1
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Mahboobipour AA, Ala M, Safdari Lord J, Yaghoobi A. Clinical manifestation, epidemiology, genetic basis, potential molecular targets, and current treatment of polycystic liver disease. Orphanet J Rare Dis 2024; 19:175. [PMID: 38671465 PMCID: PMC11055360 DOI: 10.1186/s13023-024-03187-w] [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: 07/04/2023] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Polycystic liver disease (PLD) is a rare condition observed in three genetic diseases, including autosomal dominant polycystic liver disease (ADPLD), autosomal dominant polycystic kidney disease (ADPKD), and autosomal recessive polycystic kidney disease (ARPKD). PLD usually does not impair liver function, and advanced PLD becomes symptomatic when the enlarged liver compresses adjacent organs or increases intra-abdominal pressure. Currently, the diagnosis of PLD is mainly based on imaging, and genetic testing is not required except for complex cases. Besides, genetic testing may help predict patients' prognosis, classify patients for genetic intervention, and conduct early treatment. Although the underlying genetic causes and mechanisms are not fully understood, previous studies refer to primary ciliopathy or impaired ciliogenesis as the main culprit. Primarily, PLD occurs due to defective ciliogenesis and ineffective endoplasmic reticulum quality control. Specifically, loss of function mutations of genes that are directly involved in ciliogenesis, such as Pkd1, Pkd2, Pkhd1, and Dzip1l, can lead to both hepatic and renal cystogenesis in ADPKD and ARPKD. In addition, loss of function mutations of genes that are involved in endoplasmic reticulum quality control and protein folding, trafficking, and maturation, such as PRKCSH, Sec63, ALG8, ALG9, GANAB, and SEC61B, can impair the production and function of polycystin1 (PC1) and polycystin 2 (PC2) or facilitate their degradation and indirectly promote isolated hepatic cystogenesis or concurrent hepatic and renal cystogenesis. Recently, it was shown that mutations of LRP5, which impairs canonical Wnt signaling, can lead to hepatic cystogenesis. PLD is currently treated by somatostatin analogs, percutaneous intervention, surgical fenestration, resection, and liver transplantation. In addition, based on the underlying molecular mechanisms and signaling pathways, several investigational treatments have been used in preclinical studies, some of which have shown promising results. This review discusses the clinical manifestation, complications, prevalence, genetic basis, and treatment of PLD and explains the investigational methods of treatment and future research direction, which can be beneficial for researchers and clinicians interested in PLD.
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Affiliation(s)
- Amir Ali Mahboobipour
- Tracheal Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Moein Ala
- Experimental Medicine Research Center, School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
| | - Javad Safdari Lord
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Yaghoobi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- School of Biological Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
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2
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Chen H, Wu Z, Yan Z, Chen C, Zhang Y, Wang Q, Gao Y, Ling K, Hu J, Wei Q. The ARPKD Protein DZIP1L Regulates Ciliary Protein Entry by Modulating the Architecture and Function of Ciliary Transition Fibers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308820. [PMID: 38634253 DOI: 10.1002/advs.202308820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/13/2024] [Indexed: 04/19/2024]
Abstract
Serving as the cell's sensory antennae, primary cilia are linked to numerous human genetic diseases when they malfunction. DZIP1L, identified as one of the genetic causes of human autosomal recessive polycystic kidney disease (ARPKD), is an evolutionarily conserved ciliary basal body protein. Although it has been reported that DZIP1L is involved in the ciliary entry of PKD proteins, the underlying mechanism remains elusive. Here, an uncharacterized role of DZIP1L is reported in modulating the architecture and function of transition fibers (TFs), striking ciliary base structures essential for selective cilia gating. Using C. elegans as a model, C01G5.7 (hereafter termed DZIP-1) is identified as the sole homolog of DZIP1L, which specifically localizes to TFs. While DZIP-1 or ANKR-26 (the ortholog of ANKRD26) deficiency shows subtle impact on TFs, co-depletion of DZIP-1 and ANKR-26 disrupts TF assembly and cilia gating for soluble and membrane proteins, including the ortholog of ADPKD protein polycystin-2. Notably, the synergistic role for DZIP1L and ANKRD26 in the formation and function of TFs is highly conserved in mammalian cilia. Hence, the findings illuminate an evolutionarily conserved role of DZIP1L in TFs architecture and function, highlighting TFs as a vital part of the ciliary gate implicated in ciliopathies ARPKD.
