein composition in the photoreceptor cilium. Nat Commun 2023; 14:5671. [PMID: 37704658 PMCID: PMC10500017 DOI: 10.1038/s41467-023-41450-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
The primary cilium is a signaling organelle with a unique membrane composition maintained by a diffusional barrier residing at the transition zone. Many transition zone proteins, such as the tectonic complex, are linked to preserving ciliary composition but the mechanism remains unknown. To understand tectonic's role, we generate a photoreceptor-specific Tctn1 knockout mouse. Loss of Tctn1 results in the absence of the entire tectonic complex and associated MKS proteins yet has minimal effects on the transition zone structure of rod photoreceptors. We find that the protein composition of the photoreceptor cilium is disrupted as non-resident membrane proteins accumulate in the cilium over time, ultimately resulting in photoreceptor degeneration. We further show that fluorescent rhodopsin moves faster through the transition zone in photoreceptors lacking tectonic, which suggests that the tectonic complex acts as a physical barrier to slow down membrane protein diffusion in the photoreceptor transition zone to ensure proper removal of non-resident membrane proteins.
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Affiliation(s)
- Hanh M Truong
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
| | - Kevin O Cruz-Colón
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | | | - Jason R Willer
- Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI, USA
| | - Amanda M Travis
- Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI, USA
| | - Sondip K Biswas
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Woo-Kuen Lo
- Department of Neurobiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Hanno J Bolz
- Senckenberg Centre for Human Genetics, Frankfurt am Main, Germany
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Jillian N Pearring
- Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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23
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Tian X, Zhao H, Zhou J. Organization, functions, and mechanisms of the BBSome in development, ciliopathies, and beyond. eLife 2023; 12:e87623. [PMID: 37466224 DOI: 10.7554/elife.87623] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
The BBSome is an octameric protein complex that regulates ciliary transport and signaling. Mutations in BBSome subunits are closely associated with ciliary defects and lead to ciliopathies, notably Bardet-Biedl syndrome. Over the past few years, there has been significant progress in elucidating the molecular organization and functions of the BBSome complex. An improved understanding of BBSome-mediated biological events and molecular mechanisms is expected to help advance the development of diagnostic and therapeutic approaches for BBSome-related diseases. Here, we review the current literature on the structural assembly, transport regulation, and molecular functions of the BBSome, emphasizing its roles in cilium-related processes. We also provide perspectives on the pathological role of the BBSome in ciliopathies as well as how these can be exploited for therapeutic benefit.
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Affiliation(s)
- Xiaoyu Tian
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Huijie Zhao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
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24
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Mill P, Christensen ST, Pedersen LB. Primary cilia as dynamic and diverse signalling hubs in development and disease. Nat Rev Genet 2023; 24:421-441. [PMID: 37072495 PMCID: PMC7615029 DOI: 10.1038/s41576-023-00587-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2023] [Indexed: 04/20/2023]
Abstract
Primary cilia, antenna-like sensory organelles protruding from the surface of most vertebrate cell types, are essential for regulating signalling pathways during development and adult homeostasis. Mutations in genes affecting cilia cause an overlapping spectrum of >30 human diseases and syndromes, the ciliopathies. Given the immense structural and functional diversity of the mammalian cilia repertoire, there is a growing disconnect between patient genotype and associated phenotypes, with variable severity and expressivity characteristic of the ciliopathies as a group. Recent technological developments are rapidly advancing our understanding of the complex mechanisms that control biogenesis and function of primary cilia across a range of cell types and are starting to tackle this diversity. Here, we examine the structural and functional diversity of primary cilia, their dynamic regulation in different cellular and developmental contexts and their disruption in disease.
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Affiliation(s)
- Pleasantine Mill
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, Scotland
| | | | - Lotte B Pedersen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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25
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Linnert J, Knapp B, Güler BE, Boldt K, Ueffing M, Wolfrum U. Usher syndrome proteins ADGRV1 (USH2C) and CIB2 (USH1J) interact and share a common interactome containing TRiC/CCT-BBS chaperonins. Front Cell Dev Biol 2023; 11:1199069. [PMID: 37427378 PMCID: PMC10323441 DOI: 10.3389/fcell.2023.1199069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
The human Usher syndrome (USH) is the most common form of a sensory hereditary ciliopathy characterized by progressive vision and hearing loss. Mutations in the genes ADGRV1 and CIB2 have been associated with two distinct sub-types of USH, namely, USH2C and USH1J. The proteins encoded by the two genes belong to very distinct protein families: the adhesion G protein-coupled receptor ADGRV1 also known as the very large G protein-coupled receptor 1 (VLGR1) and the Ca2+- and integrin-binding protein 2 (CIB2), respectively. In the absence of tangible knowledge of the molecular function of ADGRV1 and CIB2, pathomechanisms underlying USH2C and USH1J are still unknown. Here, we aimed to enlighten the cellular functions of CIB2 and ADGRV1 by the identification of interacting proteins, a knowledge that is commonly indicative of cellular functions. Applying affinity proteomics by tandem affinity purification in combination with mass spectrometry, we identified novel potential binding partners of the CIB2 protein and compared these with the data set we previously obtained for ADGRV1. Surprisingly, the interactomes of both USH proteins showed a high degree of overlap indicating their integration in common networks, cellular pathways and functional modules which we confirmed by GO term analysis. Validation of protein interactions revealed that ADGRV1 and CIB2 mutually interact. In addition, we showed that the USH proteins also interact with the TRiC/CCT chaperonin complex and the Bardet Biedl syndrome (BBS) chaperonin-like proteins. Immunohistochemistry on retinal sections demonstrated the co-localization of the interacting partners at the photoreceptor cilia, supporting the role of USH proteins ADGRV1 and CIB2 in primary cilia function. The interconnection of protein networks involved in the pathogenesis of both syndromic retinal dystrophies BBS and USH suggest shared pathomechanisms for both syndromes on the molecular level.
