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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 2023:1-11. [PMID: 37932244 DOI: 10.1080/13816810.2023.2270570] [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: 07/14/2023] [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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2
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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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3
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Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR. Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. BMC Bioinformatics 2022; 23:482. [PMCID: PMC9664736 DOI: 10.1186/s12859-022-05041-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background
Despite numerous molecular and computational advances, roughly half of patients with a rare disease remain undiagnosed after exome or genome sequencing. A particularly challenging barrier to diagnosis is identifying variants that cause deleterious alternative splicing at intronic or exonic loci outside of canonical donor or acceptor splice sites.
Results
Several existing tools predict the likelihood that a genetic variant causes alternative splicing. We sought to extend such methods by developing a new metric that aids in discerning whether a genetic variant leads to deleterious alternative splicing. Our metric combines genetic variation in the Genome Aggregate Database with alternative splicing predictions from SpliceAI to compare observed and expected levels of splice-altering genetic variation. We infer genic regions with significantly less splice-altering variation than expected to be constrained. The resulting model of regional splicing constraint captures differential splicing constraint across gene and exon categories, and the most constrained genic regions are enriched for pathogenic splice-altering variants. Building from this model, we developed ConSpliceML. This ensemble machine learning approach combines regional splicing constraint with multiple per-nucleotide alternative splicing scores to guide the prediction of deleterious splicing variants in protein-coding genes. ConSpliceML more accurately distinguishes deleterious and benign splicing variants than state-of-the-art splicing prediction methods, especially in “cryptic” splicing regions beyond canonical donor or acceptor splice sites.
Conclusion
Integrating a model of genetic constraint with annotations from existing alternative splicing tools allows ConSpliceML to prioritize potentially deleterious splice-altering variants in studies of rare human diseases.
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Venkataramany AS, Schieffer KM, Lee K, Cottrell CE, Wang PY, Mardis ER, Cripe TP, Chandler DS. Alternative RNA Splicing Defects in Pediatric Cancers: New Insights in Tumorigenesis and Potential Therapeutic Vulnerabilities. Ann Oncol 2022; 33:578-592. [PMID: 35339647 DOI: 10.1016/j.annonc.2022.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Compared to adult cancers, pediatric cancers are uniquely characterized by a genomically stable landscape and lower tumor mutational burden. However, alternative splicing, a global cellular process that produces different mRNA/protein isoforms from a single mRNA transcript, has been increasingly implicated in the development of pediatric cancers. DESIGN We review the current literature on the role of alternative splicing in adult cancer, cancer predisposition syndromes, and pediatric cancers. We also describe multiple splice variants identified in adult cancers and confirmed through comprehensive genomic profiling in our institutional cohort of rare, refractory and relapsed pediatric and adolescent young adult cancer patients. Finally, we summarize the contributions of alternative splicing events to neoantigens and chemoresistance and prospects for splicing-based therapies. RESULTS Published dysregulated splicing events can be categorized as exon inclusion, exon exclusion, splicing factor upregulation, or splice site alterations. We observe these phenomena in cancer predisposition syndromes (Lynch syndrome, Li-Fraumeni syndrome, CHEK2) and pediatric leukemia (B-ALL), sarcomas (Ewing sarcoma, rhabdomyosarcoma, osteosarcoma), retinoblastoma, Wilms tumor, and neuroblastoma. Within our institutional cohort, we demonstrate splice variants in key regulatory genes (CHEK2, TP53, PIK3R1, MDM2, KDM6A, NF1) that resulted in exon exclusion or splice site alterations, which were predicted to impact functional protein expression and promote tumorigenesis. Differentially spliced isoforms and splicing proteins also impact neoantigen creation and treatment resistance, such as imatinib or glucocorticoid regimens. Additionally, splice-altering strategies with the potential to change the therapeutic landscape of pediatric cancers include antisense oligonucleotides, adeno-associated virus gene transfers, and small molecule inhibitors. CONCLUSIONS Alternative splicing plays a critical role in the formation and growth of pediatric cancers, and our institutional cohort confirms and highlights the broad spectrum of affected genes in a variety of cancers. Further studies that elucidate the mechanisms of disease-inducing splicing events will contribute toward the development of novel therapeutics.
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Affiliation(s)
- A S Venkataramany
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States; Medical Scientist Training Program, The Ohio State University, Columbus, Ohio, United States
| | - K M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States
| | - K Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - C E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Department of Pathology, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - P Y Wang
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States
| | - E R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States
| | - T P Cripe
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, United States; Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States; Division of Hematology, Oncology and Blood and Marrow Transplant, Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States
| | - D S Chandler
- Center for Childhood Cancer and Blood Diseases, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, Ohio, United States; Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States.
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5
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Keegan NP, Wilton SD, Fletcher S. Analysis of Pathogenic Pseudoexons Reveals Novel Mechanisms Driving Cryptic Splicing. Front Genet 2022; 12:806946. [PMID: 35140743 PMCID: PMC8819188 DOI: 10.3389/fgene.2021.806946] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Understanding pre-mRNA splicing is crucial to accurately diagnosing and treating genetic diseases. However, mutations that alter splicing can exert highly diverse effects. Of all the known types of splicing mutations, perhaps the rarest and most difficult to predict are those that activate pseudoexons, sometimes also called cryptic exons. Unlike other splicing mutations that either destroy or redirect existing splice events, pseudoexon mutations appear to create entirely new exons within introns. Since exon definition in vertebrates requires coordinated arrangements of numerous RNA motifs, one might expect that pseudoexons would only arise when rearrangements of intronic DNA create novel exons by chance. Surprisingly, although such mutations do occur, a far more common cause of pseudoexons is deep-intronic single nucleotide variants, raising the question of why these latent exon-like tracts near the mutation sites have not already been purged from the genome by the evolutionary advantage of more efficient splicing. Possible answers may lie in deep intronic splicing processes such as recursive splicing or poison exon splicing. Because these processes utilize intronic motifs that benignly engage with the spliceosome, the regions involved may be more susceptible to exonization than other intronic regions would be. We speculated that a comprehensive study of reported pseudoexons might detect alignments with known deep intronic splice sites and could also permit the characterisation of novel pseudoexon categories. In this report, we present and analyse a catalogue of over 400 published pseudoexon splice events. In addition to confirming prior observations of the most common pseudoexon mutation types, the size of this catalogue also enabled us to suggest new categories for some of the rarer types of pseudoexon mutation. By comparing our catalogue against published datasets of non-canonical splice events, we also found that 15.7% of pseudoexons exhibit some splicing activity at one or both of their splice sites in non-mutant cells. Importantly, this included seven examples of experimentally confirmed recursive splice sites, confirming for the first time a long-suspected link between these two splicing phenomena. These findings have the potential to improve the fidelity of genetic diagnostics and reveal new targets for splice-modulating therapies.
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Affiliation(s)
- Niall P. Keegan
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Niall P. Keegan,
| | - Steve D. Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, Australia
- Centre for Neuromuscular and Neurological Disorders, Perron Institute for Neurological and Translational Science, The University of Western Australia, Perth, WA, Australia
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6
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Parental Origin of the RB1 Gene Mutations in Families with Low Penetrance Hereditary Retinoblastoma. Cancers (Basel) 2021; 13:cancers13205068. [PMID: 34680218 PMCID: PMC8534066 DOI: 10.3390/cancers13205068] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Some families with hereditary retinoblastoma exhibit mild phenotype with low penetrance and variable expressivity, including complete absence of clinical signs of the disease in some carriers of the germline RB1 mutation. The identification of low-penetrance mutations in the RB1 gene and the study of their inheritance in pedigrees is contributing to understanding the mechanisms underlying the development of retinoblastoma with low penetrance. It is important both for further expansion of knowledge in the field of molecular genetics of retinoblastoma, and for competent genetic counseling and subsequent clinical management of families with this form of the disease. Our results support an assumption that parental origin of an RB1 mutation influences the likelihood of developing retinoblastoma. We also revealed a relatively high frequency of asymptomatic carriage of the RB1 mutations among the parents of retinoblastoma patients, highlighting the utmost necessity for molecular analysis among the probands’ relatives irrespective of their clinical status and family history of retinoblastoma. Abstract Our aim was to identify RB1 alterations causing hereditary low penetrance retinoblastoma and to evaluate how the parental origin of an RB1 mutation affects its phenotypic expression. By NGS and MLPA, RB1 mutations were found in 191 from 332 unrelated retinoblastoma patients. Among patients with identified RB1 mutations but without clinical family history of retinoblastoma, 7% (12/175) were found to have hereditary disease with one of the parents being an asymptomatic carrier of an RB1 mutation. Additionally, in two families with retinoblastoma history, mutations were inherited by probands from unaffected parents. Overall, nine probands inherited RB1 mutations from clinically unaffected fathers and five, from mothers. Yet, we gained explanations of maternal “unaffectedness” in most cases, either as somatic mosaicism or as clinical presentation of retinomas in involution, rendering the proportion of paternal to maternal truly asymptomatic mutation carriers as 9:1 (p = 0.005). This observation supports an assumption that parental origin of an RB1 mutation influences the likelihood of developing retinoblastoma. Additionally, our study revealed a relatively high frequency of asymptomatic carriage of the RB1 mutations among the parents of retinoblastoma patients, highlighting the utmost necessity of molecular analysis among the probands’ relatives irrespective of their clinical status and family history of retinoblastoma.
