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Gregersen PA, Jensen PS, Christensen R, Lohmann D, Racher H, Gallie B, Urbak SF. Retinoblastoma caused by an RB1 variant with unusually low penetrance in a Danish family. Eur J Med Genet 2024; 70:104956. [PMID: 38897371 DOI: 10.1016/j.ejmg.2024.104956] [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: 02/12/2024] [Revised: 04/23/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024]
Abstract
Retinoblastoma is the most common eye cancer in children. It is caused by pathogenic alterations of both alleles of the tumor suppressor gene RB1. In heritable retinoblastoma, a constitutional RB1 variant predisposes the cells to tumor formation, and loss of the other allele is a prerequisite for the development of retinoblastoma. Heritable retinoblastoma is inherited in an autosomal dominant manner; however, the majority of cases are the result of a de novo pathogenic RB1 variant. Penetrance is usually high (>90%), but with marked inter-familial variability. In some families, penetrance is incomplete and family members who develop tumors tend to remain unilaterally affected. Moreover, some families with low penetrance also show a parent-of-origin effect. We describe a patient with unilateral retinoblastoma caused by a previously unreported likely pathogenic RB1 variant (c.1199T>C) that disrupts a highly conserved amino acid residue within the A-box functional domain. Segregation analysis showed that the variant had unusually low penetrance as nine non-affected family members carried the same variant. We emphasize the use of genetic analysis on tumor DNA for classifying the RB1 variant, and underline the challenges in clinical management and counseling of families carrying the specific RB1 variant.
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Affiliation(s)
- Pernille A Gregersen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Centre for Rare Diseases, Department of Paediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Peter S Jensen
- Department of Ophthalmology, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Dietmar Lohmann
- Institut für Humangenetik, Universitätsklinikum Essen, University Duisburg-Essen, Essen, Germany
| | - Hilary Racher
- Impact Genetics, Brampton, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Brenda Gallie
- Ophthalmology, The Hospital for Sick Children, Toronto, Canada; Departments Ophthalmology and Molecular Genetics, University of Toronto, Canada
| | - Steen F Urbak
- Department of Ophthalmology, Aarhus University Hospital, Aarhus, Denmark
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Price EA, Sagoo MS, Reddy MA, Onadim Z. An overview of RB1 transcript alterations detected during retinoblastoma genetic screening. Ophthalmic Genet 2024; 45:235-245. [PMID: 37932244 DOI: 10.1080/13816810.2023.2270570] [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: 07/14/2023] [Revised: 08/24/2023] [Accepted: 10/09/2023] [Indexed: 11/08/2023]
Abstract
Identification of pathogenic RB1 variants aids in the clinical management of families with retinoblastoma. We routinely screen DNA for RB1 variants, but transcript analysis can also be used for variant screening, and to help decide variant pathogenicity. DNA was screened by conformation analysis followed by Sanger sequencing. Large deletion/insertions were detected by polymorphism analysis, MLPA and quantitative-PCR. Methylation-specific PCR was used to detect hypermethylation. RNA screening was performed when a DNA pathogenic variant was missing, or to determine effects on splicing.Two hundred and thirteen small coding variants were predicted to affect splicing in 207 patients. Splice donor (sd) variants were nearly twice as frequent as splice acceptor (sa) with the most affected positions being sd + 1 and sa-1. Some missense and nonsense codons altered splicing, while some splice consensus variants did not. Large deletion/insertions can disrupt splicing, but RNA analysis showed that some of these are more complex than indicated by DNA testing. RNA screening found pathogenic variants in 53.8% of samples where DNA analysis did not. RB1 splicing is altered by changes at consensus splice sites, some missense and nonsense codons, deep intronic changes and large deletion/insertions. Common alternatively spliced transcripts may complicate analysis. An effective molecular screening strategy would include RNA analysis to help determine pathogenicity.
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Affiliation(s)
- Elizabeth A Price
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
| | - Mandeep S Sagoo
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK
- NIHR Biomedical Research Centre for Ophthalmology, Moorfields Eye Hospital, Institute of Ophthalmology, University College London, London, UK
| | - M Ashwin Reddy
- Retinoblastoma Service, Royal London Hospital, Barts Health NHS Trust, London, UK
- Faculty of Medicine, Queen Mary University of London, London, UK
| | - Zerrin Onadim
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
- Faculty of Medicine, Queen Mary University of London, London, UK
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3
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Mendonça V, Pereira Sena P, Evangelista Dos Santos AC, Rodrigues Bonvicino C, Ashton-Prolla P, Epelman S, Ferman SE, Lapunzina P, Nevado J, Grigorovski N, Mattosinho C, Seuànez H, Regla Vargas F. Diverse mutational spectrum in the 13q14 chromosomal region in a Brazilian cohort of retinoblastoma. Exp Eye Res 2022; 224:109211. [PMID: 35985532 DOI: 10.1016/j.exer.2022.109211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/19/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022]
Abstract
Retinoblastoma is a rare childhood tumor caused by the inactivation of both copies of the RB1 gene. Early diagnosis and identification of heritable RB1 mutation carriers can improve the disease outcome and management via genetic counseling. We used the Multiplex Ligation-dependent Probe Amplification (MLPA) method to analyze the RB1 gene and flanking regions in blood samples from 159 retinoblastoma patients previously negative for RB1 point mutations via Sanger sequencing. We detected a wide spectrum of germline chromosomal alterations, ranging from partial loss or duplication of RB1 to large deletions spanning RB1 and adjacent genes. Mutations were validated via karyotyping, fluorescent in situ hybridization (FISH), SNP-arrays (Single Nucleotide Polymorphism-arrays) and/or quantitative relative real-time PCR. Patients with leukocoria as a presenting symptom showed reduced death rate (p = 0.013) and this sign occurred more frequently among carriers of two breakpoints within RB1 (p = 0.05). All unilateral cases presented both breakpoints outside of RB1 (p = 0.0075). Patients with one breakpoint within RB1 were diagnosed at earlier ages (p = 0.017). Our findings characterize the mutational spectrum of a Brazilian cohort of retinoblastoma patients and point to a possible relationship between the mutation breakpoint location and tumor outcome, contributing to a better prospect of the genotype/phenotype correlation and adding to the wide diversity of germline mutations involving RB1 and adjacent regions in retinoblastoma.
