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Yoshioka Y, Yamashita H, Uchida T, Shinzato C, Kawamitsu M, Fourreau CJL, Castelló GM, Fiedler BK, van den Eeckhout TM, Borghi S, Reimer JD, Shoguchi E. Azooxanthellate Palythoa (Cnidaria: Anthozoa) Genomes Reveal Toxin-related Gene Clusters and Loss of Neuronal Genes in Hexacorals. Genome Biol Evol 2024; 16:evae197. [PMID: 39240721 DOI: 10.1093/gbe/evae197] [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: 05/07/2024] [Revised: 08/20/2024] [Accepted: 09/02/2024] [Indexed: 09/08/2024] Open
Abstract
Zoantharia is an order among the Hexacorallia (Anthozoa: Cnidaria), and includes at least 300 species. Previously reported genomes from scleractinian corals and actiniarian sea anemones have illuminated part of the hexacorallian diversification. However, little is known about zoantharian genomes and the early evolution of hexacorals. To explore genome evolution in this group of hexacorals, here, we report de novo genome assemblies of the zoantharians Palythoa mizigama (Pmiz) and Palythoa umbrosa (Pumb), both of which are members of the family Sphenopidae, and uniquely live in comparatively dark coral reef caves without symbiotic Symbiodiniaceae dinoflagellates. Draft genomes generated from ultra-low input PacBio sequencing totaled 373 and 319 Mbp for Pmiz and Pumb, respectively. Protein-coding genes were predicted in each genome, totaling 30,394 in Pmiz and 24,800 in Pumb, with each set having ∼93% BUSCO completeness. Comparative genomic analyses identified 3,036 conserved gene families, which were found in all analyzed hexacoral genomes. Some of the genes related to toxins, chitin degradation, and prostaglandin biosynthesis were expanded in these two Palythoa genomes and many of which aligned tandemly. Extensive gene family loss was not detected in the Palythoa lineage and five of ten putatively lost gene families likely had neuronal function, suggesting biased gene loss in Palythoa. In conclusion, our comparative analyses demonstrate evolutionary conservation of gene families in the Palythoa lineage from the common ancestor of hexacorals. Restricted loss of gene families may imply that lost neuronal functions were effective for environmental adaptation in these two Palythoa species.
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Affiliation(s)
- Yuki Yoshioka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa 907-0451, Japan
| | - Taiga Uchida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa 277-8564, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa 277-8564, Japan
| | - Mayumi Kawamitsu
- Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Guillermo Mironenko Castelló
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Britta Katharina Fiedler
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Timotheus Maximilian van den Eeckhout
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Stefano Borghi
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum Network, Townsville, QLD, Australia
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
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2
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Megaw R, Moye A, Zhang Z, Newton F, McPhie F, Murphy LC, McKie L, He F, Jungnickel MK, von Kriegsheim A, Tennant PA, Brotherton C, Gurniak C, Gross AK, Machesky LM, Wensel TG, Mill P. Ciliary tip actin dynamics regulate photoreceptor outer segment integrity. Nat Commun 2024; 15:4316. [PMID: 38773095 PMCID: PMC11109262 DOI: 10.1038/s41467-024-48639-w] [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: 06/05/2023] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
As signalling organelles, cilia regulate their G protein-coupled receptor content by ectocytosis, a process requiring localised actin dynamics to alter membrane shape. Photoreceptor outer segments comprise an expanse of folded membranes (discs) at the tip of highly-specialised connecting cilia, into which photosensitive GPCRs are concentrated. Discs are shed and remade daily. Defects in this process, due to mutations, cause retinitis pigmentosa (RP). Whilst fundamental for vision, the mechanism of photoreceptor disc generation is poorly understood. Here, we show membrane deformation required for disc genesis is driven by dynamic actin changes in a process akin to ectocytosis. We show RPGR, a leading RP gene, regulates actin-binding protein activity central to this process. Actin dynamics, required for disc formation, are perturbed in Rpgr mouse models, leading to aborted membrane shedding as ectosome-like vesicles, photoreceptor death and visual loss. Actin manipulation partially rescues this, suggesting the pathway could be targeted therapeutically. These findings help define how actin-mediated dynamics control outer segment turnover.
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Affiliation(s)
- Roly Megaw
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK.
- Princess Alexandra Eye Pavilion, NHS Lothian, Edinburgh, EH3 9HA, UK.
| | - Abigail Moye
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhixian Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Fay Newton
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Fraser McPhie
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Laura C Murphy
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Lisa McKie
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Feng He
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Melissa K Jungnickel
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Alex von Kriegsheim
- Edinburgh Cancer Research United Kingdom Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Peter A Tennant
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Chloe Brotherton
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Christine Gurniak
- Institute fur Genetik, Universitat Bonn, Karlrobert-Kreiten-Strasse, 53115, Bonn, Germany
| | - Alecia K Gross
- University of Alabama at Birmingham, 2nd Ave South, Birmingham, AL, 35294, USA
| | - Laura M Machesky
- CRUK Scotland Institute, Switchback Road, Bearsden, Glasgow, G61 1BD, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB1 7UY, UK
| | - Theodore G Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pleasantine Mill
- MRC Human Genetics Unit, MRC Institute of Genetics & Cancer, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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3
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Zhang Z, Moye AR, He F, Chen M, Agosto MA, Wensel TG. Centriole and transition zone structures in photoreceptor cilia revealed by cryo-electron tomography. Life Sci Alliance 2024; 7:e202302409. [PMID: 38182160 PMCID: PMC10770417 DOI: 10.26508/lsa.202302409] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Primary cilia mediate sensory signaling in multiple organisms and cell types but have structures adapted for specific roles. Structural defects in them lead to devastating diseases known as ciliopathies in humans. Key to their functions are structures at their base: the basal body, the transition zone, the "Y-shaped links," and the "ciliary necklace." We have used cryo-electron tomography with subtomogram averaging and conventional transmission electron microscopy to elucidate the structures associated with the basal region of the "connecting cilia" of rod outer segments in mouse retina. The longitudinal variations in microtubule (MT) structures and the lumenal scaffold complexes connecting them have been determined, as well as membrane-associated transition zone structures: Y-shaped links connecting MT to the membrane, and ciliary beads connected to them that protrude from the cell surface and form a necklace-like structure. These results represent a clearer structural scaffold onto which molecules identified by genetics, proteomics, and superresolution fluorescence can be placed in our emerging model of photoreceptor sensory cilia.