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Affiliation(s)
- Huicheng Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Zhimao Wu
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Ziwei Yan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yingying Zhang
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Qiaoling Wang
- Institute of Medicine and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 430000, China
| | - Yuqing Gao
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qing Wei
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, 518055, China
- School of Synthetic Biology, Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, Taiyuan, 030006, China
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Wu Z, Chen H, Zhang Y, Wang Y, Wang Q, Augière C, Hou Y, Fu Y, Peng Y, Durand B, Wei Q. Cep131-Cep162 and Cby-Fam92 complexes cooperatively maintain Cep290 at the basal body and contribute to ciliogenesis initiation. PLoS Biol 2024; 22:e3002330. [PMID: 38442096 PMCID: PMC10914257 DOI: 10.1371/journal.pbio.3002330] [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: 08/28/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Cilia play critical roles in cell signal transduction and organ development. Defects in cilia function result in a variety of genetic disorders. Cep290 is an evolutionarily conserved ciliopathy protein that bridges the ciliary membrane and axoneme at the basal body (BB) and plays critical roles in the initiation of ciliogenesis and TZ assembly. How Cep290 is maintained at BB and whether axonemal and ciliary membrane localized cues converge to determine the localization of Cep290 remain unknown. Here, we report that the Cep131-Cep162 module near the axoneme and the Cby-Fam92 module close to the membrane synergistically control the BB localization of Cep290 and the subsequent initiation of ciliogenesis in Drosophila. Concurrent deletion of any protein of the Cep131-Cep162 module and of the Cby-Fam92 module leads to a complete loss of Cep290 from BB and blocks ciliogenesis at its initiation stage. Our results reveal that the first step of ciliogenesis strictly depends on cooperative and retroactive interactions between Cep131-Cep162, Cby-Fam92 and Cep290, which may contribute to the complex pathogenesis of Cep290-related ciliopathies.
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Affiliation(s)
- Zhimao Wu
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Huicheng Chen
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Yingying Zhang
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Yaru Wang
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Qiaoling Wang
- Institute of Medicine and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Céline Augière
- University Claude Bernard Lyon 1, MeLiS—UCBL—CNRS UMR 5284—INSERM U1314, Lyon, France
| | - Yanan Hou
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Yuejun Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Ying Peng
- Institute of Medicine and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Bénédicte Durand
- University Claude Bernard Lyon 1, MeLiS—UCBL—CNRS UMR 5284—INSERM U1314, Lyon, France
| | - Qing Wei
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
- Shenzhen Key Laboratory of Metabolic Health, Shenzhen, China
- School of Synthetic Biology, Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, Taiyuan, China
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4
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Bocquet B, Borday C, Erkilic N, Mamaeva D, Donval A, Masson C, Parain K, Kaminska K, Quinodoz M, Perea-Romero I, Garcia-Garcia G, Jimenez-Medina C, Boukhaddaoui H, Coget A, Leboucq N, Calzetti G, Gandolfi S, Percesepe A, Barili V, Uliana V, Delsante M, Bozzetti F, Scholl HP, Corton M, Ayuso C, Millan JM, Rivolta C, Meunier I, Perron M, Kalatzis V. TBC1D32 variants disrupt retinal ciliogenesis and cause retinitis pigmentosa. JCI Insight 2023; 8:e169426. [PMID: 37768732 PMCID: PMC10721274 DOI: 10.1172/jci.insight.169426] [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: 02/07/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4 patients presenting with RP from 3 unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human induced pluripotent stem cell-derived (iPSC-derived) retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition-like phenotype. Last, our results suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data highlight a critical role for TBC1D32 in the retina and demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD-causative gene.
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Affiliation(s)
- Béatrice Bocquet
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Caroline Borday
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Nejla Erkilic
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Daria Mamaeva
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Alicia Donval
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Christel Masson
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karine Parain
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Garcia-Garcia
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carla Jimenez-Medina
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Hassan Boukhaddaoui
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Arthur Coget
- Department of Neuroradiology and
- Institute for Human Functional Imaging (I2FH), University of Montpellier, CHU, Montpellier, France
| | | | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Medicine and Surgery
| | | | | | | | | | | | - Francesca Bozzetti
- Neuroradiology Unit, Diagnostic Department, University Hospital of Parma, Parma, Italy
| | - Hendrik P.N. Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Marta Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose M. Millan
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Muriel Perron
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
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Hou Y, Zheng S, Wu Z, Augière C, Morel V, Cortier E, Duteyrat JL, Zhang Y, Chen H, Peng Y, Durand B, Wei Q. Drosophila transition fibers are essential for IFT-dependent ciliary elongation but not basal body docking and ciliary budding. Curr Biol 2023; 33:727-736.e6. [PMID: 36669498 DOI: 10.1016/j.cub.2022.12.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 09/22/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023]
Abstract
Cilia are highly conserved organelles critical for animal development and perception. Dysfunction of cilia has been linked to a wide spectrum of human genetic diseases, termed ciliopathies.1,2 Transition fibers (TFs) are striking ciliary base structures essential for cilia assembly. Vertebrates' TFs that originate from centriole distal appendages (DAs) mediate basal body docking to ciliary vesicles to initiate ciliogenesis and regulate the entry of ciliary proteins for axoneme assembly via intraflagellar transport (IFT) machinery.3 Although no distal appendages can be observed on Drosophila centrioles,4,5 three key TF proteins, FBF1, CEP164, and CEP89, have obvious homologs in Drosophila. We aimed to compare their functions with their mammalian counterparts in Drosophila ciliogenesis. Here, we show that all three proteins are localized like TF proteins at the ciliary base in both sensory neurons and spermatocytes, the only two types of ciliated cells in flies. Fbf1 and Cep89 are essential for the formation of IFT-dependent neuronal cilia, but Cep164 is dispensable for ciliogenesis in flies. Strikingly, none are required for basal body docking and transition zone (TZ) assembly in IFT-dependent neuronal cilia or IFT-independent spermatocyte cilia. Furthermore, we demonstrate that Unc is essential to recruit all three TF proteins and establish a hierarchical order, with Cep89 acting on Fbf1. Collectively, our results not only demonstrate that TF proteins are required for IFT-dependent ciliogenesis in Drosophila, in agreement with an evolutionarily conserved function of these proteins in regulating ciliary protein entry, but also that the basal body docking function of TFs has diverged during evolution.