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Affiliation(s)
- Vanessa Mendonça
- Genetics Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Priscila Pereira Sena
- Genetics Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | | | | | | | - Sidnei Epelman
- Pediatric Oncology Service, Hospital Santa Marcelina, São Paulo, Brazil
| | - Sima Esther Ferman
- Department of Pediatric Oncology, Clinical Division, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Pablo Lapunzina
- INGEMM, Hospital La Paz, Universidad de Madrid, Madrid, Spain; CIBERER (Centro de Investigación Médica en Red de Enfermedades Raras), Madrid, Spain; ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Julián Nevado
- INGEMM, Hospital La Paz, Universidad de Madrid, Madrid, Spain; CIBERER (Centro de Investigación Médica en Red de Enfermedades Raras), Madrid, Spain; ITHACA-European Reference Network, Hospital La Paz, Madrid, Spain
| | - Nathalia Grigorovski
- Department of Pediatric Oncology, Clinical Division, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Clarissa Mattosinho
- Department of Ocular Oncology, Division of Surgery, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Hector Seuànez
- Genetics Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil; Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fernando Regla Vargas
- Birth Defects Epidemiology Laboratory, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil; Department of Genetics and Molecular Biology, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
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Five novel RB1 gene mutations and genotype-phenotype correlations in Chinese children with retinoblastoma. Int Ophthalmol 2022; 42:3421-3430. [PMID: 35960463 PMCID: PMC9587959 DOI: 10.1007/s10792-022-02341-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/18/2022] [Indexed: 11/22/2022]
Abstract
Purpose To identify the spectrum of RB1 gene mutations in 114 Chinese patients with retinoblastoma. Methods Genomic DNA was extracted from the peripheral blood of 114 Rb patients. Polymerase chain reactions (PCRs) followed by direct Sanger sequencing were used to screen for mutations in the RB1 gene, which contains 26 exons with flanking intronic sequences, except exon 15. Clinical data, including gender, age at diagnosis, laterality of ocular lesions, and associated symptoms, were recorded and compared. Results We identified five novel mutations in the RB1 gene. Twenty-five other mutations found in this study have been previously reported. A higher rate of RB1 mutations, with 47.3% of mutations among bilaterally affected patients vs. 6.8% within unilaterally affected patients, was also observed (p < 0.0001). Bilaterally affected patients were diagnosed earlier when compared to unilaterally affected patients (11 ± 7 months versus 20 ± 14 months, p = 0.0002). Furthermore, nonsense mutations were abundant (n = 14), followed by frameshift mutations (n = 8), splicing site mutations (n = 5), while missense mutations were few (n = 3). Conclusions We found five novel mutations in RB1 genes, which expands the mutational spectrum of the gene. Children with bilateral Rb exhibited higher mutation rates and were diagnosed earlier than those with unilateral Rb. These findings will inform clinical diagnosis and genetic therapeutic targeting in Rb patients. Supplementary Information The online version contains supplementary material available at 10.1007/s10792-022-02341-2.
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Yao Y, Gu X, Xu X, Ge S, Jia R. Novel insights into RB1 mutation. Cancer Lett 2022; 547:215870. [PMID: 35964818 DOI: 10.1016/j.canlet.2022.215870] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 01/09/2023]
Abstract
Since the discovery of the retinoblastoma susceptibility gene (RB1) decades ago, RB1 has been regarded as a prototype tumor suppressor gene providing a paradigm for tumor genetic research. Constant research has updated the understanding of RB1-related pathways and their impact on tumor and nontumor diseases. Mutation of RB1 gene has been observed in multiple types of malignant tumors including prostate cancer, lung cancer, breast cancer, and almost every familial and sporadic case of retinoblastoma. Even if well-known and long-investigated, the application potential of RB1 mutation has not been fully tapped. In this review, we focus on the mechanism underlying RB1 mutation during oncogenesis. Therapeutically, we have further discussed potential clinical strategies by targeting RB1-mutated cancers. The unsolved problems and prospects of RB1 mutation are also discussed.
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Affiliation(s)
- Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Xiaofang Xu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China.
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Le Gall J, Dehainault C, Benoist C, Matet A, Lumbroso-Le Rouic L, Aerts I, Jiménez I, Schleiermacher G, Houdayer C, Radvanyi F, Frouin E, Renault V, Doz F, Stoppa-Lyonnet D, Gauthier-Villars M, Cassoux N, Golmard L. Highly Sensitive Detection Method of Retinoblastoma Genetic Predisposition and Biomarkers. J Mol Diagn 2021; 23:1714-1721. [PMID: 34656762 DOI: 10.1016/j.jmoldx.2021.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/15/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022] Open
Abstract
Retinoblastoma is a malignant tumor of the infant retina. Nearly half of patients are predisposed to retinoblastoma by a germline RB1 pathogenic variant. Nonhereditary retinoblastoma is mainly caused by inactivation of both RB1 alleles at a somatic level. Several polymorphisms have been reported as biomarkers of retinoblastoma risk, aggressiveness, or invasion. The most informative genetic testing is obtained from tumor DNA. Historically, access to tumor DNA has been warranted by the frequent indication of enucleation, which has decreased because of advances in conservative approaches. Recent studies showed that tumor cell-free DNA can be analyzed in aqueous humor from retinoblastoma patients. This report describes a next-generation sequencing method relying on unique molecular identifiers for a highly sensitive detection of retinoblastoma genetic predisposition and biomarkers in a single analysis. It is the first use of unique molecular identifiers for retinoblastoma genetics. This gene panel enables the detection of RB1 point variants, large genome rearrangements, and loss of heterozygosity. It is adapted for genomic DNA extracted from blood or tumor DNA extracted from tumor fragment, aqueous humor, or plasma. The access to tumor cell-free DNA improves the diagnosis of genetic predisposition in case of conservative ocular therapy and provides access to biomarkers guiding the treatment strategy. The analysis of a gene panel is cost-effective and can be easily implemented in diagnostic laboratories.
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Affiliation(s)
- Jessica Le Gall
- Department of Genetics, Institut Curie, Paris, France; PSL Research University, Paris, France
| | - Catherine Dehainault
- Department of Genetics, Institut Curie, Paris, France; PSL Research University, Paris, France
| | - Camille Benoist
- PSL Research University, Paris, France; Bioinformatics Unit, Institut Curie, Paris, France
| | - Alexandre Matet
- Department of Ocular Oncology, Institut Curie, Paris, France; Université de Paris, Paris, France
| | - Livia Lumbroso-Le Rouic
- PSL Research University, Paris, France; Department of Ophthalmology, Institut Curie, Paris, France
| | - Isabelle Aerts
- PSL Research University, Paris, France; Oncology Center SIREDO, Institut Curie, Paris, France
| | - Irene Jiménez
- PSL Research University, Paris, France; Oncology Center SIREDO, Institut Curie, Paris, France; INSERM U830, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- PSL Research University, Paris, France; Oncology Center SIREDO, Institut Curie, Paris, France; INSERM U830, Institut Curie, Paris, France
| | - Claude Houdayer
- Department of Genetics, Rouen University Hospital and Inserm U1245, Rouen University (UNIROUEN), Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - François Radvanyi
- PSL Research University, Paris, France; Molecular Oncology Team, CNRS, UMR144, Institut Curie, Paris, France
| | - Eleonore Frouin
- PSL Research University, Paris, France; Bioinformatics Unit, Institut Curie, Paris, France
| | - Victor Renault
- PSL Research University, Paris, France; Bioinformatics Unit, Institut Curie, Paris, France
| | - François Doz
- Université de Paris, Paris, France; Oncology Center SIREDO, Institut Curie, Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR144, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France; Université de Paris, Paris, France; INSERM U830, Institut Curie, Paris, France
| | - Marion Gauthier-Villars
- Department of Genetics, Institut Curie, Paris, France; PSL Research University, Paris, France
| | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, Paris, France; Université de Paris, Paris, France
| | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France; PSL Research University, Paris, France.
