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Atkinson R, Georgiou M, Yang C, Szymanska K, Lahat A, Vasconcelos EJR, Ji Y, Moya Molina M, Collin J, Queen R, Dorgau B, Watson A, Kurzawa-Akanbi M, Laws R, Saxena A, Shyan Beh C, Siachisumo C, Goertler F, Karwatka M, Davey T, Inglehearn CF, McKibbin M, Lührmann R, Steel DH, Elliott DJ, Armstrong L, Urlaub H, Ali RR, Grellscheid SN, Johnson CA, Mozaffari-Jovin S, Lako M. PRPF8-mediated dysregulation of hBrr2 helicase disrupts human spliceosome kinetics and 5´-splice-site selection causing tissue-specific defects. Nat Commun 2024; 15:3138. [PMID: 38605034 PMCID: PMC11009313 DOI: 10.1038/s41467-024-47253-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
The carboxy-terminus of the spliceosomal protein PRPF8, which regulates the RNA helicase Brr2, is a hotspot for mutations causing retinitis pigmentosa-type 13, with unclear role in human splicing and tissue-specificity mechanism. We used patient induced pluripotent stem cells-derived cells, carrying the heterozygous PRPF8 c.6926 A > C (p.H2309P) mutation to demonstrate retinal-specific endophenotypes comprising photoreceptor loss, apical-basal polarity and ciliary defects. Comprehensive molecular, transcriptomic, and proteomic analyses revealed a role of the PRPF8/Brr2 regulation in 5'-splice site (5'SS) selection by spliceosomes, for which disruption impaired alternative splicing and weak/suboptimal 5'SS selection, and enhanced cryptic splicing, predominantly in ciliary and retinal-specific transcripts. Altered splicing efficiency, nuclear speckles organisation, and PRPF8 interaction with U6 snRNA, caused accumulation of active spliceosomes and poly(A)+ mRNAs in unique splicing clusters located at the nuclear periphery of photoreceptors. Collectively these elucidate the role of PRPF8/Brr2 regulatory mechanisms in splicing and the molecular basis of retinal disease, informing therapeutic approaches.
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Affiliation(s)
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | - Albert Lahat
- Department of Biosciences, Durham University, Durham, UK
| | | | - Yanlong Ji
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Marina Moya Molina
- Biosciences Institute, Newcastle University, Newcastle, UK
- Newcells Biotech, Newcastle, UK
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Rachel Queen
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Birthe Dorgau
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Avril Watson
- Biosciences Institute, Newcastle University, Newcastle, UK
- Newcells Biotech, Newcastle, UK
| | | | - Ross Laws
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | - Abhijit Saxena
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Chia Shyan Beh
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | | | | | - Tracey Davey
- Electron Microscopy Research Services, Newcastle University, Newcastle, UK
| | | | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Reinhard Lührmann
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - David H Steel
- Biosciences Institute, Newcastle University, Newcastle, UK
| | | | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Henning Urlaub
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg August University of Göttingen, Göttingen, Germany
| | - Robin R Ali
- Centre for Cell and Gene Therapy, Kings College London, London, UK
| | - Sushma-Nagaraja Grellscheid
- Department of Biosciences, Durham University, Durham, UK
- Department of Informatics, University of Bergen, Bergen, Norway
| | - Colin A Johnson
- Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
| | - Sina Mozaffari-Jovin
- Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.
- Department of Medical Genetics and Medical Genetics Research Center, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle, UK.
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2
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Aweidah H, Xi Z, Sahel JA, Byrne LC. PRPF31-retinitis pigmentosa: Challenges and opportunities for clinical translation. Vision Res 2023; 213:108315. [PMID: 37714045 PMCID: PMC10872823 DOI: 10.1016/j.visres.2023.108315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/17/2023]
Abstract
Mutations in pre-mRNA processing factor 31 cause autosomal dominant retinitis pigmentosa (PRPF31-RP), for which there is currently no efficient treatment, making this disease a prime target for the development of novel therapeutic strategies. PRPF31-RP exhibits incomplete penetrance due to haploinsufficiency, in which reduced levels of gene expression from the mutated allele result in disease. A variety of model systems have been used in the investigation of disease etiology and therapy development. In this review, we discuss recent advances in both in vivo and in vitro model systems, evaluating their advantages and limitations in the context of therapy development for PRPF31-RP. Additionally, we describe the latest approaches for treatment, including AAV-mediated gene augmentation, genome editing, and late-stage therapies such as optogenetics, cell transplantation, and retinal prostheses.
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Affiliation(s)
- Hamzah Aweidah
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhouhuan Xi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Ophthalmology, Eye Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
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3
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Keuthan CJ, Karma S, Zack DJ. Alternative RNA Splicing in the Retina: Insights and Perspectives. Cold Spring Harb Perspect Med 2023; 13:a041313. [PMID: 36690463 PMCID: PMC10547393 DOI: 10.1101/cshperspect.a041313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Alternative splicing is a fundamental and highly regulated post-transcriptional process that enhances transcriptome and proteome diversity. This process is particularly important in neuronal tissues, such as the retina, which exhibit some of the highest levels of differentially spliced genes in the body. Alternative splicing is regulated both temporally and spatially during neuronal development, can be cell-type-specific, and when altered can cause a number of pathologies, including retinal degeneration. Advancements in high-throughput sequencing technologies have facilitated investigations of the alternative splicing landscape of the retina in both healthy and disease states. Additionally, innovations in human stem cell engineering, specifically in the generation of 3D retinal organoids, which recapitulate many aspects of the in vivo retinal microenvironment, have aided studies of the role of alternative splicing in human retinal development and degeneration. Here we review these advances and discuss the ongoing development of strategies for the treatment of alternative splicing-related retinal disease.
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Affiliation(s)
- Casey J Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Sadik Karma
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Donald J Zack
- Departments of Ophthalmology, Wilmer Eye Institute, Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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4
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Hristov BH, Noble WS, Bertero A. Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558852. [PMID: 37790381 PMCID: PMC10542540 DOI: 10.1101/2023.09.21.558852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Most studies of genome organization have focused on intra-chromosomal (cis) contacts because they harbor key features such as DNA loops and topologically associating domains. Inter-chromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework to identify sets of loci that jointly interact in trans from Hi-C data. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts: the Plasmodium falciparum var genes, the mouse olfactory receptor "Greek islands", and the human RBM20 cardiac splicing factory. We then apply trans-C to systematically test the hypothesis that genes co-regulated by the same trans-acting element (i.e., a transcription or splicing factor) co-localize in three dimensions to form "RNA factories" that maximize the efficiency and accuracy of RNA biogenesis. We find that many loci with multiple binding sites of the same transcription factor interact with one another in trans, especially those bound by transcription factors with intrinsically disordered domains. Similarly, clustered binding of a subset of RNA binding proteins correlates with trans interaction of the encoding loci. These findings support the existence of trans interacting chromatin domains (TIDs) driven by RNA biogenesis. Trans-C provides an efficient computational framework for studying these and other types of trans interactions, empowering studies of a poorly understood aspect of genome architecture.
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Affiliation(s)
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | - Alessandro Bertero
- Molecular Biotechnology Center “Guido Tarone”, Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy
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5
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Lu J, Zheng KQ, Bertrand RE, Quinlan J, Ferdous S, Srinivasan T, Oh S, Wang K, Chen R. Gene augmentation therapy to rescue degenerative photoreceptors in a Cwc27 mutant mouse model. Exp Eye Res 2023; 234:109596. [PMID: 37479075 DOI: 10.1016/j.exer.2023.109596] [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: 04/24/2023] [Revised: 06/18/2023] [Accepted: 07/18/2023] [Indexed: 07/23/2023]
Abstract
Previous reports have demonstrated that defects in the spliceosome-associated protein CWC27 can lead to the degeneration of retinal cells in Cwc27 mutant mouse models. However, it is unknown whether gene replacement therapy can rescue this phenotype. The purpose of this study was to evaluate whether AAV based gene therapy could rescue the retinal degeneration observed in Cwc27 mutant mice. By 6 months of age, Cwc27 mutant mice show a retinal degenerative phenotype, including morphological and functional abnormalities, primarily driven by the death of photoreceptors. We hypothesize that subretinal injection of AAV8 to drive exogenous CWC27 protein expression will improve the retinal phenotype. We evaluated these improvements after gene therapy with electroretinography (ERG) and histology, either hematoxylin and eosin (H&E) or immunostaining. In this study, we demonstrated that subretinal injection of AAV8-GRK-Cwc27-FLAG in mutant mice can improve the functionality and morphology of the retina. Immunostaining analyses revealed a notable decrease in photoreceptor degeneration, including cone cell degeneration, in the AAV-injected eyes compared to the PBS-injected eyes. Based on these results, gene replacement therapy could be a promising method for treating retinal degeneration caused by mutations in Cwc27.
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Affiliation(s)
- Jiaxiong Lu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Karen Q Zheng
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of BioSciences, Rice University, Houston, TX, USA
| | - Renae Elaine Bertrand
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph Quinlan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Bioengineering, Rice University, Houston, TX, USA
| | - Salma Ferdous
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tanmay Srinivasan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of BioSciences, Rice University, Houston, TX, USA
| | - Soo Oh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Keqing Wang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rui Chen
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA; Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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6
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Krausová M, Kreplová M, Banik P, Cvačková Z, Kubovčiak J, Modrák M, Zudová D, Lindovský J, Kubik-Zahorodna A, Pálková M, Kolář M, Procházka J, Sedláček R, Staněk D. Retinitis pigmentosa-associated mutations in mouse Prpf8 cause misexpression of circRNAs and degeneration of cerebellar granule cells. Life Sci Alliance 2023; 6:e202201855. [PMID: 37019475 PMCID: PMC10078954 DOI: 10.26508/lsa.202201855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 04/07/2023] Open
Abstract
A subset of patients with retinitis pigmentosa (RP) carry mutations in several spliceosomal components including the PRPF8 protein. Here, we established two alleles of murine Prpf8 that genocopy or mimic aberrant PRPF8 found in RP patients-the substitution p.Tyr2334Asn and an extended protein variant p.Glu2331ValfsX15. Homozygous mice expressing the aberrant Prpf8 variants developed within the first 2 mo progressive atrophy of the cerebellum because of extensive granule cell loss, whereas other cerebellar cells remained unaffected. We further show that a subset of circRNAs were deregulated in the cerebellum of both Prpf8-RP mouse strains. To identify potential risk factors that sensitize the cerebellum for Prpf8 mutations, we monitored the expression of several splicing proteins during the first 8 wk. We observed down-regulation of all selected splicing proteins in the WT cerebellum, which coincided with neurodegeneration onset. The decrease in splicing protein expression was further pronounced in mouse strains expressing mutated Prpf8. Collectively, we propose a model where physiological reduction in spliceosomal components during postnatal tissue maturation sensitizes cells to the expression of aberrant Prpf8 and the subsequent deregulation of circRNAs triggers neuronal death.
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Affiliation(s)
- Michaela Krausová
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Michaela Kreplová
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Poulami Banik
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Zuzana Cvačková
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Kubovčiak
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Modrák
- Core Facility Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Dagmar Zudová
- Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec, Czech Republic
| | - Jiří Lindovský
- Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec, Czech Republic
| | - Agnieszka Kubik-Zahorodna
- Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec, Czech Republic
| | - Marcela Pálková
- Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec, Czech Republic
| | - Michal Kolář
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Procházka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec, Czech Republic
| | - Radislav Sedláček
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
- Czech Centre for Phenogenomics, Institute of Molecular Genetics, Czech Academy of Sciences, Vestec, Czech Republic
| | - David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
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7
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Challenges and Opportunities in the Genetic Analysis of Inherited Retinal Dystrophies in Africa, a Literature Review. J Pers Med 2023; 13:jpm13020239. [PMID: 36836473 PMCID: PMC9964248 DOI: 10.3390/jpm13020239] [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: 12/26/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 01/31/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are a global problem that is largely unaddressed, especially in Africa. Black indigenous Africans are rarely represented in research that develops genetic tests and genetic therapies for IRDs, yet their genomes are more diverse. The aim of this literature review is to synthesize information on the IRD genetic research conducted among indigenous black Africans to identify challenges and opportunities for progress. PubMed was searched to identify empirical publications reporting the genetic analysis of IRDs among indigenous Africans. A total of 11 articles were selected for the review. Based on the information in the articles, the main genetic testing methods in use include next-generation, whole exome, and Sanger sequencing. The main IRDs characterized by the genetic tests include retinitis pigmentosa, Leber Congenital Amaurosis, Stagardt disease, and cone dystrophy. Examples of implicated genes include MERTK, GUCY2D, ABCA4, and KCNV2 for the four IRDs, respectively. Research activities on the genetics of IRDs are generally scanty in Africa. Even in South Africa and North Africa where some research activities were noted, only a few indigenous black Africans were included in the study cohorts. There is an urgent need for genetic research on IRDs, especially in East, Central, and West Africa.