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Affiliation(s)
- Yanan Hou
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Shirui Zheng
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Zhimao Wu
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen 518055, China
| | - Céline Augière
- University of Lyon, Université Claude Bernard Lyon 1, MeLiS - UCBL-CNRS UMR 5284 - INSERM U1314, Institut NeuroMyoGène, Lyon 69008, France
| | - Véronique Morel
- University of Lyon, Université Claude Bernard Lyon 1, MeLiS - UCBL-CNRS UMR 5284 - INSERM U1314, Institut NeuroMyoGène, Lyon 69008, France
| | - Elisabeth Cortier
- University of Lyon, Université Claude Bernard Lyon 1, MeLiS - UCBL-CNRS UMR 5284 - INSERM U1314, Institut NeuroMyoGène, Lyon 69008, France
| | - Jean-Luc Duteyrat
- University of Lyon, Université Claude Bernard Lyon 1, MeLiS - UCBL-CNRS UMR 5284 - INSERM U1314, Institut NeuroMyoGène, Lyon 69008, France
| | - Yingying Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Huicheng Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ying Peng
- Institute of Medicine and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 430000, China
| | - Bénédicte Durand
- University of Lyon, Université Claude Bernard Lyon 1, MeLiS - UCBL-CNRS UMR 5284 - INSERM U1314, Institut NeuroMyoGène, Lyon 69008, France.
| | - Qing Wei
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen 518055, China; Shenzhen Key Laboratory of Metabolic Health, Shenzhen 518055, China.
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6
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Chee JM, Lanoue L, Clary D, Higgins K, Bower L, Flenniken A, Guo R, Adams DJ, Bosch F, Braun RE, Brown SDM, Chin HJG, Dickinson ME, Hsu CW, Dobbie M, Gao X, Galande S, Grobler A, Heaney JD, Herault Y, de Angelis MH, Mammano F, Nutter LMJ, Parkinson H, Qin C, Shiroishi T, Sedlacek R, Seong JK, Xu Y, Brooks B, McKerlie C, Lloyd KCK, Westerberg H, Moshiri A. Genome-wide screening reveals the genetic basis of mammalian embryonic eye development. BMC Biol 2023; 21:22. [PMID: 36737727 PMCID: PMC9898963 DOI: 10.1186/s12915-022-01475-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 11/23/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. RESULTS Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. CONCLUSIONS Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.
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Affiliation(s)
- Justine M Chee
- Oakland University William Beaumont School of Medicine, Rochester, MI, USA
| | - Louise Lanoue
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Dave Clary
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Kendall Higgins
- University of Miami: Miller School of Medicine, Miami, FL, USA
| | - Lynette Bower
- Mouse Biology Program, University of California Davis, Davis, CA, USA
| | - Ann Flenniken
- The Centre for Phenogenomics, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
| | - Ruolin Guo
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - David J Adams
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fatima Bosch
- Centre of Animal Biotechnology and Gene Therapy (CBATEG), Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Steve D M Brown
- Medical Research Council Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, UK
| | - H-J Genie Chin
- National Laboratory Animal Center, National Applied Research Laboratories (NARLabs), Taipei City, Taiwan
| | - Mary E Dickinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chih-Wei Hsu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Michael Dobbie
- Phenomics Australia, The John Curtin School of Medical Research, Canberra, Australia
| | - Xiang Gao
- Nanjing Biomedical Research Institute, Nanjing University, Nanjing, China
| | - Sanjeev Galande
- Indian Institutes of Science Education and Research, Pune, India
| | - Anne Grobler
- Faculty of Health Sciences, PCDDP North-West University, Potchefstroom, South Africa
| | - Jason D Heaney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yann Herault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Illkirch, France
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Fabio Mammano
- Monterotondo Mouse Clinic, Italian National Research Council (CNR), Monterotondo Scalo, Italy
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Helen Parkinson
- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Chuan Qin
- National Laboratory Animal Center, National Applied Research Laboratories, Beijing, China
| | | | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - J-K Seong
- Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul, South Korea
| | - Ying Xu
- CAM-SU Genomic Resource Center, Soochow University, Suzhou, China
| | - Brian Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, NIH, Bethesda, MD, 20892, USA
| | - Colin McKerlie
- The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine & Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - K C Kent Lloyd
- Mouse Biology Program, University of California Davis, Davis, CA, USA
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, CA, USA
| | - Henrik Westerberg
- Medical Research Council Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, UK
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, University of California Davis, Sacramento, CA, USA.