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Affiliation(s)
- Joshua Linnert
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Barbara Knapp
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Baran E. Güler
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karls University of Tuebingen, Tubingen, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Eberhard Karls University of Tuebingen, Tubingen, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg University Mainz, Mainz, Germany
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26
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Wang H, Zaiser F, Eckert P, Ruf J, Kayser N, Veenstra AC, Müller M, Haas R, Walz G, Yakulov TA. Inversin (NPHP2) and Vangl2 are required for normal zebrafish cloaca formation. Biochem Biophys Res Commun 2023; 673:9-15. [PMID: 37352572 DOI: 10.1016/j.bbrc.2023.06.058] [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: 05/30/2023] [Revised: 05/31/2023] [Accepted: 06/17/2023] [Indexed: 06/25/2023]
Abstract
Nephronophthisis (NPH), an autosomal recessive ciliopathy, results from mutations in more than 20 different genes (NPHPs). These gene products form protein complexes that regulate trafficking within the cilium, a microtubular structure that plays a crucial role in developmental processes. Several NPHPs, including NPHP2/Inversin, have been linked to extraciliary functions. In addition to defining a specific segment of primary cilia (Inversin compartment), NPHP2 participates in planar cell polarity (PCP) signaling along with Dishevelled and Vangl family members. We used the mutant zebrafish line invssa36157, containing a stop codon at amino acid 314, to characterize tissue-specific functions of zebrafish Nphp2. The invssa36157 line exhibits mild ciliopathy phenotypes and increased glomerular and cloaca cyst formation. These mutants showed enhanced susceptibility to the simultaneous depletion of the nphp1/nphp2/nphp8 module, known to be involved in the cytoskeletal organization of epithelial cells. Notably, simultaneous depletion of zebrafish nphp1 and vangl2 led to a pronounced increase in cloaca malformations in the invssa36157 mutant embryos. Time-lapse imaging showed that the pronephric cells correctly migrated towards the ectodermal cells in these embryos, but failed to form the cloaca opening. Despite these abnormal developments, cellular fate does not seem to be affected in nphp1 and vangl2 MO-depleted invssa36157 mutants, as shown by in situ hybridizations for markers of pronephros and ectodermal cell development. However, significantly reduced apoptotic activity was observed in this double knockdown model, signifying the role of apoptosis in cloacal morphogenesis. Our findings underscore the critical interplay of nphp1, nphp2/Inversin, and vangl2 in orchestrating normal cloaca formation in zebrafish, shedding light on the complex molecular mechanisms underlying ciliopathy-associated phenotypes.
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Affiliation(s)
- Hui Wang
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Friedemann Zaiser
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Priska Eckert
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Johannes Ruf
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Nicolas Kayser
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Anna C Veenstra
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Merle Müller
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Rebecca Haas
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Gerd Walz
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Albertstrasse 19, 79104, Freiburg, Germany
| | - Toma A Yakulov
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, University of Freiburg, Germany.
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27
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Benmerah A, Briseño-Roa L, Annereau JP, Saunier S. Repurposing small molecules for Nephronophthisis and related renal ciliopathies. Kidney Int 2023:S0085-2538(23)00390-3. [PMID: 37244473 DOI: 10.1016/j.kint.2023.04.027] [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: 12/20/2022] [Revised: 03/10/2023] [Accepted: 04/10/2023] [Indexed: 05/29/2023]
Abstract
Nephronophthisis is an autosomal recessive tubulo-interstitial nephropathy, belonging to the ciliopathy disorders, characterized by fibrosis and/or cysts. It is the most common genetic cause of renal failure in children and young adults. Clinically and genetically heterogeneous, it is caused by variants in ciliary genes resulting in either an isolated kidney disease or syndromic forms in association with other manifestations of ciliopathy disorders. No curative treatment is currently available. Over the past two decades, advances in understanding disease mechanisms have identified several dysregulated signaling pathways, some shared with other cystic kidney diseases. Notably, molecules previously developed to target these pathways have shown promising beneficial effects in orthologous mouse models. In addition to these knowledge-based repurposing approaches, unbiased "in cellulo" phenotypic screens of "repurposing" libraries identified small molecules able to rescue the ciliogenesis defects observed in nephronophthisis conditions. Those compounds appeared to act on relevant pathways and, when tested, showed beneficial nephronophthisis-associated kidney and/or extra-renal defects in mice. In this review, we have summarized those studies which highlight the drug repurposing strategies in the context of a rare disorders such as nephronophthisis-related ciliopathies, with broad genetic heterogeneity and systemic manifestations but with shared disease mechanisms.
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Affiliation(s)
- Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, Université Paris Cité, INSERM UMR 1163, 75015 Paris, France
| | | | | | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, Imagine Institute, Université Paris Cité, INSERM UMR 1163, 75015 Paris, France.
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28
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Safavian D, Kim MS, Xie H, El-Zeiry M, Palander O, Dai L, Collins RF, Froese C, Shannon R, Nagata KI, Trimble WS. Septin-mediated RhoA activation engages the exocyst complex to recruit the cilium transition zone. J Cell Biol 2023; 222:e201911062. [PMID: 36912772 PMCID: PMC10039714 DOI: 10.1083/jcb.201911062] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/25/2022] [Accepted: 01/05/2023] [Indexed: 03/14/2023] Open
Abstract
Septins are filamentous GTPases that play important but poorly characterized roles in ciliogenesis. Here, we show that SEPTIN9 regulates RhoA signaling at the base of cilia by binding and activating the RhoA guanine nucleotide exchange factor, ARHGEF18. GTP-RhoA is known to activate the membrane targeting exocyst complex, and suppression of SEPTIN9 causes disruption of ciliogenesis and mislocalization of an exocyst subunit, SEC8. Using basal body-targeted proteins, we show that upregulating RhoA signaling at the cilium can rescue ciliary defects and mislocalization of SEC8 caused by global SEPTIN9 depletion. Moreover, we demonstrate that the transition zone components, RPGRIP1L and TCTN2, fail to accumulate at the transition zone in cells lacking SEPTIN9 or depleted of the exocyst complex. Thus, SEPTIN9 regulates the recruitment of transition zone proteins on Golgi-derived vesicles by activating the exocyst via RhoA to allow the formation of primary cilia.
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Affiliation(s)
- Darya Safavian
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Moshe S. Kim
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hong Xie
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maha El-Zeiry
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Oliva Palander
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Lu Dai
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Richard F. Collins
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Carol Froese
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rachel Shannon
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Koh-ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Human Service Center, Kasugai, Aichi, Japan
| | - William S. Trimble
- Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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29
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Dyke E, Bijnagte-Schoenmaker C, Wu KM, Oudakker A, Roepman R, Nadif Kasri N. Generation of induced pluripotent stem cell line carrying frameshift variants in NPHP1 (UCSFi001-A-68) using CRISPR/Cas9. Stem Cell Res 2023; 68:103053. [PMID: 36842376 DOI: 10.1016/j.scr.2023.103053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
NPHP1 (Nephrocystin 1) is a protein that localizes to the transition zone of the cilium, a small organelle that projects from the plasma membrane of most cells and allows for integration and coordination of signalling pathways during development and homeostasis. Loss of NPHP1 function due to biallelic NPHP1 gene mutations can lead to the development of ciliopathies - a heterogeneous spectra of disorders characterized by ciliary dysfunction. Here we report the generation of an NPHP1-null hiPSC line (UCSFi001-A-68) via CRISPR/Cas9-mediated non-homologous end joining in the UCSFi001-A background, for study of the role that this protein plays in different tissues.
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Affiliation(s)
- Emma Dyke
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Chantal Bijnagte-Schoenmaker
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Ka Man Wu
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Astrid Oudakker
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, Netherlands
| | - Ronald Roepman
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, Netherlands.