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Hülsenbeck I, Frank M, Biewald E, Kanber D, Lohmann DR, Ketteler P. Introduction of a Variant Classification System for Analysis of Genotype-Phenotype Relationships in Heritable Retinoblastoma. Cancers (Basel) 2021; 13:cancers13071605. [PMID: 33807189 PMCID: PMC8037437 DOI: 10.3390/cancers13071605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Heritable retinoblastoma is a genetic disease that predisposes to develop multiple retinoblastomas in childhood and other extraocular tumors later in life. It is caused by genetic variants in the RB1 gene. Here we present a new classification for genetic variants in the RB1 gene (REC) that focuses on the variant’s effect. The different classes, REC-I to -V, correlate with different risks of tumor predisposition. REC correlated with different clinical courses when applied in our study cohort. REC aims to facilitate risk estimation for physicians, patients and their families, and researchers and to improve the definition of the necessity of screening examination. Abstract Constitutional haploinsufficiency of the RB1 gene causes heritable retinoblastoma, a tumor predisposition syndrome. Patients with heritable retinoblastoma develop multiple retinoblastomas early in childhood and other extraocular tumors later in life. Constitutional pathogenic variants in RB1 are heterogeneous, and a few genotype-phenotype correlations have been described. To identify further genotype-phenotype relationships, we developed the retinoblastoma variant effect classification (REC), which considers each variant’s predicted effects on the common causal mediator, RB1 protein pRB. For validation, the RB1 variants of 287 patients were grouped according to REC. Multiple aspects of phenotypic expression were analyzed, known genotype-phenotype associations were revised, and new relationships were explored. Phenotypic expression of patients with REC-I, -II, and -III was distinct. Remarkably, the phenotype of patients with variants causing residual amounts of truncated pRB (REC-I) was more severe than patients with complete loss of RB1 (REC-II). The age of diagnosis of REC-I variants appeared to be distinct depending on truncation’s localization relative to pRB structure domains. REC classes identify genotype-phenotype relationships and, therefore, this classification framework may serve as a tool to develop tailored tumor screening programs depending on the type of RB1 variant.
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Affiliation(s)
- Isabel Hülsenbeck
- Department of Pediatric Hematology and Oncology, University Duisburg-Essen, University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany;
- Eye Oncogenetics Research Group, University Hospital Essen, 45122 Essen, Germany; (D.K.); (D.R.L.)
| | - Mirjam Frank
- Institute for Medical Informatics, Biometry and Epidemiology, University Duisburg-Essen, University Hospital Essen, 45122 Essen, Germany;
| | - Eva Biewald
- Department of Ophthalmology, University Duisburg-Essen, University Hospital Essen, 45122 Essen, Germany;
| | - Deniz Kanber
- Eye Oncogenetics Research Group, University Hospital Essen, 45122 Essen, Germany; (D.K.); (D.R.L.)
- Institute of Human Genetics, University Duisburg-Essen, 45122 Essen, Germany
| | - Dietmar R. Lohmann
- Eye Oncogenetics Research Group, University Hospital Essen, 45122 Essen, Germany; (D.K.); (D.R.L.)
- Institute of Human Genetics, University Duisburg-Essen, 45122 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, 69120 Heidelberg, Germany
| | - Petra Ketteler
- Department of Pediatric Hematology and Oncology, University Duisburg-Essen, University Hospital Essen, Hufelandstrasse 55, 45122 Essen, Germany;
- Eye Oncogenetics Research Group, University Hospital Essen, 45122 Essen, Germany; (D.K.); (D.R.L.)
- Institute of Human Genetics, University Duisburg-Essen, 45122 Essen, Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf, 69120 Heidelberg, Germany
- Correspondence:
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Parkhitko AA, Singh A, Hsieh S, Hu Y, Binari R, Lord CJ, Hannenhalli S, Ryan CJ, Perrimon N. Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells. PLoS Genet 2021; 17:e1009354. [PMID: 33591981 PMCID: PMC7909629 DOI: 10.1371/journal.pgen.1009354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/26/2021] [Accepted: 01/11/2021] [Indexed: 01/02/2023] Open
Abstract
The RB1 tumor suppressor is recurrently mutated in a variety of cancers including retinoblastomas, small cell lung cancers, triple-negative breast cancers, prostate cancers, and osteosarcomas. Finding new synthetic lethal (SL) interactions with RB1 could lead to new approaches to treating cancers with inactivated RB1. We identified 95 SL partners of RB1 based on a Drosophila screen for genetic modifiers of the eye phenotype caused by defects in the RB1 ortholog, Rbf1. We validated 38 mammalian orthologs of Rbf1 modifiers as RB1 SL partners in human cancer cell lines with defective RB1 alleles. We further show that for many of the RB1 SL genes validated in human cancer cell lines, low activity of the SL gene in human tumors, when concurrent with low levels of RB1 was associated with improved patient survival. We investigated higher order combinatorial gene interactions by creating a novel Drosophila cancer model with co-occurring Rbf1, Pten and Ras mutations, and found that targeting RB1 SL genes in this background suppressed the dramatic tumor growth and rescued fly survival whilst having minimal effects on wild-type cells. Finally, we found that drugs targeting the identified RB1 interacting genes/pathways, such as UNC3230, PYR-41, TAK-243, isoginkgetin, madrasin, and celastrol also elicit SL in human cancer cell lines. In summary, we identified several high confidence, evolutionarily conserved, novel targets for RB1-deficient cells that may be further adapted for the treatment of human cancer.