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8
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PRPF8 increases the aggressiveness of hepatocellular carcinoma by regulating FAK/AKT pathway via fibronectin 1 splicing. Exp Mol Med 2023; 55:132-142. [PMID: 36609600 PMCID: PMC9898568 DOI: 10.1038/s12276-022-00917-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/18/2022] [Accepted: 11/08/2022] [Indexed: 01/09/2023] Open
Abstract
Hepatocellular carcinoma (HCC) pathogenesis is associated with alterations in splicing machinery components (spliceosome and splicing factors) and aberrant expression of oncogenic splice variants. We aimed to analyze the expression and potential role of the spliceosome component PRPF8 (pre-mRNA processing factor 8) in HCC. PRPF8 expression (mRNA/protein) was analyzed in a retrospective cohort of HCC patients (n = 172 HCC and nontumor tissues) and validated in two in silico cohorts (TCGA and CPTAC). PRPF8 expression was silenced in liver cancer cell lines and in xenograft tumors to understand the functional and mechanistic consequences. In silico RNAseq and CLIPseq data were also analyzed. Our results indicate that PRPF8 is overexpressed in HCC and associated with increased tumor aggressiveness (patient survival, etc.), expression of HCC-related splice variants, and modulation of critical genes implicated in cancer-related pathways. PRPF8 silencing ameliorated aggressiveness in vitro and decreased tumor growth in vivo. Analysis of in silico CLIPseq data in HepG2 cells demonstrated that PRPF8 binds preferentially to exons of protein-coding genes, and RNAseq analysis showed that PRPF8 silencing alters splicing events in multiple genes. Integrated and in vitro analyses revealed that PRPF8 silencing modulates fibronectin (FN1) splicing, promoting the exclusion of exon 40.2, which is paramount for binding to integrins. Consistent with this finding, PRPF8 silencing reduced FAK/AKT phosphorylation and blunted stress fiber formation. Indeed, HepG2 and Hep3B cells exhibited a lower invasive capacity in membranes treated with conditioned medium from PRPF8-silenced cells compared to medium from scramble-treated cells. This study demonstrates that PRPF8 is overexpressed and associated with aggressiveness in HCC and plays important roles in hepatocarcinogenesis by altering FN1 splicing, FAK/AKT activation and stress fiber formation.
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9
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Gene augmentation prevents retinal degeneration in a CRISPR/Cas9-based mouse model of PRPF31 retinitis pigmentosa. Nat Commun 2022; 13:7695. [PMID: 36509783 PMCID: PMC9744804 DOI: 10.1038/s41467-022-35361-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa, an untreatable form of blindness. Gene therapy is a promising treatment for PRPF31-retinitis pigmentosa, however, there are currently no suitable animal models in which to develop AAV-mediated gene augmentation. Here we establish Prpf31 mutant mouse models using AAV-mediated CRISPR/Cas9 knockout, and characterize the resulting retinal degeneration phenotype. Mouse models with early-onset morphological and functional impairments like those in patients were established, providing new platforms in which to investigate pathogenetic mechanisms and develop therapeutic methods. AAV-mediated PRPF31 gene augmentation restored the retinal structure and function in a rapidly degenerating mouse model, demonstrating the first in vivo proof-of-concept for AAV-mediated gene therapy to treat PRPF31-retinitis pigmentosa. AAV-CRISPR/Cas9-PRPF31 knockout constructs also mediated efficient PRPF31 knockout in human and non-human primate retinal explants, laying a foundation for establishing non-human primate models using the method developed here.
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10
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Nazlamova L, Villa Vasquez SS, Lord J, Karthik V, Cheung MK, Lakowski J, Wheway G. Microtubule modification defects underlie cilium degeneration in cell models of retinitis pigmentosa associated with pre-mRNA splicing factor mutations. Front Genet 2022; 13:1009430. [PMID: 36176300 PMCID: PMC9513239 DOI: 10.3389/fgene.2022.1009430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common cause of hereditary blindness, and may occur in isolation as a non-syndromic condition or alongside other features in a syndromic presentation. Biallelic or monoallelic mutations in one of eight genes encoding pre-mRNA splicing factors are associated with non-syndromic RP. The molecular mechanism of disease remains incompletely understood, limiting opportunities for targeted treatment. Here we use CRISPR and base edited PRPF6 and PRPF31 mutant cell lines, and publicly-available data from human PRPF31+/− patient derived retinal organoids and PRPF31 siRNA-treated organotypic retinal cultures to confirm an enrichment of differential splicing of microtubule, centrosomal, cilium and DNA damage response pathway genes in these cells. We show that genes with microtubule/centrosome/centriole/cilium gene ontology terms are enriched for weak 3′ and 5′ splice sites, and that subtle defects in spliceosome activity predominantly affect efficiency of splicing of these exons. We suggest that the primary defect in PRPF6 or PRPF31 mutant cells is microtubule and centrosomal defects, leading to defects in cilium and mitotic spindle stability, with the latter leading to DNA damage, triggering differential splicing of DNA damage response genes to activate this pathway. Finally, we expand understanding of “splicing factor RP” by investigating the function of TTLL3, one of the most statistically differentially expressed genes in PRPF6 and PRPF31 mutant cells. We identify that TTLL3 is the only tubulin glycylase expressed in the human retina, essential for monoglycylation of microtubules of the cilium, including the retinal photoreceptor cilium, to prevent cilium degeneration and retinal degeneration. Our preliminary data suggest that rescue of tubulin glycylation through overexpression of TTLL3 is sufficient to rescue cilium number in PRPF6 and PRPF31 mutant cells, suggesting that this defect underlies the cellular defect and may represent a potential target for therapeutic intervention in this group of disorders.
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Affiliation(s)
- Liliya Nazlamova
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Suly Saray Villa Vasquez
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jenny Lord
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Varshini Karthik
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Man-Kim Cheung
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Jörn Lakowski
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gabrielle Wheway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- *Correspondence: Gabrielle Wheway,
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11
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O'Grady L, Schrier Vergano SA, Hoffman TL, Sarco D, Cherny S, Bryant E, Schultz-Rogers L, Chung WK, Sacharow S, Immken LL, Holder S, Blackwell RR, Buchanan C, Yusupov R, Lecoquierre F, Guerrot AM, Rodan L, de Vries BBA, Kamsteeg EJ, Santos Simarro F, Palomares-Bralo M, Brown N, Pais L, Ferrer A, Klee EW, Babovic-Vuksanovic D, Rhodes L, Person R, Begtrup A, Keller-Ramey J, Santiago-Sim T, Schnur RE, Sweetser DA, Gold NB. Heterozygous variants in PRPF8 are associated with neurodevelopmental disorders. Am J Med Genet A 2022; 188:2750-2759. [PMID: 35543142 DOI: 10.1002/ajmg.a.62772] [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: 03/15/2022] [Revised: 03/22/2022] [Accepted: 04/05/2022] [Indexed: 01/25/2023]
Abstract
The pre-mRNA-processing factor 8, encoded by PRPF8, is a scaffolding component of a spliceosome complex involved in the removal of introns from mRNA precursors. Previously, heterozygous pathogenic variants in PRPF8 have been associated with autosomal dominant retinitis pigmentosa. More recently, PRPF8 was suggested as a candidate gene for autism spectrum disorder due to the enrichment of sequence variants in this gene in individuals with neurodevelopmental disorders. We report 14 individuals with various forms of neurodevelopmental conditions, found to have heterozygous, predominantly de novo, missense, and loss-of-function variants in PRPF8. These individuals have clinical features that may represent a new neurodevelopmental syndrome.
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Affiliation(s)
- Lauren O'Grady
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA.,MGH Institute of Health Professions, Charlestown, Massachusetts, USA
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughter, Norfolk, Virginia, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia, USA
| | - Trevor L Hoffman
- Department of Genetics, Southern California Kaiser Permanente Medical Group, Anaheim, California, USA
| | - Dean Sarco
- Department of Neurology, Kaiser Permanente-Los Angeles Medical Center, Los Angeles, California, USA
| | - Sara Cherny
- Division of Cardiology, Ann & Robert H. Lurie Children's Hospital, Chicago, Illinois, USA
| | - Emily Bryant
- Division of Neurology, Ann & Robert H. Lurie Children's Hospital, Chicago, Illinois, USA
| | - Laura Schultz-Rogers
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Stephanie Sacharow
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Ladonna L Immken
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Susan Holder
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Rebecca R Blackwell
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Catherine Buchanan
- Department of Clinical & Metabolic Genetics, Dell Children's Medical Group, Austin, Texas, USA
| | - Roman Yusupov
- Division of Pediatric Genetics, Joe DiMaggio Children's Hospital, Hollywood, Florida, USA
| | - François Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, Rouen, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, FHU G4 Génomique, Normandie University, UNIROUEN, Inserm U1245, CHU Rouen, Rouen, France
| | - Lance Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - Erik Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center and Donders Institute for Brain, Cognition and Behavior, Nijmegen, The Netherlands
| | - Fernando Santos Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Maria Palomares-Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Natasha Brown
- Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia.,Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Lynn Pais
- Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | | | | | | - David A Sweetser
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
| | - Nina B Gold
- Division of Medical Genetics and Metabolism, Massachusetts General Hospital for Children, Boston, Massachusetts, USA
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12
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Autophagy regulation by RNA alternative splicing and implications in human diseases. Nat Commun 2022; 13:2735. [PMID: 35585060 PMCID: PMC9117662 DOI: 10.1038/s41467-022-30433-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Autophagy and RNA alternative splicing are two evolutionarily conserved processes involved in overlapping physiological and pathological processes. However, the extent of functional connection is not well defined. Here, we consider the role for alternative splicing and generation of autophagy-related gene isoforms in the regulation of autophagy in recent work. The impact of changes to the RNA alternative splicing machinery and production of alternative spliced isoforms on autophagy are reviewed with particular focus on disease relevance. The use of drugs targeting both alternative splicing and autophagy as well as the selective regulation of single autophagy-related protein isoforms, are considered as therapeutic strategies. Both alternative splicing and autophagy are core cell biological processes, but where they intersect has received little attention. Here, the authors reflect on recent connections identified between these pathways and consider their impact on human disease.
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13
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Wang J, Tao Z, Deng H, Cui Y, Xu Z, Lyu Q, Zhao J. Therapeutic implications of nanodrug and tissue engineering for retinal pigment epithelium-related diseases. NANOSCALE 2022; 14:5657-5677. [PMID: 35352082 DOI: 10.1039/d1nr08337f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The retinal pigment epithelium (RPE), as a single layer of cells that performs multiple functions posteriorly in the eye, is a promising target site for the prevention and treatment of several clinical diseases, including proliferative diabetic retinopathy, age-related macular degeneration, chorionic neovascularization, and retinitis pigmentosa. In recent decades, several nanodrug delivery platforms and tissue-engineered RPE have been widely developed to treat RPE-related diseases. This work summarizes the recent advances in nanoplatforms and tissue engineering scaffolds developed in these fields. The diseases associated with pathological RPE and their common therapy strategies are first introduced. Then, the recent progress made with a variety of drug delivery systems is presented, with an emphasis on the modification strategies of nanomaterials for targeted delivery. Tissue engineering-mediated RPE transplantation for treating these diseases is subsequently described. Finally, the clinical translation challenges in these fields are discussed in depth. This article will offer readers a better understanding of emerging nanotechnology and tissue engineering related to the treatment of RPE-related diseases and could facilitate their widespread use in experiments in vivo and in clinical applications.