- UC Davis Eye Center, 4860 Y St., Ste. 2400, Sacramento, CA, 95817, USA.
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7
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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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8
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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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9
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Satoda Y, Noguchi T, Fujii T, Taniguchi A, Katoh Y, Nakayama K. BROMI/TBC1D32 together with CCRK/CDK20 and FAM149B1/JBTS36 contributes to intraflagellar transport turnaround involving ICK/CILK1. Mol Biol Cell 2022; 33:ar79. [PMID: 35609210 PMCID: PMC9582636 DOI: 10.1091/mbc.e22-03-0089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Primary cilia are antenna-like organelles that contain specific proteins, and are crucial for tissue morphogenesis. Anterograde and retrograde trafficking of ciliary proteins are mediated by the intraflagellar transport (IFT) machinery. BROMI/TBC1D32 interacts with CCRK/CDK20, which phosphorylates and activates the intestinal cell kinase (ICK)/CILK1 kinase, to regulate the change in direction of the IFT machinery at the ciliary tip. Mutations in BROMI, CCRK, and ICK in humans cause ciliopathies, and mice defective in these genes are also known to demonstrate ciliopathy phenotypes. We show here that BROMI interacts not only with CCRK but also with CFAP20, an evolutionarily conserved ciliary protein, and with FAM149B1/ Joubert syndrome (JBTS)36, a protein in which mutations cause JBTS. In addition, we show that FAM149B1 interacts directly with CCRK as well as with BROMI. Ciliary defects observed in CCRK-knockout (KO), BROMI-KO, and FAM149B1-KO cells, including abnormally long cilia and accumulation of the IFT machinery and ICK at the ciliary tip, resembled one another, and BROMI mutants that are defective in binding to CCRK and CFAP20 were unable to rescue the ciliary defects of BROMI-KO cells. These data indicate that CCRK, BROMI, FAM149B1, and probably CFAP20 altogether regulate the IFT turnaround process under the control of ICK.
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Affiliation(s)
- Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Taiju Fujii
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Aoi Taniguchi
- 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
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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10
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Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes. Commun Biol 2022; 5:312. [PMID: 35383272 PMCID: PMC8983713 DOI: 10.1038/s42003-022-03269-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Obtaining the high-resolution structures of proteins and their complexes is a crucial aspect of understanding the mechanisms of life. Experimental structure determination methods are time-consuming, expensive and cannot keep pace with the growing number of protein sequences available through genomic DNA sequencing. Thus, the ability to accurately predict the structure of proteins from their sequence is a holy grail of structural and computational biology that would remove a bottleneck in our efforts to understand as well as rationally engineer living systems. Recent advances in protein structure prediction, in particular the breakthrough with the AI-based tool AlphaFold2 (AF2), hold promise for achieving this goal, but the practical utility of AF2 remains to be explored. Focusing on proteins with essential roles in centrosome and centriole biogenesis, we demonstrate the quality and usability of the AF2 prediction models and we show that they can provide important insights into the modular organization of two key players in this process, CEP192 and CEP44. Furthermore, we used the AF2 algorithm to elucidate and then experimentally validate previously unknown prime features in the structure of TTBK2 bound to CEP164, as well as the Chibby1-FAM92A complex for which no structural information was available to date. These findings have important implications in understanding the regulation and function of these complexes. Finally, we also discuss some practical limitations of AF2 and anticipate the implications for future research approaches in the centriole/centrosome field. Using experimental data, the authors assess the quality and discuss the limitations of AlphaFold2 predictions of protein structures and protein-protein interactions essential for centrosome and centriole biogenesis.
