51
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Davy G, Rousselin A, Goardon N, Castéra L, Harter V, Legros A, Muller E, Fouillet R, Brault B, Smirnova AS, Lemoine F, de la Grange P, Guillaud-Bataille M, Caux-Moncoutier V, Houdayer C, Bonnet F, Blanc-Fournier C, Gaildrat P, Frebourg T, Martins A, Vaur D, Krieger S. Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer. Eur J Hum Genet 2017; 25:1147-1154. [PMID: 28905878 DOI: 10.1038/ejhg.2017.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/13/2017] [Accepted: 06/13/2017] [Indexed: 12/15/2022] Open
Abstract
Interpretation of variants of unknown significance (VUS) is a major challenge for laboratories performing molecular diagnosis of hereditary breast and ovarian cancer (HBOC), especially considering that many genes are now known to be involved in this syndrome. One important way these VUS can have a functional impact is through their effects on RNA splicing. Here we present a custom RNA-Seq assay plus bioinformatics and biostatistics pipeline to analyse specifically alternative and abnormal splicing junctions in 11 targeted HBOC genes. Our pipeline identified 14 new alternative splices in BRCA1 and BRCA2 in addition to detecting the majority of known alternative spliced transcripts therein. We provide here the first global splicing pattern analysis for the other nine genes, which will enable a comprehensive interpretation of splicing defects caused by VUS in HBOC. Previously known splicing alterations were consistently detected, occasionally with a more complex splicing pattern than expected. We also found that splicing in the 11 genes is similar in blood and breast tissue, supporting the utility and simplicity of blood splicing assays. Our pipeline is ready to be integrated into standard molecular diagnosis for HBOC, but it could equally be adapted for an integrative analysis of any multigene disorder.
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Affiliation(s)
- Grégoire Davy
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Antoine Rousselin
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Nicolas Goardon
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Laurent Castéra
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Valentin Harter
- Cancéropôle Nord-Ouest Data Processing Centre, CLCC François Baclesse, Caen, France
| | - Angelina Legros
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France
| | - Etienne Muller
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Robin Fouillet
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France
| | - Baptiste Brault
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Anna S Smirnova
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Fréderic Lemoine
- GenoSplice Technology, iPEPS-ICM, Pitié-Salpétrière Hospital, Paris, France
| | | | | | | | - Claude Houdayer
- Department of Genetics, Institut Curie, Paris, France.,Inserm U830, Paris, France.,Université Paris-Descartes, Sorbonne Paris Cité, Paris, France
| | - Françoise Bonnet
- Laboratory of Molecular Genetics, Institut Bergonié, Bordeaux, France
| | - Cécile Blanc-Fournier
- Department of Pathology, CLCC François Baclesse, Caen, France.,Tumorothèque de Caen Basse-Normandie, Caen, France
| | - Pascaline Gaildrat
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Thierry Frebourg
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Dominique Vaur
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Sophie Krieger
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.,University of Caen Normandy, Caen, France
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52
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Wang Y, Bernhardy AJ, Cruz C, Krais JJ, Nacson J, Nicolas E, Peri S, van der Gulden H, van der Heijden I, O'Brien SW, Zhang Y, Harrell MI, Johnson SF, Candido Dos Reis FJ, Pharoah PDP, Karlan B, Gourley C, Lambrechts D, Chenevix-Trench G, Olsson H, Benitez JJ, Greene MH, Gore M, Nussbaum R, Sadetzki S, Gayther SA, Kjaer SK, D'Andrea AD, Shapiro GI, Wiest DL, Connolly DC, Daly MB, Swisher EM, Bouwman P, Jonkers J, Balmaña J, Serra V, Johnson N. The BRCA1-Δ11q Alternative Splice Isoform Bypasses Germline Mutations and Promotes Therapeutic Resistance to PARP Inhibition and Cisplatin. Cancer Res 2017; 76:2778-90. [PMID: 27197267 DOI: 10.1158/0008-5472.can-16-0186] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/15/2016] [Indexed: 12/19/2022]
Abstract
Breast and ovarian cancer patients harboring BRCA1/2 germline mutations have clinically benefitted from therapy with PARP inhibitor (PARPi) or platinum compounds, but acquired resistance limits clinical impact. In this study, we investigated the impact of mutations on BRCA1 isoform expression and therapeutic response. Cancer cell lines and tumors harboring mutations in exon 11 of BRCA1 express a BRCA1-Δ11q splice variant lacking the majority of exon 11. The introduction of frameshift mutations to exon 11 resulted in nonsense-mediated mRNA decay of full-length, but not the BRCA1-Δ11q isoform. CRISPR/Cas9 gene editing as well as overexpression experiments revealed that the BRCA1-Δ11q protein was capable of promoting partial PARPi and cisplatin resistance relative to full-length BRCA1, both in vitro and in vivo Furthermore, spliceosome inhibitors reduced BRCA1-Δ11q levels and sensitized cells carrying exon 11 mutations to PARPi treatment. Taken together, our results provided evidence that cancer cells employ a strategy to remove deleterious germline BRCA1 mutations through alternative mRNA splicing, giving rise to isoforms that retain residual activity and contribute to therapeutic resistance. Cancer Res; 76(9); 2778-90. ©2016 AACR.
