1
|
Tusseau M, Eyries M, Chatron N, Coulet F, Guichet A, Colin E, Demeer B, Maillard H, Thevenon J, Lavigne C, Saillour V, Paris C, De Sainte Agathe JM, Pujalte M, Guilhem A, Dupuis-Girod S, Lesca G. Genome sequencing identify chromosome 9 inversions disrupting ENG in 2 unrelated HHT families. Eur J Med Genet 2024; 68:104919. [PMID: 38355093 DOI: 10.1016/j.ejmg.2024.104919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/05/2024] [Accepted: 02/04/2024] [Indexed: 02/16/2024]
Abstract
Hereditary hemorrhagic telangiectasia (HHT), also known as Rendu-Osler-Weber disease, is a dominant inherited vascular disorder. The clinical diagnosis is based on the Curaçao criteria and pathogenic variants in the ENG and ACVRL1 genes are responsible for most cases of HHT. Four families with a negative targeted gene panel and selected by a multidisciplinary team were selected and whole-genome sequencing was performed according to the recommendations of the French National Plan for Genomic Medicine. Structural variations were confirmed by standard molecular cytogenetic analysis (FISH). In two families with a definite diagnosis of HHT, we identified two different paracentric inversions of chromosome 9, both disrupting the ENG gene. These inversions are considered as pathogenic and causative for the HHT phenotype of the patients. This is the first time structural variations are reported to cause HHT. As such balanced events are often missed by exon-based sequencing (panel, exome), structural variations may be an under-recognized cause of HHT. Genome sequencing for the detection of these events could be suggested for patients with a definite diagnosis of HHT and in whom no causative pathogenic variant was identified.
Collapse
Affiliation(s)
- M Tusseau
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France; Laboratoire AURAGEN, Lyon, France
| | - M Eyries
- Department of Medical Genetics, AP-HP Sorbonne University, Paris, France; Laboratoire Multisites SeqOIA, Paris, France
| | - N Chatron
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France; Laboratoire AURAGEN, Lyon, France
| | - F Coulet
- Department of Medical Genetics, AP-HP Sorbonne University, Paris, France; Laboratoire Multisites SeqOIA, Paris, France
| | - A Guichet
- Service de Génétique Médicale, CHU D'Angers, Angers, France
| | - E Colin
- Service de Génétique Médicale, CHU D'Angers, Angers, France
| | - B Demeer
- Genetics Department, CLAD Nord de France, CHU Amiens, France; CHIMERE, UR UPJV 7516, Université Picardie Jules Verne, Amiens, France
| | - H Maillard
- Department of Internal Medicine and Clinical Immunology, Referral Centre for Rare Systemic Autoimmune Diseases for North and North-West France (CeRAINO), CHU Lille, 59000, Lille, France
| | | | - C Lavigne
- Department of Internal Medicine and Clinical Immunology, Angers University Hospital, Angers, France
| | - V Saillour
- Laboratoire Multisites SeqOIA, Paris, France
| | - C Paris
- Laboratoire AURAGEN, Lyon, France
| | - J M De Sainte Agathe
- Department of Medical Genetics, AP-HP Sorbonne University, Paris, France; Laboratoire Multisites SeqOIA, Paris, France
| | - M Pujalte
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France; Laboratoire AURAGEN, Lyon, France
| | - A Guilhem
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France
| | - S Dupuis-Girod
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France
| | - G Lesca
- Hospices Civils de Lyon, Department of Medical Genetics and National HHT Reference Center, University Hospital of Lyon, Lyon, France; Laboratoire AURAGEN, Lyon, France.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Xiao YS, He WJ, Jiang HC, Tan L, Ma J, Zhang Z. Clinical and whole exome sequencing findings in children from Yunnan Yi minority ethnic group with retinitis pigmentosa: two case reports. J Med Case Rep 2023; 17:226. [PMID: 37264419 DOI: 10.1186/s13256-023-03830-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/20/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Retinitis pigmentosa is a group of rare hereditary retinal dystrophy diseases that lead to difficulty seeing at night, progressive loss of peripheral field vision (tunnel vision), and eventual loss of central vision. However, a genetic cause cannot be determined in approximately 60% of cases. CASE PRESENTATION Two non-consanguineous Yi minority ethnic group families who have a 6.4-year-old boy and a 0.5-year-old boy, respectively, were recruited for genetic diagnosis. Here, we used whole-exome sequencing to detect mutations in the genes of the probands of the retinitis pigmentosa families, and Sanger sequencing to confirm the causal mutations identified by whole exome sequencing. In addition, we report two cases with retinitis pigmentosa caused by RDH12 (c.524C > T) and PRPF4 (c.1273G > A) pathogenic mutations. CONCLUSIONS These results might extend the mutation spectrum of known retinitis pigmentosa genes and give these two Yi minority ethnic group families from Yunnan more precise genetic counseling and more specific prognoses.
Collapse
Affiliation(s)
- Yi-Shuang Xiao
- Department of Ophthalmology, Kunming Children's Hospital, Kunming Medical University, Kunming, 650228, Yunnan, People's Republic of China
| | - Wen-Ji He
- Kunming Children's Hospital, Kunming Medical University, Kunming, 650228, Yunnan, People's Republic of China
| | - Hong-Chao Jiang
- Kunming Children's Hospital, Kunming Medical University, Kunming, 650228, Yunnan, People's Republic of China
| | - Li Tan
- Kunming Children's Hospital, Kunming Medical University, Kunming, 650228, Yunnan, People's Republic of China
| | - Jing Ma
- Department of Otolaryngology-Head and Neck Surgery, Kunming Children's Hospital, Kunming Medical University, Kunming, 650228, Yunnan, People's Republic of China.
| | - Zhen Zhang
- Kunming Children's Hospital, Kunming Medical University, Kunming, 650228, Yunnan, People's Republic of China.