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Affiliation(s)
- Zhixian Zhang
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Abigail R Moye
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Department of Ophthalmic Genetics, Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Feng He
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Muyuan Chen
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Melina A Agosto
- Department of Physiology and Biophysics and Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Canada
| | - Theodore G Wensel
- https://ror.org/02pttbw34 Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
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Yue F, Ku AT, Stevens PD, Michalski MN, Jiang W, Tu J, Shi Z, Dou Y, Wang Y, Feng XH, Hostetter G, Wu X, Huang S, Shroyer NF, Zhang B, Williams BO, Liu Q, Lin X, Li Y. Loss of ZNRF3/RNF43 Unleashes EGFR in Cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.10.574969. [PMID: 38260423 PMCID: PMC10802575 DOI: 10.1101/2024.01.10.574969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
ZNRF3 and RNF43 are closely related transmembrane E3 ubiquitin ligases with significant roles in development and cancer. Conventionally, their biological functions have been associated with regulating WNT signaling receptor ubiquitination and degradation. However, our proteogenomic studies have revealed EGFR as the most negatively correlated protein with ZNRF3/RNF43 mRNA levels in multiple human cancers. Through biochemical investigations, we demonstrate that ZNRF3/RNF43 interact with EGFR via their extracellular domains, leading to EGFR ubiquitination and subsequent degradation facilitated by the E3 ligase RING domain. Overexpression of ZNRF3 reduces EGFR levels and suppresses cancer cell growth in vitro and in vivo, whereas knockout of ZNRF3/RNF43 stimulates cell growth and tumorigenesis through upregulated EGFR signaling. Together, these data highlight ZNRF3 and RNF43 as novel E3 ubiquitin ligases of EGFR and establish the inactivation of ZNRF3/RNF43 as a driver of increased EGFR signaling, ultimately promoting cancer progression. This discovery establishes a connection between two fundamental signaling pathways, EGFR and WNT, at the level of cytoplasmic membrane receptor, uncovering a novel mechanism underlying the frequent co-activation of EGFR and WNT signaling in development and cancer.
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Affiliation(s)
- Fei Yue
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amy T. Ku
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Payton D. Stevens
- Van Andel Institute, Department of Cell Biology, Grand Rapids, Michigan, 49503, USA
| | - Megan N. Michalski
- Van Andel Institute, Department of Cell Biology, Grand Rapids, Michigan, 49503, USA
| | - Weiyu Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jianghua Tu
- Texas Therapeutics Institute and Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Zhongcheng Shi
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xin-Hua Feng
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Galen Hostetter
- Van Andel Institute, Core Technologies and Services, Grand Rapids, Michigan 49503, USA
| | - Xiangwei Wu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Shixia Huang
- Advanced Technology Cores, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Education, Innovation & Technology, Baylor College of Medicine, Houston, Texas 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Noah F. Shroyer
- Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bart O. Williams
- Van Andel Institute, Department of Cell Biology, Grand Rapids, Michigan, 49503, USA
- Van Andel Institute, Core Technologies and Services, Grand Rapids, Michigan 49503, USA
| | - Qingyun Liu
- Texas Therapeutics Institute and Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Xia Lin
- The First Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
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5
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Li X, Wang Y, Wang J, Wang P, Zhang Q. Double Hyperautofluorescence Rings as a Sign of CFAP410-related Retinopathy. Invest Ophthalmol Vis Sci 2023; 64:44. [PMID: 38153748 PMCID: PMC10756245 DOI: 10.1167/iovs.64.15.44] [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: 07/29/2023] [Accepted: 12/04/2023] [Indexed: 12/29/2023] Open
Abstract
Purpose Variants in CFAP410 have been reported to cause retinal dystrophy with or without systemic symptoms. This study was designed to characterize the fundus changes of patients with biallelic variants in CFAP410. Methods Variants in CFAP410 were identified through whole exome sequencing and targeted exome sequencing of 10,530 probands. Biallelic variants in CFAP410 were evaluated by comprehensive in silico analysis and confirmed by Sanger sequencing and segregation analysis. Ocular phenotypes including fundus photographs, scanning laser ophthalmoscopy, autofluorescence images, ERG, and optical coherence tomography were characterized. Results Nine patients from eight families were homozygotes or compound heterozygotes for a total of four variants in CFAP410, including c.144-6_159del (novel), c.340_351dup, c.347C>T, and c.545+1G>A. Three patients were diagnosed with cone-rod dystrophy, and the remaining six patients with RP. Among eight patients performed with ultra-wide scanning laser ophthalmoscopy, double hyperautofluorescence rings inside and outside of the macular vascular arcades were observed in six patients, and the remaining two older patients demonstrated single hyperautofluorescence ring surrounded by pigmentation. CFAP410-associated retinopathy in early stage was generally tapetoretinal degeneration without noticeable bone spicule pigmentation, with more severe degeneration in the inferior nasal retina. ERG recordings delineated a severely reduced cone response and mildly to severely reduced rod response. Posterior staphyloma was seen in seven patients who underwent optical coherence tomography examinations. Conclusions The present study demonstrates the fundus characteristics of patients with biallelic variants in CFAP410 and expands the genotype-phenotype spectrum of CFAP410-related retinal degeneration, in which posterior staphyloma together with double hyperautofluorescence rings might be common peculiar signs.
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Affiliation(s)
- Xueqing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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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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7
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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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8
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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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9
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Moye AR, Robichaux MA, Wensel T. Expansion Microscopy of Mouse Photoreceptor Cilia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:395-402. [PMID: 37440063 PMCID: PMC10697808 DOI: 10.1007/978-3-031-27681-1_58] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
The small size of ciliary structures that underlies photoreceptor function and inherited ciliopathies requires imaging techniques adapted to visualizing them at the highest possible resolution. In addition to powerful super-resolution imaging modalities, emerging approaches to sample preparation, including expansion microscopy (ExM), can provide a robust route to imaging specific molecules at the nanoscale level in the retina. We describe a protocol for applying ExM to whole retinas in order to achieve nanoscale fluorescence imaging of ciliary markers, including tubulin, CEP290, centrin, and CEP164. The results are consistent with those from other super-resolution fluorescence techniques and reveal new insights into their arrangements with respect to the subcompartments of photoreceptor cilia. This technique is complimentary to other imaging modalities used in retinal imaging, and can be carried out in virtually any laboratory, without the need for expensive specialized equipment.