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Affiliation(s)
- Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Andrea J Bernhardy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Cristina Cruz
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain. Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Joseph Nacson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Emmanuelle Nicolas
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Suraj Peri
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | | | - Shane W O'Brien
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yong Zhang
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Maribel I Harrell
- Department of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, Washington
| | - Shawn F Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Francisco J Candido Dos Reis
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil. Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Beth Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Charlie Gourley
- University of Edinburgh Cancer Research UK Centre, MRC IGMM, Edinburgh, United Kingdom
| | | | | | - Håkan Olsson
- Departments of Cancer Epidemiology and Oncology, Lund University, Lund, Sweden
| | - Javier J Benitez
- Human Genetics Group and Human Genotyping Unit Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark H Greene
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Martin Gore
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Robert Nussbaum
- University of California San Francisco, Cancer Risk Program, San Francisco, California
| | - Siegal Sadetzki
- Gertner Institute for Epidemiology and Health Policy Research, Sheba Medical Center, Tel Hashomer, Israel
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. Department of Pediatrics, Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David L Wiest
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Denise C Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mary B Daly
- Risk Assessment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, Washington
| | - Peter Bouwman
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jos Jonkers
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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53
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Gradishar W, Johnson K, Brown K, Mundt E, Manley S. Clinical Variant Classification: A Comparison of Public Databases and a Commercial Testing Laboratory. Oncologist 2017; 22:797-803. [PMID: 28408614 PMCID: PMC5507641 DOI: 10.1634/theoncologist.2016-0431] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/05/2017] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND There is a growing move to consult public databases following receipt of a genetic test result from a clinical laboratory; however, the well-documented limitations of these databases call into question how often clinicians will encounter discordant variant classifications that may introduce uncertainty into patient management. Here, we evaluate discordance in BRCA1 and BRCA2 variant classifications between a single commercial testing laboratory and a public database commonly consulted in clinical practice. MATERIALS AND METHODS BRCA1 and BRCA2 variant classifications were obtained from ClinVar and compared with the classifications from a reference laboratory. Full concordance and discordance were determined for variants whose ClinVar entries were of the same pathogenicity (pathogenic, benign, or uncertain). Variants with conflicting ClinVar classifications were considered partially concordant if ≥1 of the listed classifications agreed with the reference laboratory classification. RESULTS Four thousand two hundred and fifty unique BRCA1 and BRCA2 variants were available for analysis. Overall, 73.2% of classifications were fully concordant and 12.3% were partially concordant. The remaining 14.5% of variants had discordant classifications, most of which had a definitive classification (pathogenic or benign) from the reference laboratory compared with an uncertain classification in ClinVar (14.0%). CONCLUSION Here, we show that discrepant classifications between a public database and single reference laboratory potentially account for 26.7% of variants in BRCA1 and BRCA2. The time and expertise required of clinicians to research these discordant classifications call into question the practicality of checking all test results against a database and suggest that discordant classifications should be interpreted with these limitations in mind. IMPLICATIONS FOR PRACTICE With the increasing use of clinical genetic testing for hereditary cancer risk, accurate variant classification is vital to ensuring appropriate medical management. There is a growing move to consult public databases following receipt of a genetic test result from a clinical laboratory; however, we show that up to 26.7% of variants in BRCA1 and BRCA2 have discordant classifications between ClinVar and a reference laboratory. The findings presented in this paper serve as a note of caution regarding the utility of database consultation.
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Affiliation(s)
- William Gradishar
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
| | - KariAnne Johnson
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
| | - Krystal Brown
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
| | - Erin Mundt
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
| | - Susan Manley
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Myriad Genetic Laboratories, Inc., Salt Lake City, Utah, USA
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54
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Byrjalsen A, Steffensen AY, Hansen TVO, Wadt K, Gerdes AM. Classification of the spliceogenic BRCA1 c.4096+3A>G variant as likely benign based on cosegregation data and identification of a healthy homozygous carrier. Clin Case Rep 2017; 5:876-879. [PMID: 28588830 PMCID: PMC5458035 DOI: 10.1002/ccr3.944] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 12/06/2016] [Accepted: 03/13/2017] [Indexed: 12/16/2022] Open
Abstract
BRCA1, c.4096+3A>G was identified in a consanguineous Danish family with several cases of breast/ovarian cancer. In silico analysis and splicing assays indicated that the variant caused aberrant splicing. However, based on segregation data and the finding of a healthy homozygous carrier, we classify the BRCA1 c.4096+3A>G variant as likely benign.
