1
|
Donato L, Scimone C, Alibrandi S, Mordà D, Anchesi I, Scalinci SZ, Rinaldi C, D'Angelo R, Sidoti A. Investigating G-quadruplex structures in RPGR gene: Implications for understanding X-linked retinal degeneration. Heliyon 2024; 10:e29828. [PMID: 38699732 PMCID: PMC11063440 DOI: 10.1016/j.heliyon.2024.e29828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/31/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
Aims This pilot study investigates the potential pathogenic role of G-quadruplex (G4) structures in RPGR-associated retinal degeneration, starting from a case of suspected X-linked form affected family. We hypothesize that the stabilization of these structures might alter DNA replication and transcription, inducing genetic instability and influencing gene expression. Main methods We conducted whole genome amplification experiments and next-generation sequencing to detect the blockade of polymerase activity by G4 structures. Our specific focus was the RPGR gene, which hosts a high concentration of predicted G4-forming motifs and is implicated in most X-linked retinal degeneration cases. To understand the potential interference of G4 structures, we applied computational and 3D molecular modeling to visualize interferences in DNA replication and transcription regulation. Key findings Our data confirmed the obstruction of DNA polymerase enzymes by G4 structures, particularly when stabilized by the compound pyridostatin. This obstruction was evident in the reduced amplification of RPGR gene regions and a shift in the start/end sites of putative G4 motifs. Moreover, the modeling indicated a potential disruption of critical promoter elements and RNA polymerase binding, which could drastically alter gene expression. Significance Our findings suggest that G4 formation in the RPGR gene could lead to genetic instability and affect the expression of RPGR, contributing to retinal dystrophy. Moreover, this study underscores the broader implications of G4 structures in other genetic disorders. Improved understanding of G4 structures could reveal novel therapeutic targets to combat genetic disorders, promoting the advancement of personalized medicine and precision health.
Collapse
Affiliation(s)
- Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-Edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-Edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-Edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
| | - Domenico Mordà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
- Department of Biomolecular Strategies, Genetics and Cutting-Edge Therapies, I.E.ME.S.T., Palermo, 90139, Italy
- Department of Veterinary Sciences, University of Messina, 98122, Messina, Italy
| | - Ivan Anchesi
- IRCCS Centro Neurolesi "Bonino-Pulejo", Via Provinciale Palermo, Contrada Casazza, 98124, Messina, Italy
| | | | - Carmela Rinaldi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
| | - Rosalia D'Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, Messina, 98125, Italy
| |
Collapse
|
2
|
Moran AL, Louzao-Martinez L, Norris DP, Peters DJM, Blacque OE. Transport and barrier mechanisms that regulate ciliary compartmentalization and ciliopathies. Nat Rev Nephrol 2024; 20:83-100. [PMID: 37872350 DOI: 10.1038/s41581-023-00773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
Primary cilia act as cell surface antennae, coordinating cellular responses to sensory inputs and signalling molecules that regulate developmental and homeostatic pathways. Cilia are therefore critical to physiological processes, and defects in ciliary components are associated with a large group of inherited pleiotropic disorders - known collectively as ciliopathies - that have a broad spectrum of phenotypes and affect many or most tissues, including the kidney. A central feature of the cilium is its compartmentalized structure, which imparts its unique molecular composition and signalling environment despite its membrane and cytosol being contiguous with those of the cell. Such compartmentalization is achieved via active transport pathways that bring protein cargoes to and from the cilium, as well as gating pathways at the ciliary base that establish diffusion barriers to protein exchange into and out of the organelle. Many ciliopathy-linked proteins, including those involved in kidney development and homeostasis, are components of the compartmentalizing machinery. New insights into the major compartmentalizing pathways at the cilium, namely, ciliary gating, intraflagellar transport, lipidated protein flagellar transport and ciliary extracellular vesicle release pathways, have improved our understanding of the mechanisms that underpin ciliary disease and associated renal disorders.