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Affiliation(s)
- Abigail R Moye
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Genetics and Ophthalmology, Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Michael A Robichaux
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, WV, USA
| | - Theodore Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
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10
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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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11
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Reed M, Takemaru KI, Ying G, Frederick JM, Baehr W. Deletion of CEP164 in mouse photoreceptors post-ciliogenesis interrupts ciliary intraflagellar transport (IFT). PLoS Genet 2022; 18:e1010154. [PMID: 36074756 PMCID: PMC9488791 DOI: 10.1371/journal.pgen.1010154] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 09/20/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Centrosomal protein of 164 kDa (CEP164) is located at distal appendages of primary cilia and is necessary for basal body (BB) docking to the apical membrane. To investigate the function of photoreceptor CEP164 before and after BB docking, we deleted CEP164 during retina embryonic development (Six3Cre), in postnatal rod photoreceptors (iCre75) and in mature retina using tamoxifen induction (Prom1-ETCre). BBs dock to the cell cortex during postnatal day 6 (P6) to extend a connecting cilium (CC) and an axoneme. P6 retina-specific knockouts (retCep164-/-) are unable to dock BBs, thereby preventing formation of CC or outer segments (OSs). In rod-specific knockouts (rodCep164-/-), Cre expression starts after P7 and CC/OS form. P16 rodCep164-/- rods have nearly normal OS lengths, and maintain OS attachment through P21 despite loss of CEP164. Intraflagellar transport components (IFT88, IFT57 and IFT140) were reduced at P16 rodCep164-/- BBs and CC tips and nearly absent at P21, indicating impaired intraflagellar transport. Nascent OS discs, labeled with a fluorescent dye on P14 and P18 and harvested on P19, showed continued rodCep164-/- disc morphogenesis but absence of P14 discs mid-distally, indicating OS instability. Tamoxifen induction with PROM1ETCre;Cep164F/F (tamCep164-/-) adult mice affected maintenance of both rod and cone OSs. The results suggest that CEP164 is key towards recruitment and stabilization of IFT-B particles at the BB/CC. IFT impairment may be the main driver of ciliary malfunction observed with hypomorphic CEP164 mutations.
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Affiliation(s)
- Michelle Reed
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, Utah, United States of America
| | - Ken-Ichi Takemaru
- Stony Brook University, Department of Pharmacological Sciences, Stony Brook, New York, United States of America
| | - Guoxin Ying
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, Utah, United States of America
| | - Jeanne M. Frederick
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, Utah, United States of America
| | - Wolfgang Baehr
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, Utah, United States of America
- Department of Neurobiology & Anatomy, University of Utah, Salt Lake City, Utah, United States of America
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
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12
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Faber S, Roepman R. A defective structural zipper in photoreceptors causes inherited blindness. PLoS Biol 2022; 20:e3001672. [PMID: 35714125 PMCID: PMC9205488 DOI: 10.1371/journal.pbio.3001672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
This Primer explores a PLOS Biology study which uses ultrastructure expansion microscopy to study the inner scaffold of the photoreceptor connecting cilium, the location of multiple proteins implicated in inherited forms of progressive sight loss such as retinitis pigmentosa and Leber congenital amaurosis.
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Affiliation(s)
- Siebren Faber
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ronald Roepman
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- * E-mail:
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13
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Mercey O, Kostic C, Bertiaux E, Giroud A, Sadian Y, Gaboriau DCA, Morrison CG, Chang N, Arsenijevic Y, Guichard P, Hamel V. The connecting cilium inner scaffold provides a structural foundation that protects against retinal degeneration. PLoS Biol 2022; 20:e3001649. [PMID: 35709082 PMCID: PMC9202906 DOI: 10.1371/journal.pbio.3001649] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 04/27/2022] [Indexed: 12/17/2022] Open
Abstract
Inherited retinal degeneration due to loss of photoreceptor cells is a leading cause of human blindness. These cells possess a photosensitive outer segment linked to the cell body through the connecting cilium (CC). While structural defects of the CC have been associated with retinal degeneration, its nanoscale molecular composition, assembly, and function are barely known. Here, using expansion microscopy and electron microscopy, we reveal the molecular architecture of the CC and demonstrate that microtubules are linked together by a CC inner scaffold containing POC5, CENTRIN, and FAM161A. Dissecting CC inner scaffold assembly during photoreceptor development in mouse revealed that it acts as a structural zipper, progressively bridging microtubule doublets and straightening the CC. Furthermore, we show that Fam161a disruption in mouse leads to specific CC inner scaffold loss and triggers microtubule doublet spreading, prior to outer segment collapse and photoreceptor degeneration, suggesting a molecular mechanism for a subtype of retinitis pigmentosa. Inherited retinal degeneration due to loss of photoreceptor cells is a leading cause of human blindness. Ultrastructure expansion microscopy on mouse retina reveals the presence of a novel structure inside the photoreceptor connecting cilium, the inner scaffold, that protects the outer segment against degeneration.
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Affiliation(s)
- Olivier Mercey
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Corinne Kostic
- Group for Retinal Disorder Research, Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Eloïse Bertiaux
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Alexia Giroud
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Yashar Sadian
- CryoGenic Facility, University of Geneva, Geneva, Switzerland
| | - David C. A. Gaboriau
- Centre for Chromosome Biology, National University of Ireland Galway, Galway, Ireland
| | - Ciaran G. Morrison
- Centre for Chromosome Biology, National University of Ireland Galway, Galway, Ireland
| | - Ning Chang
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Yvan Arsenijevic
- Unit of Retinal Degeneration and Regeneration, Department of Ophthalmology, University Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Paul Guichard
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (PG); (VH)
| | - Virginie Hamel
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- * E-mail: (PG); (VH)
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14
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Lu J, Xiong K, Qian X, Choi J, Shim YK, Burnett J, Mardon G, Chen R. Spata7 is required for maintenance of the retinal connecting cilium. Sci Rep 2022; 12:5575. [PMID: 35368022 PMCID: PMC8976851 DOI: 10.1038/s41598-022-09530-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
SPATA7, an early onset LCA3 retinal disease gene, encodes a putative scaffold protein that is essential for the proper assembly of the connecting cilium (CC) complex in photoreceptors. Previous studies have shown that SPATA7 interacts with other photoreceptor-specific ciliary proteins, such as RPGR and RPGRIP1, and maintains the integrity of CC integrity. However, although it is known that Spata7 is required for early formation of the CC, it is unclear if Spata7 is also required for the maintenance of the CC. To investigate Spata7 function in the retina at the adult stage, loss of function was induced in the adult retina upon tamoxifen induction of an inducible Spata7 knockout allele (Spata7flox/-; UbcCreERT2/+). The phenotype of mutant retina was characterized by a combination of histology, immunobiochemistry, and electroretinography (ERG). Our results demonstrated that Spata7 is also essential for maintaining the integrity of the mature retinal CC. Loss of Spata7 in adults caused phenotypes similar to those seen in germline mutant mice, including photoreceptor cell degeneration and defective ERG responses. Close examination of the CC revealed significantly shortened NPHP1 length as a result of Spata7 deletion. Furthermore, mislocalization of rhodopsin, leading to ER stress-mediated apoptosis, was observed in the retinal layers. Our results indicate that Spata7 is required not only for the establishment but also for the maintenance of the CC of photoreceptors.