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Affiliation(s)
- Jiao Wang
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Shenzhen Eye Hospital affiliated to Jinan University, School of Optometry, Shenzhen University, Shenzhen 518000, China.
| | - Zhengyang Tao
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Shenzhen Eye Hospital affiliated to Jinan University, School of Optometry, Shenzhen University, Shenzhen 518000, China.
| | - Hongwei Deng
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Shenzhen Eye Hospital affiliated to Jinan University, School of Optometry, Shenzhen University, Shenzhen 518000, China.
| | - Yubo Cui
- Department of Ophthalmology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China.
| | - Zhirong Xu
- Jinzhou Medical University, Jinzhou, Liaoning 121000, P.R. China
| | - Qinghua Lyu
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Shenzhen Eye Hospital affiliated to Jinan University, School of Optometry, Shenzhen University, Shenzhen 518000, China.
- Institute of Microscale Optoelectronics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jun Zhao
- Department of Ophthalmology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China.
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14
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Georgiou M, Yang C, Atkinson R, Pan K, Buskin A, Molina MM, Collin J, Al‐Aama J, Goertler F, Ludwig SEJ, Davey T, Lührmann R, Nagaraja‐Grellscheid S, Johnson CA, Ali R, Armstrong L, Korolchuk V, Urlaub H, Mozaffari‐Jovin S, Lako M. Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells. Clin Transl Med 2022; 12:e759. [PMID: 35297555 PMCID: PMC8926896 DOI: 10.1002/ctm2.759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION Mutations in pre-mRNA processing factor 31 (PRPF31), a core protein of the spliceosomal tri-snRNP complex, cause autosomal-dominant retinitis pigmentosa (adRP). It has remained an enigma why mutations in ubiquitously expressed tri-snRNP proteins result in retina-specific disorders, and so far, the underlying mechanism of splicing factors-related RP is poorly understood. METHODS We used the induced pluripotent stem cell (iPSC) technology to generate retinal organoids and RPE models from four patients with severe and very severe PRPF31-adRP, unaffected individuals and a CRISPR/Cas9 isogenic control. RESULTS To fully assess the impacts of PRPF31 mutations, quantitative proteomics analyses of retinal organoids and RPE cells were carried out showing RNA splicing, autophagy and lysosome, unfolded protein response (UPR) and visual cycle-related pathways to be significantly affected. Strikingly, the patient-derived RPE and retinal cells were characterised by the presence of large amounts of cytoplasmic aggregates containing the mutant PRPF31 and misfolded, ubiquitin-conjugated proteins including key visual cycle and other RP-linked tri-snRNP proteins, which accumulated progressively with time. The mutant PRPF31 variant was not incorporated into splicing complexes, but reduction of PRPF31 wild-type levels led to tri-snRNP assembly defects in Cajal bodies of PRPF31 patient retinal cells, altered morphology of nuclear speckles and reduced formation of active spliceosomes giving rise to global splicing dysregulation. Moreover, the impaired waste disposal mechanisms further exacerbated aggregate formation, and targeting these by activating the autophagy pathway using Rapamycin reduced cytoplasmic aggregates, leading to improved cell survival. CONCLUSIONS Our data demonstrate that it is the progressive aggregate accumulation that overburdens the waste disposal machinery rather than direct PRPF31-initiated mis-splicing, and thus relieving the RPE cells from insoluble cytoplasmic aggregates presents a novel therapeutic strategy that can be combined with gene therapy studies to fully restore RPE and retinal cell function in PRPF31-adRP patients.
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Affiliation(s)
- Maria Georgiou
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Chunbo Yang
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Robert Atkinson
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Kuan‐Ting Pan
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Adriana Buskin
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | - Joseph Collin
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Jumana Al‐Aama
- Faculty of MedicineKing Abdulaziz UniversitySaudi Arabia
| | | | | | - Tracey Davey
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | | | | | | | - Lyle Armstrong
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | - Henning Urlaub
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Bioanalytics, Department of Clinical ChemistryUniversity Medical CenterGoettingenGermany
| | - Sina Mozaffari‐Jovin
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Medical Genetics Research CenterMashhad University of Medical SciencesMashhadIran
- Department of Medical Genetics, Faculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Majlinda Lako
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
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15
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Shen XL, Yuan JF, Qin XH, Song GP, Hu HB, Tu HQ, Song ZQ, Li PY, Xu YL, Li S, Jian XX, Li JN, He CY, Yu XP, Liang LY, Wu M, Han QY, Wang K, Li AL, Zhou T, Zhang YC, Wang N, Li HY. LUBAC regulates ciliogenesis by promoting CP110 removal from the mother centriole. J Cell Biol 2022; 221:212875. [PMID: 34813648 PMCID: PMC8614155 DOI: 10.1083/jcb.202105092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/13/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022] Open
Abstract
Primary cilia transduce diverse signals in embryonic development and adult tissues. Defective ciliogenesis results in a series of human disorders collectively known as ciliopathies. The CP110–CEP97 complex removal from the mother centriole is an early critical step for ciliogenesis, but the underlying mechanism for this step remains largely obscure. Here, we reveal that the linear ubiquitin chain assembly complex (LUBAC) plays an essential role in ciliogenesis by targeting the CP110–CEP97 complex. LUBAC specifically generates linear ubiquitin chains on CP110, which is required for CP110 removal from the mother centriole in ciliogenesis. We further identify that a pre-mRNA splicing factor, PRPF8, at the distal end of the mother centriole acts as the receptor of the linear ubiquitin chains to facilitate CP110 removal at the initial stage of ciliogenesis. Thus, our study reveals a direct mechanism of regulating CP110 removal in ciliogenesis and implicates the E3 ligase LUBAC as a potential therapy target of cilia-associated diseases, including ciliopathies and cancers.
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Affiliation(s)
- Xiao-Lin Shen
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Jin-Feng Yuan
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Xuan-He Qin
- School of Life Sciences and Technology, Tongji University, Shanghai, China.,Shanghai East Hospital, Tongji University, Shanghai, China
| | - Guang-Ping Song
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Huai-Bin Hu
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Hai-Qing Tu
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Zeng-Qing Song
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Pei-Yao Li
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Yu-Ling Xu
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Sen Li
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Xiao-Xiao Jian
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Jia-Ning Li
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Chun-Yu He
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Xi-Ping Yu
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Li-Yun Liang
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Min Wu
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Qiu-Ying Han
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Kai Wang
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Ai-Ling Li
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Tao Zhou
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Yu-Cheng Zhang
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Na Wang
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China
| | - Hui-Yan Li
- Nanhu Laboratory, State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Beijing, China.,School of Basic Medical Sciences, Fudan University, Shanghai, China
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16
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Rodríguez-Muñoz A, García-Bohórquez B, Udaondo P, Hervás-Ontiveros A, Salom D, Aller E, Jaijo T, García-García G, Millán J. CONCOMITANT MUTATIONS IN INHERITED RETINAL DYSTROPHIES: Why the Reproductive and Therapeutic Counseling Should Be Addressed Cautiously. Retina 2021; 41:1966-1975. [PMID: 33411470 DOI: 10.1097/iae.0000000000003103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE To highlight the challenge of correct reproductive and therapeutic counseling in complex pedigrees with different inherited retinal dystrophies (IRD). METHODS Two hundred eight patients diagnosed with nonsyndromic IRD underwent full ophthalmologic examination and molecular analysis using targeted next-generation sequencing. RESULTS Five families (4%) carried mutations in more than one gene that contribute to different IRD. Family fRPN-NB had a dominant mutation in SNRNP200, which was present in nine affected individuals and four unaffected, and a mutation in RP2 among 11 family members. Family fRPN-142 carried a mutation in RPGR that cosegregated with the disease in all affected individuals. In addition, the proband also harbored two disease-causing mutations in the genes BEST1 and SNRNP200. Family fRPN-169 beared compound heterozygous mutations in USH2A and a dominant mutation in RP1. Genetic testing of fRPN-194 determined compound heterozygous mutations in CNGA3 and a dominant mutation in PRPF8 only in the proband. Finally, fRPN-219 carried compound heterozygous mutations in the genes ABCA4 and TYR. CONCLUSION These findings reinforce the complexity of IRD and underscore the need for the combination of high-throughput genetic testing and clinical characterization. Because of these features, the reproductive and therapeutic counseling for IRD must be approached with caution.
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Affiliation(s)
- Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
| | - Belén García-Bohórquez
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
| | - Patricia Udaondo
- Department of Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Ana Hervás-Ontiveros
- Department of Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - David Salom
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Department of Ophthalmology Hospital de Manises, Valencia, Spain; and
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Unit of Genetics, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Unit of Genetics, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
| | - José Millán
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
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17
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Yang C, Georgiou M, Atkinson R, Collin J, Al-Aama J, Nagaraja-Grellscheid S, Johnson C, Ali R, Armstrong L, Mozaffari-Jovin S, Lako M. Pre-mRNA Processing Factors and Retinitis Pigmentosa: RNA Splicing and Beyond. Front Cell Dev Biol 2021; 9:700276. [PMID: 34395430 PMCID: PMC8355544 DOI: 10.3389/fcell.2021.700276] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease characterized by progressive degeneration of photoreceptors and/or retinal pigment epithelium that eventually results in blindness. Mutations in pre-mRNA processing factors (PRPF3, 4, 6, 8, 31, SNRNP200, and RP9) have been linked to 15–20% of autosomal dominant RP (adRP) cases. Current evidence indicates that PRPF mutations cause retinal specific global spliceosome dysregulation, leading to mis-splicing of numerous genes that are involved in a variety of retina-specific functions and/or general biological processes, including phototransduction, retinol metabolism, photoreceptor disk morphogenesis, retinal cell polarity, ciliogenesis, cytoskeleton and tight junction organization, waste disposal, inflammation, and apoptosis. Importantly, additional PRPF functions beyond RNA splicing have been documented recently, suggesting a more complex mechanism underlying PRPF-RPs driven disease pathogenesis. The current review focuses on the key RP-PRPF genes, depicting the current understanding of their roles in RNA splicing, impact of their mutations on retinal cell’s transcriptome and phenome, discussed in the context of model species including yeast, zebrafish, and mice. Importantly, information on PRPF functions beyond RNA splicing are discussed, aiming at a holistic investigation of PRPF-RP pathogenesis. Finally, work performed in human patient-specific lab models and developing gene and cell-based replacement therapies for the treatment of PRPF-RPs are thoroughly discussed to allow the reader to get a deeper understanding of the disease mechanisms, which we believe will facilitate the establishment of novel and better therapeutic strategies for PRPF-RP patients.