Collapse
Affiliation(s)
- Ailis L Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Laura Louzao-Martinez
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
| |
Collapse
|
3
|
Sushmita K, Sharma S, Singh Kaushik M, Kateriya S. Algal rhodopsins encoding diverse signal sequence holds potential for expansion of organelle optogenetics. Biophys Physicobiol 2023; 20:e201008. [PMID: 38362319 PMCID: PMC10865886 DOI: 10.2142/biophysico.bppb-v20.s008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Rhodopsins have been extensively employed for optogenetic regulation of bioelectrical activity of excitable cells and other cellular processes across biological systems. Various strategies have been adopted to attune the cellular processes at the desired subcellular compartment (plasma membrane, endoplasmic reticulum, Golgi, mitochondria, lysosome) within the cell. These strategies include-adding signal sequences, tethering peptides, specific interaction sites, or mRNA elements at different sites in the optogenetic proteins for plasma membrane integration and subcellular targeting. However, a single approach for organelle optogenetics was not suitable for the relevant optogenetic proteins and often led to the poor expression, mislocalization, or altered physical and functional properties. Therefore, the current study is focused on the native subcellular targeting machinery of algal rhodopsins. The N- and C-terminus signal prediction led to the identification of rhodopsins with diverse organelle targeting signal sequences for the nucleus, mitochondria, lysosome, endosome, vacuole, and cilia. Several identified channelrhodopsins and ion-pumping rhodopsins possess effector domains associated with DNA metabolism (repair, replication, and recombination) and gene regulation. The identified algal rhodopsins with diverse effector domains and encoded native subcellular targeting sequences hold immense potential to establish expanded organelle optogenetic regulation and associated cellular signaling.
Collapse
Affiliation(s)
- Kumari Sushmita
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sunita Sharma
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manish Singh Kaushik
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
4
|
Faber S, Letteboer SJF, Junger K, Butcher R, Tammana TVS, van Beersum SEC, Ueffing M, Collin RWJ, Liu Q, Boldt K, Roepman R. PDE6D Mediates Trafficking of Prenylated Proteins NIM1K and UBL3 to Primary Cilia. Cells 2023; 12:cells12020312. [PMID: 36672247 PMCID: PMC9857354 DOI: 10.3390/cells12020312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
Mutations in PDE6D impair the function of its cognate protein, phosphodiesterase 6D (PDE6D), in prenylated protein trafficking towards the ciliary membrane, causing the human ciliopathy Joubert Syndrome (JBTS22) and retinal degeneration in mice. In this study, we purified the prenylated cargo of PDE6D by affinity proteomics to gain insight into PDE6D-associated disease mechanisms. By this approach, we have identified a specific set of PDE6D-interacting proteins that are involved in photoreceptor integrity, GTPase activity, nuclear import, or ubiquitination. Among these interacting proteins, we identified novel ciliary cargo proteins of PDE6D, including FAM219A, serine/threonine-protein kinase NIM1 (NIM1K), and ubiquitin-like protein 3 (UBL3). We show that NIM1K and UBL3 localize inside the cilium in a prenylation-dependent manner. Furthermore, UBL3 also localizes in vesicle-like structures around the base of the cilium. Through affinity proteomics of UBL3, we confirmed its strong interaction with PDE6D and its association with proteins that regulate small extracellular vesicles (sEVs) and ciliogenesis. Moreover, we show that UBL3 localizes in specific photoreceptor cilium compartments in a prenylation-dependent manner. Therefore, we propose that UBL3 may play a role in the sorting of proteins towards the photoreceptor outer segment, further explaining the development of PDE6D-associated retinal degeneration.
Collapse
Affiliation(s)
- Siebren Faber
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Stef J. F. Letteboer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Katrin Junger
- Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72076 Tübingen, Germany
| | - Rossano Butcher
- Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Trinadh V. Satish Tammana
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sylvia E. C. van Beersum
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marius Ueffing
- Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72076 Tübingen, Germany
| | - Rob W. J. Collin
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Qin Liu
- Department of Ophthalmology, Ocular Genomics Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02115, USA
| | - Karsten Boldt
- Division of Experimental Ophthalmology and Medical Proteome Center, Center of Ophthalmology, University of Tübingen, 72076 Tübingen, Germany
| | - Ronald Roepman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Correspondence:
| |
Collapse
|
5
|
Cehajic-Kapetanovic J, Martinez-Fernandez de la Camara C, Birtel J, Rehman S, McClements ME, Charbel Issa P, Lotery AJ, MacLaren RE. Impaired glutamylation of RPGR ORF15 underlies the cone-dominated phenotype associated with truncating distal ORF15 variants. Proc Natl Acad Sci U S A 2022; 119:e2208707119. [PMID: 36445968 PMCID: PMC9897430 DOI: 10.1073/pnas.2208707119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pathogenic variants in the Retinitis pigmentosa GTPase regulator (RPGR) gene lead to a clinically severe form of X-linked retinal dystrophy. However, it remains unclear why some variants cause a predominant rod, while others result in a cone-dominated phenotype. Post-translational glutamylation of the photoreceptor-specific RPGRORF15 isoform by the TTLL5 enzyme is essential for its optimal function in photoreceptors, and loss of TTLL5 leads to retinal dystrophy with a cone phenotype. Here we show that RPGR retinal disease, studied in a single cohort of 116 male patients, leads to a clear progressive shift from rod- to cone-dominating phenotype as the RPGRORF15 variant location approaches the distal part of the Open Reading Frame 15 (ORF15) region. The rod photoreceptor involvement on the contrary diminishes along the RGPR sequence, and the variants associated with the cone only phenotype are located predominantly in the very distal part, including the C-terminal basic domain. Moreover, these distal truncating RPGRORF15 variants disrupt the interaction with TTLL5 and lead to a significant impairment of RPGR glutamylation. Thus, consistent with the phenotype of TTLL5 pathogenic variants, our study shows that RPGRORF15 variants, which disrupt its basic domain and the interaction with TTLL5, also impair RPGR glutamylation and lead to the cone phenotype. This has implications for ongoing gene therapy clinical trials where the application of RPGR with impaired glutamylation may be less effective in treating RGPR dystrophies and may even convert a rod-cone dystrophy into a cone dystrophy phenotype.