- Department of Clinical Pharmacy, Affiliated Hospital of Yunnan University, Kunming, 650021, Yunnan, China.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Toyama T, Kudryashova TV, Ichihara A, Lenna S, Looney A, Shen Y, Jiang L, Teos L, Avolio T, Lin D, Kaplan U, Marden G, Dambal V, Goncharov D, Delisser H, Lafyatis R, Seta F, Goncharova EA, Trojanowska M. GATA6 coordinates cross-talk between BMP10 and oxidative stress axis in pulmonary arterial hypertension. Sci Rep 2023; 13:6593. [PMID: 37087509 PMCID: PMC10122657 DOI: 10.1038/s41598-023-33779-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/19/2023] [Indexed: 04/24/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a life-threatening condition characterized by a progressive increase in pulmonary vascular resistance leading to right ventricular failure and often death. Here we report that deficiency of transcription factor GATA6 is a shared pathological feature of PA endothelial (PAEC) and smooth muscle cells (PASMC) in human PAH and experimental PH, which is responsible for maintenance of hyper-proliferative cellular phenotypes, pulmonary vascular remodeling and pulmonary hypertension. We further show that GATA6 acts as a transcription factor and direct positive regulator of anti-oxidant enzymes, and its deficiency in PAH/PH pulmonary vascular cells induces oxidative stress and mitochondrial dysfunction. We demonstrate that GATA6 is regulated by the BMP10/BMP receptors axis and its loss in PAECs and PASMC in PAH supports BMPR deficiency. In addition, we have established that GATA6-deficient PAEC, acting in a paracrine manner, increase proliferation and induce other pathological changes in PASMC, supporting the importance of GATA6 in pulmonary vascular cell communication. Treatment with dimethyl fumarate resolved oxidative stress and BMPR deficiency, reversed hemodynamic changes caused by endothelial Gata6 loss in mice, and inhibited proliferation and induced apoptosis in human PAH PASMC, strongly suggesting that targeting GATA6 deficiency may provide a therapeutic advance for patients with PAH.
Collapse
Affiliation(s)
- Tetsuo Toyama
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA
| | - Tatiana V Kudryashova
- Pittsburgh Lung, Blood and Heart Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Davis School of Medicine, University of California, Davis, CA, USA
| | - Asako Ichihara
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA
| | - Stefania Lenna
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA
| | - Agnieszka Looney
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA
| | - Yuanjun Shen
- Pittsburgh Lung, Blood and Heart Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Davis School of Medicine, University of California, Davis, CA, USA
| | - Lifeng Jiang
- Division of Pulmonary, Critical Care, and Sleep Medicine, Davis School of Medicine, University of California, Davis, CA, USA
| | - Leyla Teos
- Division of Pulmonary, Critical Care, and Sleep Medicine, Davis School of Medicine, University of California, Davis, CA, USA
| | - Theodore Avolio
- Pittsburgh Lung, Blood and Heart Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Derek Lin
- Division of Pulmonary, Critical Care, and Sleep Medicine, Davis School of Medicine, University of California, Davis, CA, USA
| | - Ulas Kaplan
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA
| | - Grace Marden
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA
| | - Vrinda Dambal
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA
| | - Dmitry Goncharov
- Pittsburgh Lung, Blood and Heart Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Davis School of Medicine, University of California, Davis, CA, USA
| | - Horace Delisser
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Rheumatology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Francesca Seta
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA
| | - Elena A Goncharova
- Pittsburgh Lung, Blood and Heart Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Division of Pulmonary, Allergy and Critical Care, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Division of Pulmonary, Critical Care, and Sleep Medicine, Davis School of Medicine, University of California, Davis, CA, USA.
- The Genome and Biomedical Science Facility (GBSF), Rm 6523, 451 Health Sciences Drive, Davis, CA, 95616, USA.
| | - Maria Trojanowska
- Arthritis and Autoimmune Diseases Center, Boston University School of Medicine, 75 E. Newton St. Evans Building, Boston, MA, 02118, USA.
| |
Collapse
|
6
|
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.
Collapse
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,
| |
Collapse
|
7
|
Bhardwaj A, Yadav A, Yadav M, Tanwar M. Genetic dissection of non-syndromic retinitis pigmentosa. Indian J Ophthalmol 2022; 70:2355-2385. [PMID: 35791117 PMCID: PMC9426071 DOI: 10.4103/ijo.ijo_46_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Retinitis pigmentosa (RP) belongs to a group of pigmentary retinopathies. It is the most common form of inherited retinal dystrophy, characterized by progressive degradation of photoreceptors that leads to nyctalopia, and ultimately, complete vision loss. RP is distinguished by the continuous retinal degeneration that progresses from the mid-periphery to the central and peripheral retina. RP was first described and named by Franciscus Cornelius Donders in the year 1857. It is one of the leading causes of bilateral blindness in adults, with an incidence of 1 in 3000 people worldwide. In this review, we are going to focus on the genetic heterogeneity of this disease, which is provided by various inheritance patterns, numerosity of variations and inter-/intra-familial variations based upon penetrance and expressivity. Although over 90 genes have been identified in RP patients, the genetic cause of approximately 50% of RP cases remains unknown. Heterogeneity of RP makes it an extremely complicated ocular impairment. It is so complicated that it is known as “fever of unknown origin”. For prognosis and proper management of the disease, it is necessary to understand its genetic heterogeneity so that each phenotype related to the various genetic variations could be treated.