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Affiliation(s)
- Andrey A. Parkhitko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Aging Institute of UPMC and the University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Arashdeep Singh
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sharon Hsieh
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Christopher J. Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Colm J. Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- School of Computer Science, University College Dublin, Dublin, Ireland
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
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9
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Salviat F, Gauthier-Villars M, Carton M, Cassoux N, Lumbroso-Le Rouic L, Dehainault C, Levy C, Golmard L, Aerts I, Doz F, Bonnet-Serrano F, Hayek S, Savignoni A, Stoppa-Lyonnet D, Houdayer C. Association Between Genotype and Phenotype in Consecutive Unrelated Individuals With Retinoblastoma. JAMA Ophthalmol 2021; 138:843-850. [PMID: 32556071 DOI: 10.1001/jamaophthalmol.2020.2100] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Importance Retinoblastoma (RB) is the most common pediatric intraocular neoplasm. RB is a complex model in which atypical pathogenic variants, modifier genes, imprinting, and mosaicism are known to be associated with the phenotype. In-depth understanding of RB therefore requires large genotype-phenotype studies. Objective To assess the association between genotype and phenotype in patients with RB. Design, Setting, and Participants This single-center, retrospective cohort study, conducted from January 1, 2000, to September 30, 2017, enrolled 1404 consecutive ascertained patients with RB who consulted an oncogeneticist. All patients had their genotype and phenotype recorded. Statistical analysis was performed from July 1, 2018, to December 31, 2018. Main Outcomes and Measures RB1 germline and somatic pathogenic variant types, family history, and disease presentation characteristics (ie, age at diagnosis, sex, laterality, and International Intraocular Retinoblastoma Classification group). Results Among 1404 patients with RB (734 [52.3%] female; mean [SD] age, 20.2 [21.2] months), 866 cases (61.7%) were unilateral and 538 cases (38.3%) were bilateral. Loss of function variants were found throughout the coding sequence, with 259 of 272 (95.2%) somatic pathogenic variants and 537 of 606 (88.6%) germline pathogenic variants (difference, 6.6%; 95% CI, 4.0%-9.2%; P < .001) after excluding tumor-specific pathogenic variants (ie, promoter methylation and loss of heterozygosity); a novel low-penetrance region was identified in exon 24. Compared with germline pathogenic variants estimated to retain RB protein expression, germline pathogenic variants estimated to abrogate RB protein expression were associated with an earlier mean (SD) age at diagnosis (12.3 [11.3] months among 457 patients vs 16.3 [13.2] months among 55 patients; difference, 4 months; 95% CI, 1.9-6.1 months; P = .01), more frequent bilateral involvement (84.2% among 452 patients vs 65.2% among 45 patients; difference, 18.9%; 95% CI, 14.5%-23.3%; P < .001), and more advanced International Intraocular Retinoblastoma Classification group (85.3% among 339 patients vs 73.9% among 34 patients; difference: 11.4%; 95% CI, 6.5%-16.3%; P = .047). Among the 765 nongermline carriers of an RB1 pathogenic variant, most were female (419 females [54.8%] vs 346 males [45.2%]; P = .008), and males were more likely to have bilateral RB (23 males [71.4%] vs 12 females [34.3%]; P = .01). Conclusions and Relevance These results suggest that RB risk is associated with the germline pathogenic variant and with maintenance of RB protein and that there is a sex-linked mechanism for nongermline carriers.
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Affiliation(s)
- Flore Salviat
- Department of Biostatistics, Institut Curie, PSL Research University, Saint-Cloud, France
| | - Marion Gauthier-Villars
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Matthieu Carton
- Department of Biostatistics, Institut Curie, PSL Research University, Saint-Cloud, France
| | - Nathalie Cassoux
- Faculty of Medicine Paris-Descartes, Paris University, Paris, France.,Service of Ophthalmology, Department of Surgical Oncology, Institut Curie, Paris, France
| | | | - Catherine Dehainault
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Christine Levy
- Service of Ophthalmology, Department of Surgical Oncology, Institut Curie, Paris, France
| | - Lisa Golmard
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Isabelle Aerts
- Oncology Center, Soins, Innovation, Recherche en Oncologie de l'Enfant, l'Adolescent et du Jeune Adulte, Institut Curie, Paris, France
| | - François Doz
- Faculty of Medicine Paris-Descartes, Paris University, Paris, France.,Oncology Center, Soins, Innovation, Recherche en Oncologie de l'Enfant, l'Adolescent et du Jeune Adulte, Institut Curie, Paris, France
| | - Fidéline Bonnet-Serrano
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Stéphanie Hayek
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France
| | - Alexia Savignoni
- Department of Biostatistics, Institut Curie, PSL Research University, Saint-Cloud, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France.,Faculty of Medicine Paris-Descartes, Paris University, Paris, France.,Research Center Institut National de la Santé et de la Recherche Médicale, Unit U830, Institut Curie, Paris, France
| | - Claude Houdayer
- Department of Genetics, Institut Curie, PSL Research University, Department of Genetics, Paris, France.,Department of Genetics, Rouen University Hospital, Rouen, France.,University of Rouen Normandy, UNIROUEN, Mont-Saint-Aignan, France.,Institut National de la Santé et de la Recherche Médicale U1245, Normandy Center for Genomic and Personalized Medicine, Rouen, France
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10
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Capasso M, Montella A, Tirelli M, Maiorino T, Cantalupo S, Iolascon A. Genetic Predisposition to Solid Pediatric Cancers. Front Oncol 2020; 10:590033. [PMID: 33194750 PMCID: PMC7656777 DOI: 10.3389/fonc.2020.590033] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
Progresses over the past years have extensively improved our capacity to use genome-scale analyses—including high-density genotyping and exome and genome sequencing—to identify the genetic basis of pediatric tumors. In particular, exome sequencing has contributed to the evidence that about 10% of children and adolescents with tumors have germline genetic variants associated with cancer predisposition. In this review, we provide an overview of genetic variations predisposing to solid pediatric tumors (medulloblastoma, ependymoma, astrocytoma, neuroblastoma, retinoblastoma, Wilms tumor, osteosarcoma, rhabdomyosarcoma, and Ewing sarcoma) and outline the biological processes affected by the involved mutated genes. A careful description of the genetic basis underlying a large number of syndromes associated with an increased risk of pediatric cancer is also reported. We place particular emphasis on the emerging view that interactions between germline and somatic alterations are a key determinant of cancer development. We propose future research directions, which focus on the biological function of pediatric risk alleles and on the potential links between the germline genome and somatic changes. Finally, the importance of developing new molecular diagnostic tests including all the identified risk germline mutations and of considering the genetic predisposition in screening tests and novel therapies is emphasized.