Collapse
Affiliation(s)
- Jasmina Cehajic-Kapetanovic
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
- 2To whom correspondence may be addressed.
| | - Cristina Martinez-Fernandez de la Camara
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
- 2To whom correspondence may be addressed.
| | - Johannes Birtel
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
- cDepartment of Ophthalmology, University of Bonn, 53127Bonn, Germany
| | - Salwah Rehman
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
| | - Michelle E. McClements
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
| | - Peter Charbel Issa
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
| | - Andrew J Lotery
- dClinical Neurosciences Research Group, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, SO16 6YDSouthampton, United Kingdom
- eUniversity Hospital Southampton NHS Foundation Trust, SO16 6YDSouthampton, United Kingdom
| | - Robert E. MacLaren
- aNuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, John Radcliffe Hospital, Level 5 & 6, West WingOX3 9DU, United Kingdom
- bOxford Eye Hospital, Oxford University Hospitals The National Health Service Trust, John Radcliffe Hospital, West WingOX3 9DU, United Kingdom
- 2To whom correspondence may be addressed.
| |
Collapse
|
6
|
Cilleros-Rodriguez D, Martin-Morales R, Barbeito P, Deb Roy A, Loukil A, Sierra-Rodero B, Herranz G, Pampliega O, Redrejo-Rodriguez M, Goetz SC, Izquierdo M, Inoue T, Garcia-Gonzalo FR. Multiple ciliary localization signals control INPP5E ciliary targeting. eLife 2022; 11:78383. [PMID: 36063381 PMCID: PMC9444247 DOI: 10.7554/elife.78383] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 08/21/2022] [Indexed: 12/04/2022] Open
Abstract
Primary cilia are sensory membrane protrusions whose dysfunction causes ciliopathies. INPP5E is a ciliary phosphoinositide phosphatase mutated in ciliopathies like Joubert syndrome. INPP5E regulates numerous ciliary functions, but how it accumulates in cilia remains poorly understood. Herein, we show INPP5E ciliary targeting requires its folded catalytic domain and is controlled by four conserved ciliary localization signals (CLSs): LLxPIR motif (CLS1), W383 (CLS2), FDRxLYL motif (CLS3) and CaaX box (CLS4). We answer two long-standing questions in the field. First, partial CLS1-CLS4 redundancy explains why CLS4 is dispensable for ciliary targeting. Second, the essential need for CLS2 clarifies why CLS3-CLS4 are together insufficient for ciliary accumulation. Furthermore, we reveal that some Joubert syndrome mutations perturb INPP5E ciliary targeting, and clarify how each CLS works: (i) CLS4 recruits PDE6D, RPGR and ARL13B, (ii) CLS2-CLS3 regulate association to TULP3, ARL13B, and CEP164, and (iii) CLS1 and CLS4 cooperate in ATG16L1 binding. Altogether, we shed light on the mechanisms of INPP5E ciliary targeting, revealing a complexity without known parallels among ciliary cargoes.