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7
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Reschke M, Biewald E, Bronstein L, Brecht IB, Dittner-Moormann S, Driever F, Ebinger M, Fleischhack G, Grabow D, Geismar D, Göricke S, Guberina M, Le Guin CHD, Kiefer T, Kratz CP, Metz K, Müller B, Ryl T, Schlamann M, Schlüter S, Schönberger S, Schulte JH, Sirin S, Süsskind D, Timmermann B, Ting S, Wackernagel W, Wieland R, Zenker M, Zeschnigk M, Reinhardt D, Eggert A, Ritter-Sovinz P, Lohmann DR, Bornfeld N, Bechrakis N, Ketteler P. Eye Tumors in Childhood as First Sign of Tumor Predisposition Syndromes: Insights from an Observational Study Conducted in Germany and Austria. Cancers (Basel) 2021; 13:cancers13081876. [PMID: 33919815 PMCID: PMC8070790 DOI: 10.3390/cancers13081876] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Eye tumors in children are very rare. In Europe, these eye tumors are nearly always diagnosed early and cure rates are high. However, eye tumors in childhood often occur as the first sign of a genetic tumor predisposition syndrome. This study collected data of children with malignant eye tumors diagnosed in five years in Germany and Austria to learn about the association of eye tumors in childhood with tumor predisposition syndrome. The study recruited 300 children with malignant eye tumors in childhood. In the here-presented cohort, more than 40% of eye tumors were associated with rare tumor predisposition syndromes. For this reason, all children with eye tumors and their families should receive genetic counseling for a tumor predisposition syndrome. Children with a genetic predisposition to cancer should receive a tailored surveillance, including detailed history, physical examination and, if indicated, imaging to screen for other cancers later in life. Abstract Retinoblastoma and other eye tumors in childhood are rare diseases. Many eye tumors are the first signs of a genetic tumor predisposition syndrome and the affected children carry a higher risk of developing other cancers later in life. Clinical and genetic data of all children with eye tumors diagnosed between 2013–2018 in Germany and Austria were collected in a multicenter prospective observational study. In five years, 300 children were recruited into the study: 287 with retinoblastoma, 7 uveal melanoma, 3 ciliary body medulloepithelioma, 2 retinal astrocytoma, 1 meningioma of the optic nerve extending into the eye. Heritable retinoblastoma was diagnosed in 44% of children with retinoblastoma. One child with meningioma of the optic nerve extending into the eye was diagnosed with neurofibromatosis 2. No pathogenic constitutional variant in DICER1 was detected in a child with medulloepithelioma while two children did not receive genetic analysis. Because of the known association with tumor predisposition syndromes, genetic counseling should be offered to all children with eye tumors. Children with a genetic predisposition to cancer should receive a tailored surveillance including detailed history, physical examinations and, if indicated, imaging to screen for other cancer. Early detection of cancers may reduce mortality.
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Affiliation(s)
- Madlen Reschke
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin, 13353 Berlin, Germany; (M.R.); (J.H.S.); (A.E.)
| | - Eva Biewald
- Department of Ophthalmology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (E.B.); (C.H.D.L.G.); (T.K.); (S.S.); (N.B.); (N.B.)
| | - Leo Bronstein
- Institute of Biostatistics and Clinical Research, University of Muenster, 48149 Münster, Germany;
| | - Ines B. Brecht
- Department of Pediatric Hematology and Oncology, Children’s University Hospital Tübingen, 72076 Tübingen, Germany; (I.B.B.); (M.E.)
| | - Sabine Dittner-Moormann
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (S.D.-M.); (G.F.); (T.R.); (S.S.); (R.W.); (D.R.)
| | - Frank Driever
- Institute of Pathology, University Hospital Essen, University Duisburg-Essen, 45122 Essen, Germany; (F.D.); (K.M.); (S.T.)
| | - Martin Ebinger
- Department of Pediatric Hematology and Oncology, Children’s University Hospital Tübingen, 72076 Tübingen, Germany; (I.B.B.); (M.E.)
| | - Gudrun Fleischhack
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (S.D.-M.); (G.F.); (T.R.); (S.S.); (R.W.); (D.R.)
| | - Desiree Grabow
- Division of Childhood Cancer Epidemiology, German Childhood Cancer Registry at Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, 55131 Mainz, Germany;
| | - Dirk Geismar
- Clinic for Particle Therapy, West German Proton Therapy Centre Essen (WPE), University Hospital Essen, 45122 Essen, Germany; (D.G.); (B.T.)
| | - Sophia Göricke
- Department of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, 45122 Essen, Germany; (S.G.); (S.S.)
| | - Maja Guberina
- Department for Radiotherapy, University Hospital Essen, 45122 Essen, Germany;
| | - Claudia H. D. Le Guin
- Department of Ophthalmology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (E.B.); (C.H.D.L.G.); (T.K.); (S.S.); (N.B.); (N.B.)
| | - Tobias Kiefer
- Department of Ophthalmology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (E.B.); (C.H.D.L.G.); (T.K.); (S.S.); (N.B.); (N.B.)
| | - Christian P. Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany;
| | - Klaus Metz
- Institute of Pathology, University Hospital Essen, University Duisburg-Essen, 45122 Essen, Germany; (F.D.); (K.M.); (S.T.)
| | - Bert Müller
- Department of Ophthalmology, Charité-Universitätsmedizin, 13353 Berlin, Germany;
| | - Tatsiana Ryl
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (S.D.-M.); (G.F.); (T.R.); (S.S.); (R.W.); (D.R.)
| | - Marc Schlamann
- Department of Neuroradiology, University Hospital Köln, 50937 Köln, Germany;
| | - Sabrina Schlüter
- Department of Ophthalmology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (E.B.); (C.H.D.L.G.); (T.K.); (S.S.); (N.B.); (N.B.)
| | - Stefan Schönberger
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (S.D.-M.); (G.F.); (T.R.); (S.S.); (R.W.); (D.R.)
| | - Johannes H. Schulte
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin, 13353 Berlin, Germany; (M.R.); (J.H.S.); (A.E.)
| | - Selma Sirin
- Department of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen, 45122 Essen, Germany; (S.G.); (S.S.)
| | - Daniela Süsskind
- Department of Ophthalmology, University Hospital Tübingen, 72076 Tübingen, Germany;
| | - Beate Timmermann
- Clinic for Particle Therapy, West German Proton Therapy Centre Essen (WPE), University Hospital Essen, 45122 Essen, Germany; (D.G.); (B.T.)
- German Consortium for Translational Cancer Research (DKTK), Standort Essen/Düsseldorf, 45122 Essen, Germany;
| | - Saskia Ting
- Institute of Pathology, University Hospital Essen, University Duisburg-Essen, 45122 Essen, Germany; (F.D.); (K.M.); (S.T.)
| | - Werner Wackernagel
- Department of Ophthalmology, Medical University of Graz, 8036 Graz, Austria;
| | - Regina Wieland
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (S.D.-M.); (G.F.); (T.R.); (S.S.); (R.W.); (D.R.)
| | - Martin Zenker
- Institute of Human Genetics, University Magdeburg, 39120 Magdeburg, Germany;
| | - Michael Zeschnigk
- Institute of Human Genetics, Medical Faculty, University Duisburg-Essen, 45122 Essen, Germany;
| | - Dirk Reinhardt
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (S.D.-M.); (G.F.); (T.R.); (S.S.); (R.W.); (D.R.)
| | - Angelika Eggert
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin, 13353 Berlin, Germany; (M.R.); (J.H.S.); (A.E.)
| | - Petra Ritter-Sovinz
- Division of Pediatric Hematology/Oncology, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria;
| | - Dietmar R. Lohmann
- German Consortium for Translational Cancer Research (DKTK), Standort Essen/Düsseldorf, 45122 Essen, Germany;
- Institute of Human Genetics, Medical Faculty, University Duisburg-Essen, 45122 Essen, Germany;
| | - Norbert Bornfeld
- Department of Ophthalmology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (E.B.); (C.H.D.L.G.); (T.K.); (S.S.); (N.B.); (N.B.)
| | - Nikolaos Bechrakis
- Department of Ophthalmology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (E.B.); (C.H.D.L.G.); (T.K.); (S.S.); (N.B.); (N.B.)
- German Consortium for Translational Cancer Research (DKTK), Standort Essen/Düsseldorf, 45122 Essen, Germany;
| | - Petra Ketteler
- Department of Pediatric Hematology and Oncology, University Hospital Essen, University Duisburg Essen, 45122 Essen, Germany; (S.D.-M.); (G.F.); (T.R.); (S.S.); (R.W.); (D.R.)
- German Consortium for Translational Cancer Research (DKTK), Standort Essen/Düsseldorf, 45122 Essen, Germany;
- Institute of Human Genetics, Medical Faculty, University Duisburg-Essen, 45122 Essen, Germany;
- Correspondence:
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8
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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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9
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Minati R, Perreault C, Thibault P. A Roadmap Toward the Definition of Actionable Tumor-Specific Antigens. Front Immunol 2020; 11:583287. [PMID: 33424836 PMCID: PMC7793940 DOI: 10.3389/fimmu.2020.583287] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022] Open
Abstract
The search for tumor-specific antigens (TSAs) has considerably accelerated during the past decade due to the improvement of proteogenomic detection methods. This provides new opportunities for the development of novel antitumoral immunotherapies to mount an efficient T cell response against one or multiple types of tumors. While the identification of mutated antigens originating from coding exons has provided relatively few TSA candidates, the possibility of enlarging the repertoire of targetable TSAs by looking at antigens arising from non-canonical open reading frames opens up interesting avenues for cancer immunotherapy. In this review, we outline the potential sources of TSAs and the mechanisms responsible for their expression strictly in cancer cells. In line with the heterogeneity of cancer, we propose that discrete families of TSAs may be enriched in specific cancer types.
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Affiliation(s)
- Robin Minati
- École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, Lyon, France
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- Department of Chemistry, Université de Montréal, Montréal, QC, Canada
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10
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Canson D, Glubb D, Spurdle AB. Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: Strategies to enhance bioinformatic prediction using hereditary cancer genes as exemplars. Hum Mutat 2020; 41:1705-1721. [PMID: 32623769 DOI: 10.1002/humu.24074] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/15/2022]
Abstract
It is possible to estimate the prior probability of pathogenicity for germline disease gene variants based on bioinformatic prediction of variant effect/s. However, routinely used approaches have likely led to the underestimation and underreporting of variants located outside donor and acceptor splice site motifs that affect messenger RNA (mRNA) processing. This review presents information about hereditary cancer gene germline variants, outside native splice sites, with experimentally validated splicing effects. We list 95 exonic variants that impact splicing regulatory elements (SREs) in BRCA1, BRCA2, MLH1, MSH2, MSH6, and PMS2. We utilized a pre-existing large-scale BRCA1 functional data set to map functional SREs, and assess the relative performance of different tools to predict effects of 283 variants on such elements. We also describe rare examples of intronic variants that impact branchpoint (BP) sites and create pseudoexons. We discuss the challenges in predicting variant effect on BP site usage and pseudoexonization, and suggest strategies to improve the bioinformatic prioritization of such variants for experimental validation. Importantly, our review and analysis highlights the value of considering impact of variants outside donor and acceptor motifs on mRNA splicing and disease causation.