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Affiliation(s)
- Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | | | - Matilde Tirelli
- CEINGE Biotecnologie Avanzate, Naples, Italy.,European School of Molecular Medicine, Università Degli Studi di Milano, Milan, Italy
| | - Teresa Maiorino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Sueva Cantalupo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE Biotecnologie Avanzate, Naples, Italy
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11
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Dittner-Moormann S, Reschke M, Biewald E, Kuechler A, Klein B, Timmermann B, Lohmann D, Ketteler P, Kanber D. 13q deletion syndrome resulting from balanced chromosomal rearrangement in father: the significance of parental karyotyping. Mol Cytogenet 2020; 13:31. [PMID: 32760450 PMCID: PMC7379829 DOI: 10.1186/s13039-020-00500-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/30/2020] [Indexed: 11/20/2022] Open
Abstract
Background Retinoblastoma is a malignancy of the eye in children characterized by biallelic inactivation of the retinoblastoma 1 gene (RB1), located at chromosome 13q14.2. Children with interstitial chromosome 13q deletions that include the RB1 gene show a predisposition to develop retinoblastoma and variable other features. Large 13q deletions with severe clinical phenotype are nearly always the result of a de novo mutation, i.e. the pathogenic alteration is not detected in parents. This results in a low risk for siblings to develop 13q deletion syndrome. Result Here, we describe a patient with profound muscle hypotonia, severe developmental delay and bilateral retinoblastoma carrying a large deletion in 13q13.3q14 with the size of 16 Mb, involving the RB1 gene. Neither parent showed retinoblastoma, muscle hypotonia or developmental delay. Chromosome analysis and Fluorescence in situ hybridization (FISH) showed a balanced complex chromosomal rearrangement (CCR) between chromosome 12 and 13 [ins(12;13)(q21.2;q12.3q14.3)] and an additional balanced translocation of chromosome 7 and 15 [t(7;15)(q31.2;q25.3)] in the healthy father. Malsegregation of the paternal insertional translocation involving chromosome 12 and 13 resulted in a 13q deletion syndrome of the child [46,XY,ins(12;13)(q21.2;q12.3q14.3)]. Conclusion Balanced translocations in parents are a rare cause of de novo RB1 deletions in offspring. This case report emphasizes the need for parental chromosomal analysis and FISH in parents of children diagnosed with 13q deletion syndrome or large RB1 gene deletions to precisely determine the recurrence risk in siblings. Guidelines for genetic testing should be revised accordingly.
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Affiliation(s)
- Sabine Dittner-Moormann
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Hufelandstraße 55, 45147 Essen, Germany
| | - Madlen Reschke
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Eva Biewald
- Department of Ophthalmology, University Hospital Essen, Essen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Barbara Klein
- Sozialpädiatrisches Zentrum, Klinikum Frankfurt Höchst GmbH, Frankfurt a. M, Germany
| | - Beate Timmermann
- Department of Particle Therapy, West German Proton Therapy Centre Essen (WPE), West German Cancer Center (WTZ), German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Dietmar Lohmann
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Petra Ketteler
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Hufelandstraße 55, 45147 Essen, Germany
| | - Deniz Kanber
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
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12
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Hanbazazh M, Dryja TP. Molecular Genetics of Intraocular Tumors. Semin Ophthalmol 2020; 35:174-181. [PMID: 32507011 DOI: 10.1080/08820538.2020.1776343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
PURPOSE To explore the value of molecular technologies in the pathologic evaluation, diagnosis, and treatment of retinoblastoma and uveal melanoma. METHODS Review of the peer-reviewed literature on the molecular pathology of primary intraocular tumors. CONCLUSION Molecular tests are playing an increasingly important role in the diagnosis of intraocular tumors. They provide information valuable for diagnosis, prognosis, screening regimens, genetic counselling, and treatment. These technologies are becoming easier, faster, and with higher sensitivity and accuracy.
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Affiliation(s)
- Mehenaz Hanbazazh
- David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
| | - Thaddeus P Dryja
- David G Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear Infirmary, Harvard Medical School , Boston, MA, USA
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13
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Ketteler P, Hülsenbeck I, Frank M, Schmidt B, Jöckel KH, Lohmann DR. The impact of RB1 genotype on incidence of second tumours in heritable retinoblastoma. Eur J Cancer 2020; 133:47-55. [PMID: 32434110 DOI: 10.1016/j.ejca.2020.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 10/24/2022]
Abstract
BACKGROUND Patients with heritable retinoblastoma are at risk for bilateral retinoblastoma and second primary malignancies (SPMs). The incidence of SPM is significantly raised after radiotherapy. We analysed the impact of the class of constitutional RB1 variant on the incidence of SPM in survivors with and without previous radiotherapy. METHODS From 1940 to 2008, 655 national patients were treated for heritable retinoblastoma at the German referral centre. Data on SPM, therapy and constitutional RB1 variant were available for 317 patients (48.3%). Heterozygous RB1 variants were classified into variants with regular and incomplete penetrance for retinoblastoma. RESULTS SPM occurred in 51 of 317 survivors of heritable retinoblastoma. The incidence rate (IR) of SPM per 1000 person years was 8.4 (95% confidence interval (CI): 6.3-11.1) in individuals heterozygous for an oncogenic RB1 variant and 2.1 (95% CI: 0.0-11.4) with RB1 mosaicism. The incidence of SPM was higher in patients with regular penetrance compared with incomplete penetrance RB1 variants (IR 10.3 [95% CI: 7.5-13.8] vs. IR 3.2 [95% CI: 1.0-7.5]; p < 0.05). In the subgroup without previous radiotherapy SPM were only observed in patients with regular penetrance variants (IR 6.3 [95% CI: 3.0-11.5]). Carriers of incomplete penetrance variants developed similar tumour entities as those with regular penetrance. CONCLUSIONS Patients heterozygous for regular penetrance RB1 variants had a higher risk to develop SPM than patients with incomplete penetrance variants. Increased knowledge on genotype-phenotype relation regarding SPM may influence screening recommendations for SPM in survivors of heritable retinoblastoma.
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Affiliation(s)
- Petra Ketteler
- Department of Paediatric Haematology and Oncology, University Hospital Essen, Essen, Germany; Institute of Human Genetics, University Duisburg-Essen, Essen, Germany; Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany; German Consortium for Translational Cancer Research (DKTK), Partner Site Essen, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Isabel Hülsenbeck
- Department of Paediatric Haematology and Oncology, University Hospital Essen, Essen, Germany; Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany
| | - Mirjam Frank
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Börge Schmidt
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Karl-Heinz Jöckel
- German Consortium for Translational Cancer Research (DKTK), Partner Site Essen, and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Dietmar R Lohmann
- Institute of Human Genetics, University Duisburg-Essen, Essen, Germany; Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany; German Consortium for Translational Cancer Research (DKTK), Partner Site Essen, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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14
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Ren Y, Ay A, Gerke TA, Kahveci T. Identification of jointly correlated gene sets. J Bioinform Comput Biol 2019; 16:1840019. [PMID: 30419787 DOI: 10.1142/s021972001840019x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Associations between expressions of genes play a key role in deciphering their functions. Correlation score between pairs of genes is often utilized to associate two genes. However, the relationship between genes is often more complex; multiple genes might collaborate to control the transcription of a gene. In this paper, we introduce the problem of searching pairs of genes, which collectively correlate with another gene. This problem is computationally much harder than the classical problem of identifying pairwise gene associations. Exhaustive search is infeasible for transcriptomic datasets also; since for [Formula: see text] genes, there are [Formula: see text] possible gene combinations. Our method builds three filters to avoid computing the association for a large fraction of the gene combinations, which do not produce high correlation. Our experiments on a synthetic dataset and a prostate cancer dataset demonstrate that our method produces accurate results at the transcriptome level in practical time. Moreover, our method identifies biologically novel results which classical pairwise gene association studies are unlikely to discover.