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30
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Structure of the N-terminal coiled-coil domains of the ciliary protein Rpgrip1l. iScience 2023; 26:106249. [PMID: 36915689 PMCID: PMC10006689 DOI: 10.1016/j.isci.2023.106249] [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: 07/27/2022] [Revised: 12/30/2022] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Rpgrip1l is one of the key ciliary proteins located at the transition zone of the primary cilium, an important organelle for cells to sense the outer environment. Mutations in the RPGRIP1L gene are associated with various ciliopathies. Here, we focused on the N-terminal coiled-coil of Rpgrip1l. By comprehensive biochemical and structural characterizations, we demonstrated that the two predicted coiled-coil regions (CC12) located at Rpgrip1l N-terminus each can form a stable parallel dimer. We further showed that overexpression of Rpgrip1l CC12 in NIH/3T3 cells significantly shortened the length of primary cilia, and this effect depended on the dimer formation. In addition, we found that CC12 of the homolog protein Rpgrip1 in mouse and human were significantly different from Rpgrip1l. Finally, we confirmed that some disease-related mutations can alter the dimeric states of CC12 of Rpgrip1l or Rpgrip1, which might explain the pathogenic mechanisms.
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31
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A deep intronic TCTN2 variant activating a cryptic exon predicted by SpliceRover in a patient with Joubert syndrome. J Hum Genet 2023:10.1038/s10038-023-01143-3. [PMID: 36894704 DOI: 10.1038/s10038-023-01143-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 01/26/2023] [Accepted: 02/27/2023] [Indexed: 03/11/2023]
Abstract
The recent introduction of genome sequencing in genetic analysis has led to the identification of pathogenic variants located in deep introns. Recently, several new tools have emerged to predict the impact of variants on splicing. Here, we present a Japanese boy of Joubert syndrome with biallelic TCTN2 variants. Exome sequencing identified only a heterozygous maternal nonsense TCTN2 variant (NM_024809.5:c.916C >T, p.(Gln306Ter)). Subsequent genome sequencing identified a deep intronic variant (c.1033+423G>A) inherited from his father. The machine learning algorithms SpliceAI, Squirls, and Pangolin were unable to predict alterations in splicing by the c.1033+423G>A variant. SpliceRover, a tool for splice site prediction using FASTA sequence, was able to detect a cryptic exon which was 85-bp away from the variant and within the inverted Alu sequence while SpliceRover scores for these splice sites showed slight increase (donor) or decrease (acceptor) between the reference and mutant sequences. RNA sequencing and RT-PCR using urinary cells confirmed inclusion of the cryptic exon. The patient showed major symptoms of TCTN2-related disorders such as developmental delay, dysmorphic facial features and polydactyly. He also showed uncommon features such as retinal dystrophy, exotropia, abnormal pattern of respiration, and periventricular heterotopia, confirming these as one of features of TCTN2-related disorders. Our study highlights usefulness of genome sequencing and RNA sequencing using urinary cells for molecular diagnosis of genetic disorders and suggests that database of cryptic splice sites predicted in introns by SpliceRover using the reference sequences can be helpful in extracting candidate variants from large numbers of intronic variants in genome sequencing.
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32
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Hureaux M, Heidet L, Vargas-Poussou R, Dorval G. [Major advances in pediatric nephro-genetics]. Med Sci (Paris) 2023; 39:234-245. [PMID: 36943120 DOI: 10.1051/medsci/2023028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
The rise of genetics in the last decades has allowed major advances in the understanding of the mechanisms leading to inherited kidney diseases. From the first positional cloning studies to the advent of high-throughput sequencing (NGS), genome analysis technologies have become increasingly efficient, with an extraordinary level of resolution. Moreover, sequencing prices have decreased from one million dollars for the sequencing of James Watson's genome in 2008, to a few hundred dollars for the sequencing of a genome today. Thus, molecular diagnosis has a central place in the diagnosis of these patients and influences the therapeutic management in many situations. However, although NGS is a powerful tool for the identification of variants involved in diseases, it also exposes to the risk of over-interpretation of certain variants, leading to erroneous diagnoses, requiring the use of specialists. In this review, we first propose a brief retrospective of the essential steps that led to the current knowledge and the development of NGS for the study of hereditary nephropathies in children. This review is then an opportunity to present the main hereditary nephropathies and the underlying molecular mechanisms. Among them, we emphasize ciliopathies, congenital anomalies of the kidney and urinary tract, podocytopathies and tubulopathies.
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Affiliation(s)
- Marguerite Hureaux
- Service de médecine génomique des maladies rares, AP-HP, université Paris Cité, France - Inserm U970, Paris CardioVascular Research Center, université Paris Cité, faculté de médecine, France - Centre de référence des maladies rénales héréditaires de l'enfant et de l'adulte MARHEA, hôpital Necker-Enfants Malades, Paris, France
| | - Laurence Heidet
- Centre de référence des maladies rénales héréditaires de l'enfant et de l'adulte MARHEA, hôpital Necker-Enfants Malades, Paris, France - Service de néphrologie pédiatrique, AP-HP, université Paris Cité, France - CNRS, centre de recherche des Cordeliers, Inserm UMRS 1138, Sorbonne université, université Paris Cité, France
| | - Rosa Vargas-Poussou
- Service de médecine génomique des maladies rares, AP-HP, université Paris Cité, France - Centre de référence des maladies rénales héréditaires de l'enfant et de l'adulte MARHEA, hôpital Necker-Enfants Malades, Paris, France - CNRS, centre de recherche des Cordeliers, Inserm UMRS 1138, Sorbonne université, université Paris Cité, France
| | - Guillaume Dorval
- Service de médecine génomique des maladies rares, AP-HP, université Paris Cité, France - Centre de référence des maladies rénales héréditaires de l'enfant et de l'adulte MARHEA, hôpital Necker-Enfants Malades, Paris, France - Inserm U1163, Laboratoire des maladies rénales héréditaires, institut Imagine, université Paris Cité, France
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33
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Aslanyan MG, Doornbos C, Diwan GD, Anvarian Z, Beyer T, Junger K, van Beersum SEC, Russell RB, Ueffing M, Ludwig A, Boldt K, Pedersen LB, Roepman R. A targeted multi-proteomics approach generates a blueprint of the ciliary ubiquitinome. Front Cell Dev Biol 2023; 11:1113656. [PMID: 36776558 PMCID: PMC9908615 DOI: 10.3389/fcell.2023.1113656] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
Establishment and maintenance of the primary cilium as a signaling-competent organelle requires a high degree of fine tuning, which is at least in part achieved by a variety of post-translational modifications. One such modification is ubiquitination. The small and highly conserved ubiquitin protein possesses a unique versatility in regulating protein function via its ability to build mono and polyubiquitin chains onto target proteins. We aimed to take an unbiased approach to generate a comprehensive blueprint of the ciliary ubiquitinome by deploying a multi-proteomics approach using both ciliary-targeted ubiquitin affinity proteomics, as well as ubiquitin-binding domain-based proximity labelling in two different mammalian cell lines. This resulted in the identification of several key proteins involved in signaling, cytoskeletal remodeling and membrane and protein trafficking. Interestingly, using two different approaches in IMCD3 and RPE1 cells, respectively, we uncovered several novel mechanisms that regulate cilia function. In our IMCD3 proximity labeling cell line model, we found a highly enriched group of ESCRT-dependent clathrin-mediated endocytosis-related proteins, suggesting an important and novel role for this pathway in the regulation of ciliary homeostasis and function. In contrast, in RPE1 cells we found that several structural components of caveolae (CAV1, CAVIN1, and EHD2) were highly enriched in our cilia affinity proteomics screen. Consistently, the presence of caveolae at the ciliary pocket and ubiquitination of CAV1 specifically, were found likely to play a role in the regulation of ciliary length in these cells. Cilia length measurements demonstrated increased ciliary length in RPE1 cells stably expressing a ubiquitination impaired CAV1 mutant protein. Furthermore, live cell imaging in the same cells revealed decreased CAV1 protein turnover at the cilium as the possible cause for this phenotype. In conclusion, we have generated a comprehensive list of cilia-specific proteins that are subject to regulation via ubiquitination which can serve to further our understanding of cilia biology in health and disease.
