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Jeyaprakash K, Thirumalairaj K, Kim U, Muthukkaruppan V, Vanniarajan A. RB1 transcript analysis detects novel splicing aberration in retinoblastoma. Pediatr Blood Cancer 2023; 70:e30290. [PMID: 36916769 DOI: 10.1002/pbc.30290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/16/2023] [Accepted: 02/19/2023] [Indexed: 03/16/2023]
Affiliation(s)
- Kumar Jeyaprakash
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India.,Department of Molecular Biology, Aravind Medical Research Foundation, Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India
| | - Kannan Thirumalairaj
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | - Usha Kim
- Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, Tamil Nadu, India
| | - Veerappan Muthukkaruppan
- Department of Stem Cell Biology and Immunology, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
| | - Ayyasamy Vanniarajan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India.,Department of Molecular Biology, Aravind Medical Research Foundation, Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India
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Splicing-Disrupting Mutations in Inherited Predisposition to Solid Pediatric Cancer. Cancers (Basel) 2022; 14:cancers14235967. [PMID: 36497448 PMCID: PMC9739414 DOI: 10.3390/cancers14235967] [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: 10/17/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
The prevalence of hereditary cancer in children was estimated to be very low until recent studies suggested that at least 10% of pediatric cancer patients carry a germline mutation in a cancer predisposition gene. A significant proportion of pathogenic variants associated with an increased risk of hereditary cancer are variants affecting splicing. RNA splicing is an essential process involved in different cellular processes such as proliferation, survival, and differentiation, and alterations in this pathway have been implicated in many human cancers. Hereditary cancer genes are highly susceptible to splicing mutations, and among them there are several genes that may contribute to pediatric solid tumors when mutated in the germline. In this review, we have focused on the analysis of germline splicing-disrupting mutations found in pediatric solid tumors, as the discovery of pathogenic splice variants in pediatric cancer is a growing field for the development of personalized therapies. Therapies developed to correct aberrant splicing in cancer are also discussed as well as the options to improve the diagnostic yield based on the increase in the knowledge in splicing.
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Rodríguez-Martín C, Cidre F, Fernández-Teijeiro A, Gómez-Mariano G, de la Vega L, Ramos P, Zaballos Á, Monzón S, Alonso J. Familial retinoblastoma due to intronic LINE-1 insertion causes aberrant and noncanonical mRNA splicing of the RB1 gene. J Hum Genet 2016; 61:463-6. [PMID: 26763876 DOI: 10.1038/jhg.2015.173] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 12/21/2015] [Accepted: 12/25/2015] [Indexed: 01/31/2023]
Abstract
Retinoblastoma (RB, MIM 180200) is the paradigm of hereditary cancer. Individuals harboring a constitutional mutation in one allele of the RB1 gene have a high predisposition to develop RB. Here, we present the first case of familial RB caused by a de novo insertion of a full-length long interspersed element-1 (LINE-1) into intron 14 of the RB1 gene that caused a highly heterogeneous splicing pattern of RB1 mRNA. LINE-1 insertion was inferred by mRNA studies and full-length sequenced by massive parallel sequencing. Some of the aberrant mRNAs were produced by noncanonical acceptor splice sites, a new finding that up to date has not been described to occur upon LINE-1 retrotransposition. Our results clearly show that RNA-based strategies have the potential to detect disease-causing transposon insertions. It also confirms that the incorporation of new genetic approaches, such as massive parallel sequencing, contributes to characterize at the sequence level these unique and exceptional genetic alterations.
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Affiliation(s)
- Carlos Rodríguez-Martín
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Florencia Cidre
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Ana Fernández-Teijeiro
- Unidad de Gestión Clínica Intercentros de Oncología Pediátricas, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, National Reference Unit for Retinoblastoma, Sevilla, Spain
| | - Gema Gómez-Mariano
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Leticia de la Vega
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Patricia Ramos
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Ángel Zaballos
- Unidad de Genómica, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
| | - Sara Monzón
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER U758), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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Gonzalez-Paredes FJ, Ramos-Trujillo E, Claverie-Martin F. Defective pre-mRNA splicing in PKD1 due to presumed missense and synonymous mutations causing autosomal dominant polycystic disease. Gene 2014; 546:243-9. [DOI: 10.1016/j.gene.2014.06.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 05/21/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
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Nagarkatti-Gude N, Wang Y, Ali MJ, Honavar SG, Jager MJ, Chan CC. Genetics of primary intraocular tumors. Ocul Immunol Inflamm 2012; 20:244-54. [PMID: 22834783 PMCID: PMC3436423 DOI: 10.3109/09273948.2012.702843] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Primary intraocular neoplasms are tumors that originate within the eye. The most common malignant primary intraocular tumor in adults is uveal melanoma and the second is primary intraocular lymphoma or vitreoretinal (intraocular) lymphoma. The most common malignant intraocular tumor in children is retinoblastoma. Genetics plays a vital role in the diagnosis and detection of ocular tumors. In uveal melanoma, monosomy 3 is the most common genetic alteration and somatic mutations of BAP1, a tumor suppressor gene, have been reported in nearly 50% of primary uveal melanomas. The retinoblastoma gene RB1 is the prototype tumor suppressor gene-mutations in RB1 alleles lead to inactivated RB protein and the development of retinoblastoma. Immunoglobulin heavy chain (IgH) or T-cell receptor (TCR) gene rearrangement is observed in B-cell or T-cell primary vitreoretinal lymphoma, respectively. Other factors related to the genetics of these three common malignancies in the eye are discussed and reviewed.