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Affiliation(s)
- Jiaxiong Lu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Kaitlyn Xiong
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xinye Qian
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jongsu Choi
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yoon-Kyung Shim
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Jacob Burnett
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Graeme Mardon
- Department of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
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15
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Potter VL, Moye AR, Robichaux MA, Wensel TG. Super-resolution microscopy reveals photoreceptor-specific subciliary location and function of ciliopathy-associated protein CEP290. JCI Insight 2021; 6:e145256. [PMID: 34520396 PMCID: PMC8564900 DOI: 10.1172/jci.insight.145256] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 09/08/2021] [Indexed: 01/19/2023] Open
Abstract
Mutations in the cilium-associated protein CEP290 cause retinal degeneration as part of multiorgan ciliopathies or as retina-specific diseases. The precise location and the functional roles of CEP290 within cilia and, specifically, the connecting cilia (CC) of photoreceptors, remain unclear. We used super-resolution fluorescence microscopy and electron microscopy to localize CEP290 in the CC and in the primary cilia of cultured cells with subdiffraction resolution and to determine effects of CEP290 deficiency in 3 mutant models. Radially, CEP290 localizes in close proximity to the microtubule doublets in the region between the doublets and the ciliary membrane. Longitudinally, it is distributed throughout the length of the CC whereas it is confined to the very base of primary cilia in human retinal pigment epithelium-1 cells. We found Y-shaped links, ciliary substructures between microtubules and membrane, throughout the length of the CC. Severe CEP290 deficiencies in mouse models did not prevent assembly of cilia or cause obvious mislocalization of ciliary components in early stages of degeneration. There were fewer cilia and no normal outer segments in the mutants, but the Y-shaped links were clearly present. These results point to photoreceptor-specific functions of CEP290 essential for CC maturation and stability following the earliest stages of ciliogenesis.
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Affiliation(s)
- Valencia L Potter
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology.,Program in Developmental Biology, Graduate School of Biomedical Sciences, and.,Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, USA
| | - Abigail R Moye
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology
| | - Michael A Robichaux
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology.,Departments of Ophthalmology and Biochemistry, West Virginia University School of Medicine, Morgantown, West Virginia, USA
| | - Theodore G Wensel
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology
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16
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Wensel TG, Potter VL, Moye A, Zhang Z, Robichaux MA. Structure and dynamics of photoreceptor sensory cilia. Pflugers Arch 2021; 473:1517-1537. [PMID: 34050409 PMCID: PMC11216635 DOI: 10.1007/s00424-021-02564-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023]
Abstract
The rod and cone photoreceptor cells of the vertebrate retina have highly specialized structures that enable them to carry out their function of light detection over a broad range of illumination intensities with optimized spatial and temporal resolution. Most prominent are their unusually large sensory cilia, consisting of outer segments packed with photosensitive disc membranes, a connecting cilium with many features reminiscent of the primary cilium transition zone, and a pair of centrioles forming a basal body which serves as the platform upon which the ciliary axoneme is assembled. These structures form a highway through which an enormous flux of material moves on a daily basis to sustain the continual turnover of outer segment discs and the energetic demands of phototransduction. After decades of study, the details of the fine structure and distribution of molecular components of these structures are still incompletely understood, but recent advances in cellular imaging techniques and animal models of inherited ciliary defects are yielding important new insights. This knowledge informs our understanding both of the mechanisms of trafficking and assembly and of the pathophysiological mechanisms of human blinding ciliopathies.
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Affiliation(s)
- Theodore G Wensel
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology and Developmental Biology Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Valencia L Potter
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology and Developmental Biology Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program (MSTP), Baylor College of Medicine, Houston, TX, 77030, USA
| | - Abigail Moye
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhixian Zhang
- Vera and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michael A Robichaux
- Departments of Ophthalmology and Biochemistry, West Virginia University, Morgantown, WV, USA
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17
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Yue F, Jiang W, Ku AT, Young AIJ, Zhang W, Souto EP, Gao Y, Yu Z, Wang Y, Creighton CJ, Nagi C, Wang T, Hilsenbeck SG, Feng XH, Huang S, Coarfa C, Zhang XHF, Liu Q, Lin X, Li Y. A Wnt-Independent LGR4-EGFR Signaling Axis in Cancer Metastasis. Cancer Res 2021; 81:4441-4454. [PMID: 34099494 DOI: 10.1158/0008-5472.can-21-1112] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 02/02/2023]
Abstract
Leucine-rich repeat-containing G protein-coupled receptors 4, 5, and 6 (LGR4/5/6) play critical roles in development and cancer. The widely accepted mechanism is that these proteins, together with their R-spondin ligands, stabilize Wnt receptors, thus potentiating Wnt signaling. Here we show that LGR4 enhanced breast cancer cell metastasis even when Wnt signaling was deactivated pharmacologically or genetically. Furthermore, LGR4 mutants that cannot potentiate Wnt signaling nevertheless promoted breast cancer cell migration and invasion in vitro and breast cancer metastasis in vivo. Multiomic screening identified EGFR as a crucial mediator of LGR4 activity in cancer progression. Mechanistically, LGR4 interacted with EGFR and blocked EGFR ubiquitination and degradation, resulting in persistent EGFR activation. Together, these data uncover a Wnt-independent LGR4-EGFR signaling axis with broad implications for cancer progression and targeted therapy. SIGNIFICANCE: This work demonstrates a Wnt-independent mechanism by which LGR4 promotes cancer metastasis.See related commentary by Stevens and Williams, p. 4397.
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Affiliation(s)
- Fei Yue
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Weiyu Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Amy T Ku
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Adelaide I J Young
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Weijie Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Eric P Souto
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Yankun Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zihan Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Chad J Creighton
- Department of Medicine, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Chandandeep Nagi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Tao Wang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Susan G Hilsenbeck
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Xin-Hua Feng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas.,Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shixia Huang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Cristian Coarfa
- Department of Medicine, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,McNair Medical Institute, Baylor College of Medicine, Houston, Texas
| | - Qingyun Liu
- Texas Therapeutics Institute and Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas
| | - Xia Lin
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
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18
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Lee WS, Lavery L, Rousseaux MWC, Rutledge EB, Jang Y, Wan YW, Wu SR, Kim W, Al-Ramahi I, Rath S, Adamski CJ, Bondar VV, Tewari A, Soleimani S, Mota S, Yalamanchili HK, Orr HT, Liu Z, Botas J, Zoghbi HY. Dual targeting of brain region-specific kinases potentiates neurological rescue in Spinocerebellar ataxia type 1. EMBO J 2021; 40:e106106. [PMID: 33709453 DOI: 10.15252/embj.2020106106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/01/2021] [Accepted: 02/10/2021] [Indexed: 12/26/2022] Open
Abstract
A critical question in neurodegeneration is why the accumulation of disease-driving proteins causes selective neuronal loss despite their brain-wide expression. In Spinocerebellar ataxia type 1 (SCA1), accumulation of polyglutamine-expanded Ataxin-1 (ATXN1) causes selective degeneration of cerebellar and brainstem neurons. Previous studies revealed that inhibiting Msk1 reduces phosphorylation of ATXN1 at S776 as well as its levels leading to improved cerebellar function. However, there are no regulators that modulate ATXN1 in the brainstem-the brain region whose pathology is most closely linked to premature death. To identify new regulators of ATXN1, we performed genetic screens and identified a transcription factor-kinase axis (ZBTB7B-RSK3) that regulates ATXN1 levels. Unlike MSK1, RSK3 is highly expressed in the human and mouse brainstems where it regulates Atxn1 by phosphorylating S776. Reducing Rsk3 rescues brainstem-associated pathologies and deficits, and lowering Rsk3 and Msk1 together improves cerebellar and brainstem function in an SCA1 mouse model. Our results demonstrate that selective vulnerability of brain regions in SCA1 is governed by region-specific regulators of ATXN1, and targeting multiple regulators could rescue multiple degenerating brain areas.