Collapse
Affiliation(s)
- Dario Cilleros-Rodriguez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Raquel Martin-Morales
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Pablo Barbeito
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Abhijit Deb Roy
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Abdelhalim Loukil
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, United States
| | - Belen Sierra-Rodero
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Gonzalo Herranz
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Olatz Pampliega
- Department of Neurosciences, University of the Basque Country, Achucarro Basque Center for Neuroscience-UPV/EHU, Leioa, Spain
| | - Modesto Redrejo-Rodriguez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Sarah C Goetz
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, United States
| | - Manuel Izquierdo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Takanari Inoue
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Francesc R Garcia-Gonzalo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Instituto de Investigaciones Biomédicas "Alberto Sols" (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain.,Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| |
Collapse
|
7
|
Chahine Karam F, Loi TH, Ma A, Nash BM, Grigg JR, Parekh D, Riley LG, Farnsworth E, Bennetts B, Gonzalez-Cordero A, Jamieson RV. Human iPSC-Derived Retinal Organoids and Retinal Pigment Epithelium for Novel Intronic RPGR Variant Assessment for Therapy Suitability. J Pers Med 2022; 12:jpm12030502. [PMID: 35330501 PMCID: PMC8951517 DOI: 10.3390/jpm12030502] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/04/2023] Open
Abstract
The RPGR gene encodes Retinitis Pigmentosa GTPase Regulator, a known interactor with ciliary proteins, which is involved in maintaining healthy photoreceptor cells. Variants in RPGR are the main contributor to X-linked rod-cone dystrophy (RCD), and RPGR gene therapy approaches are in clinical trials. Hence, elucidation of the pathogenicity of novel RPGR variants is important for a patient therapy opportunity. Here, we describe a novel intronic RPGR variant, c.1415 − 9A>G, in a patient with RCD, which was classified as a variant of uncertain significance according to current clinical diagnostic criteria. The variant lay several base pairs intronic to the canonical splice acceptor site, raising suspicion of an RPGR RNA splicing abnormality and consequent protein dysfunction. To investigate disease causation in an appropriate disease model, induced pluripotent stem cells were generated from patient fibroblasts and differentiated to retinal pigment epithelium (iPSC-RPE) and retinal organoids (iPSC-RO). Abnormal RNA splicing of RPGR was demonstrated in patient fibroblasts, iPSC-RPE and iPSC-ROs, leading to a predicted frameshift and premature stop codon. Decreased RPGR expression was demonstrated in these cell types, with a striking loss of RPGR localization at the ciliary transitional zone, critically in the photoreceptor cilium of the patient iPSC-ROs. Mislocalisation of rhodopsin staining was present in the patient’s iPSC-RO rod photoreceptor cells, along with an abnormality of L/M opsin staining affecting cone photoreceptor cells and increased photoreceptor apoptosis. Additionally, patient iPSC-ROs displayed an increase in F-actin expression that was consistent with an abnormal actin regulation phenotype. Collectively, these studies indicate that the splicing abnormality caused by the c.1415 − 9A>G variant has an impact on RPGR function. This work has enabled the reclassification of this variant to pathogenic, allowing the consideration of patients with this variant having access to gene therapy clinical trials. In addition, we have identified biomarkers of disease suitable for the interrogation of other RPGR variants of uncertain significance.
Collapse
Affiliation(s)
- Fidelle Chahine Karam
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
| | - To Ha Loi
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
| | - Alan Ma
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Department of Clinical Genetics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
| | - Benjamin M. Nash
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - John R. Grigg
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Specialty of Ophthalmology, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia
| | - Darshan Parekh
- Rare Diseases Functional Genomics Laboratory, Sydney Children’s Hospitals Network and Children’s Medical Research Institute, Westmead, Sydney 2145, Australia; (D.P.); (L.G.R.)
| | - Lisa G. Riley
- Rare Diseases Functional Genomics Laboratory, Sydney Children’s Hospitals Network and Children’s Medical Research Institute, Westmead, Sydney 2145, Australia; (D.P.); (L.G.R.)
- Specialty of Child and Adolescent Health, University of Sydney, Westmead, Sydney 2145, Australia
| | - Elizabeth Farnsworth
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - Bruce Bennetts
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell Medicine Group, Children’s Medical Research Institute, University of Sydney, Westmead, Sydney 2145, Australia;
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia
| | - Robyn V. Jamieson
- Eye Genetics Research Unit, Children’s Medical Research Institute, Sydney Children’s Hospitals Network, Save Sight Institute, University of Sydney, Westmead, Sydney 2145, Australia; (F.C.K.); (T.H.L.); (A.M.); (B.M.N.); (J.R.G.)
- Department of Clinical Genetics, Western Sydney Genetics Program, Sydney Children’s Hospitals Network, Westmead, Sydney 2145, Australia
- Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Westmead, Sydney 2145, Australia; (E.F.); (B.B.)