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11
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Noguchi T, Nakamura K, Satoda Y, Katoh Y, Nakayama K. CCRK/CDK20 regulates ciliary retrograde protein trafficking via interacting with BROMI/TBC1D32. PLoS One 2021; 16:e0258497. [PMID: 34624068 PMCID: PMC8500422 DOI: 10.1371/journal.pone.0258497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/28/2021] [Indexed: 01/02/2023] Open
Abstract
CCRK/CDK20 was reported to interact with BROMI/TBC1D32 and regulate ciliary Hedgehog signaling. In various organisms, mutations in the orthologs of CCRK and those of the kinase ICK/CILK1, which is phosphorylated by CCRK, are known to result in cilia elongation. Furthermore, we recently showed that ICK regulates retrograde ciliary protein trafficking and/or the turnaround event at the ciliary tips, and that its mutations result in the elimination of intraflagellar transport (IFT) proteins that have overaccumulated at the bulged ciliary tips as extracellular vesicles, in addition to cilia elongation. However, how these proteins cooperate to regulate ciliary protein trafficking has remained unclear. We here show that the phenotypes of CCRK-knockout (KO) cells closely resemble those of ICK-KO cells; namely, the overaccumulation of IFT proteins at the bulged ciliary tips, which appear to be eliminated as extracellular vesicles, and the enrichment of GPR161 and Smoothened on the ciliary membrane. The abnormal phenotypes of CCRK-KO cells were rescued by the exogenous expression of wild-type CCRK but not its kinase-dead mutant or a mutant defective in BROMI binding. These results together indicate that CCRK regulates the turnaround process at the ciliary tips in concert with BROMI and probably via activating ICK.
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Affiliation(s)
- Tatsuro Noguchi
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Kentaro Nakamura
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yuuki Satoda
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
- * E-mail: (KN); (YK)
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
- * E-mail: (KN); (YK)
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12
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Cyge B, Voronina V, Hoque M, Kim EN, Hall J, Bailey-Lundberg JM, Pazour GJ, Crawford HC, Moon RT, Li FQ, Takemaru KI. Loss of the ciliary protein Chibby1 in mice leads to exocrine pancreatic degeneration and pancreatitis. Sci Rep 2021; 11:17220. [PMID: 34446743 PMCID: PMC8390639 DOI: 10.1038/s41598-021-96597-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Primary cilia protrude from the apical surface of many cell types and act as a sensory organelle that regulates diverse biological processes ranging from chemo- and mechanosensation to signaling. Ciliary dysfunction is associated with a wide array of genetic disorders, known as ciliopathies. Polycystic lesions are commonly found in the kidney, liver, and pancreas of ciliopathy patients and mouse models. However, the pathogenesis of the pancreatic phenotype remains poorly understood. Chibby1 (Cby1), a small conserved coiled-coil protein, localizes to the ciliary base and plays a crucial role in ciliogenesis. Here, we report that Cby1-knockout (KO) mice develop severe exocrine pancreatic atrophy with dilated ducts during early postnatal development. A significant reduction in the number and length of cilia was observed in Cby1-KO pancreta. In the adult Cby1-KO pancreas, inflammatory cell infiltration and fibrosis were noticeable. Intriguingly, Cby1-KO acinar cells showed an accumulation of zymogen granules (ZGs) with altered polarity. Moreover, isolated acini from Cby1-KO pancreas exhibited defective ZG secretion in vitro. Collectively, our results suggest that, upon loss of Cby1, concomitant with ciliary defects, acinar cells accumulate ZGs due to defective exocytosis, leading to cell death and progressive exocrine pancreatic degeneration after birth.
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Affiliation(s)
- Benjamin Cyge
- Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Vera Voronina
- Department of Pharmacology, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, WA, 98195, USA
| | - Mohammed Hoque
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Eunice N Kim
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Jason Hall
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Jennifer M Bailey-Lundberg
- Department of Anesthesiology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Gregory J Pazour
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Howard C Crawford
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, 32224, USA
- Henry Ford Health System, Detroit, MI, 48202, USA
| | - Randall T Moon
- Department of Pharmacology, Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine and Howard Hughes Medical Institute, Seattle, WA, 98195, USA
| | - Feng-Qian Li
- Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11974, USA
| | - Ken-Ichi Takemaru
- Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, NY, 11794, USA.
- Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY, 11794, USA.
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, 11974, USA.
- Department of Pharmacological Sciences, Stony Brook University, BST 7-182, 101 Nicolls Rd., Stony Brook, NY, 11794-8651, USA.
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13
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Abstract
Ciliogenesis describes the assembly of cilia in interphase cells. Several hundred proteins have been linked to ciliogenesis, which proceeds through a highly coordinated multistage process at the distal end of centrioles requiring membranes. In this short review, we focus on recently reported insights into the biogenesis of the primary cilium membrane and its association with other ciliogenic processes in the intracellular ciliogenesis pathway.