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Affiliation(s)
- Won-Seok Lee
- Integrative Molecular and Biomedical Science Program, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Laura Lavery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Maxime W C Rousseaux
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Eric B Rutledge
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Youjin Jang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Ying-Wooi Wan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Sih-Rong Wu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Wonho Kim
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
| | - Ismael Al-Ramahi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Smruti Rath
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Carolyn J Adamski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
| | - Vitaliy V Bondar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Ambika Tewari
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Shirin Soleimani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Samantha Mota
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Hari K Yalamanchili
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Harry T Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Juan Botas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA.,Howard Hughes Medical Institute, Houston, TX, USA
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19
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Barnes CL, Malhotra H, Calvert PD. Compartmentalization of Photoreceptor Sensory Cilia. Front Cell Dev Biol 2021; 9:636737. [PMID: 33614665 PMCID: PMC7889997 DOI: 10.3389/fcell.2021.636737] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Functional compartmentalization of cells is a universal strategy for segregating processes that require specific components, undergo regulation by modulating concentrations of those components, or that would be detrimental to other processes. Primary cilia are hair-like organelles that project from the apical plasma membranes of epithelial cells where they serve as exclusive compartments for sensing physical and chemical signals in the environment. As such, molecules involved in signal transduction are enriched within cilia and regulating their ciliary concentrations allows adaptation to the environmental stimuli. The highly efficient organization of primary cilia has been co-opted by major sensory neurons, olfactory cells and the photoreceptor neurons that underlie vision. The mechanisms underlying compartmentalization of cilia are an area of intense current research. Recent findings have revealed similarities and differences in molecular mechanisms of ciliary protein enrichment and its regulation among primary cilia and sensory cilia. Here we discuss the physiological demands on photoreceptors that have driven their evolution into neurons that rely on a highly specialized cilium for signaling changes in light intensity. We explore what is known and what is not known about how that specialization appears to have driven unique mechanisms for photoreceptor protein and membrane compartmentalization.
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Affiliation(s)
| | | | - Peter D. Calvert
- Department of Ophthalmology and Visual Sciences, Center for Vision Research, SUNY Upstate Medical University, Syracuse, NY, United States
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20
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Hsu Y, Seo S, Sheffield VC. Photoreceptor cilia, in contrast to primary cilia, grant entry to a partially assembled BBSome. Hum Mol Genet 2021; 30:87-102. [PMID: 33517424 DOI: 10.1093/hmg/ddaa284] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 11/16/2020] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
The BBSome is a protein complex consisting of BBS1, BBS2, BBS4, BBS5, BBS7, BBS8, BBS9 and BBS18 that associates with intraflagellar transport complexes and specializes in ciliary trafficking. In primary cilia, ciliary entry requires the fully assembled BBSome as well as the small GTPase, ARL6 (BBS3). Retinal photoreceptors possess specialized cilia. In light of key structural and functional differences between primary and specialized cilia, we examined the principles of BBSome recruitment to photoreceptor cilia. We performed sucrose gradient fractionation using retinal lysates of Bbs2-/-, Bbs7-/-, Bbs8-/- and Bbs3-/- mice to determine the status of BBSome assembly, then determined localization of BBSome components using immunohistochemistry. Surprisingly, we found that a subcomplex of the BBSome containing at least BBS1, BBS5, BBS8 and BBS9 is recruited to cilia in the absence of BBS2 or BBS7. In contrast, a BBSome subcomplex consisting of BBS1, BBS2, BBS5, BBS7 and BBS9 is found in Bbs8-/- retinas and is denied ciliary entry in photoreceptor cells. In addition, the BBSome remains fully assembled in Bbs3-/- retinas and can be recruited to photoreceptor cilia in the absence of BBS3. We compared phenotypic severity of their retinal degeneration phenotypes. These findings demonstrate that unlike primary cilia, photoreceptor cilia admit a partially assembled BBSome meeting specific requirements. In addition, the recruitment of the BBSome to photoreceptor cilia does not require BBS3. These findings indicate that the ciliary entry of the BBSome is subjected to cell-specific regulation, particularly in cells with highly adapted forms of cilia such as photoreceptors.
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Affiliation(s)
- Ying Hsu
- Department of Pediatrics, Division of Medical Genetics and Genomics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Seongjin Seo
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Val C Sheffield
- Department of Pediatrics, Division of Medical Genetics and Genomics, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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21
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Abstract
BACKGROUND The spermatogenesis-associated protein-7 (SPATA7) gene encodes a ciliary protein that is expressed in the photoreceptors and in spermatocytes. Mutations in the SPATA7 gene are associated with congenital and early-onset forms of retinal dystrophy. METHODS Papers and review articles on SPATA7 were retrieved from the PubMed database using the search terms "SPATA7" and "spermatogenesis-associated protein 7". Those that were relevant to retinal disease or to the function of the SPATA7 gene were selected for review. RESULTS The SPATA7 locus was mapped as LCA3 to chromosome 14, and the gene identified by screening of all genes in the refined genomic interval. Mutations in SPATA7 are associated with Leber congenital amaurosis (LCA) and early-onset retinitis pigmentosa. There are no clear-cut correlations between the genotypes and phenotypes in SPATA7-associated disease, and phenotypic heterogeneity occurs among patients with the same mutation. The SPATA7 protein is expressed in the photoreceptor connecting cilia. Murine models of Spata7 knockout have been useful in understanding the role of this gene in the retina at the cellular and molecular levels. CONCLUSION Most of the mutations in the SPATA7 are nonsense or frameshifts and are predicted to lead to loss of function. Clinical heterogeneity is often seen in patients with SPATA7 mutations. Animal models of SPATA7 knockout indicate that the protein has a key role in organizing the ciliary protein complexes.