- Correspondence: ; Tel.: +61-2-9687-2800; Fax: +61-2-9687-2120
| |
Collapse
|
8
|
Wang Y, Liu S, Zhai Y, Liu Y, Wan X, Wang W, Wang F, Sun X. Identification of a novel RPGR mutation associated with X-linked cone-rod dystrophy in a Chinese family. BMC Ophthalmol 2021; 21:401. [PMID: 34800980 PMCID: PMC8605601 DOI: 10.1186/s12886-021-02166-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/31/2021] [Indexed: 11/10/2022] Open
Abstract
Background Cone-rod dystrophy (CORD) is a group of inherited retinal dystrophies, characterized by decreased visual acuity, color vision defects, photophobia, and decreased sensitivity in the central visual field. Our study has identified a novel pathogenic variant associated with X-linked cone-rod dystrophy (XLCORD) in a Chinese family. Methods All six family members, including the proband, affected siblings, cousins and female carriers, have underwent thorough ophthalmic examinations. The whole exome sequencing was performed for the proband, followed by Sanger sequencing for spilt-sample validation. A mammalian expression vector (AAV-MCS) with mutated retinitis pigmentosa GTPase regulator (RPGR) sequence was expressed in HEK293 T cells. The mutated protein was verified by Western blotting and immunohistochemistry. Results A novel mutation in the RPGR gene (c.2383G > T, p.E795X) is identified to be responsible for CORD pathogenesis. Conclusions Our findings have expanded the spectrum of CORD-associated mutations in RPGR gene and serve as a basis for genetic diagnosis for X-linked CORD. Supplementary Information The online version contains supplementary material available at 10.1186/s12886-021-02166-0.
Collapse
Affiliation(s)
- Yafang Wang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Shu Liu
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Yuanqi Zhai
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Yang Liu
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Xiaoling Wan
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Wenqiu Wang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China.
| | - Fenghua Wang
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China.,Shanghai Key Laboratory of Ocular Fundus Diseases, 100 Haining Road, Shanghai, 200080, China.,Shanghai Engineering Center for Visual Science and Photomedicine, 100 Haining Road, Shanghai, 200080, China.,National Clinical Research Center for Eye Diseases, 100 Haining Road, Shanghai, 200080, China.,Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 100 Haining Road, Shanghai, 200080, China
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China.,Shanghai Key Laboratory of Ocular Fundus Diseases, 100 Haining Road, Shanghai, 200080, China.,Shanghai Engineering Center for Visual Science and Photomedicine, 100 Haining Road, Shanghai, 200080, China.,National Clinical Research Center for Eye Diseases, 100 Haining Road, Shanghai, 200080, China.,Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, 100 Haining Road, Shanghai, 200080, China
| |
Collapse
|
9
|
Qiu H, Fujisawa S, Nozaki S, Katoh Y, Nakayama K. Interaction of INPP5E with ARL13B is essential for its ciliary membrane retention but dispensable for its ciliary entry. Biol Open 2021; 10:bio057653. [PMID: 33372066 PMCID: PMC7860134 DOI: 10.1242/bio.057653] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Compositions of proteins and lipids within cilia and on the ciliary membrane are maintained to be distinct from those of the cytoplasm and plasma membrane, respectively, by the presence of the ciliary gate. INPP5E is a phosphoinositide 5-phosphatase that is localized on the ciliary membrane by anchorage via its C-terminal prenyl moiety. In addition, the ciliary membrane localization of INPP5E is determined by the small GTPase ARL13B. However, it remained unclear as to how ARL13B participates in the localization of INPP5E. We here show that wild-type INPP5E, INPP5E(WT), in ARL13B-knockout cells and an INPP5E mutant defective in ARL13B binding, INPP5E(ΔCTS), in control cells were unable to show steady-state localization on the ciliary membrane. However, not only INPP5E(WT) but also INPP5E(ΔCTS) was able to rescue the abnormal localization of ciliary proteins in INPP5E-knockout cells. Analysis using the chemically induced dimerization system demonstrated that INPP5E(WT) in ARL13B-knockout cells and INPP5E(ΔCTS) in control cells were able to enter cilia, but neither was retained on the ciliary membrane due to the lack of the INPP5E-ARL13B interaction. Thus, our data demonstrate that binding of INPP5E to ARL13B is essential for its steady-state localization on the ciliary membrane but is dispensable for its entry into cilia.