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Affiliation(s)
- Mariam G. Aslanyan
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Cenna Doornbos
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Gaurav D. Diwan
- BioQuant, Heidelberg University, Heidelberg, Germany,Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Zeinab Anvarian
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tina Beyer
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Sylvia E. C. van Beersum
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Robert B. Russell
- BioQuant, Heidelberg University, Heidelberg, Germany,Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Marius Ueffing
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Alexander Ludwig
- School of Biological Sciences, NTU Institute of Structural Biology, Nanyang Technological University, Singapore City, Singapore
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Lotte B. Pedersen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands,*Correspondence: Ronald Roepman,
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Jewett CE, McCurdy BL, O'Toole ET, Stemm-Wolf AJ, Given KS, Lin CH, Olsen V, Martin W, Reinholdt L, Espinosa JM, Sullivan KD, Macklin WB, Prekeris R, Pearson CG. Trisomy 21 induces pericentrosomal crowding delaying primary ciliogenesis and mouse cerebellar development. eLife 2023; 12:e78202. [PMID: 36656118 PMCID: PMC9851619 DOI: 10.7554/elife.78202] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 12/06/2022] [Indexed: 01/20/2023] Open
Abstract
Trisomy 21, the genetic cause of Down syndrome, disrupts primary cilia formation and function, in part through elevated Pericentrin, a centrosome protein encoded on chromosome 21. Yet how trisomy 21 and elevated Pericentrin disrupt cilia-related molecules and pathways, and the in vivo phenotypic relevance remain unclear. Utilizing ciliogenesis time course experiments combined with light microscopy and electron tomography, we reveal that chromosome 21 polyploidy elevates Pericentrin and microtubules away from the centrosome that corral MyosinVA and EHD1, delaying ciliary membrane delivery and mother centriole uncapping essential for ciliogenesis. If given enough time, trisomy 21 cells eventually ciliate, but these ciliated cells demonstrate persistent trafficking defects that reduce transition zone protein localization and decrease sonic hedgehog signaling in direct anticorrelation with Pericentrin levels. Consistent with cultured trisomy 21 cells, a mouse model of Down syndrome with elevated Pericentrin has fewer primary cilia in cerebellar granule neuron progenitors and thinner external granular layers at P4. Our work reveals that elevated Pericentrin from trisomy 21 disrupts multiple early steps of ciliogenesis and creates persistent trafficking defects in ciliated cells. This pericentrosomal crowding mechanism results in signaling deficiencies consistent with the neurological phenotypes found in individuals with Down syndrome.
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Affiliation(s)
- Cayla E Jewett
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Bailey L McCurdy
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Eileen T O'Toole
- Molecular, Cellular, and Developmental Biology, University of Colorado BoulderBoulderUnited States
| | - Alexander J Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Katherine S Given
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Carrie H Lin
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Valerie Olsen
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | | | | | - Joaquín M Espinosa
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pharmacology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Kelly D Sullivan
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Wendy B Macklin
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Rytis Prekeris
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Chad G Pearson
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical CampusAuroraUnited States
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical CampusAuroraUnited States
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Kanie T, Ng R, Abbott KL, Pongs O, Jackson PK. Myristoylated Neuronal Calcium Sensor-1 captures the ciliary vesicle at distal appendages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.523037. [PMID: 36712037 PMCID: PMC9881967 DOI: 10.1101/2023.01.06.523037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The primary cilium is a microtubule-based organelle that cycles through assembly and disassembly. In many cell types, formation of the cilium is initiated by recruitment of ciliary vesicles to the distal appendage of the mother centriole. However, the distal appendage mechanism that directly captures ciliary vesicles is yet to be identified. In an accompanying paper, we show that the distal appendage protein, CEP89, is important for thef ciliary vesicle recruitment, but not for other steps of cilium formation (Tomoharu Kanie, Love, Fisher, Gustavsson, & Jackson, 2023). The lack of a membrane binding motif in CEP89 suggests that it may indirectly recruit ciliary vesicles via another binding partner. Here, we identify Neuronal Calcium Sensor-1 (NCS1) as a stoichiometric interactor of CEP89. NCS1 localizes to the position between CEP89 and a ciliary vesicle marker, RAB34, at the distal appendage. This localization was completely abolished in CEP89 knockouts, suggesting that CEP89 recruits NCS1 to the distal appendage. Similarly to CEP89 knockouts, ciliary vesicle recruitment as well as subsequent cilium formation was perturbed in NCS1 knockout cells. The ability of NCS1 to recruit the ciliary vesicle is dependent on its myristoylation motif and NCS1 knockout cells expressing myristoylation defective mutant failed to rescue the vesicle recruitment defect despite localizing proper localization to the centriole. In sum, our analysis reveals the first known mechanism for how the distal appendage recruits the ciliary vesicles.