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Affiliation(s)
- Yuanfang Ren
- * Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Ahmet Ay
- † Departments of Biology and Mathematics, Colgate University, Hamilton, NY 13346, USA
| | | | - Tamer Kahveci
- * Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA
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15
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Pertesi M, Ekdahl L, Palm A, Johnsson E, Järvstråt L, Wihlborg AK, Nilsson B. Essential genes shape cancer genomes through linear limitation of homozygous deletions. Commun Biol 2019; 2:262. [PMID: 31341961 PMCID: PMC6642121 DOI: 10.1038/s42003-019-0517-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/26/2019] [Indexed: 12/26/2022] Open
Abstract
The landscape of somatic acquired deletions in cancer cells is shaped by positive and negative selection. Recurrent deletions typically target tumor suppressor, leading to positive selection. Simultaneously, loss of a nearby essential gene can lead to negative selection, and introduce latent vulnerabilities specific to cancer cells. Here we show that, under basic assumptions on positive and negative selection, deletion limitation gives rise to a statistical pattern where the frequency of homozygous deletions decreases approximately linearly between the deletion target gene and the nearest essential genes. Using DNA copy number data from 9,744 human cancer specimens, we demonstrate that linear deletion limitation exists and exposes deletion-limiting genes for seven known deletion targets (CDKN2A, RB1, PTEN, MAP2K4, NF1, SMAD4, and LINC00290). Downstream analysis of pooled CRISPR/Cas9 data provide further evidence of essentiality. Our results provide further insight into how the deletion landscape is shaped and identify potentially targetable vulnerabilities.
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Affiliation(s)
- Maroulio Pertesi
- Hematology and Transfusion Medicine Department of Laboratory Medicine, BMC, SE-221 84 Lund, Sweden
| | - Ludvig Ekdahl
- Hematology and Transfusion Medicine Department of Laboratory Medicine, BMC, SE-221 84 Lund, Sweden
| | - Angelica Palm
- Hematology and Transfusion Medicine Department of Laboratory Medicine, BMC, SE-221 84 Lund, Sweden
| | - Ellinor Johnsson
- Hematology and Transfusion Medicine Department of Laboratory Medicine, BMC, SE-221 84 Lund, Sweden
| | - Linnea Järvstråt
- Hematology and Transfusion Medicine Department of Laboratory Medicine, BMC, SE-221 84 Lund, Sweden
| | - Anna-Karin Wihlborg
- Hematology and Transfusion Medicine Department of Laboratory Medicine, BMC, SE-221 84 Lund, Sweden
| | - Björn Nilsson
- Hematology and Transfusion Medicine Department of Laboratory Medicine, BMC, SE-221 84 Lund, Sweden
- Broad Institute, 415 Main Street, Cambridge, MA 02142 USA
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16
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Chaussade A, Millot G, Wells C, Brisse H, Laé M, Savignoni A, Desjardins L, Dendale R, Doz F, Aerts I, Jimenez I, Cassoux N, Stoppa Lyonnet D, Gauthier Villars M, Houdayer C. Correlation between RB1germline mutations and second primary malignancies in hereditary retinoblastoma patients treated with external beam radiotherapy. Eur J Med Genet 2019; 62:217-223. [DOI: 10.1016/j.ejmg.2018.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 06/21/2018] [Accepted: 07/17/2018] [Indexed: 11/16/2022]
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17
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Imperatore V, Pinto AM, Gelli E, Trevisson E, Morbidoni V, Frullanti E, Hadjistilianou T, De Francesco S, Toti P, Gusson E, Roversi G, Accogli A, Capra V, Mencarelli MA, Renieri A, Ariani F. Parent-of-origin effect of hypomorphic pathogenic variants and somatic mosaicism impact on phenotypic expression of retinoblastoma. Eur J Hum Genet 2018; 26:1026-1037. [PMID: 29662154 DOI: 10.1038/s41431-017-0054-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/27/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Retinoblastoma is the most common eye cancer in children. Numerous families have been described displaying reduced penetrance and expressivity. An extensive molecular characterization of seven families led us to characterize the two main mechanisms impacting on phenotypic expression, as follows: (i) mosaicism of amorphic pathogenic variants; and (ii) parent-of-origin-effect of hypomorphic pathogenic variants. Somatic mosaicism for RB1 splicing variants (c.1960+5G>C and c.2106+2T>C), leading to a complete loss of function was demonstrated by high-depth NGS in two families. In both cases, the healthy carrier parent (one with retinoma) showed a variant frequency lower than that expected for a heterozygous individual, indicating a 56-60% mosaicism level. Previous evidences of a ~3-fold excess of RB1 maternal canonical transcript led us to hypothesize that this differential allelic expression could influence phenotypic outcome in families at risk for RB onset. Accordingly, in five families, we identified a higher tumor risk associated with paternally inherited hypomorphic pathogenic variants, namely a deletion resulting in the loss of 37 amino acids at the N-terminus (c.608-16_608del), an exonic substitution with a "leaky" splicing effect (c.1331A>G), a partially deleterious substitution (c.1981C>T) and a truncating C-terminal variant (c.2663+2T>C). The identification of these mechanisms changes the genetic/prenatal counseling and the clinical management of families, indicating a higher recurrence risk when the hypomorphic pathogenic variant is inherited from the father, and suggesting the need for second tumor surveillance in unaffected carriers at risk of developing adult-onset cancer such as osteosarcoma or leiomyosarcoma.
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Affiliation(s)
| | - Anna Maria Pinto
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Gelli
- Medical Genetics, University of Siena, Siena, Italy
| | - Eva Trevisson
- Department of Woman and Child Health, University of Padova Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy.,Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy
| | - Valeria Morbidoni
- Department of Woman and Child Health, University of Padova Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy.,Istituto di Ricerca Pediatrica, IRP, Città della Speranza, Padova, Italy
| | | | - Theodora Hadjistilianou
- Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Sonia De Francesco
- Unit of Ophthalmology and Retinoblastoma Referral Center, Department of Surgery, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Paolo Toti
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Policlinico 'Santa Maria alle Scotte', Siena, Italy
| | - Elena Gusson
- Unit of Ophthalmology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Gaia Roversi
- Department of Medicine and Surgery, University Milan-Bicocca; Ospedale San Gerardo, ASST Monza, Monza, Italy
| | | | | | - Maria Antonietta Mencarelli
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy. .,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.