Collapse
Affiliation(s)
- Aarti Bhardwaj
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Anshu Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Manoj Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Mukesh Tanwar
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| |
Collapse
|
8
|
Obuća M, Cvačková Z, Kubovčiak J, Kolář M, Staněk D. Retinitis pigmentosa-linked mutation in DHX38 modulates its splicing activity. PLoS One 2022; 17:e0265742. [PMID: 35385551 PMCID: PMC8985939 DOI: 10.1371/journal.pone.0265742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/07/2022] [Indexed: 01/21/2023] Open
Abstract
Retinitis pigmentosa (RP) is a hereditary disease affecting tens of thousands of people world-wide. Here we analyzed the effect of an amino acid substitution in the RNA helicase DHX38 (Prp16) causing RP. DHX38 has been proposed as the helicase important for the 2nd step of splicing. We showed that DHX38 associates with key splicing factors involved in both splicing steps but did not find any evidence that the RP mutations changes DHX38 interaction profile with the spliceosome. We further downregulated DHX38 and monitored changes in splicing. We observed only minor perturbations of general splicing but detected modulation of ~70 alternative splicing events. Next, we probed DHX38 function in splicing of retina specific genes and found that FSCN2 splicing is dependent on DHX38. In addition, RHO splicing was inhibited specifically by expression of DHX38 RP variant. Finally, we showed that overexpression of DHX38 promotes usage of canonical as well as cryptic 5' splice sites in HBB splicing reporter. Together, our data show that DHX38 is a splicing factor that promotes splicing of cryptic splice sites and regulate alternative splicing. We further provide evidence that the RP-linked substitution G332D modulates DHX38 splicing activity.
Collapse
Affiliation(s)
- Mina Obuća
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Zuzana Cvačková
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Kubovčiak
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Kolář
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - David Staněk
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- * E-mail:
| |
Collapse
|
9
|
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: 13] [Impact Index Per Article: 4.3] [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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Yildirim A, Mozaffari-Jovin S, Wallisch AK, Schäfer J, Ludwig SEJ, Urlaub H, Lührmann R, Wolfrum U. SANS (USH1G) regulates pre-mRNA splicing by mediating the intra-nuclear transfer of tri-snRNP complexes. Nucleic Acids Res 2021; 49:5845-5866. [PMID: 34023904 PMCID: PMC8191790 DOI: 10.1093/nar/gkab386] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Splicing is catalyzed by the spliceosome, a compositionally dynamic complex assembled stepwise on pre-mRNA. We reveal links between splicing machinery components and the intrinsically disordered ciliopathy protein SANS. Pathogenic mutations in SANS/USH1G lead to Usher syndrome—the most common cause of deaf-blindness. Previously, SANS was shown to function only in the cytosol and primary cilia. Here, we have uncovered molecular links between SANS and pre-mRNA splicing catalyzed by the spliceosome in the nucleus. We show that SANS is found in Cajal bodies and nuclear speckles, where it interacts with components of spliceosomal sub-complexes such as SF3B1 and the large splicing cofactor SON but also with PRPFs and snRNAs related to the tri-snRNP complex. SANS is required for the transfer of tri-snRNPs between Cajal bodies and nuclear speckles for spliceosome assembly and may also participate in snRNP recycling back to Cajal bodies. SANS depletion alters the kinetics of spliceosome assembly, leading to accumulation of complex A. SANS deficiency and USH1G pathogenic mutations affects splicing of genes related to cell proliferation and human Usher syndrome. Thus, we provide the first evidence that splicing dysregulation may participate in the pathophysiology of Usher syndrome.
Collapse
Affiliation(s)
- Adem Yildirim
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Sina Mozaffari-Jovin
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.,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.,Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Ann-Kathrin Wallisch
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Jessica Schäfer
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Sebastian E J Ludwig
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.,Bioanalytics, Department of Clinical Chemistry, University Medical Center Goettingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Uwe Wolfrum
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| |
Collapse
|
12
|
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: 21] [Impact Index Per Article: 7.0] [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.
Collapse
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
| |
Collapse
|
13
|
Griffin C, Saint-Jeannet JP. Spliceosomopathies: Diseases and mechanisms. Dev Dyn 2020; 249:1038-1046. [PMID: 32506634 DOI: 10.1002/dvdy.214] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 12/21/2022] Open
Abstract
The spliceosome is a complex of RNA and proteins that function together to identify intron-exon junctions in precursor messenger-RNAs, splice out the introns, and join the flanking exons. Mutations in any one of the genes encoding the proteins that make up the spliceosome may result in diseases known as spliceosomopathies. While the spliceosome is active in all cell types, with the majority of the proteins presumably expressed ubiquitously, spliceosomopathies tend to be tissue-specific as a result of germ line or somatic mutations, with phenotypes affecting primarily the retina in retinitis pigmentosa, hematopoietic lineages in myelodysplastic syndromes, or the craniofacial skeleton in mandibulofacial dysostosis. Here we describe the major spliceosomopathies, review the proposed mechanisms underlying retinitis pigmentosa and myelodysplastic syndromes, and discuss how this knowledge may inform our understanding of craniofacial spliceosomopathies.
Collapse
Affiliation(s)
- Casey Griffin
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, USA
| | - Jean-Pierre Saint-Jeannet
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, USA
| |
Collapse
|
14
|
Chen T, Zhang B, Ziegenhals T, Prusty AB, Fröhler S, Grimm C, Hu Y, Schaefke B, Fang L, Zhang M, Kraemer N, Kaindl AM, Fischer U, Chen W. A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing. PLoS Genet 2019; 15:e1008460. [PMID: 31671093 PMCID: PMC6850558 DOI: 10.1371/journal.pgen.1008460] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 11/12/2019] [Accepted: 10/04/2019] [Indexed: 12/15/2022] Open
Abstract
Malfunction of pre-mRNA processing factors are linked to several human diseases including cancer and neurodegeneration. Here we report the identification of a de novo heterozygous missense mutation in the SNRPE gene (c.65T>C (p.Phe22Ser)) in a patient with non-syndromal primary (congenital) microcephaly and intellectual disability. SNRPE encodes SmE, a basal component of pre-mRNA processing U snRNPs. We show that the microcephaly-linked SmE variant is unable to interact with the SMN complex and as a consequence fails to assemble into U snRNPs. This results in widespread mRNA splicing alterations in fibroblast cells derived from this patient. Similar alterations were observed in HEK293 cells upon SmE depletion that could be rescued by the expression of wild type but not mutant SmE. Importantly, the depletion of SmE in zebrafish causes aberrant mRNA splicing alterations and reduced brain size, reminiscent of the patient microcephaly phenotype. We identify the EMX2 mRNA, which encodes a protein required for proper brain development, as a major mis-spliced down stream target. Together, our study links defects in the SNRPE gene to microcephaly and suggests that alterations of cellular splicing of specific mRNAs such as EMX2 results in the neurological phenotype of the disease. In higher eukaryotes, the protein coding genes are first transcribed as precursor mRNAs (pre-mRNAs) and further processed by the spliceosome to form the mature mRNA for translation. Malfunction of pre-mRNA processing factors are linked to several human diseases including cancer and neurodegeneration. Here we report the identification of a de novo heterozygous missense mutation in the SNRPE/SmE gene in a patient with non-syndromal primary (congenital) microcephaly and intellectual disability. The effect of identified de novo mutation on SNRPE/SmE was characterized in vitro. The zebrafish was used as in vivo model to further dissect the physiological consequence and pathomechanism. Finally, the EMX2 gene was identified as one of the major down stream target genes responsible for the phenotype. Our study links defects in the SNRPE/SmE gene to microcephaly and provides the new pathogenic mechanism for microcephaly.