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Affiliation(s)
- Chitra Kannabiran
- Kallam Anji Reddy Molecular Genetics Laboratory, Prof Brien Holden Eye Research Centre, L.V. Prasad Eye Institute , Hyderabad, India
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22
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Chen HY, Kelley RA, Li T, Swaroop A. Primary cilia biogenesis and associated retinal ciliopathies. Semin Cell Dev Biol 2020; 110:70-88. [PMID: 32747192 PMCID: PMC7855621 DOI: 10.1016/j.semcdb.2020.07.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/14/2020] [Accepted: 07/18/2020] [Indexed: 12/19/2022]
Abstract
The primary cilium is a ubiquitous microtubule-based organelle that senses external environment and modulates diverse signaling pathways in different cell types and tissues. The cilium originates from the mother centriole through a complex set of cellular events requiring hundreds of distinct components. Aberrant ciliogenesis or ciliary transport leads to a broad spectrum of clinical entities with overlapping yet highly variable phenotypes, collectively called ciliopathies, which include sensory defects and syndromic disorders with multi-organ pathologies. For efficient light detection, photoreceptors in the retina elaborate a modified cilium known as the outer segment, which is packed with membranous discs enriched for components of the phototransduction machinery. Retinopathy phenotype involves dysfunction and/or degeneration of the light sensing photoreceptors and is highly penetrant in ciliopathies. This review will discuss primary cilia biogenesis and ciliopathies, with a focus on the retina, and the role of CP110-CEP290-CC2D2A network. We will also explore how recent technologies can advance our understanding of cilia biology and discuss new paradigms for developing potential therapies of retinal ciliopathies.
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Affiliation(s)
- Holly Y Chen
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA.
| | - Ryan A Kelley
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Tiansen Li
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, MSC0610, 6 Center Drive, Bethesda, MD 20892, USA.
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23
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Establishing and regulating the composition of cilia for signal transduction. Nat Rev Mol Cell Biol 2020; 20:389-405. [PMID: 30948801 DOI: 10.1038/s41580-019-0116-4] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The primary cilium is a hair-like surface-exposed organelle of the eukaryotic cell that decodes a variety of signals - such as odorants, light and Hedgehog morphogens - by altering the local concentrations and activities of signalling proteins. Signalling within the cilium is conveyed through a diverse array of second messengers, including conventional signalling molecules (such as cAMP) and some unusual intermediates (such as sterols). Diffusion barriers at the ciliary base establish the unique composition of this signalling compartment, and cilia adapt their proteome to signalling demands through regulated protein trafficking. Much progress has been made on the molecular understanding of regulated ciliary trafficking, which encompasses not only exchanges between the cilium and the rest of the cell but also the shedding of signalling factors into extracellular vesicles.
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24
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Frederick JM, Hanke-Gogokhia C, Ying G, Baehr W. Diffuse or hitch a ride: how photoreceptor lipidated proteins get from here to there. Biol Chem 2019; 401:573-584. [DOI: 10.1515/hsz-2019-0375] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/02/2019] [Indexed: 12/23/2022]
Abstract
Abstract
Photoreceptors are polarized neurons, with specific subcellular compartmentalization and unique requirements for protein expression and trafficking. Each photoreceptor contains an outer segment (OS) where vision begins, an inner segment (IS) where protein synthesis occurs and a synaptic terminal for signal transmission to second-order neurons. The OS is a large, modified primary cilium attached to the IS by a slender connecting cilium (CC), the equivalent of the transition zone (TZ). Daily renewal of ~10% of the OS requires massive protein biosynthesis in the IS with reliable transport and targeting pathways. Transport of lipidated (‘sticky’) proteins depends on solubilization factors, phosphodiesterase δ (PDEδ) and uncoordinated protein-119 (UNC119), and the cargo dispensation factor (CDF), Arf-like protein 3-guanosine triphosphate (ARL3-GTP). As PDE6 and transducin still reside prominently in the OS of PDEδ and UNC119 germline knockout mice, respectively, we propose the existence of an alternate trafficking pathway, whereby lipidated proteins migrate in rhodopsin-containing vesicles of the secretory pathway.
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Affiliation(s)
- Jeanne M. Frederick
- Department of Ophthalmology and Visual Sciences , University of Utah Health Science Center , 65 Mario Capecchi Drive , Salt Lake City , UT 84132 , USA
| | - Christin Hanke-Gogokhia
- Department of Ophthalmology and Visual Sciences , University of Utah Health Science Center , 65 Mario Capecchi Drive , Salt Lake City , UT 84132 , USA
| | - Guoxin Ying
- Department of Ophthalmology and Visual Sciences , University of Utah Health Science Center , 65 Mario Capecchi Drive , Salt Lake City , UT 84132 , USA
| | - Wolfgang Baehr
- Department of Ophthalmology and Visual Sciences , University of Utah Health Science Center , 65 Mario Capecchi Drive , Salt Lake City , UT 84132 , USA
- Department of Neurobiology and Anatomy , University of Utah , Salt Lake City , UT 84112 , USA
- Department of Biology , University of Utah , Salt Lake City , UT 84132 , USA
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25
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Defining the layers of a sensory cilium with STORM and cryoelectron nanoscopy. Proc Natl Acad Sci U S A 2019; 116:23562-23572. [PMID: 31690665 DOI: 10.1073/pnas.1902003116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Primary cilia carry out numerous signaling and sensory functions, and defects in them, "ciliopathies," cause a range of symptoms, including blindness. Understanding of their nanometer-scale ciliary substructures and their disruptions in ciliopathies has been hindered by limitations of conventional microscopic techniques. We have combined cryoelectron tomography, enhanced by subtomogram averaging, with superresolution stochastic optical reconstruction microscopy (STORM) to define subdomains within the light-sensing rod sensory cilium of mouse retinas and reveal previously unknown substructures formed by resident proteins. Domains are demarcated by structural features such as the axoneme and its connections to the ciliary membrane, and are correlated with molecular markers of subcompartments, including the lumen and walls of the axoneme, the membrane glycocalyx, and the intervening cytoplasm. Within this framework, we report spatial distributions of key proteins in wild-type (WT) mice and the effects on them of genetic deficiencies in 3 models of Bardet-Biedl syndrome.
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26
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Hashimoto Y, Greco TM, Cristea IM. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:143-154. [PMID: 31347046 DOI: 10.1007/978-3-030-15950-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding multicellular organism development from a molecular perspective is no small feat, yet this level of comprehension affords clinician-scientists the ability to identify root causes and mechanisms of congenital diseases. Inarguably, the maturation of molecular biology tools has significantly contributed to the identification of genetic loci that underlie normal and aberrant developmental programs. In combination with cell biology approaches, these tools have begun to elucidate the spatiotemporal expression and function of developmentally-regulated proteins. The emergence of quantitative mass spectrometry (MS) for biological applications has accelerated the pace at which these proteins can be functionally characterized, driving the construction of an increasingly detailed systems biology picture of developmental processes. Here, we review the quantitative MS-based proteomic technologies that have contributed significantly to understanding the role of proteome regulation in developmental processes. We provide a brief overview of these methodologies, focusing on their ability to provide precise and accurate proteome measurements. We then highlight the use of discovery-based and targeted mass spectrometry approaches in model systems to study cellular differentiation states, tissue phenotypes, and spatiotemporal subcellular organization. We also discuss the current application and future perspectives of MS proteomics to study PTM coordination and the role of protein complexes during development.