Collapse
Affiliation(s)
- Hantian Qiu
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Sayaka Fujisawa
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shohei Nozaki
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yohei Katoh
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuhisa Nakayama
- Department of Physiological Chemistry, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| |
Collapse
|
10
|
A novel missense variant c.G644A (p.G215E) of the RPGR gene in a Chinese family causes X-linked retinitis pigmentosa. Biosci Rep 2020; 39:220828. [PMID: 31652454 PMCID: PMC6822503 DOI: 10.1042/bsr20192235] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/11/2019] [Accepted: 09/24/2019] [Indexed: 01/01/2023] Open
Abstract
The mutations in patients with X-linked retinitis pigmentosa (xlRP) have not been well described in the Chinese population. In the present study, a five-generation Chinese retinitis pigmentosa (RP) family was recruited; targeted next-generation sequencing (TGS) was used to identify causative genes and Sanger sequencing for co-segregation. RNA-seq data analysis and revere transcriptional-polymerase chain reaction (RT-PCR) were applied to investigate gene expression patterns of RP GTPase regulator (RPGR) in human and Rpgr in mouse. A novel, hemizygous, deleterious and missense variant: c.G644A (p.G215E) in the RPGR gene (NM_000328.2) exon 7 of X-chromosome was identified in the proband, which was co-segregated with the clinical phenotypes in this family. RNA-seq data showed that RPGR is ubiquitously expressed in 27 human tissues with testis in highest, but no eye tissues data. Then the expressions for Rpgr mRNA in mice including eye tissues were conducted and showed that Rpgr transcript is ubiquitously expressed very highly in retina and testis, and highly in other eye tissues including lens, sclera, and cornea; and expressed highly in the six different developmental times of retinal tissue. Ubiquitous expression in different tissues from eye and very high expression in the retina indicated that RPGR plays a vital role in eye functions, particularly in retina. In conclusion, our study is the first to indicate that the novel missense variant c.G644A (p.G215E) in the RPGR gene might be the disease-causing mutation in this xlRP family, expanding mutation spectrum. These findings facilitate better understanding of the molecular pathogenesis of this disease; provide new insights for genetic counseling and healthcare.
Collapse
|
11
|
Zhou P, Zhou J. The Primary Cilium as a Therapeutic Target in Ocular Diseases. Front Pharmacol 2020; 11:977. [PMID: 32676032 PMCID: PMC7333185 DOI: 10.3389/fphar.2020.00977] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022] Open
Abstract
Primary cilia are microtubule-based cellular structures located on the surfaces of most mammalian cells and play important roles in detecting external stimuli, signal transduction, and cell cycle regulation. Primary cilia are also present in several structures of the eye, and their abnormal development or dysfunction can cause various ocular diseases. The rapid development of proteomics and metabolomics technologies have helped in the identification of many ocular disease-related proteins, some of which are dysregulated in primary cilia. This review focuses on ciliary dysregulation in a number of ocular diseases and discusses the potential of targeting primary cilia in gene and stem cell therapy for these diseases.
Collapse
Affiliation(s)
- Peng Zhou
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Zhou
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
12
|
Roy K, Marin EP. Lipid Modifications in Cilia Biology. J Clin Med 2019; 8:jcm8070921. [PMID: 31252577 PMCID: PMC6678300 DOI: 10.3390/jcm8070921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/22/2019] [Accepted: 06/24/2019] [Indexed: 12/17/2022] Open
Abstract
Cilia are specialized cellular structures with distinctive roles in various signaling cascades. Ciliary proteins need to be trafficked to the cilium to function properly; however, it is not completely understood how these proteins are delivered to their final localization. In this review, we will focus on how different lipid modifications are important in ciliary protein trafficking and, consequently, regulation of signaling pathways. Lipid modifications can play a variety of roles, including tethering proteins to the membrane, aiding trafficking through facilitating interactions with transporter proteins, and regulating protein stability and abundance. Future studies focusing on the role of lipid modifications of ciliary proteins will help our understanding of how cilia maintain specific protein pools strictly connected to their functions.
Collapse
Affiliation(s)
- Kasturi Roy
- Department of Internal Medicine, Section of Nephrology, Yale School of Medicine, PO Box 208029, New Haven, CT 06520-8029, USA.
| | - Ethan P Marin
- Department of Internal Medicine, Section of Nephrology, Yale School of Medicine, PO Box 208029, New Haven, CT 06520-8029, USA
| |
Collapse
|
13
|
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.