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Affiliation(s)
- Chunbo Yang
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maria Georgiou
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Robert Atkinson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Joseph Collin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jumana Al-Aama
- Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Colin Johnson
- Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Robin Ali
- King's College London, London, United Kingdom
| | - Lyle Armstrong
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Majlinda Lako
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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18
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Kukhtar D, Rubio-Peña K, Serrat X, Cerón J. Mimicking of splicing-related retinitis pigmentosa mutations in C. elegans allow drug screens and identification of disease modifiers. Hum Mol Genet 2021; 29:756-765. [PMID: 31919495 DOI: 10.1093/hmg/ddz315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas and the high conservation of the spliceosome components facilitate the mimicking of human pathological mutations in splicing factors of model organisms. The degenerative retinal disease retinitis pigmentosa (RP) is caused by mutations in distinct types of genes, including missense mutations in splicing factors that provoke RP in an autosomal dominant form (s-adRP). Using CRISPR in Caenorhabditis elegans, we generated mutant strains to mimic s-adRP mutations reported in PRPF8 and SNRNP200. Whereas these inherited mutations are present in heterozygosis in patients, C. elegans allows the maintenance of these mutations as homozygotes, which is advantageous for genetic and drug screens. We found that snrp-200(cer23[V676L]) and prp-8(cer14[H2302del]) display pleiotropic phenotypes, including reduced fertility. However, snrp-200(cer24[S1080L]) and prp-8(cer22[R2303G]) are weak alleles suitable for RNAi screens for identifying genetic interactions, which could uncover potential disease modifiers. We screened a collection of RNAi clones for splicing-related genes and identified three splicing factors: isy-1/ISY1, cyn-15/PPWD1 and mog-2/SNRPA1, whose partial inactivation may modify the course of the disease. Interestingly, these three genes act as modifiers of prp-8(cer22) but not of snrp-200(cer24). Finally, a screen of the strong allele prp-8(cer14) with FDA-approved drugs did not identify molecules capable of alleviating the temperature-sensitive sterility. Instead, we detected drugs, such as dequalinium chloride, which exacerbated the phenotype, and therefore, are potentially harmful to s-adRP patients since they may accelerate the progression of the disease.
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Affiliation(s)
- Dmytro Kukhtar
- Modeling human diseases in C. elegans Group. Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Karinna Rubio-Peña
- Modeling human diseases in C. elegans Group. Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Xènia Serrat
- Modeling human diseases in C. elegans Group. Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 08908 Barcelona, Spain
| | - Julián Cerón
- Modeling human diseases in C. elegans Group. Genes, Disease and Therapy Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, 08908 Barcelona, Spain
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19
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Yang H, Beutler B, Zhang D. Emerging roles of spliceosome in cancer and immunity. Protein Cell 2021; 13:559-579. [PMID: 34196950 PMCID: PMC9232692 DOI: 10.1007/s13238-021-00856-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is catalyzed by an intricate ribonucleoprotein complex called the spliceosome. Although the spliceosome is considered to be general cell “housekeeping” machinery, mutations in core components of the spliceosome frequently correlate with cell- or tissue-specific phenotypes and diseases. In this review, we expound the links between spliceosome mutations, aberrant splicing, and human cancers. Remarkably, spliceosome-targeted therapies (STTs) have become efficient anti-cancer strategies for cancer patients with splicing defects. We also highlight the links between spliceosome and immune signaling. Recent studies have shown that some spliceosome gene mutations can result in immune dysregulation and notable phenotypes due to mis-splicing of immune-related genes. Furthermore, several core spliceosome components harbor splicing-independent immune functions within the cell, expanding the functional repertoire of these diverse proteins.
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Affiliation(s)
- Hui Yang
- Department of Neurosurgery, Huashan Hospital, Shanghai Key laboratory of Brain Function Restoration and Neural Regeneration, MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Duanwu Zhang
- Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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20
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Maxwell DW, O'Keefe RT, Roy S, Hentges KE. The role of splicing factors in retinitis pigmentosa: links to cilia. Biochem Soc Trans 2021; 49:1221-1231. [PMID: 34060618 DOI: 10.1042/bst20200798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 01/27/2023]
Abstract
Cilia are critical to numerous biological functions, both in development and everyday homeostatic processes. Diseases arising from genetic mutations that cause cilia dysfunction are termed ciliopathies. Several ubiquitously expressed splicing factors have been implicated in the condition Retinitis Pigmentosa (RP), a group of diseases characterised by the progressive degeneration of the retina. In many types of RP the disease affects the modified primary cilium of the photoreceptor cells and thus, these types of RP are considered ciliopathies. Here, we discuss sequence variants found within a number of these splicing factors, the resulting phenotypes, and the mechanisms underpinning disease pathology. Additionally, we discuss recent evidence investigating why RP patients with mutations in globally expressed splicing factors present with retina-specific phenotypes.
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Affiliation(s)
- Dale W Maxwell
- Division of Evolution and Genome Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, U.K
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Raymond T O'Keefe
- Division of Evolution and Genome Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, U.K
| | - Sudipto Roy
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
- Department of Pediatrics, National University of Singapore, 1E Kent Ridge Road, Singapore 119228, Singapore
| | - Kathryn E Hentges
- Division of Evolution and Genome Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PT, U.K
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21
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Liang Q, Wu N, Zaneveld S, Liu H, Fu S, Wang K, Bertrand R, Wang J, Li Y, Chen R. Transcript isoforms of Reep6 have distinct functions in the retina. Hum Mol Genet 2021; 30:1907-1918. [PMID: 34104971 DOI: 10.1093/hmg/ddab157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/21/2022] Open
Abstract
Much of the complexity of the eukaryotic cell transcriptome is due to the alternative splicing of mRNA. However, knowledge on how transcriptome complexity is translated into functional complexity remains limited. For example, although different isoforms of a gene may show distinct temporal and spatial expression patterns, it is largely unknown whether these isoforms encode proteins with distinct functions matching their expression pattern. In this report, we investigated the function and relationship of the two isoforms of Reep6, namely Reep6.1 and Reep6.2, in rod photoreceptor cells. These two isoforms result from the alternative splicing of exon 5 and show mutually exclusive expression patterns. Reep6.2 is the canonical isoform that is expressed in non-retinal tissues while Reep6.1 is the only expressed isoform in the adult retina. The Reep6.1 isoform-specific knockout mouse, Reep6E5/E5, is generated by deleting exon 5 and a homozygous deletion phenotypically displayed a rod degeneration phenotype comparable to a Reep6 full knockout mouse, indicating that the Reep6.1 isoform is essential for the rod photoreceptor cell survival. Consistent with the results obtained from a loss-of-function experiment, overexpression of Reep6.2 failed to rescue the rod degeneration phenotype of Reep6 knockout mice while overexpression of Reep6.1 does lead to rescue. These results demonstrate that, consistent with the expression pattern of the isoform, Reep6.1 has rod-specific functions that cannot be substituted by its canonical isoform. Our findings suggested that a strict regulation of splicing is required for the maintenance of photoreceptor cells.
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Affiliation(s)
- Qingnan Liang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Nathaniel Wu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Smriti Zaneveld
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hehe Liu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shangyi Fu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Keqing Wang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Renae Bertrand
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jun Wang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Yumei Li
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Rui Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
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22
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Arzalluz-Luque Á, Cabrera JL, Skottman H, Benguria A, Bolinches-Amorós A, Cuenca N, Lupo V, Dopazo A, Tarazona S, Delás B, Carballo M, Pascual B, Hernan I, Erceg S, Lukovic D. Mutant PRPF8 Causes Widespread Splicing Changes in Spliceosome Components in Retinitis Pigmentosa Patient iPSC-Derived RPE Cells. Front Neurosci 2021; 15:636969. [PMID: 33994920 PMCID: PMC8116631 DOI: 10.3389/fnins.2021.636969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is a rare, progressive disease that affects photoreceptors and retinal pigment epithelial (RPE) cells with blindness as a final outcome. Despite high medical and social impact, there is currently no therapeutic options to slow down the progression of or cure the disease. The development of effective therapies was largely hindered by high genetic heterogeneity, inaccessible disease tissue, and unfaithful model organisms. The fact that components of ubiquitously expressed splicing factors lead to the retina-specific disease is an additional intriguing question. Herein, we sought to correlate the retinal cell-type-specific disease phenotype with the splicing profile shown by a patient with autosomal recessive RP, caused by a mutation in pre-mRNA splicing factor 8 (PRPF8). In order to get insight into the role of PRPF8 in homeostasis and disease, we capitalize on the ability to generate patient-specific RPE cells and reveal differentially expressed genes unique to RPE cells. We found that spliceosomal complex and ribosomal functions are crucial in determining cell-type specificity through differential expression and alternative splicing (AS) and that PRPF8 mutation causes global changes in splice site selection and exon inclusion that particularly affect genes involved in these cellular functions. This finding corroborates the hypothesis that retinal tissue identity is conferred by a specific splicing program and identifies retinal AS events as a framework toward the design of novel therapeutic opportunities.
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Affiliation(s)
- Ángeles Arzalluz-Luque
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, València, Spain
| | - Jose Luis Cabrera
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Heli Skottman
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alberto Benguria
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Arantxa Bolinches-Amorós
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Research Center Principe Felipe, Valencia, Spain.,National Stem Cell Bank-Valencia Node, Research Center Principe Felipe, Valencia, Spain
| | - Nicolás Cuenca
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Vincenzo Lupo
- Unit of Genetics and Genomics of Neuromuscular and Neurodegenerative Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC). Madrid, Spain
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València, València, Spain
| | - Bárbara Delás
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Miguel Carballo
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Beatriz Pascual
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Imma Hernan
- Unitat de Genética Molecular, Hospital de Terrassa, Terrassa, Spain
| | - Slaven Erceg
- Stem Cells Therapies in Neurodegenerative Diseases Lab, Research Center Principe Felipe, Valencia, Spain.,National Stem Cell Bank-Valencia Node, Research Center Principe Felipe, Valencia, Spain.,Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain.,Department of Neuroregeneration, Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czechia
| | - Dunja Lukovic
- Rare Diseases Joint Units, IIS La Fe-CIPF, Valencia, Spain.,Retinal Degeneration Lab, Research Centre Principe Felipe, Valencia, Spain
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23
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Wood KA, Eadsforth MA, Newman WG, O'Keefe RT. The Role of the U5 snRNP in Genetic Disorders and Cancer. Front Genet 2021; 12:636620. [PMID: 33584830 PMCID: PMC7876476 DOI: 10.3389/fgene.2021.636620] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is performed by the spliceosome, a dynamic macromolecular complex consisting of five small uridine-rich ribonucleoprotein complexes (the U1, U2, U4, U5, and U6 snRNPs) and numerous auxiliary splicing factors. A plethora of human disorders are caused by genetic variants affecting the function and/or expression of splicing factors, including the core snRNP proteins. Variants in the genes encoding proteins of the U5 snRNP cause two distinct and tissue-specific human disease phenotypes – variants in PRPF6, PRPF8, and SNRP200 are associated with retinitis pigmentosa (RP), while variants in EFTUD2 and TXNL4A cause the craniofacial disorders mandibulofacial dysostosis Guion-Almeida type (MFDGA) and Burn-McKeown syndrome (BMKS), respectively. Furthermore, recurrent somatic mutations or changes in the expression levels of a number of U5 snRNP proteins (PRPF6, PRPF8, EFTUD2, DDX23, and SNRNP40) have been associated with human cancers. How and why variants in ubiquitously expressed spliceosome proteins required for pre-mRNA splicing in all human cells result in tissue-restricted disease phenotypes is not clear. Additionally, why variants in different, yet interacting, proteins making up the same core spliceosome snRNP result in completely distinct disease outcomes – RP, craniofacial defects or cancer – is unclear. In this review, we define the roles of different U5 snRNP proteins in RP, craniofacial disorders and cancer, including how disease-associated genetic variants affect pre-mRNA splicing and the proposed disease mechanisms. We then propose potential hypotheses for how U5 snRNP variants cause tissue specificity resulting in the restricted and distinct human disorders.
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Affiliation(s)
- Katherine A Wood
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Megan A Eadsforth
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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24
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Gebauer F, Schwarzl T, Valcárcel J, Hentze MW. RNA-binding proteins in human genetic disease. Nat Rev Genet 2020; 22:185-198. [PMID: 33235359 DOI: 10.1038/s41576-020-00302-y] [Citation(s) in RCA: 287] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2020] [Indexed: 12/27/2022]
Abstract
RNA-binding proteins (RBPs) are critical effectors of gene expression, and as such their malfunction underlies the origin of many diseases. RBPs can recognize hundreds of transcripts and form extensive regulatory networks that help to maintain cell homeostasis. System-wide unbiased identification of RBPs has increased the number of recognized RBPs into the four-digit range and revealed new paradigms: from the prevalence of structurally disordered RNA-binding regions with roles in the formation of membraneless organelles to unsuspected and potentially pervasive connections between intermediary metabolism and RNA regulation. Together with an increasingly detailed understanding of molecular mechanisms of RBP function, these insights are facilitating the development of new therapies to treat malignancies. Here, we provide an overview of RBPs involved in human genetic disorders, both Mendelian and somatic, and discuss emerging aspects in the field with emphasis on molecular mechanisms of disease and therapeutic interventions.