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Affiliation(s)
- Yutaka Hashimoto
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Todd M Greco
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
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27
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Chen Y, Leng M, Gao Y, Zhan D, Choi JM, Song L, Li K, Xia X, Zhang C, Liu M, Ji S, Jain A, Saltzman AB, Malovannaya A, Qin J, Jung SY, Wang Y. A Cross-Linking-Aided Immunoprecipitation/Mass Spectrometry Workflow Reveals Extensive Intracellular Trafficking in Time-Resolved, Signal-Dependent Epidermal Growth Factor Receptor Proteome. J Proteome Res 2019; 18:3715-3730. [PMID: 31442056 DOI: 10.1021/acs.jproteome.9b00427] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ligand binding to the cell surface receptors initiates signaling cascades that are commonly transduced through a protein-protein interaction (PPI) network to activate a plethora of response pathways. However, tools to capture the membrane PPI network are lacking. Here, we describe a cross-linking-aided mass spectrometry workflow for isolation and identification of signal-dependent epidermal growth factor receptor (EGFR) proteome. We performed protein cross-linking in cell culture at various time points following EGF treatment, followed by immunoprecipitation of endogenous EGFR and analysis of the associated proteins by quantitative mass spectrometry. We identified 140 proteins with high confidence during a 2 h time course by data-dependent acquisition and further validated the results by parallel reaction monitoring. A large proportion of proteins in the EGFR proteome function in endocytosis and intracellular protein transport. The EGFR proteome was highly dynamic with distinct temporal behavior; 10 proteins that appeared in all time points constitute the core proteome. Functional characterization showed that loss of the FYVE domain-containing proteins altered the EGFR intracellular distribution but had a minor effect on EGFR proteome or signaling. Thus, our results suggest that the EGFR proteome include functional regulators that influence EGFR signaling and bystanders that are captured as the components of endocytic vesicles. The high-resolution spatiotemporal information of these molecules facilitates the delineation of many pathways that could determine the strength and duration of the signaling, as well as the location and destination of the receptor.
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Affiliation(s)
- Yue Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77003, United States
| | - Mei Leng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77003, United States
| | - Yankun Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of Lifeomics , Beijing 102206 , China
| | - Dongdong Zhan
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences , East China Normal University , Shanghai 200241 , China
| | - Jong Min Choi
- Advanced Technology Core, Baylor College of Medicine, Houston, Texas77030, United States
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of Lifeomics , Beijing 102206 , China
| | - Kai Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of Lifeomics , Beijing 102206 , China
| | - Xia Xia
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of Lifeomics , Beijing 102206 , China
| | - Chunchao Zhang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77003, United States
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of Lifeomics , Beijing 102206 , China
| | - Shuhui Ji
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of Lifeomics , Beijing 102206 , China
| | - Antrix Jain
- Advanced Technology Core, Baylor College of Medicine, Houston, Texas77030, United States
| | - Alexander B Saltzman
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77003, United States
| | - Anna Malovannaya
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77003, United States,Advanced Technology Core, Baylor College of Medicine, Houston, Texas77030, United States,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas77030, United States,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77003, United States
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of Lifeomics , Beijing 102206 , China.,The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences , East China Normal University , Shanghai 200241 , China.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77003, United States,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77003, United States
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77003, United States
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (The PHOENIX Center, Beijing), Institute of Lifeomics , Beijing 102206 , China.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77003, United States,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77003, United States
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28
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Abstract
Rods and cones are retinal photoreceptor neurons required for our visual sensation. Because of their highly polarized structures and well-characterized processes of G protein-coupled receptor-mediated phototransduction signaling, these photoreceptors have been excellent models for studying the compartmentalization and sorting of proteins. Rods and cones have a modified ciliary compartment called the outer segment (OS) as well as non-OS compartments. The distinct membrane protein compositions between OS and non-OS compartments suggest that the OS is separated from the rest of the cellular compartments by multiple barriers or gates that are selectively permissive to specific cargoes. This review discusses the mechanisms of protein sorting and compartmentalization in photoreceptor neurons. Proper sorting and compartmentalization of membrane proteins are required for signal transduction and transmission. This review also discusses the roles of compartmentalized signaling, which is compromised in various retinal ciliopathies.
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Affiliation(s)
- Yoshikazu Imanishi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA;
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29
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The photoreceptor cilium and its diseases. Curr Opin Genet Dev 2019; 56:22-33. [DOI: 10.1016/j.gde.2019.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/21/2019] [Accepted: 05/11/2019] [Indexed: 12/26/2022]
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30
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Wheway G, Nazlamova L, Turner D, Cross S. 661W Photoreceptor Cell Line as a Cell Model for Studying Retinal Ciliopathies. Front Genet 2019; 10:308. [PMID: 31024622 PMCID: PMC6459963 DOI: 10.3389/fgene.2019.00308] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 03/21/2019] [Indexed: 12/20/2022] Open
Abstract
The retina contains several ciliated cell types, including the retinal pigment epithelium (RPE) and photoreceptor cells. The photoreceptor cilium is one of the most highly modified sensory cilia in the human body. The outer segment of the photoreceptor is a highly elaborate primary cilium, containing stacks or folds of membrane where the photopigment molecules are located. Perhaps unsurprisingly, defects in cilia often lead to retinal phenotypes, either as part of syndromic conditions involving other organs, or in isolation in the so-called retinal ciliopathies. The study of retinal ciliopathies has been limited by a lack of retinal cell lines. RPE1 retinal pigment epithelial cell line is commonly used in such studies, but the existence of a photoreceptor cell line has largely been neglected in the retinal ciliopathy field. 661W cone photoreceptor cells, derived from mouse, have been widely used as a model for studying macular degeneration, but not described as a model for studying retinal ciliopathies such as retinitis pigmentosa. Here, we characterize the 661W cell line as a model for studying retinal ciliopathies. We fully characterize the expression profile of these cells, using whole transcriptome RNA sequencing, and provide this data on Gene Expression Omnibus for the advantage of the scientific community. We show that these cells express the majority of markers of cone cell origin. Using immunostaining and confocal microscopy, alongside scanning electron microscopy, we show that these cells grow long primary cilia, reminiscent of photoreceptor outer segments, and localize many cilium proteins to the axoneme, membrane and transition zone. We show that siRNA knockdown of cilia genes Ift88 results in loss of cilia, and that this can be assayed by high-throughput screening. We present evidence that the 661W cell line is a useful cell model for studying retinal ciliopathies.