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Affiliation(s)
- Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma, OK, 73112
| | - Roy Ng
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
| | - Keene L. Abbott
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
| | - Olaf Pongs
- Institute for Physiology, Center for Integrative Physiology and Molecular Medicine (CIPPM), Saarland University, Homburg, Germany
| | - Peter K. Jackson
- Baxter Laboratory, Department of Microbiology & Immunology and Department of Pathology, Stanford University, Stanford, CA, 94305
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Vasilyeva TA, Kadyshev VV, Marakhonov AV, Kanivets IV, Korostelev SA, Koshkin PA, Pyankov DV, Petrova NV, Kutsev SI, Zinchenko RA. [Molecular genetics in diagnosis of Coats disease: combination of oligogenic variants associated with different forms of hereditary retinal dystrophy]. Vestn Oftalmol 2023; 139:69-74. [PMID: 36924516 DOI: 10.17116/oftalma202313901169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Coats disease (OMIM 300216) is a form of hereditary retinal dystrophy, which occurs due to congenital abnormality of retinal vessels and features unilateral exudative vitreoretinopathy. Coats disease mostly occurs sporadically; its genetic cause is still undetermined. Molecular genetic research including whole exome sequencing by the NGS method was used to define a genetic cause of the observed phenotype. Two heterozygous variants in different genomic loci associated with other forms of hereditary retinal dystrophy were detected, a rare variant in the HMCN1 gene c.9571C>T, p.(Arg3191Cys), and a known pathogenic variant in the NPHP4 gene c.2930C>T, p.(Thr977Met). The HMCN1 gene is responsible for dominant age-related macular degeneration (OMIM 603075), pathogenic variants in the NPHP4 gene cause recessive Senior-Løken syndrome 4 (OMIM 266900). These genes encode the proteins that are involved in the regulation of integrity of the blood-retinal barrier in the vascular endothelium (NPHP4) and retinal pigment epithelium (HMCN1). The identified mutation in the NPHP4 gene could lead to decreased function of the NPHP4 protein and contribute to the development of retinal degeneration, potentially of oligogenic nature.
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Affiliation(s)
- T A Vasilyeva
- Research Centre for Medical Genetics, Moscow, Russia
| | - V V Kadyshev
- Research Centre for Medical Genetics, Moscow, Russia
| | | | - I V Kanivets
- Russian Medical Academy of Continuous Professional Education, Moscow, Russia.,OOO Genomed, Moscow, Russia
| | - S A Korostelev
- OOO Genomed, Moscow, Russia.,I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | | | | | - N V Petrova
- Research Centre for Medical Genetics, Moscow, Russia
| | - S I Kutsev
- Research Centre for Medical Genetics, Moscow, Russia
| | - R A Zinchenko
- Research Centre for Medical Genetics, Moscow, Russia.,N.A. Semashko National Research Institute of Public Health, Moscow, Russia
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37
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Morleo M, Vieira HL, Pennekamp P, Palma A, Bento-Lopes L, Omran H, Lopes SS, Barral DC, Franco B. Crosstalk between cilia and autophagy: implication for human diseases. Autophagy 2023; 19:24-43. [PMID: 35613303 PMCID: PMC9809938 DOI: 10.1080/15548627.2022.2067383] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Macroautophagy/autophagy is a self-degradative process necessary for cells to maintain their energy balance during development and in response to nutrient deprivation. Autophagic processes are tightly regulated and have been found to be dysfunctional in several pathologies. Increasing experimental evidence points to the existence of an interplay between autophagy and cilia. Cilia are microtubule-based organelles protruding from the cell surface of mammalian cells that perform a variety of motile and sensory functions and, when dysfunctional, result in disorders known as ciliopathies. Indeed, selective autophagic degradation of ciliary proteins has been shown to control ciliogenesis and, conversely, cilia have been reported to control autophagy. Moreover, a growing number of players such as lysosomal and mitochondrial proteins are emerging as actors of the cilia-autophagy interplay. However, some of the published data on the cilia-autophagy axis are contradictory and indicate that we are just starting to understand the underlying molecular mechanisms. In this review, the current knowledge about this axis and challenges are discussed, as well as the implication for ciliopathies and autophagy-associated disorders.
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Affiliation(s)
- Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), 80078, Pozzuoli, Italy,Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Helena L.A. Vieira
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal,UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal,Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Petra Pennekamp
- Department of General Pediatrics, University Hospital Münster, University of Münster, Münster48149, Germany,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Alessandro Palma
- Department of Onco-hematology, Gene and Cell Therapy, Bambino Gesù Children’s Hospital - IRCCS, Rome, Italy
| | - Liliana Bento-Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Münster, University of Münster, Münster48149, Germany,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Susana S. Lopes
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal,Member of the European Reference Networks ERN-LUNG, Lisbon, Portugal
| | - Duarte C. Barral
- CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), 80078, Pozzuoli, Italy,Medical Genetics, Department of Translational Medical Science, University of Naples “Federico II”, Naples, Italy,Scuola Superiore Meridionale, School for Advanced Studies, Naples, Italy,CONTACT Brunella Franco CEDOC, NOVA Medical School, NMS, Universidade NOVA de Lisboa, Lisboa1169-056, Portugal
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38
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Janas JA, Zhang L, Luu JH, Demeter J, Meng L, Marro SG, Mall M, Mooney NA, Schaukowitch K, Ng YH, Yang N, Huang Y, Neumayer G, Gozani O, Elias JE, Jackson PK, Wernig M. Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation. Mol Cell 2022; 82:4627-4646.e14. [PMID: 36417913 PMCID: PMC9779922 DOI: 10.1016/j.molcel.2022.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Cell lineage specification is accomplished by a concerted action of chromatin remodeling and tissue-specific transcription factors. However, the mechanisms that induce and maintain appropriate lineage-specific gene expression remain elusive. Here, we used an unbiased proteomics approach to characterize chromatin regulators that mediate the induction of neuronal cell fate. We found that Tip60 acetyltransferase is essential to establish neuronal cell identity partly via acetylation of the histone variant H2A.Z. Despite its tight correlation with gene expression and active chromatin, loss of H2A.Z acetylation had little effect on chromatin accessibility or transcription. Instead, loss of Tip60 and acetyl-H2A.Z interfered with H3K4me3 deposition and activation of a unique subset of silent, lineage-restricted genes characterized by a bivalent chromatin configuration at their promoters. Altogether, our results illuminate the mechanisms underlying bivalent chromatin activation and reveal that H2A.Z acetylation regulates neuronal fate specification by establishing epigenetic competence for bivalent gene activation and cell lineage transition.
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Affiliation(s)
- Justyna A Janas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lichao Zhang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacklyn H Luu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingjun Meng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samuele G Marro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Moritz Mall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katie Schaukowitch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yi Han Ng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nan Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuhao Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gernot Neumayer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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39
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Life-Saver or Undertaker: The Relationship between Primary Cilia and Cell Death in Vertebrate Embryonic Development. J Dev Biol 2022; 10:jdb10040052. [PMID: 36547474 PMCID: PMC9783631 DOI: 10.3390/jdb10040052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The development of multicellular organisms requires a tightly coordinated network of cellular processes and intercellular signalling. For more than 20 years, it has been known that primary cilia are deeply involved in the mediation of intercellular signalling and that ciliary dysfunction results in severe developmental defects. Cilia-mediated signalling regulates cellular processes such as proliferation, differentiation, migration, etc. Another cellular process ensuring proper embryonic development is cell death. While the effect of cilia-mediated signalling on many cellular processes has been extensively studied, the relationship between primary cilia and cell death remains largely unknown. This article provides a short review on the current knowledge about this relationship.