Collapse
Affiliation(s)
- Tao Chen
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical System Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Bin Zhang
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Thomas Ziegenhals
- Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Archana B. Prusty
- Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Sebastian Fröhler
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical System Biology, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Clemens Grimm
- Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Yuhui Hu
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Bernhard Schaefke
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Liang Fang
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Min Zhang
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
| | - Nadine Kraemer
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Department of Pediatric Neurology, Berlin, Germany
| | - Angela M. Kaindl
- Charité-Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Department of Pediatric Neurology, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Center for Chronically Sick Children, Berlin, Germany
- * E-mail: (UF); (AK); (WC)
| | - Utz Fischer
- Department of Biochemistry, Theodor-Boveri-Institute, University of Würzburg, Würzburg, Germany
- * E-mail: (UF); (AK); (WC)
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, China
- * E-mail: (UF); (AK); (WC)
| |
Collapse
|
15
|
Park S, Han SH, Kim HG, Jeong J, Choi M, Kim HY, Kim MG, Park JK, Han JE, Cho GJ, Kim MO, Ryoo ZY, Choi SK. Suppression of PRPF4 regulates pluripotency, proliferation, and differentiation in mouse embryonic stem cells. Cell Biochem Funct 2019; 37:608-617. [PMID: 31502671 DOI: 10.1002/cbf.3437] [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] [Received: 06/23/2019] [Revised: 08/17/2019] [Accepted: 08/26/2019] [Indexed: 01/03/2023]
Abstract
Mouse embryonic stem cells (mESCs) are characterized by their self-renewal and pluripotency and are capable of differentiating into all three germ layers. For this reason, mESCs are considered a very important model for stem cell research and clinical applications in regenerative medicine. The pre-mRNA processing factor 4 (PRPF4) gene is known to have a major effect on pre-mRNA splicing and is also known to affect tissue differentiation during development. In this study, we investigated the effects of PRPF4 knockdown on mESCs. First, we allowed mESCs to differentiate naturally and observed a significant decrease in PRPF4 expression during the differentiation process. We then artificially induced the knockdown of PRPF4 in mESCs and observed the changes in the phenotype. When PRPF4 was knocked down, various genes involved in mESC pluripotency showed significantly decreased expression. In addition, mESC proliferation increased abnormally, accompanied by a significant increase in mESC colony size. The formation of mESC embryoid bodies and teratomas was delayed following PRPF4 knockdown. Based on these results, the reduced expression of PRPF4 affects mESC phenotypes and is a key factor in mESC. SIGNIFICANCE OF THE STUDY: Our results indicate that PRPF4 affects the properties of mESCs. Suppression of PRPF4 resulted in a decrease in pluripotency of mESC and promoted proliferation. In addition, suppression of PRPF4 also resulted in decreased apoptosis. Moreover, the inhibition of PRPF4 reduced the ability to differentiate and formation of teratoma in mESC. Our results demonstrated that PRPF4 is a key factor of controlling mESC abilities.
Collapse
Affiliation(s)
- Song Park
- Core Protein Resources Center, DGIST, Daegu, Republic of Korea
| | - Se-Hyeon Han
- Department of News-team, SBS (Seoul Broadcasting Station), Yangchungu, Seoul, South Korea.,School of Media Communication, Hanyang University, Seongdonggu, Seoul, South Korea
| | - Hyeon-Gyeom Kim
- Core Protein Resources Center, DGIST, Daegu, Republic of Korea.,School of Life Science, BK21 Plus KNU Creative Bioresearch Group, Kyungpook National University, Daegu, Korea
| | - Jain Jeong
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Minjee Choi
- Core Protein Resources Center, DGIST, Daegu, Republic of Korea.,School of Life Science, BK21 Plus KNU Creative Bioresearch Group, Kyungpook National University, Daegu, Korea
| | - Hee-Yeon Kim
- Core Protein Resources Center, DGIST, Daegu, Republic of Korea
| | - Min-Gi Kim
- Core Protein Resources Center, DGIST, Daegu, Republic of Korea
| | - Jin-Kyu Park
- College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
| | - Jee Eun Han
- College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
| | - Gil-Jae Cho
- College of Veterinary Medicine, Kyungpook National University, Daegu, Korea
| | - Myoung Ok Kim
- Department of Animal Science, College of Ecology and Environment Science, Kyungpook National University, Sangju, Korea
| | - Zae Young Ryoo
- School of Life Science, BK21 Plus KNU Creative Bioresearch Group, Kyungpook National University, Daegu, Korea
| | - Seong-Kyoon Choi
- Core Protein Resources Center, DGIST, Daegu, Republic of Korea.,Division of Biotechnology, DGIST, Daegu, Republic of Korea
| |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Holger Dill
- Department of Biochemistry, Biocentre, University of Wuerzburg, Würzburg, Germany
| | - Utz Fischer
- Department of Biochemistry, Biocentre, University of Wuerzburg, Würzburg, Germany.