Collapse
Affiliation(s)
- Yoshikazu Imanishi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA;
| |
Collapse
|
14
|
Hu R, Huang W, Liu J, Jin M, Wu Y, Li J, Wang J, Yu Z, Wang H, Cao Y. Mutagenesis of putative ciliary genes with the CRISPR/Cas9 system in zebrafish identifies genes required for retinal development. FASEB J 2019; 33:5248-5256. [PMID: 30624971 DOI: 10.1096/fj.201802140r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cilia are conserved microtubule-based organelles that function as mechanical and chemical sensors in various cell types. By bioinformatic, genomic, and proteomic studies, more than 2000 proteins have been identified as cilium-associated proteins or putative ciliary proteins; these proteins are referred to as the ciliary proteome or the ciliome. However, little is known about the function of these numerous putative ciliary proteins in cilia. To identify the possible new functional proteins or pathways in cilia, we carried out a small-scale genetic screen targeting 54 putative ciliary genes by using the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system. We successfully constructed 54 zebrafish mutants, and 8 of them displayed microphthalmias. Three of these 8 genes encode proteins for protein transport, suggesting the important roles of protein transport in retinal development. In situ hybridization revealed that all these genes are expressed in zebrafish eyes. Furthermore, polo-like kinase 1 was required for ciliogenesis in neural tube. We uncovered the potential function of the ciliary genes for the retinal development of zebrafish.-Hu, R., Huang, W., Liu, J., Jin, M., Wu, Y., Li, J., Wang, J., Yu, Z., Wang, H., Cao, Y. Mutagenesis of putative ciliary genes with the CRISPR/Cas9 system in zebrafish identifies genes required for retinal development.
Collapse
Affiliation(s)
- Ruikun Hu
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Weilai Huang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiangfang Liu
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Miaomiao Jin
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yue Wu
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jingyu Li
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jingyi Wang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zehao Yu
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hong Wang
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Ying Cao
- Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| |
Collapse
|
15
|
Dietrich P, Hellerbrand C, Bosserhoff A. The Delta Subunit of Rod-Specific Photoreceptor cGMP Phosphodiesterase (PDE6D) Contributes to Hepatocellular Carcinoma Progression. Cancers (Basel) 2019; 11:cancers11030398. [PMID: 30901922 PMCID: PMC6468542 DOI: 10.3390/cancers11030398] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 02/28/2019] [Accepted: 03/11/2019] [Indexed: 12/25/2022] Open
Abstract
Emerging evidence reveals crucial roles of wild type RAS in liver cancer. The delta subunit of rod-specific photoreceptor cGMP phosphodiesterase (PDE6D) regulates the trafficking of RAS proteins to the plasma membrane and thereby contributes to RAS activation. However, the expression and specific function of PDE6D in hepatocellular carcinoma (HCC) were completely unknown. In this study, PDE6D was newly found to be markedly upregulated in HCC tissues and cell lines. Overexpression of PDE6D in HCC correlated with enhanced tumor stages, tumor grading, and ERK activation. PDE6D depletion significantly reduced proliferation, clonogenicity, and migration of HCC cells. Moreover, PDE6D was induced by TGF-β1, the mediator of stemness, epithelial-mesenchymal transition (EMT), and chemoresistance. In non-resistant cells, overexpression of PDE6D conferred resistance to sorafenib-induced toxicity. Further, PDE6D was overexpressed in sorafenib resistance, and inhibition of PDE6D reduced proliferation and migration in sorafenib-resistant HCC cells. Together, PDE6D was found to be overexpressed in liver cancer and correlated with tumor stages, grading, and ERK activation. Moreover, PDE6D contributed to migration, proliferation, and sorafenib resistance in HCC cells, therefore representing a potential novel therapeutic target.
Collapse
Affiliation(s)
- Peter Dietrich
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University, Erlangen-Nürnberg, 91054 Erlangen, Germany.
- Department of Medicine 1, University Hospital Erlangen, Friedrich-Alexander-University, Erlangen-Nürnberg, 91054 Erlangen, Germany.
| | - Claus Hellerbrand
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University, Erlangen-Nürnberg, 91054 Erlangen, Germany.
- Comprehensive Cancer Center (CCC) Erlangen-EMN, 91054 Erlangen, Germany.
| | - Anja Bosserhoff
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University, Erlangen-Nürnberg, 91054 Erlangen, Germany.
- Comprehensive Cancer Center (CCC) Erlangen-EMN, 91054 Erlangen, Germany.
| |
Collapse
|
16
|
Donato L, Scimone C, Nicocia G, D'Angelo R, Sidoti A. Role of oxidative stress in Retinitis pigmentosa: new involved pathways by an RNA-Seq analysis. Cell Cycle 2018; 18:84-104. [PMID: 30569795 DOI: 10.1080/15384101.2018.1558873] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is a very heterogeneous inherited ocular disorder group characterized by progressive retinal disruption. Retinal pigment epithelium (RPE) degeneration, due to oxidative stress which arrests the metabolic support to photoreceptors, represents one of the principal causes of RP. Here, the role of oxidative stress in RP onset and progression was analyzed by a comparative whole transcriptome analysis of human RPE cells, treated with 100 µg/ml of oxLDL and untreated, at different time points. Experiment was thrice repeated and performed on Ion ProtonTM sequencing system. Data analysis, including low quality reads trimming and gene expression quantification, was realized by CLC Genomics Workbench software. The whole analysis highlighted 14 clustered "macro-pathways" and many sub-pathways, classified by selection of 5271 genes showing the highest alteration of expression. Among them, 23 genes were already known to be RP causative ones (15 over-expressed and 8 down-expressed), and their enrichment and intersection analyses highlighted new 77 candidate related genes (49 over-expressed and 28 down-expressed). A final filtering analysis then highlighted 29 proposed candidate genes. This data suggests that many new genes, not yet associated with RP, could influence its etiopathogenesis.