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40
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Park K, Leroux MR. Composition, organization and mechanisms of the transition zone, a gate for the cilium. EMBO Rep 2022; 23:e55420. [PMID: 36408840 PMCID: PMC9724682 DOI: 10.15252/embr.202255420] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/08/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The cilium evolved to provide the ancestral eukaryote with the ability to move and sense its environment. Acquiring these functions required the compartmentalization of a dynein-based motility apparatus and signaling proteins within a discrete subcellular organelle contiguous with the cytosol. Here, we explore the potential molecular mechanisms for how the proximal-most region of the cilium, termed transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins and helps to ensure ciliary autonomy and homeostasis. These include a unique complement and spatial organization of proteins that span from the microtubule-based axoneme to the ciliary membrane; a protein picket fence; a specialized lipid microdomain; differential membrane curvature and thickness; and lastly, a size-selective molecular sieve. In addition, the TZ must be permissive for, and functionally integrates with, ciliary trafficking systems (including intraflagellar transport) that cross the barrier and make the ciliary compartment dynamic. The quest to understand the TZ continues and promises to not only illuminate essential aspects of human cell signaling, physiology, and development, but also to unravel how TZ dysfunction contributes to ciliopathies that affect multiple organ systems, including eyes, kidney, and brain.
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Affiliation(s)
- Kwangjin Park
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
- Present address:
Terry Fox LaboratoryBC CancerVancouverBCCanada
- Present address:
Department of Medical GeneticsUniversity of British ColumbiaVancouverBCCanada
| | - Michel R Leroux
- Department of Molecular Biology and BiochemistrySimon Fraser UniversityBurnabyBCCanada
- Centre for Cell Biology, Development, and DiseaseSimon Fraser UniversityBurnabyBCCanada
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41
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Valentini G, Saia M, Farello G, Salpietro V, Mancuso A, Ceravolo I, Colucci PV, Torre M, Iapadre G, Rosa GD, Cucinotta F. Meckel Syndrome: A Clinical and Molecular Overview. JOURNAL OF PEDIATRIC NEUROLOGY 2022. [DOI: 10.1055/s-0042-1759531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AbstractMeckel syndrome (MKS) is a lethal, autosomal recessive, congenital syndrome caused by mutations in genes that encode proteins structurally or functionally related to the primary cilium. MKS is a malformative syndrome, most commonly characterized by occipital meningoencephalocele, polycystic kidney disease, liver fibrosis, and post- and (occasionally) preaxial polydactyly. To date, more than 10 genes are known to constitute the molecular background of MKS, displaying genetic heterogeneity. Individuals with MKS may resemble some phenotypic features of Joubert syndrome and related disorders, thus making diagnostic setting quite challenging. Here, we systematically reviewed the main clinical and genetic characteristics of MKS and its role among ciliopathies.
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Affiliation(s)
- Giulia Valentini
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age “G. Barresi,” University Hospital of Messina, Messina, Italy
| | - Maria Saia
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age “G. Barresi,” University Hospital of Messina, Messina, Italy
| | - Giovanni Farello
- Pediatric Clinic–Department of Life, Health and Environmental Sciences–Piazzale Salvatore Tommasi 1, Coppito (AQ), Italy
| | | | - Alessio Mancuso
- Unit of Pediatric Emergency, Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” University of Messina, Messina, Italy
| | - Ida Ceravolo
- Department of Clinical and Experimental Medicine, University of Messina, Via C. Valeria, Messina, Italy
| | - Pia V. Colucci
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age “G. Barresi,” University Hospital of Messina, Messina, Italy
| | - Manuela Torre
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age “G. Barresi,” University Hospital of Messina, Messina, Italy
| | - Giulia Iapadre
- Department of Pediatrics, University of L'Aquila, L'Aquila, Italy
| | - Gabriella Di Rosa
- Unit of Child Neurology and Psychiatry, Department of Human Pathology of the Adult and Developmental Age “G. Barresi,” University Hospital of Messina, Messina, Italy
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42
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Primary cilia suppress Ripk3-mediated necroptosis. Cell Death Dis 2022; 8:477. [PMID: 36460631 PMCID: PMC9718801 DOI: 10.1038/s41420-022-01272-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
Abstract
Cilia are sensory organelles that project from the surface of almost all cells. Nephronophthisis (NPH) and NPH-related ciliopathies are degenerative genetic diseases caused by mutation of cilia-associated genes. These kidney disorders are characterized by progressive loss of functional tubular epithelial cells which is associated with inflammation, progressive fibrosis, and cyst formation, ultimately leading to end-stage renal disease. However, disease mechanisms remain poorly understood. Here, we show that targeted deletion of cilia in renal epithelial cells enhanced susceptibility to necroptotic cell death under inflammatory conditions. Treatment of non-ciliated cells with tumor necrosis factor (TNF) α and the SMAC mimetic birinapant resulted in Ripk1-dependent cell death, while viability of ciliated cells was almost not affected. Cell death could be enhanced and shifted toward necroptosis by the caspase inhibitor emricasan, which could be blocked by inhibitors of Ripk1 and Ripk3. Moreover, combined treatment of ciliated and non-ciliated cells with TNFα and cycloheximide induced a cell death response that could be partially rescued with emricasan in ciliated cells. In contrast, non-ciliated cells responded with pronounced cell death that was blocked by necroptosis inhibitors. Consistently, combined treatment with interferon-γ and emricasan induced cell death only in non-ciliated cells. Mechanistically, enhanced necroptosis induced by loss of cilia could be explained by induction of Ripk3 and increased abundance of autophagy components, including p62 and LC3 associated with the Ripk1/Ripk3 necrosome. Genetic ablation of cilia in renal tubular epithelial cells in mice resulted in TUNEL positivity and increased expression of Ripk3 in kidney tissue. Moreover, loss of Nphp1, the most frequent cause of NPH, further increased susceptibility to necroptosis in non-ciliated epithelial cells, suggesting that necroptosis might contribute to the pathogenesis of the disease. Together, these data provide a link between cilia-related signaling and cell death responses and shed new light on the disease pathogenesis of NPH-related ciliopathies.