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Affiliation(s)
- Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain. .,University Pompeu Fabra (UPF), Barcelona, Spain.
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Juan Valcárcel
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,University Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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25
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Spliceosomal factor mutations and mis-splicing in MDS. Best Pract Res Clin Haematol 2020; 33:101199. [PMID: 33038983 DOI: 10.1016/j.beha.2020.101199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Somatic, heterozygous missense and nonsense mutations in at least seven proteins that function in the spliceosome are found at high frequency in MDS patients. These proteins act at various steps in the process of splicing by the spliceosome and lead to characteristic alterations in the alternative splicing of a subset of genes. Several studies have investigated the effects of these mutations and have attempted to identify a commonly affected gene or pathway. Here, we summarize what is known about the normal function of these proteins and how the mutations alter the splicing landscape of the genome. We also summarize the commonly mis-spliced gene targets and discuss the state of mechanistic unification that has been achieved. Finally, we discuss alternative mechanisms by which these mutations may lead to disease.
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26
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Oxidative Stress, a Crossroad Between Rare Diseases and Neurodegeneration. Antioxidants (Basel) 2020; 9:antiox9040313. [PMID: 32326494 PMCID: PMC7222183 DOI: 10.3390/antiox9040313] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/06/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
Oxidative stress is an imbalance between production and accumulation of oxygen reactive species and/or reactive nitrogen species in cells and tissues, and the capacity of detoxifying these products, using enzymatic and non-enzymatic components, such as glutathione. Oxidative stress plays roles in several pathological processes in the nervous system, such as neurotoxicity, neuroinflammation, ischemic stroke, and neurodegeneration. The concepts of oxidative stress and rare diseases were formulated in the eighties, and since then, the link between them has not stopped growing. The present review aims to expand knowledge in the pathological processes associated with oxidative stress underlying some groups of rare diseases: Friedreich’s ataxia, diseases with neurodegeneration with brain iron accumulation, Charcot-Marie-Tooth as an example of rare neuromuscular disorders, inherited retinal dystrophies, progressive myoclonus epilepsies, and pediatric drug-resistant epilepsies. Despite the discrimination between cause and effect may not be easy on many occasions, all these conditions are Mendelian rare diseases that share oxidative stress as a common factor, and this may represent a potential target for therapies.
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27
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Ribeiro M, Furtado M, Martins S, Carvalho T, Carmo-Fonseca M. RNA Splicing Defects in Hypertrophic Cardiomyopathy: Implications for Diagnosis and Therapy. Int J Mol Sci 2020; 21:ijms21041329. [PMID: 32079122 PMCID: PMC7072897 DOI: 10.3390/ijms21041329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/27/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM), the most common inherited heart disease, is predominantly caused by mutations in genes that encode sarcomere-associated proteins. Effective gene-based diagnosis is critical for the accurate clinical management of patients and their family members. However, the introduction of high-throughput DNA sequencing approaches for clinical diagnostics has vastly expanded the number of variants of uncertain significance, leading to many inconclusive results that limit the clinical utility of genetic testing. More recently, developments in RNA analysis have been improving diagnostic outcomes by identifying new variants that interfere with splicing. This review summarizes recent discoveries of RNA mis-splicing in HCM and provides an overview of research that aims to apply the concept of RNA therapeutics to HCM.
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Affiliation(s)
- Marta Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
- Department of Bioengineering and iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Marta Furtado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Sandra Martins
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Teresa Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
- Correspondence:
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28
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Hamieh A, Nandrot EF. Retinal Pigment Epithelial Cells: The Unveiled Component in the Etiology of Prpf Splicing Factor-Associated Retinitis Pigmentosa. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1185:227-231. [PMID: 31884616 DOI: 10.1007/978-3-030-27378-1_37] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pre-mRNA splicing is a critical step in RNA processing in all eukaryotic cells. It consists of introns removal and requires the assembly of a large RNA-protein complex called the spliceosome. This complex of small nuclear ribonucleoproteins is associated with accessory proteins from the pre-mRNA processing factor (PRPF) family. Mutations in different splicing factor-encoding genes were identified in retinitis pigmentosa (RP) patients. A surprising feature of these ubiquitous factors is that the outcome of their alteration is restricted to the retina. Because of their high metabolic demand, most studies focused on photoreceptors dysfunction and associated degeneration. However, cells from the retinal pigment epithelium (RPE) are also crucial to maintaining retinal homeostasis and photoreceptor function. Moreover, mutations in RPE-specific genes are associated with some RP cases. Indeed, we identified major RPE defects in Prpf31-mutant mice: circadian rhythms of both photoreceptor outer segments (POS) phagocytosis and retinal adhesion were attenuated or lost, leading to ultrastructural anomalies and vacuoles. Taken together, our published and ongoing data suggest that (1) similar molecular events take place in human and mouse cells and (2) these functional defects generate various stress processes.
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Affiliation(s)
- Abdallah Hamieh
- Therapeutics Department, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Emeline F Nandrot
- Therapeutics Department, Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
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29
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Ritter M, Arno G, Ba-Abbad R, Holder GE, Webster AR. Macular maldevelopment in ATF6-mediated retinal dysfunction. Ophthalmic Genet 2020; 40:564-569. [PMID: 31900015 DOI: 10.1080/13816810.2019.1706749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background: Achromatopsia has been previously associated with mutations in the ATF6 gene. Rod-monochromatism, foveal hypoplasia, and disruption of the subfoveal photoreceptor layer are described as phenotypical features. We report detailed structural and electrophysiological assessment of two patients from two families, one manifesting severe macular maldevelopment and one with foveal hypoplasia.Materials and methods: The patients underwent a complete ophthalmic examination including electroretinography (ERG), spectral-domain optical coherence tomography (SD-OCT), fundus autofluorescence, and fundus photography. Genetic testing was performed by next-generation sequencing.Results: In one patient, fundoscopy and SD-OCT revealed well-demarcated coloboma-like excavated lesions at the central macula of both eyes. Genetic analysis identified a novel homozygous p.Asp140Ter mutation in the ATF6 gene. The second patient had foveal hypoplasia in association with a homozygous ATF6 mutation affecting a splice donor site (c.1187 + 5G>C). In both patients, electrophysiological assessment showed normal rod-specific (DA 0.01) and dark-adapted bright white-flash ERGs (DA 10.0). 30 Hz flicker ERGs were undetectable. There were low-amplitude single-flash photopic ERGs (LA 3.0) with timing and shape suggesting S-cone origin.Conclusions: The findings, particularly a case with severe macular maldevelopment, may expand on the phenotype previously associated with ATF6-mediated achromatopsia. In addition, the comprehensive electrophysiological assessment suggests that preserved S-cone activity can be detected in this particular molecular sub-type of cone dysfunction.
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Affiliation(s)
- Markus Ritter
- Moorfields Eye Hospital, London, UK.,Department of Ophthalmology, Medical University of Vienna, Vienna, Austria
| | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Rola Ba-Abbad
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, University College London, London, UK
| | - Graham E Holder
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, University College London, London, UK.,National University of Singapore, Department of Ophthalmology, National University Hospital, Singapore
| | - Andrew R Webster
- Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, University College London, London, UK
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30
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Zhang T, Bai J, Zhang X, Zheng X, Lu N, Liang Z, Lin L, Chen Y. SNRNP200 Mutations Cause Autosomal Dominant Retinitis Pigmentosa. Front Med (Lausanne) 2020; 7:588991. [PMID: 33553197 PMCID: PMC7859630 DOI: 10.3389/fmed.2020.588991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/18/2020] [Indexed: 02/05/2023] Open
Abstract
The small nuclear ribonucleoprotein 200 kDa (SNRNP200) gene plays a key role in the maturation of pre-message RNA (pre-mRNA) splicing with the indication for the etiology of retinitis pigmentosa (RP). Gene recognition can facilitate the diagnosis of these patients for better clinical management, treatment and counseling. This study aimed to outline the causative mutation in a Chinese family and the pathogenic mechanism of this SNRNP200 mutation in RP. Eighteen individuals from the affected family underwent a complete ophthalmic examination. Whole exome sequencing (WES) was conducted to identify the pathogenic variant in the proband, which was then confirmed by Sanger sequencing. Expression of the SNRNP200 transcript in zebrafish was identified via whole mount in situ hybridization. Morpholino oligonucleotide (MO) and SNRNP200 wild and mutant mRNA were injected into zebrafish embryos followed by analyses of the systemic changes and retinal phenotypes using immunofluorescence. Heterozygous SNRNP200c.C6088T (p.Arg2030Cys) mutation was ascertained in two members of this family: the proband and his father (II-2). Overexpression of SNRNP200Arg2030Cys, but not SNRNP200WT caused systemic deformities in the wild-type zebrafish embryos with the retina primarily injured, and significantly increased death rates in the morphant embryos, in which the orthologous zebrafish SNRNP200 gene was blocked. In conclusion, this study reports a novel heterozygous SNRNP200c.C6088T mutation, which is evidenced to cause RP via a dominant-negative effect.
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Affiliation(s)
- Tao Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jingshan Bai
- Department of Ophthalmology, The Second People's Hospital of Dongying, Dongying, China
- Department of Ophthalmology, The Dawang Hospital of Guangrao of Dongying, Dongying, China
| | - Xinyi Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xiaowei Zheng
- Department of Ophthalmology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Nan Lu
- Department of Cardiology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Zhongyin Liang
- Department of Bioinformatics, Berry Genomics Co., Ltd., Beijing, China
| | - Ling Lin
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Rheumatology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- *Correspondence: Ling Lin
| | - Yongsong Chen
- The Clinical Research Center of the First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Endocrinology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Yongsong Chen
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31
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Avela K, Salonen‐Kajander R, Laitinen A, Ramsden S, Barton S, Rudanko S. The genetic aetiology of retinal degeneration in children in Finland - new founder mutations identified. Acta Ophthalmol 2019; 97:805-814. [PMID: 31087526 DOI: 10.1111/aos.14128] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/10/2019] [Indexed: 01/22/2023]
Abstract
PURPOSE To study the genetic aetiology and phenotypes of retinal degeneration (RD) in Finnish children born during 1993-2009. METHODS Children with retinal degeneration (N = 68) were investigated during 2012-2014 with a targeted gene analysis or a next-generation sequencing (NGS) based gene panel. Also, a full clinical ophthalmological examination was performed. RESULTS The cohort covered 44% (68/153) of the Finnish children with inherited RD born 1993-2009. X-linked retinoschisis, retinitis pigmentosa, Leber congenital amaurosis and cone-rod dystrophy were the most common clinical diagnoses in the study group. Pathogenic mutations were found in 17 retinal genes. The molecular genetic aetiology was identified in 77% of the patients (in 77% of the families) analysed by NGS method. Several founder mutations were detected including three novel founder mutations c.148delG in TULP1, c.2314C>R (p.Gln772Ter) in RPGRIP1 and c.533G>A (Trp178Ter) in TYR. We also confirmed the previous tentative finding of c.2944 + 1delG in GYCU2D being the most frequent cause of Leber congenital amaurosis (LCA) in Finland. CONCLUSIONS Globally, RD is genetically heterogeneous with over 260 disease genes reported so far. This was shown not to be the case in Finland, where the genetic aetiology of RD is caused by a small group of genes, due to several founder mutations that are enriched in the population. We found that X-chromosomal retinoschisis constitutes the major group in Finnish paediatric RD population and is almost exclusively caused by two founder mutations. Several other founder mutations were detected including three novel founder mutations. All in all, the genetic aetiology of 77% of families was identified which is higher than previously reported from other populations, likely due to the specific genomic constitution of the Finns.