| | - Francesca Ariani
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
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18
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Mediator complex components are frequent targets for genetic alterations in various types of human cancer. J Genet Genomics 2017; 44:587-591. [PMID: 29246864 DOI: 10.1016/j.jgg.2017.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/26/2017] [Accepted: 08/25/2017] [Indexed: 11/22/2022]
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19
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Soliman SE, Racher H, Zhang C, MacDonald H, Gallie BL. Genetics and Molecular Diagnostics in Retinoblastoma--An Update. Asia Pac J Ophthalmol (Phila) 2017; 6:197-207. [PMID: 28399338 DOI: 10.22608/apo.201711] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/09/2017] [Indexed: 11/08/2022] Open
Abstract
Retinoblastoma is the prototype genetic cancer: in one or both eyes of young children, most retinoblastomas are initiated by biallelic mutation of the retinoblastoma tumor suppressor gene, RB1, in a developing retinal cell. All those with bilateral retinoblastoma have heritable cancer, although 95% have not inherited the RB1 mutation. Non-heritable retinoblastoma is always unilateral, with 98% caused by loss of both RB1 alleles from the tumor, whereas 2% have normal RB1 in tumors initiated by amplification of the MYCN oncogene. Good understanding of retinoblastoma genetics supports optimal care for retinoblastoma children and their families. Retinoblastoma is the first cancer to officially acknowledge the seminal role of genetics in cancer, by incorporating "H" into the eighth edition of cancer staging (2017): those who carry the RB1 cancer-predisposing gene are H1; those proven to not carry the familial RB1 mutation are H0; and those at unknown risk are HX. We suggest H0* be used for those with residual <1% risk to carry a RB1 mutation due to undetectable mosaicism. Loss of RB1 from a susceptible developing retinal cell initiates the benign precursor, retinoma. Progressive genomic changes result in retinoblastoma, and cancer progression ensues with increasing genomic disarray. Looking forward, novel therapies are anticipated from studies of retinoblastoma and metastatic tumor cells and the second primary cancers that the carriers of RB1 mutations are at high risk to develop. Here, we summarize the concepts of retinoblastoma genetics for ophthalmologists in a question/answer format to assist in the care of patients and their families.
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Affiliation(s)
- Sameh E Soliman
- Department of Ophthalmology and Vision Sciences, University of Toronto, Ontario, Canada
- Department of Ophthalmology, Faculty of Medicine, University of Alexandria, Alexandria, Egypt
| | | | - Chengyue Zhang
- Department of Ophthalmology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Heather MacDonald
- Department of Ophthalmology and Vision Sciences, University of Toronto, Ontario, Canada
| | - Brenda L Gallie
- Department of Ophthalmology and Vision Sciences, University of Toronto, Ontario, Canada
- Departments of Ophthalmology, Molecular Genetics, and Medical Biophysics, University of Toronto, Toronto, Canada
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20
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Nagel R, Semenova EA, Berns A. Drugging the addict: non-oncogene addiction as a target for cancer therapy. EMBO Rep 2016; 17:1516-1531. [PMID: 27702988 PMCID: PMC5090709 DOI: 10.15252/embr.201643030] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022] Open
Abstract
Historically, cancers have been treated with chemotherapeutics aimed to have profound effects on tumor cells with only limited effects on normal tissue. This approach was followed by the development of small‐molecule inhibitors that can target oncogenic pathways critical for the survival of tumor cells. The clinical targeting of these so‐called oncogene addictions, however, is in many instances hampered by the outgrowth of resistant clones. More recently, the proper functioning of non‐mutated genes has been shown to enhance the survival of many cancers, a phenomenon called non‐oncogene addiction. In the current review, we will focus on the distinct non‐oncogenic addictions found in cancer cells, including synthetic lethal interactions, the underlying stress phenotypes, and arising therapeutic opportunities.
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Affiliation(s)
- Remco Nagel
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ekaterina A Semenova
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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21
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Francis JH, Levin AM, Abramson DH. Update on Ophthalmic Oncology 2014: Retinoblastoma and Uveal Melanoma. Asia Pac J Ophthalmol (Phila) 2016; 5:368-82. [PMID: 27632029 DOI: 10.1097/apo.0000000000000213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE The aim of this study was to review peer-reviewed articles on ophthalmic oncology (specifically retinoblastoma and uveal melanoma) published from January to December 2014. DESIGN This study is a literature review. METHODS The terms retinoblastoma and uveal melanoma were used in a MEDLINE literature search. Abstracts were studied, and the most relevant articles were selected for inclusion and further in-depth review. RESULTS In retinoblastoma, more eyes are being salvaged due to intravitreal melphalan. The year 2014 marks a deepening in our understanding of the biological basis of the disease and the cell of origin. Knowledge on the genetic underpinnings of uveal melanoma has broadened to include other pathways, interactions, and potential therapeutic targets. CONCLUSIONS In 2014, there were valuable advancements in our knowledge of retinoblastoma and uveal melanoma. Some of these resulted in improved patient management.
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Affiliation(s)
- Jasmine H Francis
- From the *Memorial Sloan Kettering Cancer Center; and †Weill Cornell Medical Center, New York, NY
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22
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Sagi M, Frenkel A, Eilat A, Weinberg N, Frenkel S, Pe'er J, Abeliovich D, Lerer I. Genetic screening in patients with Retinoblastoma in Israel. Fam Cancer 2016; 14:471-80. [PMID: 25754945 DOI: 10.1007/s10689-015-9794-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Retinoblastoma (Rb) is a childhood tumor (~1 in 20,000 live births) developing in the retina due to mutations in the RB1 gene. Identification of the oncogenic mutations in the RB1 gene is important for the clinical management and for genetic counseling to families with a child or a parent affected with the tumor. Here we present our experience in detecting the pathogenic mutations in blood samples, from 150 unrelated Rb patients and highlight the relevant counseling issues. Mutation screening in the RB1 gene was based on Sanger sequencing, mosaicism of recurrent CpG transition mutations was detected by allele specific PCR and multiplex ligation dependent probe amplification for detecting of large deletions/duplications. The overall detection rate of mutations in our cohort was 55% (82/150). In the familial cases it was 100% (17/17), in bilateral and unilateral-multifocal sporadic cases 91% (50/55), and in the unilateral sporadic cases 19% (15/78). Nonsense mutations and small deletions or insertions that results in transcripts with premature termination codons that are subject to nonsense mediated decay were the most frequent, detected in 50/82 (61%) of the patients. The rest were large deletions detected in 14/82 (17%), splice site mutations detected in 11/82 (13%), missense mutations in four patients and mutations in the promoter sequence in three patients. Mutation mosaicism ranging from 10 to 30% was detected by allele specific PCR in ten patients, 9% (5/55) of patients with bilateral tumor and 33% (5/15) of the patients with unilateral tumor. In three patients rare variants were detected as the only finding which was also detected in other healthy family members. Allele specific amplification of recurrent mutations raises in our cohort the identification rate from 82 to 91% in the sporadic bilateral cases and from 13 to 19% in the unilateral sporadic cases. Most mosaic cases could not be identified by Sanger sequencing and therefore screening for recurrent CpG transition mutations by allele specific amplification is of utmost importance. Molecular screening is important for the genetic counseling regarding the risk for tumor development and the relevance for prenatal diagnosis but in several families is accompanied by detecting rare variants that might be rare polymorphisms or low penetrant mutations.