| |
Collapse
|
17
|
Wang Y, Han Y, Xu P, Ding S, Li G, Jin H, Meng Y, Meng A, Jia S. prpf4 is essential for cell survival and posterior lateral line primordium migration in zebrafish. J Genet Genomics 2018; 45:443-453. [DOI: 10.1016/j.jgg.2018.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 04/20/2018] [Accepted: 05/17/2018] [Indexed: 11/16/2022]
|
18
|
Dias MF, Joo K, Kemp JA, Fialho SL, da Silva Cunha A, Woo SJ, Kwon YJ. Molecular genetics and emerging therapies for retinitis pigmentosa: Basic research and clinical perspectives. Prog Retin Eye Res 2017; 63:107-131. [PMID: 29097191 DOI: 10.1016/j.preteyeres.2017.10.004] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/19/2017] [Accepted: 10/25/2017] [Indexed: 02/06/2023]
Abstract
Retinitis Pigmentosa (RP) is a hereditary retinopathy that affects about 2.5 million people worldwide. It is characterized with progressive loss of rods and cones and causes severe visual dysfunction and eventual blindness in bilateral eyes. In addition to more than 3000 genetic mutations from about 70 genes, a wide genetic overlap with other types of retinal dystrophies has been reported with RP. This diversity of genetic pathophysiology makes treatment extremely challenging. Although therapeutic attempts have been made using various pharmacologic agents (neurotrophic factors, antioxidants, and anti-apoptotic agents), most are not targeted to the fundamental cause of RP, and their clinical efficacy has not been clearly proven. Current therapies for RP in ongoing or completed clinical trials include gene therapy, cell therapy, and retinal prostheses. Gene therapy, a strategy to correct the genetic defects using viral or non-viral vectors, has the potential to achieve definitive treatment by replacing or silencing a causative gene. Among many clinical trials of gene therapy for hereditary retinal diseases, a phase 3 clinical trial of voretigene neparvovec (AAV2-hRPE65v2, Luxturna) recently showed significant efficacy for RPE65-mediated inherited retinal dystrophy including Leber congenital amaurosis and RP. It is about to be approved as the first ocular gene therapy biologic product. Despite current limitations such as limited target genes and indicated patients, modest efficacy, and the invasive administration method, development in gene editing technology and novel gene delivery carriers make gene therapy a promising therapeutic modality for RP and other hereditary retinal dystrophies in the future.
Collapse
Affiliation(s)
- Marina França Dias
- School of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Brazil; Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jessica A Kemp
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Silvia Ligório Fialho
- Pharmaceutical Research and Development, Ezequiel Dias Foundation, Belo Horizonte, Brazil
| | | | - Se Joon Woo
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA; Department of Ophthalmology, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
| | - Young Jik Kwon
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA; Department of Chemical Engineering and Materials Sciences, University of California, Irvine, CA, USA; Department of Biomedical Engineering, University of California, Irvine, CA, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
| |
Collapse
|
19
|
The spliceosomal proteins PPIH and PRPF4 exhibit bi-partite binding. Biochem J 2017; 474:3689-3704. [PMID: 28935721 DOI: 10.1042/bcj20170366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 09/05/2017] [Accepted: 09/15/2017] [Indexed: 01/04/2023]
Abstract
Pre-mRNA splicing is a dynamic, multistep process that is catalyzed by the RNA (ribonucleic acid)-protein complex called the spliceosome. The spliceosome contains a core set of RNAs and proteins that are conserved in all organisms that perform splicing. In higher organisms, peptidyl-prolyl isomerase H (PPIH) directly interacts with the core protein pre-mRNA processing factor 4 (PRPF4) and both integrate into the pre-catalytic spliceosome as part of the tri-snRNP (small nuclear RNA-protein complex) subcomplex. As a first step to understand the protein interactions that dictate PPIH and PRPF4 function, we expressed and purified soluble forms of each protein and formed a complex between them. We found two sites of interaction between PPIH and the N-terminus of PRPF4, an unexpected result. The N-terminus of PRPF4 is an intrinsically disordered region and does not adopt secondary structure in the presence of PPIH. In the absence of an atomic resolution structure, we used mutational analysis to identify point mutations that uncouple these two binding sites and find that mutations in both sites are necessary to break up the complex. A discussion of how this bipartite interaction between PPIH and PRPF4 may modulate spliceosomal function is included.
Collapse
|
20
|
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: 19] [Impact Index Per Article: 2.7] [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.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Ayoubian H, Fröhlich T, Pogodski D, Flatley A, Kremmer E, Schepers A, Feederle R, Arnold GJ, Grässer FA. Antibodies against the mono-methylated arginine-glycine repeat (MMA-RG) of the Epstein-Barr virus nuclear antigen 2 (EBNA2) identify potential cellular proteins targeted in viral transformation. J Gen Virol 2017; 98:2128-2142. [PMID: 28758620 DOI: 10.1099/jgv.0.000870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The Epstein-Barr virus is a human herpes virus with oncogenic potential. The virus-encoded nuclear antigen 2 (EBNA2) is a key mediator of viral tumorigenesis. EBNA2 features an arginine-glycine (RG) repeat at amino acids (aa)339-354 that is essential for the transformation of lymphocytes and contains symmetrically (SDMA) and asymmetrically (ADMA) di-methylated arginine residues. The SDMA-modified EBNA2 binds the survival motor neuron protein (SMN), thus mimicking SMD3, a cellular SDMA-containing protein that interacts with SMN. Accordingly, a monoclonal antibody (mAb) specific for the SDMA-modified RG repeat of EBNA2 also binds to SMD3. With the novel mAb 19D4 we now show that EBNA2 contains mono-methylated arginine (MMA) residues within the RG repeat. Using 19D4, we immune-precipitated and analysed by mass spectrometry cellular proteins in EBV-transformed B-cells that feature MMA motifs that are similar to the one in EBNA2. Among the cellular proteins identified, we confirmed by immunoprecipitation and/or Western blot analyses Aly/REF, Coilin, DDX5, FXR1, HNRNPK, LSM4, MRE11, NRIP, nucleolin, PRPF8, RBM26, SMD1 (SNRDP1) and THRAP3 proteins that are either known to contain MMA residues or feature RG repeat sequences that probably serve as methylation substrates. The identified proteins are involved in splicing, tumorigenesis, transcriptional activation, DNA stability and RNA processing or export. Furthermore, we found that several proteins involved in energy metabolism are associated with MMA-modified proteins. Interestingly, the viral EBNA1 protein that features methylated RG repeat motifs also reacted with the antibodies. Our results indicate that the region between aa 34-52 of EBNA1 contains ADMA or SDMA residues, while the region between aa 328-377 mainly contains MMA residues.