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Affiliation(s)
- Kristiina Avela
- The Department of Clinical Genetics Helsinki University Hospital, HUSLAB Helsinki Finland
| | | | - Arja Laitinen
- The Department of Ophthalmology Helsinki University Hospital Helsinki Finland
| | - Simon Ramsden
- St Mary′s Hospital Central Manchester University Hospitals and Manchester Centre for Genomic Medicine Manchester UK
| | - Stephanie Barton
- St Mary′s Hospital Central Manchester University Hospitals and Manchester Centre for Genomic Medicine Manchester UK
| | - Sirkka‐Liisa Rudanko
- Visio Low Vision Research Centre Finnish Federation of the Visually Impaired Helsinki Finland
- Finnish Register of Visual Impairment by National Institute for Health and Welfare Helsinki Finland
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Shakhmantsir I, Dooley SJ, Kishore S, Chen D, Pierce E, Bennett J, Sehgal A. RNA Splicing Factor Mutations That Cause Retinitis Pigmentosa Result in Circadian Dysregulation. J Biol Rhythms 2019; 35:72-83. [PMID: 31726916 DOI: 10.1177/0748730419887876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Circadian clocks regulate multiple physiological processes in the eye, but their requirement for retinal health remains unclear. We previously showed that Drosophila homologs of spliceosome proteins implicated in human retinitis pigmentosa (RP), the most common genetically inherited cause of blindness, have a role in the brain circadian clock. In this study, we report circadian phenotypes in murine models of RP. We found that mice carrying a homozygous H2309P mutation in Pre-mRNA splicing factor 8 (Prpf8) display a lengthened period of the circadian wheel-running activity rhythm. We show also that the daily cycling of circadian gene expression is dampened in the retina of Prpf8-H2309P mice. Surprisingly, molecular rhythms are intact in the eye cup, which includes the retinal pigment epithelium (RPE), even though the RPE is thought to be the primary tissue affected in this form of RP. Downregulation of Prp31, another RNA splicing factor implicated in RP, leads to period lengthening in a human cell culture model. The period of circadian bioluminescence in primary fibroblasts of human RP patients is not significantly altered. Together, these studies link a prominent retinal disorder to circadian deficits, which could contribute to disease pathology.
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Affiliation(s)
- Iryna Shakhmantsir
- Chronobiology and Sleep institute (CSI) and Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Graduate Program in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott J Dooley
- Graduate Program in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Siddharth Kishore
- Graduate Program in Cell and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dechun Chen
- Chronobiology and Sleep institute (CSI) and Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Eric Pierce
- Ocular Genomics Institute, Mass Eye and Ear, Harvard Medical School, Boston, Massachusetts
| | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amita Sehgal
- Chronobiology and Sleep institute (CSI) and Howard Hughes Medical Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Vijayakumari D, Sharma AK, Bawa PS, Kumar R, Srinivasan S, Vijayraghavan U. Early splicing functions of fission yeast Prp16 and its unexpected requirement for gene Silencing is governed by intronic features. RNA Biol 2019; 16:754-769. [PMID: 30810475 DOI: 10.1080/15476286.2019.1585737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Prp16 is a DEAH box pre-mRNA splicing factor that triggers a key spliceosome conformational switch to facilitate second step splicing in Saccharomyces cerevisiae. However, Prp16 functions are largely unexplored in Schizosaccharomyces pombe, an attractive model with exon-intron architecture more relevant to several other eukaryotes. Here, we generated mis-sense alleles in SpPrp16 whose consequences on genome-wide splicing uncover its nearly global splicing role with only a small subset of unaffected introns. Prp16 dependent and independent intron categories displayed a striking difference in the strength of intronic 5' splice site (5'SS)-U6 snRNA and branch site (BS)-U2 snRNA interactions. Selective weakening of these interactions could convert a Prp16 dependent intron into an independent one. These results point to the role of SpPrp16 in destabilizing 5'SS-U6snRNA and BS-U2snRNA interactions which plausibly trigger structural alterations in the spliceosome to facilitate first step catalysis. Our data suggest that SpPrp16 interactions with early acting factors, its enzymatic activities and association with intronic elements collectively account for efficient and accurate first step catalysis. In addition to splicing derangements in the spprp16F528S mutant, we show that SpPrp16 influences cell cycle progression and centromeric heterochromatinization. We propose that strong 5'SS-U6 snRNA and BS-U2 snRNA complementarity of intron-like elements in non-coding RNAs which lead to complete splicing arrest and impaired Seb1 functions at the pericentromeric loci may cumulatively account for the heterochromatin defects in spprp16F528S cells. These findings suggest that the diverse Prp16 functions within a genome are likely governed by its intronic features that influence splice site-snRNA interaction strength.
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Affiliation(s)
- Drisya Vijayakumari
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | - Amit Kumar Sharma
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | | | - Rakesh Kumar
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | | | - Usha Vijayraghavan
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
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34
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Martin-Merida I, Aguilera-Garcia D, Fernandez-San JP, Blanco-Kelly F, Zurita O, Almoguera B, Garcia-Sandoval B, Avila-Fernandez A, Arteche A, Minguez P, Carballo M, Corton M, Ayuso C. Toward the Mutational Landscape of Autosomal Dominant Retinitis Pigmentosa: A Comprehensive Analysis of 258 Spanish Families. Invest Ophthalmol Vis Sci 2019; 59:2345-2354. [PMID: 29847639 DOI: 10.1167/iovs.18-23854] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To provide a comprehensive overview of the molecular basis of autosomal dominant retinitis pigmentosa (adRP) in Spanish families. Thus, we established the molecular characterization rate, gene prevalence, and mutational spectrum in the largest European cohort reported to date. Methods A total of 258 unrelated Spanish families with a clinical diagnosis of RP and suspected autosomal dominant inheritance were included. Clinical diagnosis was based on complete ophthalmologic examination and family history. Retrospective and prospective analysis of Spanish adRP families was carried out using a combined strategy consisting of classic genetic techniques and next-generation sequencing (NGS) for single-nucleotide variants and copy number variation (CNV) screening. Results Overall, 60% of our families were genetically solved. Interestingly, 3.1% of the cohort carried pathogenic CNVs. Disease-causing variants were found in an autosomal dominant gene in 55% of the families; however, X-linked and autosomal recessive forms were also identified in 3% and 2%, respectively. Four genes (RHO, PRPF31, RP1, and PRPH2) explained up to 62% of the solved families. Missense changes were most frequently found in adRP-associated genes; however, CNVs represented a relevant disease cause in PRPF31- and CRX-associated forms. Conclusions Implementation of NGS technologies in the adRP study clearly increased the diagnostic yield compared with classic approaches. Our study outcome expands the spectrum of disease-causing variants, provides accurate data on mutation gene prevalence, and highlights the implication of CNVs as important contributors to adRP etiology.
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Affiliation(s)
- Inmaculada Martin-Merida
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Domingo Aguilera-Garcia
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Jose P Fernandez-San
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Olga Zurita
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Berta Almoguera
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Blanca Garcia-Sandoval
- Department of Ophthalmology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Almudena Avila-Fernandez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Ana Arteche
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Miguel Carballo
- Molecular Genetics Unit, Hospital de Terrassa, Terrassa, Barcelona, Spain
| | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital-Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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35
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Dill H, Fischer U. Gene Knockdown in Zebrafish (Danio rerio) as a Tool to Model Photoreceptor Diseases. Methods Mol Biol 2019; 1834:209-219. [PMID: 30324447 DOI: 10.1007/978-1-4939-8669-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Disturbances in the general mRNA metabolism have been recognized as a major defect in a growing number of hereditary human diseases. One prominent example of this disease group is retinitis pigmentosa (RP), characterized by selective loss of photoreceptor cells. RP can be caused by dominant mutations in key factors of the pre-mRNA processing spliceosome. In these cases, the complex events leading to the RP phenotype can only insufficiently be analyzed in animal knockout models due to the essential functions of splice factors. Furthermore knockout animals frequently miss the specific phenotypes caused by knockdown of the respective genes. Here we introduce the zebrafish Danio rerio as a valuable vertebrate model system to study RP and related diseases in knockdown case scenarios.
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Affiliation(s)
- Holger Dill
- Department of Biochemistry, Biocentre, University of Wuerzburg, Würzburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Biocentre, University of Wuerzburg, Würzburg, Germany.
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36
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Foltz LP, Howden SE, Thomson JA, Clegg DO. Functional Assessment of Patient-Derived Retinal Pigment Epithelial Cells Edited by CRISPR/Cas9. Int J Mol Sci 2018; 19:E4127. [PMID: 30572641 PMCID: PMC6321630 DOI: 10.3390/ijms19124127] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa is the most common form of inherited blindness and can be caused by a multitude of different genetic mutations that lead to similar phenotypes. Specifically, mutations in ubiquitously expressed splicing factor proteins are known to cause an autosomal dominant form of the disease, but the retina-specific pathology of these mutations is not well understood. Fibroblasts from a patient with splicing factor retinitis pigmentosa caused by a missense mutation in the PRPF8 splicing factor were used to produce three diseased and three CRISPR/Cas9-corrected induced pluripotent stem cell (iPSC) clones. We differentiated each of these clones into retinal pigment epithelial (RPE) cells via directed differentiation and analyzed the RPE cells in terms of gene and protein expression, apicobasal polarity, and phagocytic ability. We demonstrate that RPE cells can be produced from patient-derived and corrected cells and they exhibit morphology and functionality similar but not identical to wild-type RPE cells in vitro. Functionally, the RPE cells were able to establish apicobasal polarity and phagocytose photoreceptor outer segments at the same capacity as wild-type cells. These data suggest that patient-derived iPSCs, both diseased and corrected, are able to differentiate into RPE cells with a near normal phenotype and without differences in phagocytosis, a result that differs from previous mouse models. These RPE cells can now be studied to establish a disease-in-a-dish system relevant to retinitis pigmentosa.
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Affiliation(s)
- Leah P Foltz
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
| | - Sara E Howden
- Murdoch Children's Research Institute, University of Melbourne, Parkville 3052, Australia.
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - James A Thomson
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - Dennis O Clegg
- Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA.
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37
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Disrupted alternative splicing for genes implicated in splicing and ciliogenesis causes PRPF31 retinitis pigmentosa. Nat Commun 2018; 9:4234. [PMID: 30315276 PMCID: PMC6185938 DOI: 10.1038/s41467-018-06448-y] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/03/2018] [Indexed: 12/23/2022] Open
Abstract
Mutations in pre-mRNA processing factors (PRPFs) cause autosomal-dominant retinitis pigmentosa (RP), but it is unclear why mutations in ubiquitously expressed genes cause non-syndromic retinal disease. Here, we generate transcriptome profiles from RP11 (PRPF31-mutated) patient-derived retinal organoids and retinal pigment epithelium (RPE), as well as Prpf31+/− mouse tissues, which revealed that disrupted alternative splicing occurred for specific splicing programmes. Mis-splicing of genes encoding pre-mRNA splicing proteins was limited to patient-specific retinal cells and Prpf31+/− mouse retinae and RPE. Mis-splicing of genes implicated in ciliogenesis and cellular adhesion was associated with severe RPE defects that include disrupted apical – basal polarity, reduced trans-epithelial resistance and phagocytic capacity, and decreased cilia length and incidence. Disrupted cilia morphology also occurred in patient-derived photoreceptors, associated with progressive degeneration and cellular stress. In situ gene editing of a pathogenic mutation rescued protein expression and key cellular phenotypes in RPE and photoreceptors, providing proof of concept for future therapeutic strategies. Mutations in pre-mRNA processing factors cause autosomal dominant retinitis pigmentosa. Here the authors provide insights into the pathophysiological mechanisms underlying non-syndromic retinal disease caused by heterozygous mutations in genes encoding ubiquitously expressed splicing factors.