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Affiliation(s)
- Daffodil Canson
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Dylan Glubb
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
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11
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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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12
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Berry JL, Polski A, Cavenee WK, Dryja TP, Murphree AL, Gallie BL. The RB1 Story: Characterization and Cloning of the First Tumor Suppressor Gene. Genes (Basel) 2019; 10:genes10110879. [PMID: 31683923 PMCID: PMC6895859 DOI: 10.3390/genes10110879] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 12/26/2022] Open
Abstract
The RB1 gene is the first described human tumor suppressor gene and plays an integral role in the development of retinoblastoma, a pediatric malignancy of the eye. Since its discovery, the stepwise characterization and cloning of RB1 have laid the foundation for numerous advances in the understanding of tumor suppressor genes, retinoblastoma tumorigenesis, and inheritance. Knowledge of RB1 led to a paradigm shift in the field of cancer genetics, including widespread acceptance of the concept of tumor suppressor genes, and has provided crucial diagnostic and prognostic information through genetic testing for patients affected by retinoblastoma. This article reviews the long history of RB1 gene research, characterization, and cloning, and also discusses recent advances in retinoblastoma genetics that have grown out of this foundational work.
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Affiliation(s)
- Jesse L Berry
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.
| | - Ashley Polski
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.
| | - Webster K Cavenee
- Ludwig Institute for Cancer Research, University of California, San Diego, CA 92093, USA.
- Department of Medicine, UCSD School of Medicine, San Diego, CA 92093, USA.
- Moores Cancer Center, UCSD School of Medicine, San Diego, CA 92093, USA.
| | - Thaddeus P Dryja
- Cogan Eye Pathology Laboratory, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - A Linn Murphree
- USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.
| | - Brenda L Gallie
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON M5T 3A9, Canada.
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON M5T 3A9, Canada.
- Departments of Molecular Genetics and Medical Biophysics, University of Toronto, Toronto, ON M5T 3A9, Canada.
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13
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Nahon-Esteve S, Martel A, Maschi C, Caujolle JP, Baillif S, Lassalle S, Hofman P. The Molecular Pathology of Eye Tumors: A 2019 Update Main Interests for Routine Clinical Practice. Curr Mol Med 2019; 19:632-664. [DOI: 10.2174/1566524019666190726161044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 12/17/2022]
Abstract
Over the last few years, we have seen constant development of molecular
pathology for the care of patients with cancer. The information obtained from molecular
data has transformed our thinking about the biological diversity of cancers, particularly in
the field of ophthalmic oncology. It has reoriented the way in which therapeutic decisions
and decisions concerning patient surveillance are made, both in the area of pediatric
cancers, including rhabdomyosarcoma and retinoblastoma, and adult cancers, such as
uveal melanoma and lymphomas. A better definition of the molecular classification of
these cancers and of the different biological pathways involved is essential to the
understanding of both the pathologist and the onco-ophthalmologist. Molecular tests
based on targeted or expanded analysis of gene panels are now available. These tests
can be performed with tumor tissue or biofluids (especially blood) to predict the
prognosis of tumors and, above all, the benefit of targeted therapies, immunotherapy or
even chemotherapy. Looking for the BAP1 mutation in uveal melanoma is essential
because of the associated metastatic risk. When treating retinoblastoma, it is mandatory
to assess the heritable status of RB1. Conjunctival melanoma requires investigation into
the BRAF mutation in the case of a locally advanced tumor. The understanding of
genomic alterations, the results of molecular tests and/or other biological tests predictive
of a therapeutic response, but also of the limits of these tests with respect to the
available biological resources, represents a major challenge for optimal patient
management in ophthalmic oncology. In this review, we present the current state of
knowledge concerning the different molecular alterations and therapeutic targets of
interest in ophthalmic oncology.
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Affiliation(s)
| | - Arnaud Martel
- Department of Ophthalmology, University Cote d'Azur, Nice, France
| | - Célia Maschi
- Department of Ophthalmology, University Cote d'Azur, Nice, France
| | | | | | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, University Cote d'Azur, Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, University Cote d'Azur, Nice, France
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14
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Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep 2019; 23:270-281.e3. [PMID: 29617666 PMCID: PMC6055527 DOI: 10.1016/j.celrep.2018.03.052] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 02/21/2018] [Accepted: 03/13/2018] [Indexed: 12/31/2022] Open
Abstract
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential. Here, we applied a bioinformatic tool, MiSplice, for the large-scale discovery of splice-site-creating mutations (SCMs) across 8,656 TCGA tumors. We report 1,964 originally mis-annotated mutations having clear evidence of creating alternative splice junctions. TP53 and GATA3 have 26 and 18 SCMs, respectively, and ATRX has 5 from lower-grade gliomas. Mutations in 11 genes, including PARP1, BRCA1, and BAP1, were experimentally validated for splice-site-creating function. Notably, we found that neoantigens induced by SCMs are likely several folds more immunogenic compared to missense mutations, exemplified by the recurrent GATA3 SCM. Further, high expression of PD-1 and PD-L1 was observed in tumors with SCMs, suggesting candidates for immune blockade therapy. Our work highlights the importance of integrating DNA and RNA data for understanding the functional and the clinical implications of mutations in human diseases.
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Affiliation(s)
- Reyka G Jayasinghe
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Song Cao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Qingsong Gao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Michael C Wendl
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Mathematics, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nam Sy Vo
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Yanyan Zhao
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Héctor Climente-González
- Institut Curie, 75248 Paris Cedex, France; MINES ParisTech, PSL-Research University, CBIO-Centre for Computational Biology, 77300 Fontainebleau, France; INSERM U900, 75248 Paris Cedex, France
| | - Shengjie Chai
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajees Varghese
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mo Huang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Sohini Sengupta
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Zhi Li
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA
| | - Samuel H Payne
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Institute for Systems Genetics, New York University School of Medicine, New York, NY 10016, USA
| | - Jeffrey H Miner
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Matthew J Walter
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA
| | | | - Benjamin Vincent
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eduardo Eyras
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain; Computational RNA Biology Group, Pompeu Fabra University (UPF), 08003 Barcelona, Spain
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Feng Chen
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; Division of Nephrology, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA; Division of Oncology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63110, USA.
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15
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Smith CC, Selitsky SR, Chai S, Armistead PM, Vincent BG, Serody JS. Alternative tumour-specific antigens. Nat Rev Cancer 2019; 19:465-478. [PMID: 31278396 PMCID: PMC6874891 DOI: 10.1038/s41568-019-0162-4] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
The study of tumour-specific antigens (TSAs) as targets for antitumour therapies has accelerated within the past decade. The most commonly studied class of TSAs are those derived from non-synonymous single-nucleotide variants (SNVs), or SNV neoantigens. However, to increase the repertoire of available therapeutic TSA targets, 'alternative TSAs', defined here as high-specificity tumour antigens arising from non-SNV genomic sources, have recently been evaluated. Among these alternative TSAs are antigens derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other processes. Unlike the patient-specific nature of SNV neoantigens, some alternative TSAs may have the advantage of being widely shared by multiple tumours, allowing for universal, off-the-shelf therapies. In this Opinion article, we will outline the biology, available computational tools, preclinical and/or clinical studies and relevant cancers for each alternative TSA class, as well as discuss both current challenges preventing the therapeutic application of alternative TSAs and potential solutions to aid in their clinical translation.
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Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sara R Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Bioinformatics Core, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Marsico Hall, Chapel Hill, NC, USA
| | - Shengjie Chai
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jonathan S Serody
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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16
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Coltri PP, Dos Santos MGP, da Silva GHG. Splicing and cancer: Challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1527. [PMID: 30773852 DOI: 10.1002/wrna.1527] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/14/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
Abstract
Cancer arises from alterations in several metabolic processes affecting proliferation, growth, replication and death of cells. A fundamental challenge in the study of cancer biology is to uncover molecular mechanisms that lead to malignant cellular transformation. Recent genomic analyses revealed that many molecular alterations observed in cancers come from modifications in the splicing process, including mutations in pre-mRNA regulatory sequences, mutations in spliceosome components, and altered ratio of specific splicing regulators. While alterations in splice site preferences might generate alternative isoforms enabling different biological functions, these might also be responsible for nonfunctional isoforms that can eventually cause dysregulation in cellular processes. Molecular characteristics of regulatory sequences and proteins might also be important prognostic tools revealing a cancer-specific splicing pattern and linking splicing control to cancer development. The connection between cancer biology and splicing regulation is of primary importance to understand the mechanisms leading to disease and also to improve development of therapeutic approaches. Splicing modulation is being explored in new anti-cancer therapies and further investigation of targeted splicing factors is critical for the success of these strategies. This article is categorized under: RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Patricia P Coltri
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria G P Dos Santos
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Guilherme H G da Silva
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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17
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Condorelli R, Spring L, O’Shaughnessy J, Lacroix L, Bailleux C, Scott V, Dubois J, Nagy R, Lanman R, Iafrate A, Andre F, Bardia A. Polyclonal RB1 mutations and acquired resistance to CDK 4/6 inhibitors in patients with metastatic breast cancer. Ann Oncol 2018; 29:640-645. [DOI: 10.1093/annonc/mdx784] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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18
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Betancor-Fernández I, Timson DJ, Salido E, Pey AL. Natural (and Unnatural) Small Molecules as Pharmacological Chaperones and Inhibitors in Cancer. Handb Exp Pharmacol 2018; 245:155-190. [PMID: 28993836 DOI: 10.1007/164_2017_55] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations causing single amino acid exchanges can dramatically affect protein stability and function, leading to disease. In this chapter, we will focus on several representative cases in which such mutations affect protein stability and function leading to cancer. Mutations in BRAF and p53 have been extensively characterized as paradigms of loss-of-function/gain-of-function mechanisms found in a remarkably large fraction of tumours. Loss of RB1 is strongly associated with cancer progression, although the molecular mechanisms by which missense mutations affect protein function and stability are not well known. Polymorphisms in NQO1 represent a remarkable example of the relationships between intracellular destabilization and inactivation due to dynamic alterations in protein ensembles leading to loss of function. We will review the function of these proteins and their dysfunction in cancer and then describe in some detail the effects of the most relevant cancer-associated single amino exchanges using a translational perspective, from the viewpoints of molecular genetics and pathology, protein biochemistry and biophysics, structural, and cell biology. This will allow us to introduce several representative examples of natural and synthetic small molecules applied and developed to overcome functional, stability, and regulatory alterations due to cancer-associated amino acid exchanges, which hold the promise for using them as potential pharmacological cancer therapies.