Collapse
Affiliation(s)
- Hiresh Ayoubian
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Dagmar Pogodski
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| | - Andrew Flatley
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Elisabeth Kremmer
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Aloys Schepers
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, Marchioninistrasse 25, 81377 Munich, Germany
| | - Georg J Arnold
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Strasse 25, 81377, Munich, Germany
| | - Friedrich A Grässer
- Institute of Virology, Saarland University Medical School, Kirrbergerstrasse, Haus 47, D-66421 Homburg/Saar, Germany
| |
Collapse
|
23
|
Malinová A, Cvačková Z, Matějů D, Hořejší Z, Abéza C, Vandermoere F, Bertrand E, Staněk D, Verheggen C. Assembly of the U5 snRNP component PRPF8 is controlled by the HSP90/R2TP chaperones. J Cell Biol 2017; 216:1579-1596. [PMID: 28515276 PMCID: PMC5461031 DOI: 10.1083/jcb.201701165] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/22/2017] [Accepted: 04/04/2017] [Indexed: 12/23/2022] Open
Abstract
The pre-mRNA splicing factor PRPF8 is a crucial component of the U5 snRNP. Using quantitative proteomics, Malinová et al. show that assembly of the U5 snRNP is controlled by the HSP90/R2TP chaperones and that Retinitis pigmentosa–associated mutations in PRPF8 impair PRPF8 quality control and U5 snRNP chaperone-mediated assembly. Splicing is catalyzed by the spliceosome, a complex of five major small nuclear ribonucleoprotein particles (snRNPs). The pre-mRNA splicing factor PRPF8 is a crucial component of the U5 snRNP, and together with EFTUD2 and SNRNP200, it forms a central module of the spliceosome. Using quantitative proteomics, we identified assembly intermediates containing PRPF8, EFTUD2, and SNRNP200 in association with the HSP90/R2TP complex, its ZNHIT2 cofactor, and additional proteins. HSP90 and R2TP bind unassembled U5 proteins in the cytoplasm, stabilize them, and promote the formation of the U5 snRNP. We further found that PRPF8 mutants causing Retinitis pigmentosa assemble less efficiently with the U5 snRNP and bind more strongly to R2TP, with one mutant retained in the cytoplasm in an R2TP-dependent manner. We propose that the HSP90/R2TP chaperone system promotes the assembly of a key module of U5 snRNP while assuring the quality control of PRPF8. The proteomics data further reveal new interactions between R2TP and the tuberous sclerosis complex (TSC), pointing to a potential link between growth signals and the assembly of key cellular machines.
Collapse
Affiliation(s)
- Anna Malinová
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic.,Faculty of Science, Charles University in Prague, 128 00 Prague, Czech Republic
| | - Zuzana Cvačková
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Daniel Matějů
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Zuzana Hořejší
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Claire Abéza
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
| | - Franck Vandermoere
- Institut de Génomique Fonctionnelle, Centre National de la Recherche Scientifique, University of Montpellier, 34090 Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
| | - David Staněk
- Institute of Molecular Genetics, Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Céline Verheggen
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique, University of Montpellier, 34293 Montpellier, France
| |
Collapse
|
24
|
Blanco-Sánchez B, Clément A, Phillips JB, Westerfield M. Zebrafish models of human eye and inner ear diseases. Methods Cell Biol 2016; 138:415-467. [PMID: 28129854 DOI: 10.1016/bs.mcb.2016.10.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Eye and inner ear diseases are the most common sensory impairments that greatly impact quality of life. Zebrafish have been intensively employed to understand the fundamental mechanisms underlying eye and inner ear development. The zebrafish visual and vestibulo-acoustic systems are very similar to these in humans, and although not yet mature, they are functional by 5days post-fertilization (dpf). In this chapter, we show how the zebrafish has significantly contributed to the field of biomedical research and how researchers, by establishing disease models and meticulously characterizing their phenotypes, have taken the first steps toward therapies. We review here models for (1) eye diseases, (2) ear diseases, and (3) syndromes affecting eye and/or ear. The use of new genome editing technologies and high-throughput screening systems should increase considerably the speed at which knowledge from zebrafish disease models is acquired, opening avenues for better diagnostics, treatments, and therapies.