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Amack JD. Structures and functions of cilia during vertebrate embryo development. Mol Reprod Dev 2022; 89:579-596. [PMID: 36367893 PMCID: PMC9805515 DOI: 10.1002/mrd.23650] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/05/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022]
Abstract
Cilia are hair-like structures that project from the surface of cells. In vertebrates, most cells have an immotile primary cilium that mediates cell signaling, and some specialized cells assemble one or multiple cilia that are motile and beat synchronously to move fluids in one direction. Gene mutations that alter cilia structure or function cause a broad spectrum of disorders termed ciliopathies that impact virtually every system in the body. A wide range of birth defects associated with ciliopathies underscores critical functions for cilia during embryonic development. In many cases, the mechanisms underlying cilia functions during development and disease remain poorly understood. This review describes different types of cilia in vertebrate embryos and discusses recent research results from diverse model systems that provide novel insights into how cilia form and function during embryo development. The work discussed here not only expands our understanding of in vivo cilia biology, but also opens new questions about cilia and their roles in establishing healthy embryos.
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Affiliation(s)
- Jeffrey D. Amack
- Department of Cell and Developmental Biology, State University of New York Upstate Medical University, Syracuse, New York, USA,,BioInspired Syracuse: Institute for Material and Living Systems, Syracuse, New York, USA
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Wang J, Thomas HR, Thompson RG, Waldrep SC, Fogerty J, Song P, Li Z, Ma Y, Santra P, Hoover JD, Yeo NC, Drummond IA, Yoder BK, Amack JD, Perkins B, Parant JM. Variable phenotypes and penetrance between and within different zebrafish ciliary transition zone mutants. Dis Model Mech 2022; 15:dmm049568. [PMID: 36533556 PMCID: PMC9844136 DOI: 10.1242/dmm.049568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022] Open
Abstract
Meckel syndrome, nephronophthisis, Joubert syndrome and Bardet-Biedl syndrome are caused by mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest that these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes, suggesting that the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants, including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1 and nphp4, as well as mutants in ift88 and ift172. Our data indicate that variations in phenotypes exist between different TZ mutants, supporting different tissue-specific functions of these TZ genes. Further, we observed phenotypic variations within progeny of a single TZ mutant, reminiscent of multiple disease syndromes being associated with mutations in one gene. In some mutants, the dynamics of the phenotype became complex with transitory phenotypes that are corrected over time. We also demonstrated that multiple-guide-derived CRISPR/Cas9 F0 'crispant' embryos recapitulate zygotic null phenotypes, and rapidly identified ciliary phenotypes in 11 cilia-associated gene candidates (ankfn1, ccdc65, cfap57, fhad1, nme7, pacrg, saxo2, c1orf194, ttc26, zmynd12 and cfap52).
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Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Robert G. Thompson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Stephanie C. Waldrep
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Joseph Fogerty
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Zhang Li
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Yongjie Ma
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Peu Santra
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jonathan D. Hoover
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Iain A. Drummond
- Davis Center for Aging and Regeneration, Mount Desert Island Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609, USA
| | - Bradley K. Yoder
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Jeffrey D. Amack
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Brian Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
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Wang D, Chen X, Wen Q, Li Z, Chen W, Chen W, Wang X. A single heterozygous nonsense mutation in the TTC21B gene causes adult-onset nephronophthisis 12: A case report and review of literature. Mol Genet Genomic Med 2022; 10:e2076. [PMID: 36263627 PMCID: PMC9747551 DOI: 10.1002/mgg3.2076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/25/2022] [Accepted: 09/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Nephronophthisis type 12 (NPHP 12) is a rare cilia-related cystic kidney disease, caused by TTC21B mutation, mainly involving the kidneys, which generally occurs in children. Our study aimed to illustrate its clinical, pathological and genetic characteristics by reporting an adult-onset case of NPHP 12 caused by a single heterozygous nonsense mutation of TTC21B confirmed by renal histology and whole exome sequencing and reviewing related literature with a comparative analysis of the clinical features of each case. It will further increase the recognition of this rare kidney genetic disease, which sometimes can manifest as an adult disease. RESULTS A 33-years-old man showed a chronic disease course, and he exhibited slight renal dysfunction (CKD stage 3, eGFR = 49 ml/[min* 1.73 m2]) with renal tubular proteinuria, without any extrarenal manifestations, congenital malformation history of kidney disease, or family hereditary disease. Renal histological findings showed substantial interstitial fibrosis with some irregular and tortuous tubules with complex branches and segmental thickening and splitting of the tubular basement membrane. The patient was diagnosed with chronic interstitial nephritis for an unknown reason clinically. Further genetic analysis revealed a single heterozygous nonsense mutation in the TTC21B gene and NPHP 12 was diagnosed finally. CONCLUSION A single heterozygous mutation in the TTC21B gene may cause atypical NPHP12, which had a relatively later onset and milder clinical symptoms without developmental abnormalities. Therefore, for unexplained adult-onset chronic interstitial nephritis with unusual changes of renal tubules and interstitial fibrosis, even without a clear history of hereditary kidney disease, genetic testing is still recommended. The correct diagnosis of this rare adult-onset hereditary nephropathy can avoid unnecessary treatment.
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Affiliation(s)
- Dan Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Xionghui Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Qiong Wen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Zhijian Li
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Wei Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
| | - Wenfang Chen
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,Department of PathologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina
| | - Xin Wang
- Department of NephrologyThe First Affiliated Hospital, Sun Yat‐sen UniversityGuangzhouChina,NHC Key Laboratory of Clinical Nephrology (Sun Yat‐sen University) and Guangdong Provincial Key Laboratory of NephrologySun Yat‐sen UniversityGuangzhouChina
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Kruczek K, Qu Z, Welby E, Shimada H, Hiriyanna S, English MA, Zein WM, Brooks BP, Swaroop A. In vitro modeling and rescue of ciliopathy associated with IQCB1/NPHP5 mutations using patient-derived cells. Stem Cell Reports 2022; 17:2172-2186. [PMID: 36084637 PMCID: PMC9561628 DOI: 10.1016/j.stemcr.2022.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
Abstract
Mutations in the IQ calmodulin-binding motif containing B1 (IQCB1)/NPHP5 gene encoding the ciliary protein nephrocystin 5 cause early-onset blinding disease Leber congenital amaurosis (LCA), together with kidney dysfunction in Senior-Løken syndrome. For in vitro disease modeling, we obtained dermal fibroblasts from patients with NPHP5-LCA that were reprogrammed into induced pluripotent stem cells (iPSCs) and differentiated into retinal pigment epithelium (RPE) and retinal organoids. Patient fibroblasts and RPE demonstrated aberrantly elongated ciliary axonemes. Organoids revealed impaired development of outer segment structures, which are modified primary cilia, and mislocalization of visual pigments to photoreceptor cell soma. All patient-derived cells showed reduced levels of CEP290 protein, a critical cilia transition zone component interacting with NPHP5, providing a plausible mechanism for aberrant ciliary gating and cargo transport. Disease phenotype in NPHP5-LCA retinal organoids could be rescued by adeno-associated virus (AAV)-mediated IQCB1/NPHP5 gene augmentation therapy. Our studies thus establish a human disease model and a path for treatment of NPHP5-LCA.