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Xu G, Li T, Chen J, Li C, Zhao H, Yao C, Dong H, Wen K, Wang K, Zhao J, Xia Q, Zhou T, Zhang H, Gao P, Li A, Pan X. Autosomal dominant retinitis pigmentosa-associated gene PRPF8 is essential for hypoxia-induced mitophagy through regulating ULK1 mRNA splicing. Autophagy 2018; 14:1818-1830. [PMID: 30103670 DOI: 10.1080/15548627.2018.1501251] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aged and damaged mitochondria can be selectively degraded by specific autophagic elimination, termed mitophagy. Defects in mitophagy have been increasingly linked to several diseases including neurodegenerative diseases, metabolic diseases and other aging-related diseases. However, the molecular mechanisms of mitophagy are not fully understood. Here, we identify PRPF8 (pre-mRNA processing factor 8), a core component of the spliceosome, as an essential mediator in hypoxia-induced mitophagy from an RNAi screen based on a fluorescent mitophagy reporter, mt-Keima. Knockdown of PRPF8 significantly impairs mitophagosome formation and subsequent mitochondrial clearance through the aberrant mRNA splicing of ULK1, which mediates macroautophagy/autophagy initiation. Importantly, autosomal dominant retinitis pigmentosa (adRP)-associated PRPF8 mutant R2310K is defective in regulating mitophagy. Moreover, knockdown of other adRP-associated splicing factors, including PRPF6, PRPF31 and SNRNP200, also lead to ULK1 mRNA mis-splicing and mitophagy defects. Thus, these findings demonstrate that PRPF8 is essential for mitophagy and suggest that dysregulation of spliceosome-mediated mitophagy may contribute to pathogenesis of retinitis pigmentosa.
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Affiliation(s)
- Guang Xu
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Ting Li
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Jiayi Chen
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Changyan Li
- b State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Lifeomics , Beijing , China
| | - Haixin Zhao
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Chengcheng Yao
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Hua Dong
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Kaiqing Wen
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Kai Wang
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Jie Zhao
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Qing Xia
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Tao Zhou
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Huafeng Zhang
- c Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Sciences , University of Science and Technology of China , Hefei , China
| | - Ping Gao
- c Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Signaling Network, School of Life Sciences , University of Science and Technology of China , Hefei , China
| | - Ailing Li
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China
| | - Xin Pan
- a State Key Laboratory of Proteomics, Institute of Basic Medical Sciences , National Center of Biomedical Analysis , Beijing , China.,d State Key Laboratory of Toxicology and Medical Countermeasures , Beijing Institute of Pharmacology and Toxicology , Beijing , China
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Bhatia V, Valdés-Sánchez L, Rodriguez-Martinez D, Bhattacharya SS. Formation of 53BP1 foci and ATM activation under oxidative stress is facilitated by RNA:DNA hybrids and loss of ATM-53BP1 expression promotes photoreceptor cell survival in mice. F1000Res 2018; 7:1233. [PMID: 30345028 PMCID: PMC6171737 DOI: 10.12688/f1000research.15579.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 01/18/2023] Open
Abstract
Background: Photoreceptors, light-sensing neurons in retina, are central to vision. Photoreceptor cell death (PCD) is observed in most inherited and acquired retinal dystrophies. But the underlying molecular mechanism of PCD is unclear. Photoreceptors are sturdy neurons that survive high oxidative and phototoxic stress, which are known threats to genome stability. Unexpectedly, DNA damage response in mice photoreceptors is compromised; mainly due to loss of crucial DNA repair proteins, ATM and 53BP1. We tried to understand the molecular function of ATM and 53BP1 in response to oxidative stress and how suppression of DNA repair response in mice retina affect photoreceptor cell survival. Methods: We use the state of art cell biology methods and structure-function analysis of mice retina. RNA:DNA hybrids (S9.6 antibody and Hybrid-binding domain of RNaseH1) and DNA repair foci (gH2AX and 53BP1) are quantified by confocal microscopy, in retinal sections and cultured cell lines. Oxidative stress, DNA double strand break, RNaseH1 expression and small-molecule kinase-inhibitors were used to understand the role of ATM and RNA:DNA hybrids in DNA repair. Lastly, retinal structure and function of ATM deficient mice, in Retinal degeneration 1 (Pde6brd1) background, is studied using Immunohistochemistry and Electroretinography. Results: Our work has three novel findings: firstly, both human and mice photoreceptor cells specifically accumulate RNA:DNA hybrids, a structure formed by re-hybridization of nascent RNA with template DNA during transcription. Secondly, RNA:DNA-hybrids promote ataxia-telangiectasia mutated (ATM) activation during oxidative stress and 53BP1-foci formation during downstream DNA repair process. Thirdly, loss of ATM -in murine photoreceptors- protract DNA repair but also promote their survival. Conclusions: We propose that due to high oxidative stress and accumulation of RNA:DNA-hybrids in photoreceptors, expression of ATM is tightly regulated to prevent PCD. Inefficient regulation of ATM expression could be central to PCD and inhibition of ATM-activation could suppress PCD in retinal dystrophy patients.
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Affiliation(s)
- Vaibhav Bhatia
- CABIMER (Centro Andaluz de Biología Molecular y Medicina Regenerativa), (FPS) Fundacion Progreso y Salud, Sevilla, Andalucia, 41092, Spain
| | - Lourdes Valdés-Sánchez
- CABIMER (Centro Andaluz de Biología Molecular y Medicina Regenerativa), (FPS) Fundacion Progreso y Salud, Sevilla, Andalucia, 41092, Spain
| | - Daniel Rodriguez-Martinez
- CABIMER (Centro Andaluz de Biología Molecular y Medicina Regenerativa), (FPS) Fundacion Progreso y Salud, Sevilla, Andalucia, 41092, Spain
| | - Shom Shankar Bhattacharya
- CABIMER (Centro Andaluz de Biología Molecular y Medicina Regenerativa), (FPS) Fundacion Progreso y Salud, Sevilla, Andalucia, 41092, Spain
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40
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Li L, Jiao X, D’Atri I, Ono F, Nelson R, Chan CC, Nakaya N, Ma Z, Ma Y, Cai X, Zhang L, Lin S, Hameed A, Chioza BA, Hardy H, Arno G, Hull S, Khan MI, Fasham J, Harlalka GV, Michaelides M, Moore AT, Coban Akdemir ZH, Jhangiani S, Lupski JR, Cremers FPM, Qamar R, Salman A, Chilton J, Self J, Ayyagari R, Kabir F, Naeem MA, Ali M, Akram J, Sieving PA, Riazuddin S, Baple EL, Riazuddin SA, Crosby AH, Hejtmancik JF. Mutation in the intracellular chloride channel CLCC1 associated with autosomal recessive retinitis pigmentosa. PLoS Genet 2018; 14:e1007504. [PMID: 30157172 PMCID: PMC6133373 DOI: 10.1371/journal.pgen.1007504] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 09/11/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
We identified a homozygous missense alteration (c.75C>A, p.D25E) in CLCC1, encoding a presumptive intracellular chloride channel highly expressed in the retina, associated with autosomal recessive retinitis pigmentosa (arRP) in eight consanguineous families of Pakistani descent. The p.D25E alteration decreased CLCC1 channel function accompanied by accumulation of mutant protein in granules within the ER lumen, while siRNA knockdown of CLCC1 mRNA induced apoptosis in cultured ARPE-19 cells. TALEN KO in zebrafish was lethal 11 days post fertilization. The depressed electroretinogram (ERG) cone response and cone spectral sensitivity of 5 dpf KO zebrafish and reduced eye size, retinal thickness, and expression of rod and cone opsins could be rescued by injection of wild type CLCC1 mRNA. Clcc1+/- KO mice showed decreased ERGs and photoreceptor number. Together these results strongly suggest that intracellular chloride transport by CLCC1 is a critical process in maintaining retinal integrity, and CLCC1 is crucial for survival and function of retinal cells.
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Affiliation(s)
- Lin Li
- Department of Ophthalmology, Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, P.R. China
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ilaria D’Atri
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Fumihito Ono
- Section on Model Synaptic Systems, Laboratory of Molecular Physiology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Physiology, Osaka Medical College, Takatsuki, Japan
| | - Ralph Nelson
- Unit on Neural Circuits, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Chao Chan
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Naoki Nakaya
- Section of Molecular Mechanisms of Glaucoma, Laboratory of Molecular and Developmental Biology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Zhiwei Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Yan Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Xiaoying Cai
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P.R. China
| | - Longhua Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, P.R. China
| | - Siying Lin
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Abdul Hameed
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan
| | - Barry A. Chioza
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Holly Hardy
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Gavin Arno
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Sarah Hull
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Muhammad Imran Khan
- Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - James Fasham
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Department of Clinical Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Gaurav V. Harlalka
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Michel Michaelides
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
| | - Anthony T. Moore
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Biosciences, Moorfields Eye Hospital, London, United Kingdom
- Ophthalmology Department, UCSF School of Medicine, San Francisco, California, United States of America
| | - Zeynep Hande Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children’s Hospital, Houston, Texas, United States of America
| | - Frans P. M. Cremers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Raheel Qamar
- Faculty of Science, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Ahmed Salman
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - John Chilton
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Jay Self
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Firoz Kabir
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ali
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Javed Akram
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
- National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Paul A. Sieving
- National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
- National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Emma L. Baple
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Department of Clinical Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - S. Amer Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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Xie D, Peng K, Yi Q, Liu W, Yang Y, Sun K, Zhu X, Lu F. Targeted Next Generation Sequencing Revealed Novel PRPF31 Mutations in Autosomal Dominant Retinitis Pigmentosa. Genet Test Mol Biomarkers 2018; 22:425-432. [PMID: 29957067 DOI: 10.1089/gtmb.2018.0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Retinitis pigmentosa (RP) is a rare type of inherited retinal dystrophy that can result in progressive vision loss. Molecular diagnosis of RP is challenging due to phenotypic and genotypic heterogeneities. AIMS This study aimed to identify the pathogenic mutations in two Chinese families with autosomal dominant RP (adRP) and in a patient with sporadic RP. MATERIALS AND METHODS Peripheral blood DNA samples were obtained from the participants. Targeted next generation sequencing (NGS) was applied to identify mutations in these patients. For pathogenic mutation analyses, stringent NGS data analyses and segregation analyses were applied. Primers were designed to validate the identified mutations by Sanger sequencing analyses. RESULTS A novel heterozygous insertion frameshift mutation c.1226_1227insA, p.T410Dfs*65, and a novel heterozygous stopgain mutation c.1015C>T, p.Q339* were identified in PRPF31. A known c.527 + 3A>G splicing mutation was identified in one of the adRP-074 families. All mutations were found to co-segregate with the disease, and none of these mutations were detected in 500 control samples. CONCLUSIONS Our data identified two new autosomal dominant mutations in PRPF31, expanding the mutational spectrum of this gene.
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Affiliation(s)
- Dan Xie
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Kun Peng
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Qian Yi
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Wenjinag Liu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Yeming Yang
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Kuanxiang Sun
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Xianjun Zhu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China .,3 Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Fang Lu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
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Zelinger L, Swaroop A. RNA Biology in Retinal Development and Disease. Trends Genet 2018; 34:341-351. [PMID: 29395379 DOI: 10.1016/j.tig.2018.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/28/2017] [Accepted: 01/03/2018] [Indexed: 02/06/2023]
Abstract
For decades, RNA has served in a supporting role between the genetic carrier (DNA) and the functional molecules (proteins). It is finally time for RNA to take center stage in all aspects of biology. The retina provides a unique opportunity to dissect the molecular underpinnings of neuronal diversity and disease. Transcriptome profiles of the retina and its resident cell types have unraveled unique features of the RNA landscape. The discovery of distinct RNA molecules and the recognition that RNA processing is a major cause of retinal neurodegeneration have prompted the design of biomarkers and novel therapeutic paradigms. We review here RNA biology as it pertains to the retina, emphasizing new avenues for investigations in development and disease.