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Affiliation(s)
- Saurabh Shakya
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Laboratory of Cellular and Developmental Signaling, Frederick, MD 21702, USA
| | - Christopher J Westlake
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Laboratory of Cellular and Developmental Signaling, Frederick, MD 21702, USA
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14
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Role of DZIP1-CBY-FAM92 transition zone complex in the basal body to membrane attachment and ciliary budding. Biochem Soc Trans 2021; 48:1067-1075. [PMID: 32491167 DOI: 10.1042/bst20191007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/20/2020] [Accepted: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Cilia play important signaling or motile functions in various organisms. In Human, cilia dysfunctions are responsible for a wide range of diseases, called ciliopathies. Cilia assembly is a tightly controlled process, which starts with the conversion of the centriole into a basal body, leading to the formation of the ciliary bud that protrudes inside a ciliary vesicle and/or ultimately at the cell surface. Ciliary bud formation is associated with the assembly of the transition zone (TZ), a complex architecture of proteins of the ciliary base which plays critical functions in gating proteins in and out of the ciliary compartment. Many proteins are involved in the assembly of the TZ, which shows structural and functional variations in different cell types or organisms. In this review, we discuss how a particular complex, composed of members of the DZIP1, CBY and FAM92 families of proteins, is required for the initial stages of cilia assembly leading to ciliary bud formation and how their functional hierarchy contributes to TZ assembly. Moreover, we summarize how evidences in Drosophila reveal functional differences of the DZIP1-CBY-FAM92 complex in the different ciliated tissues of this organism. Whereas it is essential for proper TZ assembly in the two types of ciliated tissues, it is involved in stable anchoring of basal bodies to the plasma membrane in male germ cells. Overall, the DZIP1-CBY-FAM92 complex reveals a molecular assembly pathway required for the initial stages of ciliary bud formation and that is conserved from Drosophila to Human.
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15
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Wu Z, Pang N, Zhang Y, Chen H, Peng Y, Fu J, Wei Q. CEP290 is essential for the initiation of ciliary transition zone assembly. PLoS Biol 2020; 18:e3001034. [PMID: 33370260 PMCID: PMC7793253 DOI: 10.1371/journal.pbio.3001034] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 01/08/2021] [Accepted: 12/16/2020] [Indexed: 11/24/2022] Open
Abstract
Cilia play critical roles during embryonic development and adult homeostasis. Dysfunction of cilia leads to various human genetic diseases, including many caused by defects in transition zones (TZs), the "gates" of cilia. The evolutionarily conserved TZ component centrosomal protein 290 (CEP290) is the most frequently mutated human ciliopathy gene, but its roles in ciliogenesis are not completely understood. Here, we report that CEP290 plays an essential role in the initiation of TZ assembly in Drosophila. Mechanistically, the N-terminus of CEP290 directly recruits DAZ interacting zinc finger protein 1 (DZIP1), which then recruits Chibby (CBY) and Rab8 to promote early ciliary membrane formation. Complete deletion of CEP290 blocks ciliogenesis at the initiation stage of TZ assembly, which can be mimicked by DZIP1 deletion mutants. Remarkably, expression of the N-terminus of CEP290 alone restores the TZ localization of DZIP1 and subsequently ameliorates the defects in TZ assembly initiation in cep290 mutants. Our results link CEP290 to DZIP1-CBY/Rab8 module and uncover a previously uncharacterized important function of CEP290 in the coordination of early ciliary membrane formation and TZ assembly.
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Affiliation(s)
- Zhimao Wu
- Chinese Academy of Sciences Key Laboratory of Insect Developmental and Evolutionary Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Nan Pang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yingying Zhang
- Chinese Academy of Sciences Key Laboratory of Insect Developmental and Evolutionary Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huicheng Chen
- Chinese Academy of Sciences Key Laboratory of Insect Developmental and Evolutionary Biology, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ying Peng
- Institute of Medicine and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jingyan Fu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qing Wei
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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16
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Kolapalli SP, Sahu R, Chauhan NR, Jena KK, Mehto S, Das SK, Jain A, Rout M, Dash R, Swain RK, Lee DY, Rusten TE, Chauhan S, Chauhan S. RNA-Binding RING E3-Ligase DZIP3/hRUL138 Stabilizes Cyclin D1 to Drive Cell-Cycle and Cancer Progression. Cancer Res 2020; 81:315-331. [PMID: 33067265 DOI: 10.1158/0008-5472.can-20-1871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/02/2020] [Accepted: 10/13/2020] [Indexed: 11/16/2022]
Abstract
DZIP3/hRUL138 is a poorly characterized RNA-binding RING E3-ubiquitin ligase with functions in embryonic development. Here we demonstrate that DZIP3 is a crucial driver of cancer cell growth, migration, and invasion. In mice and zebrafish cancer models, DZIP3 promoted tumor growth and metastasis. In line with these results, DZIP3 was frequently overexpressed in several cancer types. Depletion of DZIP3 from cells resulted in reduced expression of Cyclin D1 and a subsequent G1 arrest and defect in cell growth. Mechanistically, DZIP3 utilized its two different domains to interact and stabilize Cyclin D1 both at mRNA and protein levels. Using an RNA-binding lysine-rich region, DZIP3 interacted with the AU-rich region in 3' untranslated region of Cyclin D1 mRNA and stabilized it. Using a RING E3-ligase domain, DZIP3 interacted and increased K63-linked ubiquitination of Cyclin D1 protein to stabilize it. Remarkably, DZIP3 interacted with, ubiquitinated, and stabilized Cyclin D1 predominantly in the G1 phase of the cell cycle, where it is needed for cell-cycle progression. In agreement with this, a strong positive correlation of mRNA expression between DZIP3 and Cyclin D1 in different cancer types was observed. Additionally, DZIP3 regulated several cell cycle proteins by modulating the Cyclin D1-E2F axes. Taken together, this study demonstrates for the first time that DZIP3 uses a unique two-pronged mechanism in its stabilization of Cyclin D1 to drive cell-cycle and cancer progression. SIGNIFICANCE: These findings show that DZIP3 is a novel driver of cell-cycle and cancer progression via its control of Cyclin D1 mRNA and protein stability in a cell-cycle phase-dependent manner. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/2/315/F1.large.jpg.