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Affiliation(s)
- Kamil Kruczek
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Zepeng Qu
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Emily Welby
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Hiroko Shimada
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Suja Hiriyanna
- Ocular Gene Therapy Core, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Milton A English
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA.
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Yinsheng Z, Miyoshi K, Qin Y, Fujiwara Y, Yoshimura T, Katayama T. TMEM67 is required for the gating function of the transition zone that controls entry of membrane-associated proteins ARL13B and INPP5E into primary cilia. Biochem Biophys Res Commun 2022; 636:162-169. [DOI: 10.1016/j.bbrc.2022.10.078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/23/2022] [Indexed: 11/26/2022]
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Primary Cilia Influence Progenitor Function during Cortical Development. Cells 2022; 11:cells11182895. [PMID: 36139475 PMCID: PMC9496791 DOI: 10.3390/cells11182895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/29/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022] Open
Abstract
Corticogenesis is an intricate process controlled temporally and spatially by many intrinsic and extrinsic factors. Alterations during this important process can lead to severe cortical malformations. Apical neuronal progenitors are essential cells able to self-amplify and also generate basal progenitors and/or neurons. Apical radial glia (aRG) are neuronal progenitors with a unique morphology. They have a long basal process acting as a support for neuronal migration to the cortical plate and a short apical process directed towards the ventricle from which protrudes a primary cilium. This antenna-like structure allows aRG to sense cues from the embryonic cerebrospinal fluid (eCSF) helping to maintain cell shape and to influence several key functions of aRG such as proliferation and differentiation. Centrosomes, major microtubule organising centres, are crucial for cilia formation. In this review, we focus on how primary cilia influence aRG function during cortical development and pathologies which may arise due to defects in this structure. Reporting and cataloguing a number of ciliary mutant models, we discuss the importance of primary cilia for aRG function and cortical development.
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Chang KJ, Wu HY, Yarmishyn AA, Li CY, Hsiao YJ, Chi YC, Lo TC, Dai HJ, Yang YC, Liu DH, Hwang DK, Chen SJ, Hsu CC, Kao CL. Genetics behind Cerebral Disease with Ocular Comorbidity: Finding Parallels between the Brain and Eye Molecular Pathology. Int J Mol Sci 2022; 23:ijms23179707. [PMID: 36077104 PMCID: PMC9456058 DOI: 10.3390/ijms23179707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Cerebral visual impairments (CVIs) is an umbrella term that categorizes miscellaneous visual defects with parallel genetic brain disorders. While the manifestations of CVIs are diverse and ambiguous, molecular diagnostics stand out as a powerful approach for understanding pathomechanisms in CVIs. Nevertheless, the characterization of CVI disease cohorts has been fragmented and lacks integration. By revisiting the genome-wide and phenome-wide association studies (GWAS and PheWAS), we clustered a handful of renowned CVIs into five ontology groups, namely ciliopathies (Joubert syndrome, Bardet–Biedl syndrome, Alstrom syndrome), demyelination diseases (multiple sclerosis, Alexander disease, Pelizaeus–Merzbacher disease), transcriptional deregulation diseases (Mowat–Wilson disease, Pitt–Hopkins disease, Rett syndrome, Cockayne syndrome, X-linked alpha-thalassaemia mental retardation), compromised peroxisome disorders (Zellweger spectrum disorder, Refsum disease), and channelopathies (neuromyelitis optica spectrum disorder), and reviewed several mutation hotspots currently found to be associated with the CVIs. Moreover, we discussed the common manifestations in the brain and the eye, and collated animal study findings to discuss plausible gene editing strategies for future CVI correction.
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Affiliation(s)
- Kao-Jung Chang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Hsin-Yu Wu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | | | - Cheng-Yi Li
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yu-Jer Hsiao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yi-Chun Chi
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Tzu-Chen Lo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - He-Jhen Dai
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yi-Chiang Yang
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Ding-Hao Liu
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - De-Kuang Hwang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chih-Chien Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Correspondence: (C.-C.H.); (C.-L.K.); Tel.: +886-2-287-573-25 (C.-C.H.); +886-2-287-573-63 (C.-L.K.)
| | - Chung-Lan Kao
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Department of Physical Medicine and Rehabilitation, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Correspondence: (C.-C.H.); (C.-L.K.); Tel.: +886-2-287-573-25 (C.-C.H.); +886-2-287-573-63 (C.-L.K.)
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Kayser N, Zaiser F, Veenstra AC, Wang H, Göcmen B, Eckert P, Franz H, Köttgen A, Walz G, Yakulov TA. Clock genes rescue nphp mutations in zebrafish. Hum Mol Genet 2022; 31:4143-4158. [PMID: 35861640 PMCID: PMC9759334 DOI: 10.1093/hmg/ddac160] [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: 05/16/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 01/21/2023] Open
Abstract
The zebrafish pronephros model, using morpholino oligonucleotides (MO) to deplete target genes, has been extensively used to characterize human ciliopathy phenotypes. Recently, discrepancies between MO and genetically defined mutants have questioned this approach. We analyzed zebrafish with mutations in the nphp1-4-8 module to determine the validity of MO-based results. While MO-mediated depletion resulted in glomerular cyst and cloaca malformation, these ciliopathy-typical manifestations were observed at a much lower frequency in zebrafish embryos with defined nphp mutations. All nphp1-4-8 mutant zebrafish were viable and displayed decreased manifestations in the next (F2) generation, lacking maternal RNA contribution. While genetic compensation was further supported by the observation that nphp4-deficient mutants became partially refractory to MO-based nphp4 depletion, zebrafish embryos, lacking one nphp gene, became more sensitive to MO-based depletion of additional nphp genes. Transcriptome analysis of nphp8 mutant embryos revealed an upregulation of the circadian clock genes cry1a and cry5. MO-mediated depletion of cry1a and cry5 caused ciliopathy phenotypes in wild-type embryos, while cry1a and cry5 depletion in maternal zygotic nphp8 mutant embryos increased the frequency of glomerular cysts compared to controls. Importantly, cry1a and cry5 rescued the nephropathy-related phenotypes in nphp1, nphp4 or nphp8-depleted zebrafish embryos. Our results reveal that nphp mutant zebrafish resemble the MO-based phenotypes, albeit at a much lower frequency. Rapid adaption through upregulation of circadian clock genes seems to ameliorate the loss of nphp genes, contributing to phenotypic differences.
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Affiliation(s)
| | | | | | | | - Burulca Göcmen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79106, Germany
| | - Priska Eckert
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Henriette Franz
- Department of Biomedicine, University of Basel, Pestalozzistr. 20, Basel CH-4056, Switzerland
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg 79106, Germany
| | - Gerd Walz
- Renal Division, University Freiburg Medical Center, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Albertstrasse 19, Freiburg 79104, Germany
| | - Toma A Yakulov
- To whom correspondence should be addressed. Tel: +49 76127063036;
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