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Affiliation(s)
- Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - David J Timson
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Huxley Building, Lewes Road, Brighton, BN2 4GJ, UK
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, Tenerife, 38320, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, 18071, Spain.
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19
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Jyotsana N, Heuser M. Exploiting differential RNA splicing patterns: a potential new group of therapeutic targets in cancer. Expert Opin Ther Targets 2017; 22:107-121. [PMID: 29235382 DOI: 10.1080/14728222.2018.1417390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Mutations in genes associated with splicing have been found in hematologic malignancies, but also in solid cancers. Aberrant cancer specific RNA splicing either results from mutations or misexpression of the spliceosome genes directly, or from mutations in splice sites of oncogenes or tumor suppressors. Areas covered: In this review, we present molecular targets of aberrant splicing in various malignancies, information on existing and emerging therapeutics against such targets, and strategies for future drug development. Expert opinion: Alternative splicing is an important mechanism that controls gene expression, and hence pharmacologic and genetic control of aberrant alternative RNA splicing has been proposed as a potential therapy in cancer. To identify and validate aberrant RNA splicing patterns as therapeutic targets we need to (1) characterize the most common genetic aberrations of the spliceosome and of splice sites, (2) understand the dysregulated downstream pathways and (3) exploit in-vivo disease models of aberrant splicing. Antisense oligonucleotides show promising activity, but will benefit from improved delivery tools. Inhibitors of mutated splicing factors require improved specificity, as alternative and aberrant splicing are often intertwined like two sides of the same coin. In summary, targeting aberrant splicing is an early but emerging field in cancer treatment.
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Affiliation(s)
- Nidhi Jyotsana
- a Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation , Hannover Medical School , Hannover , Germany
| | - Michael Heuser
- a Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation , Hannover Medical School , Hannover , Germany
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20
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Soliman SE, Racher H, Lambourne M, Matevski D, MacDonald H, Gallie B. A novel deep intronic low penetrance RB1 variant in a retinoblastoma family. Ophthalmic Genet 2017; 39:288-290. [PMID: 29099630 DOI: 10.1080/13816810.2017.1393828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sameh E Soliman
- a The Department of Ophthalmology and Vision Sciences , Hospital for Sick Children, University of Toronto , Toronto , Ontario , Canada.,b The Department of Ophthalmology, Faculty of Medicine , University of Alexandria , Alexandria , Egypt
| | | | | | | | - Heather MacDonald
- a The Department of Ophthalmology and Vision Sciences , Hospital for Sick Children, University of Toronto , Toronto , Ontario , Canada
| | - Brenda Gallie
- a The Department of Ophthalmology and Vision Sciences , Hospital for Sick Children, University of Toronto , Toronto , Ontario , Canada
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21
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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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22
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Ewens KG, Bhatti TR, Moran KA, Richards-Yutz J, Shields CL, Eagle RC, Ganguly A. Phosphorylation of pRb: mechanism for RB pathway inactivation in MYCN-amplified retinoblastoma. Cancer Med 2017; 6:619-630. [PMID: 28211617 PMCID: PMC5345671 DOI: 10.1002/cam4.1010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 12/18/2022] Open
Abstract
A small, but unique subgroup of retinoblastoma has been identified with no detectable mutation in the retinoblastoma gene (RB1) and with high levels of MYCN gene amplification. This manuscript investigated alternate pathways of inactivating pRb, the encoded protein in these tumors. We analyzed the mutation status of the RB1 gene and MYCN copy number in a series of 245 unilateral retinoblastomas, and the phosphorylation status of pRb in a subset of five tumors using immunohistochemistry. There were 203 tumors with two mutations in RB1 (RB1-/- , 83%), 29 with one (RB1+/- , 12%) and 13 with no detectable mutations (RB1+/+ , 5%). Eighteen tumors carried MYCN amplification between 29 and 110 copies: 12 had two (RB1-/- ) or one RB1 (RB1+/- ) mutations, while six had no mutations (RB1+/+ ). Immunohistochemical staining of tumor sections with antibodies against pRb and phosphorylated Rb (ppRb) displayed high levels of pRb and ppRb in both RB1+/+ and RB1+/- tumors with MYCN amplification compared to no expression of these proteins in a classic RB1-/- , MYCN-low tumor. These results establish that high MYCN amplification can be present in retinoblastoma with or without coding sequence mutations in the RB1 gene. The functional state of pRb is inferred to be inactive due to phosphorylation of pRb in the MYCN-amplified retinoblastoma without coding sequence mutations. This makes inactivation of RB1 by gene mutation or its protein product, pRb, by protein phosphorylation, a necessary condition for initiating retinoblastoma tumorigenesis, independent of MYCN amplification.
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Affiliation(s)
- Kathryn G Ewens
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tricia R Bhatti
- Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kimberly A Moran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer Richards-Yutz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Carol L Shields
- Oncology Services, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Ralph C Eagle
- Department of Pathology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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23
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Aggarwala V, Ganguly A, Voight BF. De novo mutational profile in RB1 clarified using a mutation rate modeling algorithm. BMC Genomics 2017; 18:155. [PMID: 28193182 PMCID: PMC5307739 DOI: 10.1186/s12864-017-3522-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/27/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Studies of de novo mutations offer great promise to improve our understanding of human disease. After a causal gene has been identified, it is natural to hypothesize that disease relevant mutations accumulate within a sub-sequence of the gene - for example, an exon, a protein domain, or at CpG sites. These assessments are typically qualitative, because we lack methodology to assess the statistical significance of sub-gene mutational burden ultimately to infer disease-relevant biology. METHODS To address this issue, we present a generalized algorithm to grade the significance of de novo mutational burden within a gene ascertained from affected probands, based on our model for mutation rate informed by local sequence context. RESULTS We applied our approach to 268 newly identified de novo germline mutations by re-sequencing the coding exons and flanking intronic regions of RB1 in 642 sporadic, bilateral probands affected with retinoblastoma (RB). We confirm enrichment of loss-of-function mutations, but demonstrate that previously noted 'hotspots' of nonsense mutations in RB1 are compatible with the elevated mutation rates expected at CpG sites, refuting a RB specific pathogenic mechanism. Our approach demonstrates an enrichment of splice-site donor mutations of exon 6 and 12 but depletion at exon 5, indicative of previously unappreciated heterogeneity in penetrance within this class of substitution. We demonstrate the enrichment of missense mutations to the pocket domain of RB1, which contains the known Arg661Trp low-penetrance mutation. CONCLUSION Our approach is generalizable to any phenotype, and affirms the importance of statistical interpretation of de novo mutations found in human genomes.
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Affiliation(s)
- Varun Aggarwala
- Genomics and Computational Biology Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Arupa Ganguly
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Perelman School of Medicine, University of Pennsylvania, 415 Anatomy Chemistry Building, 3620 Hamilton Walk, Philadelphia, PA 19104 USA
| | - Benjamin F. Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Perelman School of Medicine, 10–126 Smilow Center for Translational Research, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
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24
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Temming P, Arendt M, Viehmann A, Eisele L, Le Guin CHD, Schündeln MM, Biewald E, Astrahantseff K, Wieland R, Bornfeld N, Sauerwein W, Eggert A, Jöckel KH, Lohmann DR. Incidence of second cancers after radiotherapy and systemic chemotherapy in heritable retinoblastoma survivors: A report from the German reference center. Pediatr Blood Cancer 2017; 64:71-80. [PMID: 27567086 DOI: 10.1002/pbc.26193] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/24/2016] [Accepted: 07/12/2016] [Indexed: 11/07/2022]
Abstract
BACKGROUND Survivors of heritable retinoblastoma carry a high risk to develop second cancers. Eye-preserving radiotherapy raises this risk, while the impact of chemotherapy remains less defined. PROCEDURE This population-based study characterizes the impact of all treatment modalities on second cancers incidence and type after retinoblastoma treatment in Germany. Data on second cancer incidence in 648 patients with heritable retinoblastoma treated between 1940 and 2008 at the German national reference center for retinoblastoma were analyzed to identify associations with treatment. RESULTS The cumulative incidence ratio (per 1,000 person years) of second cancers was 8.6 (95% confidence interval 7.0-10.4). Second cancer incidence was influenced by type of retinoblastoma treatment but not by the year of diagnosis or by sex. Radiotherapy and systemic chemotherapy increased the incidence of second cancers (by 3.0- and 1.8-fold, respectively). While radiotherapy was specifically associated with second cancers arising within the periorbital region in the previously irradiated field, chemotherapy was the strongest risk factor for second cancers in other localizations. Soft tissue sarcomas and osteosarcomas were the most prevalent second cancers (standardized incidence ratio 179.35 compared to the German population). CONCLUSIONS Second cancers remain a major concern in heritable retinoblastoma survivors. Consistent with previous reports, radiotherapy increased second cancer incidence and influenced type and localization. However, chemotherapy was the strongest risk factor for second malignancies outside the periorbital region. Our results provide screening priorities during life-long oncological follow-up based on the curative therapy the patient has received and emphasize the need for less-detrimental therapies for children with heritable retinoblastoma.