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Affiliation(s)
- Gabrielle Wheway
- Centre for Research in Biosciences, University of the West of England, Bristol, Bristol, United Kingdom.,Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Human Development and Health, Southampton General Hospital, Southampton, United Kingdom
| | - Liliya Nazlamova
- Centre for Research in Biosciences, University of the West of England, Bristol, Bristol, United Kingdom.,Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Human Development and Health, Southampton General Hospital, Southampton, United Kingdom
| | - Dann Turner
- Centre for Research in Biosciences, University of the West of England, Bristol, Bristol, United Kingdom
| | - Stephen Cross
- Wolfson Bioimaging Facility, University of Bristol, Bristol, United Kingdom
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31
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Ying G, Frederick JM, Baehr W. Deletion of both centrin 2 (CETN2) and CETN3 destabilizes the distal connecting cilium of mouse photoreceptors. J Biol Chem 2019; 294:3957-3973. [PMID: 30647131 DOI: 10.1074/jbc.ra118.006371] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/09/2019] [Indexed: 02/03/2023] Open
Abstract
Centrins (CETN1-4) are ubiquitous and conserved EF-hand-family Ca2+-binding proteins associated with the centrosome, basal body, and transition zone. Deletion of CETN1 or CETN2 in mice causes male infertility or dysosmia, respectively, without affecting photoreceptor function. However, it remains unclear to what extent centrins are redundant with each other in photoreceptors. Here, to explore centrin redundancy, we generated Cetn3 GT/GT single-knockout and Cetn2 -/-;Cetn3 GT/GT double-knockout mice. Whereas the Cetn3 deletion alone did not affect photoreceptor function, simultaneous ablation of Cetn2 and Cetn3 resulted in attenuated scotopic and photopic electroretinography (ERG) responses in mice at 3 months of age, with nearly complete retina degeneration at 1 year. Removal of CETN2 and CETN3 activity from the lumen of the connecting cilium (CC) destabilized the photoreceptor axoneme and reduced the CC length as early as postnatal day 22 (P22). In Cetn2 -/-;Cetn3 GT/GT double-knockout mice, spermatogenesis-associated 7 (SPATA7), a key organizer of the photoreceptor-specific distal CC, was depleted gradually, and CETN1 was condensed to the mid-segment of the CC. Ultrastructural analysis revealed that in this double knockout, the axoneme of the CC expanded radially at the distal end, with vertically misaligned outer segment discs and membrane whorls. These observations suggest that CETN2 and CETN3 cooperate in stabilizing the CC/axoneme structure.
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Affiliation(s)
- Guoxin Ying
- From the Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, Utah 84132,
| | - Jeanne M Frederick
- From the Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, Utah 84132
| | - Wolfgang Baehr
- From the Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, Utah 84132, .,the Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, Utah 84112, and.,the Department of Biology, University of Utah, Salt Lake City, Utah 84132
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32
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Igeta H, Watanabe Y, Morikawa R, Ikeda M, Otsuka I, Hoya S, Koizumi M, Egawa J, Hishimoto A, Iwata N, Someya T. Rare compound heterozygous missense SPATA7 variations and risk of schizophrenia; whole-exome sequencing in a consanguineous family with affected siblings, follow-up sequencing and a case-control study. Neuropsychiatr Dis Treat 2019; 15:2353-2363. [PMID: 31695380 PMCID: PMC6707433 DOI: 10.2147/ndt.s218773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Whole-exome sequencing (WES) of multiplex families is a promising strategy for identifying causative variations for common diseases. To identify rare recessive risk variations for schizophrenia, we performed a WES study in a consanguineous family with affected siblings. We then performed follow-up sequencing of SPATA7 in schizophrenia-affected families. In addition, we performed a case-control study to investigate association between SPATA7 variations and schizophrenia. PATIENTS AND METHODS WES was performed on two affected siblings and their unaffected parents, who were second cousins, of a multiplex schizophrenia family. Subsequently, we sequenced the coding region of SPATA7, a potential risk gene identified by the WES analysis, in 142 affected offspring from 137 families for whom parental DNA samples were available. We further tested rare recessive SPATA7 variations, identified by WES and sequencing, for associations with schizophrenia in 2,756 patients and 2,646 controls. RESULTS Our WES analysis identified rare compound heterozygous missense SPATA7 variations, p.Asp134Gly and p.Ile332Thr, in both affected siblings. Sequencing SPATA7 coding regions from 137 families identified no rare recessive variations in affected offspring. In the case-control study, we did not detect the rare compound heterozygous SPATA7 missense variations in patients or controls. CONCLUSION Our data does not support the role of the rare compound heterozygous SPATA7 missense variations p.Asp134Gly and p.Ile332Thr in conferring a substantial risk of schizophrenia.
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Affiliation(s)
- Hirofumi Igeta
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryo Morikawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Satoshi Hoya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masataka Koizumi
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Baehr W, Hanke-Gogokhia C, Sharif A, Reed M, Dahl T, Frederick JM, Ying G. Insights into photoreceptor ciliogenesis revealed by animal models. Prog Retin Eye Res 2018; 71:26-56. [PMID: 30590118 DOI: 10.1016/j.preteyeres.2018.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022]
Abstract
Photoreceptors are polarized neurons, with very specific subcellular compartmentalization and unique requirements for protein expression and trafficking. Each photoreceptor contains an outer segment, the site of photon capture that initiates vision, an inner segment that houses the biosynthetic machinery and a synaptic terminal for signal transmission to downstream neurons. Outer segments and inner segments are connected by a connecting cilium (CC), the equivalent of a transition zone (TZ) of primary cilia. The connecting cilium is part of the basal body/axoneme backbone that stabilizes the outer segment. This report will update the reader on late developments in photoreceptor ciliogenesis and transition zone formation, specifically in mouse photoreceptors, focusing on early events in photoreceptor ciliogenesis. The connecting cilium, an elongated and narrow structure through which all outer segment proteins and membrane components must traffic, functions as a gate that controls access to the outer segment. Here we will review genes and their protein products essential for basal body maturation and for CC/TZ genesis, sorted by phenotype. Emphasis is given to naturally occurring mouse mutants and gene knockouts that interfere with CC/TZ formation and ciliogenesis.
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Affiliation(s)
- Wolfgang Baehr
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA.
| | - Christin Hanke-Gogokhia
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Ali Sharif
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Michelle Reed
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Tiffanie Dahl
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Jeanne M Frederick
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
| | - Guoxin Ying
- Department of Ophthalmology and Visual Sciences, University of Utah Health Sciences, Salt Lake City, UT, 84132, USA
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