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Affiliation(s)
| | - Rinku Sahu
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Nishant R Chauhan
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Kautilya K Jena
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Subhash Mehto
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Saroj K Das
- Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | - Ashish Jain
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo; Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Manaswini Rout
- Vascular Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Rupesh Dash
- Gene Therapy and Cancer Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Rajeeb K Swain
- Vascular Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - David Y Lee
- Department of Internal Medicine, Radiation Oncology, and University of New Mexico Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico
| | - Tor Erik Rusten
- Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo; Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Santosh Chauhan
- Cell and Cancer Biology Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
| | - Swati Chauhan
- Gene Therapy and Cancer Lab, Institute of Life Sciences, Bhubaneswar, Odisha, India.
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17
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Lapart JA, Gottardo M, Cortier E, Duteyrat JL, Augière C, Mangé A, Jerber J, Solassol J, Gopalakrishnan J, Thomas J, Durand B. Dzip1 and Fam92 form a ciliary transition zone complex with cell type specific roles in Drosophila. eLife 2019; 8:49307. [PMID: 31821146 PMCID: PMC6904220 DOI: 10.7554/elife.49307] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022] Open
Abstract
Cilia and flagella are conserved eukaryotic organelles essential for cellular signaling and motility. Cilia dysfunctions cause life-threatening ciliopathies, many of which are due to defects in the transition zone (TZ), a complex structure of the ciliary base. Therefore, understanding TZ assembly, which relies on ordered interactions of multiprotein modules, is of critical importance. Here, we show that Drosophila Dzip1 and Fam92 form a functional module which constrains the conserved core TZ protein, Cep290, to the ciliary base. We identify cell type specific roles of this functional module in two different tissues. While it is required for TZ assembly in all Drosophila ciliated cells, it also regulates basal-body growth and docking to the plasma membrane during spermatogenesis. We therefore demonstrate a novel regulatory role for Dzip1 and Fam92 in mediating membrane/basal-body interactions and show that these interactions exhibit cell type specific functions in basal-body maturation and TZ organization. Many animal cells have hair-like structures called cilia on their surface, which help them to sense and interact with their surroundings. The cilia are supported by protein filaments and must assemble correctly because faulty cilia can lead to several life-threatening diseases. Problems in an area at the base of the cilia, known as the ‘transition zone’, account for the most severe forms of these diseases in humans. The transition zone is responsible for selecting which proteins are allowed in and out of the cilia. The transition zone itself is made up of many proteins that work together to determine the cilia composition. But not all of these proteins are known, and it is unclear how those that are known affect cilia structure. One protein found in transition zones of several animals, including fruit flies and mice, is called Cby. Lapart et al. set out to understand which other proteins interact with Cby in fruit flies to better understand what this protein does in the transition zone. A series of experiments showed that Cby interacts with two proteins called Dzip1 and Fam92 to regulate the assembly of transition zones. Together these three proteins constrain a core component of the transition zone, a fourth protein called Cep290, to the base of the cilia. Fruit flies only have cilia on cells in their sensory organs and testes and, in both types of tissue, cilia could only form properly when Dzip1 and Fam92 were present. Lapart et al. also showed that, in the fruit fly testes, Dzip1 and Fam92 helped to anchor the newly forming cilia to the cell surface. This anchoring role was particularly important for the fruit flies’ sperm to grow their characteristic whip-like tails, which are a specialized type of cilia that allow sperm cells to move. Overall, the findings show how some transition zone proteins work together and that they can have different effects in different tissues. Understanding the mechanisms behind healthy cilia assembly will likely be key to tackling cilia-related diseases.