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Affiliation(s)
- Petra Temming
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany.,Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany
| | - Marina Arendt
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Anja Viehmann
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany.,Institute of General Medicine, University Hospital Essen, Essen, Germany
| | - Lewin Eisele
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Claudia H D Le Guin
- Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany.,Department of Ophthalmology, University Hospital Essen, Essen, Germany
| | - Michael M Schündeln
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Eva Biewald
- Department of Ophthalmology, University Hospital Essen, Essen, Germany
| | - Kathy Astrahantseff
- Department of Pediatric Oncology, Hematology and BMT, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Regina Wieland
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany
| | - Norbert Bornfeld
- Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany.,Department of Ophthalmology, University Hospital Essen, Essen, Germany
| | | | - Angelika Eggert
- Department of Pediatric Oncology, Hematology and BMT, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karl-Heinz Jöckel
- German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Dietmar R Lohmann
- Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany.,German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany.,Institute of Human Genetics, University Hospital Essen, Essen, Germany
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25
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SALIMINEJAD KIOOMARS, BEHNAM BABAK, AKBARI MOHAMMADTAGHI, KHORSHID HAMIDREZAKHORRAM, GHASSEMI FARRIBA, AMOLI FAHIMEHASADI, AKHONDI MOHAMMADMEHDI, VOSOOGH PARVANEH, NASERIPOUR MASOOD, AHANI ALI. Rapid detection of RB1 recurrent mutations in retinoblastoma by ARMS-PCR. J Genet 2016. [DOI: 10.1007/s12041-013-0237-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Temming P, Arendt M, Viehmann A, Eisele L, Le Guin CH, Schündeln MM, Biewald E, Mäusert J, Wieland R, Bornfeld N, Sauerwein W, Eggert A, Lohmann DR, Jöckel KH. How Eye-Preserving Therapy Affects Long-Term Overall Survival in Heritable Retinoblastoma Survivors. J Clin Oncol 2016; 34:3183-8. [DOI: 10.1200/jco.2015.65.4012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Purpose Intraocular retinoblastoma is curable, but survivors with a heritable predisposition are at high risk for second malignancies. Because second malignancies are associated with high mortality, prognostic factors for second malignancy influence long-term overall survival. This study investigates the impact of all types of eye-preserving therapies on long-term survival in the complete German cohort of patients with heritable retinoblastoma. Patients and Methods Overall survival, disease staging using international scales, time period of diagnosis, and treatment type were analyzed in the 633 German children treated at the national reference center for heritable retinoblastoma. Results The 5-year overall survival of children diagnosed in Germany with heritable retinoblastoma between 1940 and 2008 was 93.2% (95% CI, 91.2% to 95.1%), but long-term mortality was increased compared with patients with nonheritable disease. Overall survival correlated with tumor staging, and 92% of patients were diagnosed with a favorable tumor stage (International Retinoblastoma Staging System stage 0 or I). Despite a 5-year overall survival of 97.4% (95% CI, 96.0% to 98.8%) in patients with stage 0 or I, only 79.5% (95% CI, 74.2% to 84.8%) of these patients survived 40 years after diagnosis. Long-term overall survival was reduced in children treated with eye-preserving radiotherapy compared with enucleation alone, and adding chemotherapy aggravated this effect. Conclusion The benefits of preserving vision must be balanced with the impact of eye-preserving treatments on long-term survival in heritable retinoblastoma, and the genetic background of the patient influences choice of eye-preserving treatment. Germline RB1 genetic analysis is important to identify heritable retinoblastoma among unilateral retinoblastoma cases. Eye-preserving radiotherapy should be carefully considered in patients with germline RB1 mutations. Life-long oncologic follow-up is crucial for all retinoblastoma survivors, and less detrimental eye-preserving therapies must be developed.
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Affiliation(s)
- Petra Temming
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Marina Arendt
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Anja Viehmann
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Lewin Eisele
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia H.D. Le Guin
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Michael M. Schündeln
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Eva Biewald
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jennifer Mäusert
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Regina Wieland
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Norbert Bornfeld
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Wolfgang Sauerwein
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Angelika Eggert
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Dietmar R. Lohmann
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karl-Heinz Jöckel
- Petra Temming, Marina Arendt, Anja Viehmann, Lewin Eisele, Claudia H.D. Le Guin, Michael M. Schündeln, Eva Biewald, Jennifer Mäusert, Regina Wieland, Norbert Bornfeld, Wolfgang Sauerwein, Dietmar R. Lohmann, and Karl-Heinz Jöckel, University Hospital Essen, Essen; Petra Temming, Dietmar R. Lohmann, and Karl-Heinz Jöckel, German Consortium for Translational Cancer Research, Heidelberg; and Angelika Eggert, Charité-Universitätsmedizin Berlin, Berlin, Germany
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27
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Li WL, Buckley J, Sanchez-Lara PA, Maglinte DT, Viduetsky L, Tatarinova TV, Aparicio JG, Kim JW, Au M, Ostrow D, Lee TC, O'Gorman M, Judkins A, Cobrinik D, Triche TJ. A Rapid and Sensitive Next-Generation Sequencing Method to Detect RB1 Mutations Improves Care for Retinoblastoma Patients and Their Families. J Mol Diagn 2016; 18:480-93. [PMID: 27155049 DOI: 10.1016/j.jmoldx.2016.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 01/14/2016] [Accepted: 02/01/2016] [Indexed: 01/26/2023] Open
Abstract
Retinoblastoma is a childhood eye malignancy that can lead to the loss of vision, eye(s), and sometimes life. The tumors are initiated by inactivating mutations in both alleles of the tumor-suppressor gene, RB1, or, rarely, by MYCN amplification. Timely identification of a germline RB1 mutation in blood samples or either somatic RB1 mutation or MYCN amplification in tumors is important for effective care and management of retinoblastoma patients and their families. However, current procedures to thoroughly test RB1 mutations are complicated and lengthy. Herein, we report a next-generation sequencing-based method capable of detecting point mutations, small indels, and large deletions or duplications across the entire RB1 gene and amplification of MYCN gene on a single platform. From DNA extraction to clinical interpretation requires only 3 days, enabling early molecular diagnosis of retinoblastoma and optimal treatment outcomes. This method can also detect low-level mosaic mutations in blood samples that can be missed by routine Sanger sequencing. In addition, it can differentiate between RB1 mutation- and MYCN amplification-driven retinoblastomas. This rapid, comprehensive, and sensitive method for detecting RB1 mutations and MYCN amplification can readily identify RB1 mutation carriers and thus improve the management and genetic counseling for retinoblastoma patients and their families.
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Affiliation(s)
- Wenhui L Li
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, USC Roski Eye Institute, University of Southern California, Los Angeles, California.
| | - Jonathan Buckley
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, USC Roski Eye Institute, University of Southern California, Los Angeles, California
| | - Pedro A Sanchez-Lara
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, USC Roski Eye Institute, University of Southern California, Los Angeles, California; Department of Pediatrics, USC Roski Eye Institute, University of Southern California, Los Angeles, California
| | - Dennis T Maglinte
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Lucy Viduetsky
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Tatiana V Tatarinova
- Department of Pediatrics, USC Roski Eye Institute, University of Southern California, Los Angeles, California; Spatial Sciences Institute, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California
| | | | - Jonathan W Kim
- Vision Center, Children's Hospital Los Angeles, Los Angeles, California; Department of Opthalmology, USC Roski Eye Institute, University of Southern California, Los Angeles, California
| | - Margaret Au
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Dejerianne Ostrow
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Thomas C Lee
- Vision Center, Children's Hospital Los Angeles, Los Angeles, California; Department of Opthalmology, USC Roski Eye Institute, University of Southern California, Los Angeles, California
| | - Maurice O'Gorman
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, USC Roski Eye Institute, University of Southern California, Los Angeles, California
| | - Alexander Judkins
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, USC Roski Eye Institute, University of Southern California, Los Angeles, California
| | - David Cobrinik
- Vision Center, Children's Hospital Los Angeles, Los Angeles, California; Department of Opthalmology, USC Roski Eye Institute, University of Southern California, Los Angeles, California; Division of Ophthalmology and Department of Surgery, and Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, California; Department of Biochemistry & Molecular Biology, USC Roski Eye Institute, University of Southern California, Los Angeles, California; Norris Comprehensive Cancer Center, USC Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Timothy J Triche
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, USC Roski Eye Institute, University of Southern California, Los Angeles, California.
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Oltean S. Modulators of alternative splicing as novel therapeutics in cancer. World J Clin Oncol 2015; 6:92-95. [PMID: 26468443 PMCID: PMC4600196 DOI: 10.5306/wjco.v6.i5.92] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/08/2015] [Accepted: 08/03/2015] [Indexed: 02/06/2023] Open
Abstract
Alternative splicing (AS), the process of removing introns from pre-mRNA and re-arrangement of exons to give several types of mature transcripts, has been described more than 40 years ago. However, until recently, it has not been clear how extensive it is. Genome-wide studies have now conclusively shown that more than 90% of genes are alternatively spliced in humans. This makes AS one of the main drivers of proteomic diversity and, consequently, determinant of cellular function repertoire. Unsurprisingly, given its extent, numerous splice isoforms have been described to be associated with several diseases including cancer. Many of them have antagonistic functions, e.g., pro- and anti-angiogenic or pro- and anti-apoptotic. Additionally several splice factors have been recently described to have oncogene or tumour suppressors activities, like SF3B1 which is frequently mutated in myelodysplastic syndromes. Beside the implications for cancer pathogenesis, de-regulated AS is recognized as one of the novel areas of cell biology where therapeutic manipulations may be designed. This editorial discusses the possibilities of manipulation of AS for therapeutic benefit in cancer. Approaches involving the use of oligonucleotides as well as small molecule splicing modulators are presented as well as thoughts on how specificity might be accomplished in splicing therapeutics.
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Temming P, Viehmann A, Arendt M, Eisele L, Spix C, Bornfeld N, Sauerwein W, Jöckel KH, Lohmann DR. Pediatric second primary malignancies after retinoblastoma treatment. Pediatr Blood Cancer 2015; 62:1799-804. [PMID: 25970657 DOI: 10.1002/pbc.25576] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/31/2015] [Indexed: 11/09/2022]
Abstract
BACKGROUND Children with retinoblastoma carry a high risk to develop second primary malignancies in childhood and adolescence. This study characterizes the type of pediatric second primary malignancies after retinoblastoma treatment and investigates the impact of different treatment strategies and prognostic factors at presentation. PROCEDURE All national patients treated for retinoblastoma at the German referral center with a current age of 6-27 years were invited to participate in a study to characterize late effects. RESULTS Data on pediatric second primary malignancies were recorded from 488 patients. Ten developed a malignancy before the age of 18 years. For children with heterozygous oncogenic RB1 alteration (heritable retinoblastoma), the cumulative incidence to develop a second malignancy at the age of 10 years was 5.2% (95% CI 1.7; 8.7%). This results in an elevated risk for sarcoma (n = 4) (SIR 147.98; 95% CI 39.81; 378.87) and leukemia (n = 4) (SIR 41.38; 95% CI 11.13; 105.95). Neither the functional type of the RB1 alteration nor its origin showed a significant impact. Treatment modality influenced incidence, latency, and type of malignancy. Previous radiotherapy increased the risk for solid tumors and 3 of 91 children developed acute leukemia after chemotherapy. However, 2 of 10 malignancies were diagnosed in patients with heritable retinoblastoma but without previous chemotherapy or external beam radiotherapy. CONCLUSIONS Screening for second primary malignancy is an important part of pediatric oncological follow-up in patients with heritable retinoblastoma. For patients with sporadic unilateral retinoblastoma, genetic information influences treatment decisions and allows tailoring of follow-up schedules.