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Affiliation(s)
- Nisha Nagarkatti-Gude
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Yujuan Wang
- Immunopathology Section, Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
- Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | | | | | - Martine J. Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chi-Chao Chan
- Immunopathology Section, Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
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Wöhlke A, Philipp U, Bock P, Beineke A, Lichtner P, Meitinger T, Distl O. A one base pair deletion in the canine ATP13A2 gene causes exon skipping and late-onset neuronal ceroid lipofuscinosis in the Tibetan terrier. PLoS Genet 2011; 7:e1002304. [PMID: 22022275 PMCID: PMC3192819 DOI: 10.1371/journal.pgen.1002304] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Accepted: 08/06/2011] [Indexed: 11/18/2022] Open
Abstract
Neuronal ceroid lipofuscinosis (NCL) is a progressive neurodegenerative disease characterized by brain and retinal atrophy and the intracellular accumulation of autofluorescent lysosomal storage bodies resembling lipofuscin in neurons and other cells. Tibetan terriers show a late-onset lethal form of NCL manifesting first visible signs at 5–7 years of age. Genome-wide association analyses for 12 Tibetan-terrier-NCL-cases and 7 Tibetan-terrier controls using the 127K canine Affymetrix SNP chip and mixed model analysis mapped NCL to dog chromosome (CFA) 2 at 83.71–84.72 Mb. Multipoint linkage and association analyses in 376 Tibetan terriers confirmed this genomic region on CFA2. A mutation analysis for 14 positional candidate genes in two NCL-cases and one control revealed a strongly associated single nucleotide polymorphism (SNP) in the MAPK PM20/PM21 gene and a perfectly with NCL associated single base pair deletion (c.1620delG) within exon 16 of the ATP13A2 gene. The c.1620delG mutation in ATP13A2 causes skipping of exon 16 presumably due to a broken exonic splicing enhancer motif. As a result of this mutation, ATP13A2 lacks 69 amino acids. All known 24 NCL cases were homozygous for this deletion and all obligate 35 NCL-carriers were heterozygous. In a sample of 144 dogs from eleven other breeds, the c.1620delG mutation could not be found. Knowledge of the causative mutation for late-onset NCL in Tibetan terrier allows genetic testing of these dogs to avoid matings of carrier animals. ATP13A2 mutations have been described in familial Parkinson syndrome (PARK9). Tibetan terriers with these mutations provide a valuable model for a PARK9-linked disease and possibly for manganese toxicity in synucleinopathies. The neuronal ceroid lipofuscinosis (NCL) is a neurodegenerative storage diseases characterized by psychomotor retardation, blindness, and premature death. NCL has been reported in several dog breeds. NCL is characterized by progressive brain and retinal atrophy and the intracellular accumulation of autofluorescent lysosomal storage bodies resembling lipofuscin. Tibetan terriers show a late-onset and lethal NCL (age of onset 5–7 years) with an autosomal recessive inheritance. The most frequently described first symptom is blindness in twilight. In the disease progress the affected dogs often appear nervous or anxious and the lack of motor coordination becomes more severe. In the final stages of this disease, mild but also severe seizures have been observed by the owner. There are no treatment options for affected dogs. Through a genome-wide association analysis using the 127K canine Affymetrix SNP chip, we found a 1 Mb candidate genomic region and identified ATP13A2 as the most likely candidate for NCL. A 1-base pair deletion mutation within exon 16 of the ATP13A2 gene caused the loss of an exonic splicing enhancer and, consequently, the alternative splicing lead to skipping of exon 16. This study provides a suitable animal model for PARK9 in man to develop therapeutic approaches.
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Affiliation(s)
- Anne Wöhlke
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Ute Philipp
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Patricia Bock
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Andreas Beineke
- Department of Pathology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Peter Lichtner
- Helmholtz Zentrum München, Institute of Human Genetics, Neuherberg, Germany
| | - Thomas Meitinger
- Helmholtz Zentrum München, Institute of Human Genetics, Neuherberg, Germany
- Technische Universität München, Institute of Human Genetics, München, Germany
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany
- * E-mail:
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