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Affiliation(s)
- Lina Zelinger
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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43
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Escher P, Passarin O, Munier FL, Tran VH, Vaclavik V. Variability in clinical phenotypes of PRPF8-linked autosomal dominant retinitis pigmentosa correlates with differential PRPF8/SNRNP200 interactions. Ophthalmic Genet 2017; 39:80-86. [DOI: 10.1080/13816810.2017.1393825] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Pascal Escher
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Lausanne, Switzerland
- Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
- Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Olga Passarin
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Lausanne, Switzerland
| | - Francis L. Munier
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Lausanne, Switzerland
| | - Viet H. Tran
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Lausanne, Switzerland
| | - Veronika Vaclavik
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Lausanne, Switzerland
- Hôpital Cantonal, Fribourg, Switzerland
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44
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snRNP proteins in health and disease. Semin Cell Dev Biol 2017; 79:92-102. [PMID: 29037818 DOI: 10.1016/j.semcdb.2017.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/09/2017] [Accepted: 10/12/2017] [Indexed: 01/16/2023]
Abstract
Split gene architecture of most human genes requires removal of intervening sequences by mRNA splicing that occurs on large multiprotein complexes called spliceosomes. Mutations compromising several spliceosomal components have been recorded in degenerative syndromes and haematological neoplasia, thereby highlighting the importance of accurate splicing execution in homeostasis of assorted adult tissues. Moreover, insufficient splicing underlies defective development of craniofacial skeleton and upper extremities. This review summarizes recent advances in the understanding of splicing factor function deduced from cryo-EM structures. We combine these data with the characterization of splicing factors implicated in hereditary or somatic disorders, with a focus on potential functional consequences the mutations may elicit in spliceosome assembly and/or performance. Given aberrant splicing or perturbations in splicing efficiency substantially underpin disease pathogenesis, profound understanding of the mis-splicing principles may open new therapeutic vistas. In three major sections dedicated to retinal dystrophies, hereditary acrofacial syndromes, and haematological malignancies, we delineate the noticeable variety of conditions associated with dysfunctional splicing and accentuate recurrent patterns in splicing defects.
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Kim J, Tsuruta F, Okajima T, Yano S, Sato B, Chiba T. KLHL7 promotes TUT1 ubiquitination associated with nucleolar integrity: Implications for retinitis pigmentosa. Biochem Biophys Res Commun 2017; 494:220-226. [PMID: 29032201 DOI: 10.1016/j.bbrc.2017.10.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/10/2017] [Indexed: 01/06/2023]
Abstract
Kelch-like protein 7 (KLHL7) is a component of Cul3-based Cullin-RING ubiquitin ligase. Recent studies have revealed that mutations in klhl7 gene cause several disorders, such as retinitis pigmentosa (RP). Although KLHL7 is considered to be crucial for regulating the protein homeostasis, little is known about its biological functions. In this study, we report that KLHL7 increases terminal uridylyl transferase 1 (TUT1) ubiquitination involved in nucleolar integrity. TUT1 is normally localized in nucleolus; however, expression of KLHL7 facilitates a vulnerability of nucleolar integrity, followed by a decrease of TUT1 localization in nucleolus. On the other hand, pathogenic KLHL7 mutants, which causes an onset of RP, have little effect on both nucleolar integrity and TUT1 localization. Finally, KLHL7 increases TUT1 ubiquitination levels. Taken together, these results imply that KLHL7 is a novel regulator of nucleolus associated with TUT1 ubiquitination. Our study may provide a valuable information to elucidate a pathogenic mechanism of RP.
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Affiliation(s)
- Jaehyun Kim
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Fuminori Tsuruta
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Tomomi Okajima
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Sarasa Yano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Ban Sato
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Tomoki Chiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
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Abstract
Much evidence is now accumulating that, in addition to their general role in splicing, the components of the core splicing machinery have extensive regulatory potential. In particular, recent evidence has demonstrated that de-regulation of these factors cause the highest extent of alternative splicing changes compared to de-regulation of the classical splicing regulators. This lack of a general inhibition of splicing resonates the differential splicing effects observed in different disease pathologies associated with specific mutations targeting core spliceosomal components. In this review we will summarize what is currently known regarding the involvement of core spliceosomal U-snRNP complexes in perturbed tissue development and human diseases and argue for the existence of a compensatory mechanism enabling cells to cope with drastic perturbations in core splicing components. This system maintains the correct balance of spliceosomal snRNPs through differential expression of variant (v)U-snRNPs.
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Affiliation(s)
- Pilar Vazquez-Arango
- a Nuffield Department of Obstetrics and Gynaecology, Level 3 , Women's Centre, John Radcliffe Hospital , Oxford , England
| | - Dawn O'Reilly
- b Sir William Dunn School of pathology , University of Oxford , South Parks Road, Oxford , England
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Carrocci TJ, Zoerner DM, Paulson JC, Hoskins AA. SF3b1 mutations associated with myelodysplastic syndromes alter the fidelity of branchsite selection in yeast. Nucleic Acids Res 2017; 45:4837-4852. [PMID: 28062854 PMCID: PMC5416834 DOI: 10.1093/nar/gkw1349] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/22/2016] [Indexed: 12/19/2022] Open
Abstract
RNA and protein components of the spliceosome work together to identify the 5΄ splice site, the 3΄ splice site, and the branchsite (BS) of nascent pre-mRNA. SF3b1 plays a key role in recruiting the U2 snRNP to the BS. Mutations in human SF3b1 have been linked to many diseases such as myelodysplasia (MDS) and cancer. We have used SF3b1 mutations associated with MDS to interrogate the role of the yeast ortholog, Hsh155, in BS selection and splicing. These alleles change how the spliceosome recognizes the BS and alter splicing when nonconsensus nucleotides are present at the −2, −1 and +1 positions relative to the branchpoint adenosine. This indicates that changes in BS usage observed in humans with SF3b1 mutations may result from perturbation of a conserved mechanism of BS recognition. Notably, different HSH155 alleles elicit disparate effects on splicing: some increase the fidelity of BS selection while others decrease fidelity. Our data support a model wherein conformational changes in SF3b1 promote U2 association with the BS independently of the action of the DEAD-box ATPase Prp5. We propose that SF3b1 functions to stabilize weak U2/BS duplexes to drive spliceosome assembly and splicing.
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Affiliation(s)
- Tucker J Carrocci
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706, USA
| | - Douglas M Zoerner
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua C Paulson
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706, USA
| | - Aaron A Hoskins
- Department of Biochemistry, U. Wisconsin-Madison, Madison, WI 53706, USA
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48
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Genetic characterization and disease mechanism of retinitis pigmentosa; current scenario. 3 Biotech 2017; 7:251. [PMID: 28721681 DOI: 10.1007/s13205-017-0878-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Retinitis pigmentosa is a group of genetically transmitted disorders affecting 1 in 3000-8000 individual people worldwide ultimately affecting the quality of life. Retinitis pigmentosa is characterized as a heterogeneous genetic disorder which leads by progressive devolution of the retina leading to a progressive visual loss. It can occur in syndromic (with Usher syndrome and Bardet-Biedl syndrome) as well as non-syndromic nature. The mode of inheritance can be X-linked, autosomal dominant or autosomal recessive manner. To date 58 genes have been reported to associate with retinitis pigmentosa most of them are either expressed in photoreceptors or the retinal pigment epithelium. This review focuses on the disease mechanisms and genetics of retinitis pigmentosa. As retinitis pigmentosa is tremendously heterogeneous disorder expressing a multiplicity of mutations; different variations in the same gene might induce different disorders. In recent years, latest technologies including whole-exome sequencing contributing effectively to uncover the hidden genesis of retinitis pigmentosa by reporting new genetic mutations. In future, these advancements will help in better understanding the genotype-phenotype correlations of disease and likely to develop new therapies.
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49
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Micheal S, Hogewind BF, Khan MI, Siddiqui SN, Zafar SN, Akhtar F, Qamar R, Hoyng CB, den Hollander AI. Variants in the PRPF8 Gene are Associated with Glaucoma. Mol Neurobiol 2017; 55:4504-4510. [PMID: 28707069 PMCID: PMC5884903 DOI: 10.1007/s12035-017-0673-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/25/2017] [Indexed: 01/05/2023]
Abstract
Glaucoma is the cause of irreversible blindness worldwide. Mutations in six genes have been associated with juvenile- and adult-onset familial primary open angle glaucoma (POAG) prior to this report but they explain only a small proportion of the genetic load. The aim of the study is to identify the novel genetic cause of the POAG in the families with adult-onset glaucoma. Whole exome sequencing (WES) was performed on DNA of two affected individuals, and predicted pathogenic variants were evaluated for segregation in four affected and three unaffected Dutch family members by Sanger sequencing. We identified a pathogenic variant (p.Val956Gly) in the PRPF8 gene, which segregates with the disease in Dutch family. Targeted Sanger sequencing of PRPF8 in a panel of 40 POAG families (18 Pakistani and 22 Dutch) revealed two additional nonsynonymous variants (p.Pro13Leu and p.Met25Thr), which segregate with the disease in two other Pakistani families. Both variants were then analyzed in a case-control cohort consisting of Pakistani 320 POAG cases and 250 matched controls. The p.Pro13Leu and p.Met25Thr variants were identified in 14 and 20 cases, respectively, while they were not detected in controls (p values 0.0004 and 0.0001, respectively). Previously, PRPF8 mutations have been associated with autosomal dominant retinitis pigmentosa (RP). The PRPF8 variants associated with POAG are located at the N-terminus, while all RP-associated mutations cluster at the C-terminus, dictating a clear genotype-phenotype correlation.
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Affiliation(s)
- Shazia Micheal
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Department of Clinical Genetics, Academic Medical Centre, Amsterdam, the Netherlands
| | - Barend F Hogewind
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sorath Noorani Siddiqui
- Department of Pediatric Ophthalmology, Al-Shifa Eye Trust Hospital, Jhelum Road, Rawalpindi, Pakistan
| | - Saemah Nuzhat Zafar
- Department of Pediatric Ophthalmology, Al-Shifa Eye Trust Hospital, Jhelum Road, Rawalpindi, Pakistan
| | - Farah Akhtar
- Department of Pediatric Ophthalmology, Al-Shifa Eye Trust Hospital, Jhelum Road, Rawalpindi, Pakistan
| | - Raheel Qamar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan.,Department of Biochemistry, Al-Nafees Medical College & Hospital, Isra University, Islamabad, Pakistan
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands. .,Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
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50
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Bujakowska KM, Fernandez-Godino R, Place E, Consugar M, Navarro-Gomez D, White J, Bedoukian EC, Zhu X, Xie HM, Gai X, Leroy BP, Pierce EA. Copy-number variation is an important contributor to the genetic causality of inherited retinal degenerations. Genet Med 2017; 19:643-651. [PMID: 27735924 PMCID: PMC6377944 DOI: 10.1038/gim.2016.158] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/30/2016] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Despite substantial progress in sequencing, current strategies can genetically solve only approximately 55-60% of inherited retinal degeneration (IRD) cases. This can be partially attributed to elusive mutations in the known IRD genes, which are not easily identified by the targeted next-generation sequencing (NGS) or Sanger sequencing approaches. We hypothesized that copy-number variations (CNVs) are a major contributor to the elusive genetic causality of IRDs. METHODS Twenty-eight cases previously unsolved with a targeted NGS were investigated with whole-genome single-nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) arrays. RESULTS Deletions in the IRD genes were detected in 5 of 28 families, including a de novo deletion. We suggest that the de novo deletion occurred through nonallelic homologous recombination (NAHR) and we constructed a genomic map of NAHR-prone regions with overlapping IRD genes. In this article, we also report an unusual case of recessive retinitis pigmentosa due to compound heterozygous mutations in SNRNP200, a gene that is typically associated with the dominant form of this disease. CONCLUSIONS CNV mapping substantially increased the genetic diagnostic rate of IRDs, detecting genetic causality in 18% of previously unsolved cases. Extending the search to other structural variations will probably demonstrate an even higher contribution to genetic causality of IRDs.Genet Med advance online publication 13 October 2016.
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Affiliation(s)
- Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rosario Fernandez-Godino
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark Consugar
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph White
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Emma C Bedoukian
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Xiaosong Zhu
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hongbo M Xie
- Department of BioMedical Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Bart P Leroy
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Ophthalmology &Center for Medical Genetics, Ghent University Hospital &Ghent University, Ghent, Belgium
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
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