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Affiliation(s)
- Petra Temming
- Department of Pediatric Hematology and Oncology, University Hospital Essen, Essen, Germany.,Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany
| | - Anja Viehmann
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Marina Arendt
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Lewin Eisele
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Claudia Spix
- German Childhood Cancer Registry, Institute of Medical Biostatistics, Epidemiology and Informatics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Norbert Bornfeld
- Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany.,Department of Ophthalmology, University Hospital Essen, Essen, Germany
| | | | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, Essen, Germany
| | - Dietmar R Lohmann
- Eye Oncogenetics Research Group, University Hospital Essen, Essen, Germany.,Institute of Human Genetics, University Hospital Essen, Essen, Germany
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Next generation sequencing in sporadic retinoblastoma patients reveals somatic mosaicism. Eur J Hum Genet 2015; 23:1523-30. [PMID: 25712084 DOI: 10.1038/ejhg.2015.6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 12/03/2014] [Accepted: 12/25/2014] [Indexed: 11/08/2022] Open
Abstract
In about 50% of sporadic cases of retinoblastoma, no constitutive RB1 mutations are detected by conventional methods. However, recent research suggests that, at least in some of these cases, there is somatic mosaicism with respect to RB1 normal and mutant alleles. The increased availability of next generation sequencing improves our ability to detect the exact percentage of patients with mosaicism. Using this technology, we re-tested a series of 40 patients with sporadic retinoblastoma: 10 of them had been previously classified as constitutional heterozygotes, whereas in 30 no RB1 mutations had been found in lymphocytes. In 3 of these 30 patients, we have now identified low-level mosaic variants, varying in frequency between 8 and 24%. In 7 out of the 10 cases previously classified as heterozygous from testing blood cells, we were able to test additional tissues (ocular tissues, urine and/or oral mucosa): in three of them, next generation sequencing has revealed mosaicism. Present results thus confirm that a significant fraction (6/40; 15%) of sporadic retinoblastoma cases are due to postzygotic events and that deep sequencing is an efficient method to unambiguously distinguish mosaics. Re-testing of retinoblastoma patients through next generation sequencing can thus provide new information that may have important implications with respect to genetic counseling and family care.
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Mercer TR, Clark MB, Andersen SB, Brunck ME, Haerty W, Crawford J, Taft RJ, Nielsen LK, Dinger ME, Mattick JS. Genome-wide discovery of human splicing branchpoints. Genome Res 2015; 25:290-303. [PMID: 25561518 PMCID: PMC4315302 DOI: 10.1101/gr.182899.114] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
During the splicing reaction, the 5′ intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3′ splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron–exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.
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Affiliation(s)
- Tim R Mercer
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - Michael B Clark
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Stacey B Andersen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marion E Brunck
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Wilfried Haerty
- MRC Functional Genomics Unit, Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia; Illumina, Inc., San Diego, California 92122, USA; School of Medicine and Health Services, Department of Integrated Systems Biology and Department of Pediatrics, George Washington University, Washington DC 20037, USA
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia
| | - John S Mattick
- Garvan Institute of Medical Research, Sydney, New South Wales 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Australia, Sydney, New South Wales 2052, Australia;
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Schedler KJE, Traine PG, Lohmann DR, Haritoglou C, Metz KA, Rodrigues EB. Hereditary Diffuse Infiltrating Retinoblastoma. Ophthalmic Genet 2014; 37:95-7. [PMID: 24892564 DOI: 10.3109/13816810.2014.921315] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Retinoblastoma is one of the most common childhood cancers. The diffuse infiltrating retinoblastoma is a rare subtype of this neoplasm. The majority of cases of diffuse infiltrating retinoblastoma are unilateral and occur sporadically. Herein we report on a family with three children affected by retinoblastoma, among them one girl with diffuse infiltrating retinoblastoma. This girl was diagnosed at the age of 8 years with a unilateral diffuse infiltrating retinoblastoma. By contrast, the two brothers became clinically apparent in the first 2 years of life with bilateral retinoblastoma. The parents were clinically unremarkable. Genetic analysis of RB1 gene was performed. The girl with diffuse infiltrating RB was found to be heterozygous for an oncogenic mutation in the RB1 gene that was also carried by both brothers and the father of the family. These results show that diffuse infiltrating retinoblastoma can develop on the background of a hereditary predisposition to retinoblastoma.
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Affiliation(s)
| | - Peter G Traine
- a Department of Ophthalmology , Clinic Pallas , Olten , Switzerland
| | - Dietmar R Lohmann
- b Institute of Human Genetics, Faculty of Medicine, University Duisburg-Essen , Essen , Germany
| | - Christos Haritoglou
- c Department of Ophthalmology , Ludwig Maximilians University , Munich , Germany
| | - Klaus A Metz
- d Institute of Pathology and Neuropathology, Faculty of Medicine, University Duisburg-Essen , Essen , Germany , and
| | - Eduardo B Rodrigues
- e Department of Ophthalmology , Vision Institute - IPEPO, Federal University of São Paulo , São Paulo , Brazil
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Genetic testing in Tunisian families with heritable retinoblastoma using a low cost approach permits accurate risk prediction in relatives and reveals incomplete penetrance in adults. Exp Eye Res 2014; 124:48-55. [PMID: 24810223 DOI: 10.1016/j.exer.2014.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 04/01/2014] [Accepted: 04/18/2014] [Indexed: 01/16/2023]
Abstract
Heritable retinoblastoma is caused by oncogenic mutations in the RB1 tumor suppressor gene. Identification of these mutations in patients is important for genetic counseling and clinical management of relatives at risk. In order to lower analytical efforts, we designed a stepwise mutation detection strategy that was adapted to the spectrum of oncogenic RB1 gene mutations. We applied this strategy on 20 unrelated patients with familial and/or de novo bilateral retinoblastoma from Tunisia. In 19 (95%) patients, we detected oncogenic mutations including base substitutions, small length mutations, and large deletions. Further analyses on the origin of the mutations showed mutational mosaicism in one unilaterally affected father of a bilateral proband and incomplete penetrance in two mothers. In a large family with several retinoblastoma patients, the mutation identified in the index patient was also detected in several non-penetrant relatives. RNA analyses showed that this mutation results in an in-frame loss of exon 9. In summary, our strategy can serve as a model for RB1 mutation identification with high analytical sensitivity. Our results point out that genetic testing is needed to reveal or exclude incomplete penetrance specifically in parents of patients with sporadic disease.
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Dommering CJ, Mol BM, Moll AC, Burton M, Cloos J, Dorsman JC, Meijers-Heijboer H, van der Hout AH. RB1 mutation spectrum in a comprehensive nationwide cohort of retinoblastoma patients. J Med Genet 2014; 51:366-74. [PMID: 24688104 DOI: 10.1136/jmedgenet-2014-102264] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Retinoblastoma (Rb) is a childhood cancer of the retina, commonly initiated by biallelic inactivation of the RB1 gene. Knowledge of the presence of a heritable RB1 mutation can help in risk management and reproductive decision making. We report here on RB1 mutation scanning in a unique nationwide cohort of Rb patients from the Netherlands. METHODS From the 1173 Rb patients registered in the Dutch National Retinoblastoma Register until January 2013, 529 patients from 433 unrelated families could be included. RB1 mutation scanning was performed with different detection methods, depending on the time period. RESULTS Our mutation detection methods revealed RB1 mutations in 92% of bilateral and/or familial Rb patients and in 10% of non-familial unilateral cases. Overall an RB1 germline mutation was detected in 187 (43%) of 433 Rb families, including 33 novel mutations. The distribution of the type of mutation was 37% nonsense, 20% frameshift, 21% splice, 9% large indel, 5% missense, 7% chromosomal deletions and 1% promoter. Ten per cent of patients were mosaic for the RB1 mutation. Six three-generation families with incomplete penetrance RB1 mutations were found. We found evidence that two variants, previously described as pathogenic RB1 mutations, are likely to be neutral variants. CONCLUSIONS The frequency of the type of mutations in the RB1 gene in our unbiased national cohort is the same as the mutation spectrum described worldwide. Furthermore, our RB1 mutation detection regimen achieves a high scanning sensitivity.
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Affiliation(s)
- Charlotte J Dommering
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Berber M Mol
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Annette C Moll
- Department of Ophthalmology, VU University Medical Center, Amsterdam, The Netherlands
| | - Margaret Burton
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jacqueline Cloos
- Department of Hematology, VU University Medical Center, Amsterdam, The Netherlands Department of Pediatric Oncology/Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Annemarie H van der Hout
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Oltean S, Bates DO. Hallmarks of alternative splicing in cancer. Oncogene 2013; 33:5311-8. [PMID: 24336324 DOI: 10.1038/onc.2013.533] [Citation(s) in RCA: 451] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 11/04/2013] [Accepted: 11/04/2013] [Indexed: 12/17/2022]
Abstract
The immense majority of genes are alternatively spliced and there are many isoforms specifically associated with cancer progression and metastasis. The splicing pattern of specific isoforms of numerous genes is altered as cells move through the oncogenic process of gaining proliferative capacity, acquiring angiogenic, invasive, antiapoptotic and survival properties, becoming free from growth factor dependence and growth suppression, altering their metabolism to cope with hypoxia, enabling them to acquire mechanisms of immune escape, and as they move through the epithelial-mesenchymal and mesenchymal-epithelial transitions and metastasis. Each of the 'hallmarks of cancer' is associated with a switch in splicing, towards a more aggressive invasive cancer phenotype. The choice of isoforms is regulated by several factors (signaling molecules, kinases, splicing factors) currently being identified systematically by a number of high-throughput, independent and unbiased methodologies. Splicing factors are de-regulated in cancer, and in some cases are themselves oncogenes or pseudo-oncogenes and can contribute to positive feedback loops driving cancer progression. Tumour progression may therefore be associated with a coordinated splicing control, meaning that there is the potential for a relatively small number of splice factors or their regulators to drive multiple oncogenic processes. The understanding of how splicing contributes to the various phenotypic traits acquired by tumours as they progress and metastasise, and in particular how alternative splicing is coordinated, can and is leading to the development of a new class of anticancer therapeutics-the alternative-splicing inhibitors.