Collapse
Affiliation(s)
| | - A Clément
- University of Oregon, Eugene, OR, United States
| | | | | |
Collapse
|
25
|
Pensado A, Diaz-Corrales FJ, De la Cerda B, Valdés-Sánchez L, Del Boz AA, Rodriguez-Martinez D, García-Delgado AB, Seijo B, Bhattacharya SS, Sanchez A. Span poly-L-arginine nanoparticles are efficient non-viral vectors for PRPF31 gene delivery: An approach of gene therapy to treat retinitis pigmentosa. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2016; 12:2251-2260. [PMID: 27381066 DOI: 10.1016/j.nano.2016.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/31/2016] [Accepted: 06/16/2016] [Indexed: 12/21/2022]
Abstract
Retinitis pigmentosa (RP) is the most common cause of inherited blindness in adults. Mutations in the PRPF31 gene produce autosomal dominant RP (adRP). To date there are no effective treatments for this disease. The purpose of this study was to design an efficient non-viral vector for human PRPF31 gene delivery as an approach to treat this form of adRP. Span based nanoparticles were developed to mediate gene transfer in the subretinal space of a mouse model of adRP carrying a point mutation (A216P) in the Prpf31 gene. Funduscopic examination, electroretinogram, optomotor test and optical coherence tomography were conducted to further in vivo evaluate the safety and efficacy of the nanosystems developed. Span-polyarginine (SP-PA) nanoparticles were able to efficiently transfect the GFP and PRPF31 plasmid in mice retinas. Statistically significant improvement in visual acuity and retinal thickness were found in Prpf31A216P/+ mice treated with the SP-PA-PRPF31 nanomedicine.
Collapse
Affiliation(s)
- Andrea Pensado
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, Spain
| | - Francisco J Diaz-Corrales
- Department of Cell Therapy and Regenerative Medicine, Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, Spain
| | - Berta De la Cerda
- Department of Cell Therapy and Regenerative Medicine, Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, Spain
| | - Lourdes Valdés-Sánchez
- Department of Cell Therapy and Regenerative Medicine, Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, Spain
| | - Ana Aramburu Del Boz
- Department of Cell Therapy and Regenerative Medicine, Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, Spain
| | - Daniel Rodriguez-Martinez
- Department of Cell Therapy and Regenerative Medicine, Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, Spain
| | - Ana B García-Delgado
- Department of Cell Therapy and Regenerative Medicine, Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, Spain
| | - Begoña Seijo
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, Spain; Molecular Image Group, Health Research Institute-University Clinical Hospital of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Shomi S Bhattacharya
- Department of Cell Therapy and Regenerative Medicine, Andalusian Molecular Biology and Regenerative Medicine Centre (CABIMER), Seville, Spain
| | - Alejandro Sanchez
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, Universidade de Santiago de Compostela, Campus Vida, Santiago de Compostela, Spain; Molecular Image Group, Health Research Institute-University Clinical Hospital of Santiago de Compostela (IDIS), Santiago de Compostela, Spain.
| |
Collapse
|
26
|
Abstract
A majority of human genes contain non-coding intervening sequences – introns that must be precisely excised from the pre-mRNA molecule. This event requires the coordinated action of five major small nuclear ribonucleoprotein particles (snRNPs) along with additional non-snRNP splicing proteins. Introns must be removed with nucleotidal precision, since even a single nucleotide mistake would result in a reading frame shift and production of a non-functional protein. Numerous human inherited diseases are caused by mutations that affect splicing, including mutations in proteins which are directly involved in splicing catalysis. One of the most common hereditary diseases associated with mutations in core splicing proteins is retinitis pigmentosa (RP). So far, mutations in more than 70 genes have been connected to RP. While the majority of mutated genes are expressed specifically in the retina, eight target genes encode for ubiquitous core snRNP proteins (Prpf3, Prpf4, Prpf6, Prpf8, Prpf31, and SNRNP200/Brr2) and splicing factors (RP9 and DHX38). Why mutations in spliceosomal proteins, which are essential in nearly every cell in the body, causes a disease that displays such a tissue-specific phenotype is currently a mystery. In this review, we recapitulate snRNP functions, summarize the missense mutations which are found in spliceosomal proteins as well as their impact on protein functions and discuss specific models which may explain why the retina is sensitive to these mutations.
Collapse
Affiliation(s)
- Šárka Růžičková
- a Department of RNA Biology , Institute of Molecular Genetics AS CR , Prague , Czech Republic
| | - David Staněk
- a Department of RNA Biology , Institute of Molecular Genetics AS CR , Prague , Czech Republic
| |
Collapse
|
27
|
Rose AM, Bhattacharya SS. Variant haploinsufficiency and phenotypic non-penetrance in PRPF31-associated retinitis pigmentosa. Clin Genet 2016; 90:118-26. [PMID: 26853529 DOI: 10.1111/cge.12758] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/30/2022]
Abstract
Retinitis pigmentosa (RP) is a genetically heterogenous group of inherited disorders, characterized by death of the retinal photoreceptor cells, leading to progressive visual impairment. One form of RP is caused by mutations in the ubiquitously expressed splicing factor, PRPF31, this form being known as RP11. An intriguing feature of RP11 is the presence of non-penetrance, which has been observed in the majority of PRPF31 mutation-carrying families. In contrast to variable expressivity, which is highly pervasive, true non-penetrance is a very rare phenomenon in Mendelian disorders. In this article, the molecular mechanisms underlying phenotypic non-penetrance in RP11 are explored. It is an elegant example of how our understanding of monogenic disorders has evolved from studying only the disease gene, to considering a mutation on the genetic background of the individual - the logical evolution in this genomic era.
Collapse
Affiliation(s)
- A M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| | - S S Bhattacharya
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| |
Collapse
|
28
|
Abstract
The human transcriptome is composed of a vast RNA population that undergoes further diversification by splicing. Detecting specific splice sites in this large sequence pool is the responsibility of the major and minor spliceosomes in collaboration with numerous splicing factors. This complexity makes splicing susceptible to sequence polymorphisms and deleterious mutations. Indeed, RNA mis-splicing underlies a growing number of human diseases with substantial societal consequences. Here, we provide an overview of RNA splicing mechanisms followed by a discussion of disease-associated errors, with an emphasis on recently described mutations that have provided new insights into splicing regulation. We also discuss emerging strategies for splicing-modulating therapy.