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Affiliation(s)
- Michal Sagi
- Department of Human Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Kiryat Hadassah, POB 12000, 91120, Jerusalem, Israel
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23
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Eloy P, Dehainault C, Sefta M, Aerts I, Doz F, Cassoux N, Lumbroso le Rouic L, Stoppa-Lyonnet D, Radvanyi F, Millot GA, Gauthier-Villars M, Houdayer C. A Parent-of-Origin Effect Impacts the Phenotype in Low Penetrance Retinoblastoma Families Segregating the c.1981C>T/p.Arg661Trp Mutation of RB1. PLoS Genet 2016; 12:e1005888. [PMID: 26925970 PMCID: PMC4771840 DOI: 10.1371/journal.pgen.1005888] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 01/30/2016] [Indexed: 01/12/2023] Open
Abstract
Retinoblastoma (Rb), the most common pediatric intraocular neoplasm, results from inactivation of both alleles of the RB1 tumor suppressor gene. The second allele is most commonly lost, as demonstrated by loss of heterozygosity studies. RB1 germline carriers usually develop bilateral tumors, but some Rb families display low penetrance and variable expressivity. In order to decipher the underlying mechanisms, 23 unrelated low penetrance pedigrees segregating the common c.1981C>T/p.Arg661Trp mutation and other low penetrance mutations were studied. In families segregating the c.1981C>T mutation, we demonstrated, for the first time, a correlation between the gender of the transmitting carrier and penetrance, as evidenced by Fisher's exact test: the probability of being unaffected is 90.3% and 32.5% when the mutation is inherited from the mother and the father, respectively (p-value = 7.10(-7). Interestingly, a similar correlation was observed in families segregating other low penetrance alleles. Consequently, we investigated the putative involvement of an imprinted, modifier gene in low penetrance Rb. We first ruled out a MED4-driven mechanism by MED4 methylation and expression analyses. We then focused on the differentially methylated CpG85 island located in intron 2 of RB1 and showing parent-of-origin-specific DNA methylation. This differential methylation promotes expression of the maternal c.1981C>T allele. We propose that the maternally inherited c.1981C>T/p.Arg661Trp allele retains sufficient tumor suppressor activity to prevent retinoblastoma development. In contrast, when the mutation is paternally transmitted, the low residual activity would mimic a null mutation and subsequently lead to retinoblastoma. This implies that the c.1981C>T mutation is not deleterious per se but needs to be destabilized in order to reach pRb haploinsufficiency and initiate tumorigenesis. We suggest that this phenomenon might be a general mechanism to explain phenotypic differences in low penetrance Rb families.
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Affiliation(s)
| | | | - Meriem Sefta
- CNRS UMR144, centre de recherche de l'Institut Curie, Paris, France
| | - Isabelle Aerts
- Département d'oncologie pédiatrique, adolescents jeunes adultes, Institut Curie, Paris, France
| | - François Doz
- Département d'oncologie pédiatrique, adolescents jeunes adultes, Institut Curie, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Nathalie Cassoux
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- Département d’oncologie chirurgicale, service d’Ophtalmologie, Institut Curie, Paris, France
| | - Livia Lumbroso le Rouic
- Département d’oncologie chirurgicale, service d’Ophtalmologie, Institut Curie, Paris, France
| | - Dominique Stoppa-Lyonnet
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- INSERM U830, centre de recherche de l'Institut Curie, Paris, France
| | | | - Gaël A. Millot
- Institut Curie, PSL Research University, Paris, France
- CNRS UMR 3244, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, Paris, France
| | | | - Claude Houdayer
- Service de Génétique, Institut Curie, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
- INSERM U830, centre de recherche de l'Institut Curie, Paris, France
- * E-mail:
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24
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Grotta S, D'Elia G, Scavelli R, Genovese S, Surace C, Sirleto P, Cozza R, Romanzo A, De Ioris MA, Valente P, Tomaiuolo AC, Lepri FR, Franchin T, Ciocca L, Russo S, Locatelli F, Angioni A. Advantages of a next generation sequencing targeted approach for the molecular diagnosis of retinoblastoma. BMC Cancer 2015; 15:841. [PMID: 26530098 PMCID: PMC4632486 DOI: 10.1186/s12885-015-1854-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 10/27/2015] [Indexed: 11/10/2022] Open
Abstract
Background Retinoblastoma (RB) is the most common malignant childhood tumor of the eye and results from inactivation of both alleles of the RB1 gene. Nowadays RB genetic diagnosis requires classical chromosome investigations, Multiplex Ligation-dependent Probe Amplification analysis (MLPA) and Sanger sequencing. Nevertheless, these techniques show some limitations. We report our experience on a cohort of RB patients using a combined approach of Next-Generation Sequencing (NGS) and RB1 custom array-Comparative Genomic Hybridization (aCGH). Methods A total of 65 patients with retinoblastoma were studied: 29 cases of bilateral RB and 36 cases of unilateral RB. All patients were previously tested with conventional cytogenetics and MLPA techniques. Fifty-three samples were then analysed using NGS. Eleven cases were analysed by RB1 custom aCGH. One last case was studied only by classic cytogenetics. Finally, it has been tested, in a lab sensitivity assay, the capability of NGS to detect artificial mosaicism series in previously recognized samples prepared at 3 different mosaicism frequencies: 10, 5, 1 %. Results Of the 29 cases of bilateral RB, 28 resulted positive (96.5 %) to the genetic investigation: 22 point mutations and 6 genomic rearrangements (four intragenic and two macrodeletion). A novel germline intragenic duplication, from exon18 to exon 23, was identified in a proband with bilateral RB. Of the 36 available cases of unilateral RB, 8 patients resulted positive (22 %) to the genetic investigation: 3 patients showed point mutations while 5 carried large deletion. Finally, we successfully validated, in a lab sensitivity assay, the capability of NGS to accurately measure level of artificial mosaicism down to 1 %. Conclusions NGS and RB1-custom aCGH have demonstrated to be an effective combined approach in order to optimize the overall diagnostic procedures of RB. Custom aCGH is able to accurately detect genomic rearrangements allowing the characterization of their extension. NGS is extremely accurate in detecting single nucleotide variants, relatively simple to perform, cost savings and efficient and has confirmed a high sensitivity and accuracy in identifying low levels of artificial mosaicisms.
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Affiliation(s)
- Simona Grotta
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy. .,Present address: S. Pietro Fatebenefratelli Hospital, UOSD Medical Genetics, Rome, Italy.
| | - Gemma D'Elia
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | | | - Silvia Genovese
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Cecilia Surace
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Pietro Sirleto
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Raffaele Cozza
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy.
| | - Antonino Romanzo
- Ophtalmology Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy.
| | - Maria Antonietta De Ioris
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy.
| | - Paola Valente
- Ophtalmology Unit, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy.
| | - Anna Cristina Tomaiuolo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Francesca Romana Lepri
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Tiziana Franchin
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Laura Ciocca
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Serena Russo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
| | - Franco Locatelli
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, Rome, Italy. .,University of Pavia, Pavia, Italy.
| | - Adriano Angioni
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165, Rome, Italy.
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