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Affiliation(s)
- S Oltean
- School of Physiology and Pharmacology, University of Bristol, Bristol, UK
| | - D O Bates
- Division of Pre-clinical Oncology, School of Clinical Sciences, University of Nottingham, Queen's Medical Center, Nottingham, UK
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Price EA, Price K, Kolkiewicz K, Hack S, Reddy MA, Hungerford JL, Kingston JE, Onadim Z. Spectrum of RB1 mutations identified in 403 retinoblastoma patients. J Med Genet 2013; 51:208-14. [PMID: 24225018 DOI: 10.1136/jmedgenet-2013-101821] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Retinoblastoma (RB) is a malignant, childhood tumour of the developing retina that occurs with an estimated frequency of 1 in 20 000. Identification of oncogenic mutations in the RB1 gene aids in the clinical management of families with a heritable predisposition to RB. Here we present the spectrum of genetic and epigenetic changes identified in 194 tumours and 209 blood samples, from 403 unrelated RB patients. METHODS Mutation screening was carried out across all 27 RB1 exons and their associated splice sites. Small coding sequence changes were detected using fluorescent conformation analysis followed by sequencing. Large exonic deletions were detected by quantitative fluorescent PCR. Methylation specific PCR of the RB1 promoter was performed to detect epigenetic alterations. Polymorphism analysis was used to determine loss of heterozygosity in tumour samples. RESULTS 95% of the expected mutations were identified in the tumour samples, with 16 samples exhibiting only one mutation, while two samples had no detectable RB1 mutation. 96% of bilateral/familial RB blood samples and 9.5% of unilateral sporadic blood samples, yielded mutations. 111 were novel mutations. CONCLUSIONS The full range of screening techniques is required to achieve a high screening sensitivity in RB patients.
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Affiliation(s)
- Elizabeth A Price
- Retinoblastoma Genetic Screening Unit, Barts Health NHS Trust, London, UK
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Dommering CJ, Marees T, van der Hout AH, Imhof SM, Meijers-Heijboer H, Ringens PJ, van Leeuwen FE, Moll AC. RB1 mutations and second primary malignancies after hereditary retinoblastoma. Fam Cancer 2012; 11:225-33. [PMID: 22205104 PMCID: PMC3365233 DOI: 10.1007/s10689-011-9505-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Survivors of hereditary retinoblastoma have a high risk of second primary malignancies, but it has not been investigated whether specific RB1 germline mutations are associated with greater risk of second primary malignancies in a large cohort. We conducted a retrospective cohort study of 199 survivors of hereditary retinoblastoma with a documented RB1 germline mutation diagnosed between 1905 and 2005. In total, 44 hereditary retinoblastoma survivors developed a second primary malignancy after a median follow-up of 30.2 years (range 1.33-76.0). A significantly increased risk of second primary malignancy was observed among carriers of one of the 11 recurrent CGA>TGA nonsense RB1 mutations (hazard ratio (HR) = 3.53; [95% confidence interval (CI) = 1.82-6.84]; P = .000), and there was a significantly lower risk for subjects with a low penetrance mutation (HR = .19; [95% CI = .05-.81]; P = .025). Our findings suggest a genotype-phenotype correlation for second primary cancers of retinoblastoma survivors and may impact on long-term surveillance protocols of patients with hereditary retinoblastoma, if confirmed by future studies.
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Affiliation(s)
- Charlotte J Dommering
- Department of Clinical Genetics, VU University Medical Center, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.
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Spier I, Horpaopan S, Vogt S, Uhlhaas S, Morak M, Stienen D, Draaken M, Ludwig M, Holinski-Feder E, Nöthen MM, Hoffmann P, Aretz S. Deep intronic APC mutations explain a substantial proportion of patients with familial or early-onset adenomatous polyposis. Hum Mutat 2012; 33:1045-50. [PMID: 22431159 DOI: 10.1002/humu.22082] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 03/05/2012] [Indexed: 01/13/2023]
Abstract
To uncover pathogenic deep intronic variants in patients with colorectal adenomatous polyposis, in whom no germline mutation in the APC or MUTYH genes can be identified by routine diagnostics, we performed a systematic APC messenger RNA analysis in 125 unrelated mutation-negative cases. Overall, we identified aberrant transcripts in 8% of the patients (familial cases 30%; early-onset manifestation 21%). In eight of them, two different out-of-frame pseudoexons were found consisting of a 167-bp insertion from intron 4 in five families with a shared founder haplotype and a 83-bp insertion from intron 10 in three patients. The pseudoexon formation was caused by three different heterozygous germline mutations, which are supposed to activate cryptic splice sites. In conclusion, a few deep intronic mutations contribute substantially to the APC mutation spectrum. Complementary DNA analysis and/or target sequencing of intronic regions should be considered as an additional mutation discovery approach in polyposis patients.
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Affiliation(s)
- Isabel Spier
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Strasse 25,Bonn, Germany.
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Abstract
Analysis of RB1 mRNA from blood leukocytes of patients with retinoblastoma identified the effects of mutations involving consensus splice site, exonic substitution and whole-exon deletions identified in genomic DNA of these patients. In addition, this study identified mutations in cases in which no mutations were detectable in the genomic DNA. One proband had mutation at the canonical splice site at +5 position of IVS22, and analysis of the transcripts in this family revealed skipping of exon 22 in three members of this family. In one proband, a missense substitution of c.652T greater than G (g.56897T greater than G; Leu218Val) in exon 7 led to splicing aberrations involving deletions of exons 7 and 8, suggesting the formation of a cryptic splice site. In two probands with no detectable changes in the genomic DNA upon screening of RB1 exons and flanking intronic sequences, transcripts were found to have deletions of exon 6 in one, and exons 21 and 22 in another family. In two probands, RNA analysis confirmed genomic deletions involving one or more exons. This study reveals novel effects of RB1 mutations on splicing and suggests the utility of RNA analysis as an adjunct to mutational screening of genomic DNA in retinoblastoma.
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RB1 gene mutations in Iranian patients with retinoblastoma: report of four novel mutations. Cancer Genet 2011; 204:316-22. [PMID: 21763628 DOI: 10.1016/j.cancergen.2011.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 04/18/2011] [Accepted: 04/25/2011] [Indexed: 11/23/2022]
Abstract
Mutations in the RB1 gene lead to retinoblastoma, which is the most common intraocular tumor in children under the age of 6. In the present survey, the mutations of 18 unrelated Iranian retinoblastoma patients were characterized. Mutation analysis of the RB1 gene was performed in patients by sequencing all coding regions and by multiplex ligation probe-dependent amplification analysis. Clinical signs and symptoms of the retinoblastoma patients were similar to those of previously described patients with retinoblastoma. Eight known mutations and four novel mutations (c.832_833insT, c.1943delC, c.1206C>T, and c.2029delG) were determined. In silico analysis of the c.1206C>T variant showed that exon 12 contained an SC-35 consensus sequence, and this variation disrupted the splicing enhancer element and caused skipping of exon 12. Molecular genetic testing of retinoblastoma patients greatly affects the genetic counseling of the families involved, as well as the management of the disease in patients and at-risk relatives.
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Hung CC, Lin SY, Lee CN, Chen CP, Lin SP, Chao MC, Chiou SS, Su YN. Low penetrance of retinoblastoma for p.V654L mutation of the RB1 gene. BMC MEDICAL GENETICS 2011; 12:76. [PMID: 21615945 PMCID: PMC3119181 DOI: 10.1186/1471-2350-12-76] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 05/26/2011] [Indexed: 02/07/2023]
Abstract
Background Retinoblastoma is caused by compound heterozygosity or homozygosity of retinoblastoma gene (RB1) mutations. In germline retinoblastoma, mutations in the RB1 gene predispose individuals to increased cancer risks during development. These mutations segregate as autosomal dominant traits with high penetrance (90%). Methods We screened 30 family members from one family using high resolution melting assay and DNA direct sequencing for mutations in the RB1 gene. We evaluate the phenotype and penetrance of germline mutations of the RB1 gene in a large Taiwanese family. Results The molecular analysis and clinical details of this family showed phenotypic variability associated with the p.V654L mutation in exon 19 of the RB1 gene in 11 family members. The phenotype varied from asymptomatic to presence of a unilateral tumor. Only four individuals (2 males and 2 females) developed unilateral retinoblastoma, which resulted in calculated low penetrance of 36% (4/11). The four individuals with retinoblastoma were diagnosed before the age of three years. None of their relatives exhibited variable severity or bilateral retinoblastoma. Conclusions The diseased-eye ratio for this family was 0.36, which is lower than current estimates. This suggests that the RB1 p.V654L mutation is a typical mutation associated with low penetrance.