Collapse
Affiliation(s)
- Marina M Scotti
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida 32610-3610 USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida 32610-3610 USA
| |
Collapse
|
29
|
Liu Y, Liu J, Wang Z, He JJ. Tip110 binding to U6 small nuclear RNA and its participation in pre-mRNA splicing. Cell Biosci 2015. [PMID: 26203351 PMCID: PMC4511435 DOI: 10.1186/s13578-015-0032-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background RNA–protein interactions play important roles in gene expression control. These interactions are mediated by several recurring RNA-binding motifs including a well-known and characterized ribonucleoprotein motif or so-called RNA recognition motif (RRM). Results In the current study, we set out to identify the RNA ligand(s) of a RRM-containing protein Tip110, also known as p110nrb, SART3, or p110, using a RNA-based yeast three-hybrid cloning strategy. Six putative RNA targets were isolated and found to contain a consensus sequence that was identical to nucleotides 34–46 of U6 small nuclear RNA. Tip110 binding to U6 was confirmed to be specific and RRM-dependent in an electrophoretic mobility shift assay. Both in vitro pre-mRNA splicing assay and in vivo splicing-dependent reporter gene assay showed that the pre-mRNA splicing was correlated with Tip110 expression. Moreover, Tip110 was found in the spliceosomes containing pre-spliced pre-mRNA and spliced mRNA products. Nonetheless, the RRM-deleted mutant (ΔRRM) that did not bind to U6 showed promotion in vitro pre-mRNA splicing, whereas the nuclear localization signal (NLS)-deleted mutant ΔNLS that bound to U6 promoted the pre-mRNA splicing both in vitro and in vivo. Lastly, RNA-Seq analysis confirmed that Tip110 regulated a number of gene pre-mRNA splicing including several splicing factors. Conclusions Taken together, these results demonstrate that Tip110 is directly involved in constitutive eukaryotic pre-mRNA splicing, likely through its binding to U6 and regulation of other splicing factors, and provide further evidence to support the global roles of Tip110 in regulation of host gene expression.
Collapse
Affiliation(s)
- Ying Liu
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 USA
| | - Jinfeng Liu
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 USA ; Department of Infectious Diseases, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi China
| | - Zenyuan Wang
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 USA ; Department of Forensic Science, College of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi China
| | - Johnny J He
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 USA
| |
Collapse
|
30
|
Deml B, Reis LM, Muheisen S, Bick D, Semina EV. EFTUD2 deficiency in vertebrates: Identification of a novel human mutation and generation of a zebrafish model. ACTA ACUST UNITED AC 2015; 103:630-40. [PMID: 26118977 DOI: 10.1002/bdra.23397] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/30/2015] [Accepted: 05/26/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND Congenital microphthalmia and coloboma are severe developmental defects that are frequently associated with additional systemic anomalies and display a high level of genetic heterogeneity. METHODS To identify the pathogenic variant in a patient with microphthalmia, coloboma, retinal dystrophy, microcephaly, and other features, whole exome sequencing analysis of the patient and parental samples was undertaken. To further explore the identified variant/gene, expression and functional studies in zebrafish were performed. RESULTS Whole exome sequencing revealed a de novo variant, c.473_474delGA, p.(Arg158Lysfs*4), in EFTUD2 which encodes a component of the spliceosome complex. Dominant mutations in EFTUD2 cause Mandibulofacial Dysostosis, Guion-Almeida type, which does not involve microphthalmia, coloboma, or retinal dystrophy; analysis of genes known to cause these ocular phenotypes identified several variants of unknown significance but no causal alleles in the affected patient. Zebrafish eftud2 demonstrated high sequence conservation with the human gene and broad embryonic expression. TALEN-mediated disruption was employed to generate a c.378_385 del, p.(Ser127Aspfs*23) truncation mutation in eftud2. Homozygous mutants displayed a reduced head size, small eye, curved body, and early embryonic lethality. Apoptosis assays demonstrated a striking increase in terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling (TUNEL)-positive cells in the developing brain, eye, spinal cord, and other tissues starting at 30 hours postfertilization. CONCLUSION This study reports a novel mutation in EFTUD2 in a Mandibulofacial Dysostosis, Guion-Almeida type patient with unusual ocular features and the generation of a first animal model of eftud2 deficiency. The severe embryonic phenotype observed in eftud2 mutants indicates an important conserved role during development of diverse tissues in vertebrates.
Collapse
Affiliation(s)
- Brett Deml
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - Sanaa Muheisen
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - David Bick
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, Wisconsin.,Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin
| |
Collapse
|
31
|
Linder B, Fischer U, Gehring NH. mRNA metabolism and neuronal disease. FEBS Lett 2015; 589:1598-606. [DOI: 10.1016/j.febslet.2015.04.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/26/2015] [Accepted: 04/27/2015] [Indexed: 12/12/2022]
|
32
|
Nash BM, Wright DC, Grigg JR, Bennetts B, Jamieson RV. Retinal dystrophies, genomic applications in diagnosis and prospects for therapy. Transl Pediatr 2015; 4:139-63. [PMID: 26835369 PMCID: PMC4729094 DOI: 10.3978/j.issn.2224-4336.2015.04.03] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Retinal dystrophies (RDs) are degenerative diseases of the retina which have marked clinical and genetic heterogeneity. Common presentations among these disorders include night or colour blindness, tunnel vision and subsequent progression to complete blindness. The known causative disease genes have a variety of developmental and functional roles with mutations in more than 120 genes shown to be responsible for the phenotypes. In addition, mutations within the same gene have been shown to cause different disease phenotypes, even amongst affected individuals within the same family highlighting further levels of complexity. The known disease genes encode proteins involved in retinal cellular structures, phototransduction, the visual cycle, and photoreceptor structure or gene regulation. This review aims to demonstrate the high degree of genetic complexity in both the causative disease genes and their associated phenotypes, highlighting the more common clinical manifestation of retinitis pigmentosa (RP). The review also provides insight to recent advances in genomic molecular diagnosis and gene and cell-based therapies for the RDs.
Collapse
Affiliation(s)
- Benjamin M Nash
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Dale C Wright
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - John R Grigg
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Bruce Bennetts
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Robyn V Jamieson
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| |
Collapse
|