Collapse
Affiliation(s)
- Luigi Donato
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Concetta Scimone
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Giacomo Nicocia
- c Department of Clinical and Experimental Medicine , University of Messina , Messina , Italy
| | - Rosalia D'Angelo
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| | - Antonina Sidoti
- a Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine , University of Messina , Messina , Italy.,b Department of Cutting-Edge Medicine and Therapies, Biomolecular Strategies and Neuroscience, Section of Applied Neuroscience, Molecular Genetics and Predictive Medicine , I.E.ME.S.T. ., Palermo , Italy
| |
Collapse
|
17
|
Kösling SK, Fansa EK, Maffini S, Wittinghofer A. Mechanism and dynamics of INPP5E transport into and inside the ciliary compartment. Biol Chem 2018; 399:277-292. [PMID: 29140789 DOI: 10.1515/hsz-2017-0226] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/03/2017] [Indexed: 11/15/2022]
Abstract
The inositol polyphosphate 5'-phosphatase E (INPP5E) localizes to cilia. We showed that the carrier protein phosphodiesterase 6 delta subunit (PDE6δ) mediates the sorting of farnesylated INPP5E into cilia due to high affinity binding and release by the ADP-ribosylation factor (Arf)-like protein Arl3·GTP. However, the dynamics of INPP5E transport into and inside the ciliary compartment are not fully understood. Here, we investigate the movement of INPP5E using live cell fluorescence microscopy and fluorescence recovery after photobleaching (FRAP) analysis. We show that PDE6δ and the dynein transport system are essential for ciliary sorting and entry of INPP5E. However, its innerciliary transport is regulated solely by the intraflagellar transport (IFT) system, independent from PDE6δ activity and INPP5E farnesylation. By contrast, movement of Arl3 into and within cilia occurs freely by diffusion and IFT-independently. The farnesylation defective INPP5E CaaX box mutant loses the exclusive ciliary localization. The accumulation of this mutant at centrioles after photobleaching suggests an affinity trap mechanism for ciliary entry, that in case of the wild type is overcome by the interaction with PDE6δ. Collectively, we postulate a three-step mechanism regulating ciliary localization of INPP5E, consisting of farnesylation- and PDE6δ-mediated targeting, INPP5E-PDE6δ complex diffusion into the cilium with transfer to the IFT system, and retention inside cilia.
Collapse
Affiliation(s)
- Stefanie Kristine Kösling
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, D-44227 Dortmund, Germany
| | - Eyad Kalawy Fansa
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, D-44227 Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, D-44227 Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, D-44227 Dortmund, Germany
| |
Collapse
|
18
|
Jensen VL, Leroux MR. Gates for soluble and membrane proteins, and two trafficking systems (IFT and LIFT), establish a dynamic ciliary signaling compartment. Curr Opin Cell Biol 2017; 47:83-91. [PMID: 28432921 DOI: 10.1016/j.ceb.2017.03.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/18/2017] [Accepted: 03/21/2017] [Indexed: 12/28/2022]
Abstract
Primary cilia are microtubule-based organelles found on most mammalian cell surfaces. They possess a soluble matrix and membrane contiguous with the cell body cytosol and plasma membrane, and yet, have distinct compositions that can be modulated to enable dynamic signal transduction. Here, we discuss how specialized ciliary compartments are established using a coordinated network of gating, trafficking and targeting activities. Cilium homeostasis is maintained by a size-selective molecular mesh that limits soluble protein entry, and by a membrane diffusion barrier localized at the transition zone. Bidirectional protein shuttling between the cell body and cilium uses IntraFlagellar Transport (IFT), and prenylated ciliary protein delivery is achieved through Lipidated protein IntraFlagellar Targeting (LIFT). Elucidating how these gates and transport systems function will help reveal the roles that cilia play in ciliary signaling and the growing spectrum of disorders termed ciliopathies.
Collapse
Affiliation(s)
- Victor L Jensen
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada; Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, Canada
| | - Michel R Leroux
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada; Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, Canada.
| |
Collapse
|