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Affiliation(s)
- Chia-Cheng Hung
- Graduate Institute of Clinical Genomics, National Taiwan University College of Medicine, Taipei, Taiwan
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Mucaki EJ, Ainsworth P, Rogan PK. Comprehensive prediction of mRNA splicing effects of BRCA1 and BRCA2 variants. Hum Mutat 2011; 32:735-42. [DOI: 10.1002/humu.21513] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Accepted: 04/08/2011] [Indexed: 12/17/2022]
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Ríos Y, Melmed S, Lin S, Liu NA. Zebrafish usp39 mutation leads to rb1 mRNA splicing defect and pituitary lineage expansion. PLoS Genet 2011; 7:e1001271. [PMID: 21249182 PMCID: PMC3020934 DOI: 10.1371/journal.pgen.1001271] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 12/08/2010] [Indexed: 11/30/2022] Open
Abstract
Loss of retinoblastoma (Rb) tumor suppressor function is associated with human malignancies. Molecular and genetic mechanisms responsible for tumorigenic Rb downregulation are not fully defined. Through a forward genetic screen and positional cloning, we identified and characterized a zebrafish ubiquitin specific peptidase 39 (usp39) mutation, the yeast and human homolog of which encodes a component of RNA splicing machinery. Zebrafish usp39 mutants exhibit microcephaly and adenohypophyseal cell lineage expansion without apparent changes in major hypothalamic hormonal and regulatory signals. Gene expression profiling of usp39 mutants revealed decreased rb1 and increased e2f4, rbl2 (p130), and cdkn1a (p21) expression. Rb1 mRNA overexpression, or antisense morpholino knockdown of e2f4, partially reversed embryonic pituitary expansion in usp39 mutants. Analysis of pre-mRNA splicing status of critical cell cycle regulators showed misspliced Rb1 pre-mRNA resulting in a premature stop codon. These studies unravel a novel mechanism for rb1 regulation by a neuronal mRNA splicing factor, usp39. Zebrafish usp39 regulates embryonic pituitary homeostasis by targeting rb1 and e2f4 expression, respectively, contributing to increased adenohypophyseal sensitivity to these altered cell cycle regulators. These results provide a mechanism for dysregulated rb1 and e2f4 pathways that may result in pituitary tumorigenesis. Previous studies have shown that Rb+/− mice develop pituitary adenomas; however, RB1 mutations have not been found in human pituitary tumors. In the present study, we uncovered a novel genetic pathway that may lead to Rb downregulation through RNA splicing mediated by usp39, a gene involved in assembly of the spliceosome. Our forward genetic study in zebrafish suggests that loss of usp39 results in aberrant rb1 mRNA splicing, which likely causes elevated expression of its target e2f4, a key regulator known to have oncogenic activity when overexpressed. We established that e2f4 upregulation is a main factor responsible for the adenohypophyseal cell lineage hyperplasia observed in the zebrafish usp39 mutant. It should be of interest to investigate if mutations or downregulation of USP39 would contribute to pituitary tumorigenesis in humans.
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Affiliation(s)
- Yesenia Ríos
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shlomo Melmed
- Department of Medicine, Cedars-Sinai Medical Center, University of California Los Angeles, Los Angeles, California, United States of America
| | - Shuo Lin
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (SL); (NAL)
| | - Ning-Ai Liu
- Department of Medicine, Cedars-Sinai Medical Center, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail: (SL); (NAL)
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Chen CY, Xu CM, Du ZF, Chen XL, Ren GL, Zhang XN. A c.1363C>T (p.R455X) nonsense mutation of RB1 gene in a southern Chinese retinoblastoma pedigree. Genet Test Mol Biomarkers 2010; 14:193-6. [PMID: 20059380 DOI: 10.1089/gtmb.2009.0162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Retinoblastoma (RB) is the most common malignant intraocular tumor in children. Fifty percent of RB patients are carriers of a predisposing germline mutation with high penetrance. RB1 has been identified as the only pathological gene. We present the rapid detection of an RB1 gene mutation in a Han pedigree of two RB patients from southern China. Total RNA was extracted from whole blood for reverse transcriptase-polymerase chain reaction (PCR) to analyze RB1 transcripts, and genomic DNA for PCR and direct sequencing to test RB1 exons. Allele-specific PCR was used to verify the mutation. The results showed that the bilaterally affected son and the unilaterally affected father were both heterozygous for the nonsense mutation c.1363C>T (p.R455X) in exon 14 of RB1. Our studies suggest the molecular basis of RB in this Chinese family and provide further evidence that codon 455 is one of the recurrent spots for mutations in RB1.
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Affiliation(s)
- Chun-Yue Chen
- Department of Biochemistry and Genetics, National Education Base for Basic Medical Sciences, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
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Khan SG, Yamanegi K, Zheng ZM, Boyle J, Imoto K, Oh KS, Baker CC, Gozukara E, Metin A, Kraemer KH. XPC branch-point sequence mutations disrupt U2 snRNP binding, resulting in abnormal pre-mRNA splicing in xeroderma pigmentosum patients. Hum Mutat 2010; 31:167-75. [PMID: 19953607 DOI: 10.1002/humu.21166] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mutations in two branch-point sequences (BPS) in intron 3 of the XPC DNA repair gene affect pre-mRNA splicing in association with xeroderma pigmentosum (XP) with many skin cancers (XP101TMA) or no skin cancer (XP72TMA), respectively. To investigate the mechanism of these abnormalities we now report that transfection of minigenes with these mutations revealed abnormal XPC pre-mRNA splicing that mimicked pre-mRNA splicing in the patients' cells. DNA oligonucleotide-directed RNase H digestion demonstrated that mutations in these BPS disrupt U2 snRNP-BPS interaction. XP101TMA cells had no detectable XPC protein but XP72TMA had 29% of normal levels. A small amount of XPC protein was detected at sites of localized ultraviolet (UV)-damaged DNA in XP72TMA cells which then recruited other nucleotide excision repair (NER) proteins. In contrast, XP101TMA cells had no detectable recruitment of XPC or other NER proteins. Post-UV survival and photoproduct assays revealed greater reduction in DNA repair in XP101TMA cells than in XP72TMA. Thus mutations in XPC BPS resulted in disruption of U2 snRNP-BPS interaction leading to abnormal pre-mRNA splicing and reduced XPC protein. At the cellular level these changes were associated with features of reduced DNA repair including diminished NER protein recruitment, reduced post-UV survival and impaired photoproduct removal.
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Affiliation(s)
- Sikandar G Khan
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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Abstract
Retinoblastoma (Rb) is a malignant tumor that originates from developing retina. Diagnosis based on clinical signs and symptoms and is usually made in children under the age of five years. Mutations in both alleles of the RB1 gene are a prerequisite for this tumor to develop. In most patients with sporadic unilateral Rb, both RB1 gene mutations occur in somatic cells and are not passed over to offspring (nonhereditary Rb). Almost all patients with sporadic bilateral and virtually all patients with familial Rb are heterozygous for RB1 gene mutations that cause predisposition to Rb (hereditary Rb). In families, Rb predisposition is transmitted as an autosomal dominant trait (familial Rb). In addition to Rb, patients with hereditary disease also have an increased risk of tumors outside the eye (second cancer). This risk is enhanced in patients who have received external beam radiotherapy. Analysis of genotype-phenotype associations has shown that the mean number of tumor foci that develop in carriers of mutant RB1 alleles is variable depending on which functions of the normal allele are retained and to what extent. Moreover, phenotypic expression of hereditary retinoblastoma is subject to genetic modification. Identification of the genetic factors that underlie these effects will not only help to arrive at a more precise prognosis but may also point to mechanisms that can be used to reduce the risk of tumor development.
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Affiliation(s)
- Dietmar Lohmann
- Institut fur Humangenetik, Universitatsklinikum Essen, Hufelandstrasse 55, D-45122 Essen, Germany.
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Castelino-Prabhu S, Stoll LM, Li QK. Metastatic retinoblastoma presenting as a left shoulder soft tissue mass: FNA findings and review of the literature. Diagn Cytopathol 2009; 38:440-6. [PMID: 19937945 DOI: 10.1002/dc.21252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Retinoblastoma is a relatively rare malignant pediatric tumor accounting for approximately 3% of childhood cancers and 1% of all cancer deaths in children under 15 years of age. During the clinical course of the disease, a metastasis usually occurs within the first year of diagnosis and is seen in 2% of retinoblastoma patients. Metastases to the intracranial region are common and account for approximately 50% of the metastatic cases. Metastasis to the soft tissue is very rare. Herein, we report a case of metastatic retinoblastoma presenting as a left shoulder soft tissue mass in a 14-year-old female with a 14-year history of familial bilateral retinoblastoma status post radiation therapy. In our case, the FNA cytology shows some features of the small round blue cell tumor group with inconspicuous Flexner-Wintersteiner or Homer-Right rosette formation. The unusual clinical presentation and morphology give rise to a diagnostic dilemma, with the differential diagnosis centering on the small round blue cell tumors such as lymphoma, rhabdomyosarcoma, nephroblastoma (Wilms' tumor), Ewing's sarcoma/PNET, and desmoplastic small round cell tumor. It also prompts concern for the development of a second primary tumor. The purpose of our study is to discuss the FNA cytology of metastatic retinoblastoma, its differential diagnoses, and the utility of immunohistochemistry. An accurate diagnosis is imperative due to the differences in prognosis and treatment implications for the various diseases.
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Affiliation(s)
- Shobha Castelino-Prabhu
- Division of Cytopathology, Department of Pathology, The Johns Hopkins Hospital, Baltimore, Maryland 21287, USA
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Bibliography. Current world literature. Curr Opin Ophthalmol 2009; 20:417-22. [PMID: 19684489 DOI: 10.1097/icu.0b013e32833079c5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rushlow D, Piovesan B, Zhang K, Prigoda-Lee NL, Marchong MN, Clark RD, Gallie BL. Detection of mosaic RB1 mutations in families with retinoblastoma. Hum Mutat 2009; 30:842-51. [PMID: 19280657 DOI: 10.1002/humu.20940] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The RB1 gene mutation detection rate in 1,020 retinoblastoma families was increased by the use of highly sensitive allele specific-PCR (AS-PCR) to detect low-level mosaicism for 11 recurrent RB1 CGA>TGA nonsense mutations. For bilaterally affected probands, AS-PCR increased the RB1 mutation detection sensitivity from 92.6% to 94.8%. Both RB1 oncogenic changes were detected in 92.7% of sporadic unilateral tumors (357/385); 14.6% (52/357) of unilateral probands with both tumor mutations identified carried one of the tumor mutations in blood. Mosaicism was evident in 5.5% of bilateral probands (23 of 421), in 3.8% of unilateral probands (22 of 572), and in one unaffected mother of a unilateral proband. Half of the mosaic mutations were only detectable by AS-PCR for the 11 recurrent CGA>TGA mutations, and not by standard sequencing. This suggests that significant numbers of low-level mosaics with other classes of RB1 mutations remain unidentified by current technology. We show that the use of linkage analysis in a two-generation retinoblastoma family resulted in the erroneous conclusion that a child carried the parental mutation, because the founder parent was mosaic for the RB1 mutation. Of 142 unaffected parental pairs tested, only one unaffected parent of a proband (0.7%) showed somatic mosaicism for the proband's mutation, in contrast to an overall 4.5% somatic mosaicism rate for retinoblastoma probands, suggesting that mosaicism for an RB1 mutation is highly likely to manifest as retinoblastoma.
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Affiliation(s)
- Diane Rushlow
- Retinoblastoma Solutions, Toronto Western Hospital, Toronto, Ontario, Canada
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