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Affiliation(s)
- Jean-André Lapart
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Marco Gottardo
- Institute of Human Genetics, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Elisabeth Cortier
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Jean-Luc Duteyrat
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Céline Augière
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Alain Mangé
- IRCM, INSERM, Université de Montpellier, ICM, Montpellier, France
| | - Julie Jerber
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Jérôme Solassol
- IRCM, INSERM, Université de Montpellier, ICM, Montpellier, France
| | - Jay Gopalakrishnan
- Institute of Human Genetics, Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Joëlle Thomas
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Bénédicte Durand
- Institut NeuroMyoGène, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
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18
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Foo JN, Xia Y. Polycystic kidney disease: new knowledge and future promises. Curr Opin Genet Dev 2019; 56:69-75. [PMID: 31476629 DOI: 10.1016/j.gde.2019.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/27/2019] [Accepted: 06/11/2019] [Indexed: 02/06/2023]
Abstract
Polycystic kidney disease (PKD) is one of the most common genetic kidney diseases, characterized by the formation of fluid-filled renal cysts, which eventually lead to end-stage renal disease. Despite several decades of investigation, explicit molecular and cellular mechanisms underpinning renal cyst formation have been unresolved until recently, severely hampering the development of effective therapeutic approaches. Currently, most PKD therapies have been developed for limiting disease complications, such as hypertension. Although Tolvaptan has been approved for treating PKD in few countries, the associated hepatic toxicity remains a major concern. In this Review, we will discuss recent advances in PKD research, covering aspects ranging from newly identified genetic/epigenetic causes, increment in mechanistic interpretation, novel therapeutic targets, to the promises offered by emerging stem cell technologies.
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Affiliation(s)
- Jia Nee Foo
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, 308232, Singapore; Human Genetics, Genome Institute of Singapore, A(⁎)STAR, 138672, Singapore.
| | - Yun Xia
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, 308232, Singapore.
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19
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Shi W, Ma Z, Zhang G, Wang C, Jiao Z. Novel functions of the primary cilium in bone disease and cancer. Cytoskeleton (Hoboken) 2019; 76:233-242. [PMID: 31108028 DOI: 10.1002/cm.21529] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/09/2022]
Abstract
The primary cilium, a sensory organelle that emanates from the cell surface of most mammalian cell types during growth arrest, has attracted the attention of many researchers over the past decade. Recently, a large number of new findings have assigned novel functions and roles to the primary cilium in signal transduction and related diseases, which has greatly augmented the importance of the cilium in human health and development. Here, we review emerging evidence supporting the primary cilium as a sensory organelle in signal transduction in microgravity, electromagnetic field sensing, chemosensation and tumorigenesis. We also present an overview of signal transduction crosstalk associated with the primary cilium in bone disease and cancer, including primary cilium-related Ca2+ signaling, parathyroid hormone signaling, cAMP signaling, BMP/Smad1/5/8 signaling and Wnt signaling. We anticipate that emerging discoveries about the function of the primary cilium will provide novel insight into the molecular mechanisms of stimulus sensation, signal transduction and pathogenesis.
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Affiliation(s)
- Wengui Shi
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Zhijian Ma
- The First Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Gengyuan Zhang
- The First Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Chen Wang
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China.,The First Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
| | - Zuoyi Jiao
- Cuiying Biomedical Research Center, Lanzhou University Second Hospital, Lanzhou, People's Republic of China.,The First Department of General Surgery, Lanzhou University Second Hospital, Lanzhou, People's Republic of China
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20
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Xu S, Liu Y, Meng Q, Wang B. Rab34 small GTPase is required for Hedgehog signaling and an early step of ciliary vesicle formation in mouse. J Cell Sci 2018; 131:jcs.213710. [PMID: 30301781 DOI: 10.1242/jcs.213710] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 09/21/2018] [Indexed: 12/30/2022] Open
Abstract
The primary cilium is a microtubule-based organelle that protrudes from the cell surface and plays essential roles in embryonic development. Ciliogenesis begins with the successive fusion of preciliary vesicles to form ciliary vesicles, which then dock onto the distal end of the mother centriole. Rab proteins have been linked to cilia formation in cultured cells, but not yet in vivo In the present study, we demonstrate that endocytic recycling protein Rab34 localizes to cilia, and that its mutation results in significant decrease of ciliogenesis in both cultured cells and mice. Rab34 is required for the successive fusion of preciliary vesicles to generate ciliary vesicles and for the migration of the mother centriole from perinuclear region to plasma membrane. We also show that Rab34 mutant mice exhibit polydactyly, and cleft-lip and -palate. These phenotypes are consistent with observations that nonciliated Rab34 mutant cells fail to respond to Hedgehog signaling and that processing of full-length Gli3 to its C-terminally truncated form is reduced in Rab34 mutant embryos. Therefore, Rab34 is required for an early step of ciliary vesicle formation and Hh signaling in vivo This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Shouying Xu
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA.,Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai 201620, China
| | - Yang Liu
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA.,Department of Veterinary Public Health, College of Veterinary Medicine, Jilin University, Jilin 130000, China
| | - Qing Meng
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai 201620, China
| | - Baolin Wang
- Department of Genetic Medicine, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA .,Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, W404, New York, NY 10065, USA
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