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Affiliation(s)
- Anna Byrjalsen
- Department of Clinical Genetics Copenhagen University Hospital Copenhagen Denmark
| | - Ane Y Steffensen
- Center for Genomic Medicine Copenhagen University Hospital Copenhagen Denmark
| | - Thomas V O Hansen
- Center for Genomic Medicine Copenhagen University Hospital Copenhagen Denmark
| | - Karin Wadt
- Department of Clinical Genetics Copenhagen University Hospital Copenhagen Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics Copenhagen University Hospital Copenhagen Denmark
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55
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Chakravorty S, Hegde M. Gene and Variant Annotation for Mendelian Disorders in the Era of Advanced Sequencing Technologies. Annu Rev Genomics Hum Genet 2017; 18:229-256. [PMID: 28415856 DOI: 10.1146/annurev-genom-083115-022545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations. We describe the emerging field of translational functional genomics, which integrates other functional "-omics" approaches that support next-generation sequencing genomic data in order to facilitate personalized diagnostics, disease management, biomarker discovery, and medicine. We also discuss the utility of this integrated approach for diagnostic clinics and medical databases and its role in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
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56
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Ocana A, Pandiella A. Targeting oncogenic vulnerabilities in triple negative breast cancer: biological bases and ongoing clinical studies. Oncotarget 2017; 8:22218-22234. [PMID: 28108739 PMCID: PMC5400659 DOI: 10.18632/oncotarget.14731] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
Triple negative breast cancer (TNBC) is still an incurable disease despite the great scientific effort performed during the last years. The huge heterogeneity of this disease has motivated the evaluation of a great number of therapies against different molecular alterations. In this article, we review the biological bases of this entity and how the known molecular evidence supports the current preclinical and clinical development of new therapies. Special attention will be given to ongoing clinical studies and potential options for future drug combinations.
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Affiliation(s)
- Alberto Ocana
- Unidad de Investigación Traslacional, Hospital Universitario de Albacete, Universidad de Castilla La Mancha, Albacete, Spain
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer and CIBERONC. CSIC-Universidad de Salamanca, Salamanca, Spain
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57
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Functional classification of DNA variants by hybrid minigenes: Identification of 30 spliceogenic variants of BRCA2 exons 17 and 18. PLoS Genet 2017; 13:e1006691. [PMID: 28339459 PMCID: PMC5384790 DOI: 10.1371/journal.pgen.1006691] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 04/07/2017] [Accepted: 03/14/2017] [Indexed: 11/30/2022] Open
Abstract
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction of variants of uncertain clinical significance (VUS) whose functional and clinical interpretations pose a challenge for genomic medicine. Likewise, an increasing amount of evidence indicates that genetic variants can have deleterious effects on pre-mRNA splicing. Our goal was to investigate the impact on splicing of a set of reported variants of BRCA2 exons 17 and 18 to assess their role in hereditary breast cancer and to identify critical regulatory elements that may constitute hotspots for spliceogenic variants. A splicing reporter minigene with BRCA2 exons 14 to-20 (MGBR2_ex14-20) was constructed in the pSAD vector. Fifty-two candidate variants were selected with splicing prediction programs, introduced in MGBR2_ex14-20 by site-directed mutagenesis and assayed in triplicate in MCF-7 cells. Wild type MGBR2_ex14-20 produced a stable transcript of the expected size (1,806 nucleotides) and structure (V1-[BRCA2_exons_14–20]–V2). Functional mapping by microdeletions revealed essential sequences for exon recognition on the 3’ end of exon 17 (c.7944-7973) and the 5’ end of exon 18 (c.7979-7988, c.7999-8013). Thirty out of the 52 selected variants induced anomalous splicing in minigene assays with >16 different aberrant transcripts, where exon skipping was the most common event. A wide range of splicing motifs were affected including the canonical splice sites (15 variants), novel alternative sites (3 variants), the polypyrimidine tract (3 variants) and enhancers/silencers (9 variants). According to the guidelines of the American College of Medical Genetics and Genomics (ACMG), 20 variants could be classified as pathogenic (c.7806-2A>G, c.7806-1G>A, c.7806-1G>T, c.7806-1_7806-2dup, c.7976+1G>A, c.7977-3_7978del, c.7977-2A>T, c.7977-1G>T, c.7977-1G>C, c.8009C>A, c.8331+1G>T and c.8331+2T>C) or likely pathogenic (c.7806-9T>G, c.7976G>C, c.7976G>A, c.7977-7C>G, c.7985C>G, c.8023A>G, c.8035G>T and c.8331G>A), accounting for 30.8% of all pathogenic/likely pathogenic variants of exons 17–18 at the BRCA Share database. The remaining 8 variants (c.7975A>G, c.7977-6T>G, c.7988A>T, c.7992T>A, c.8007A>G, c.8009C>T, c.8009C>G, and c.8072C>T) induced partial splicing anomalies with important ratios of the full-length transcript (≥70%), so that they remained classified as VUS. Aberrant splicing is therefore especially prevalent in BRCA2 exons 17 and 18 due to the presence of active ESEs involved in exon recognition. Splicing functional assays with minigenes are a valuable strategy for the initial characterization of the splicing outcomes and the subsequent clinical interpretation of variants of any disease-gene, although these results should be checked, whenever possible, against patient RNA. A significant proportion of disease-causing mutations of inherited disorders impair splicing. Massive sequencing projects of genetic diseases generate thousands of sequence variations that require functional and clinical interpretations. We have shown that splicing reporter minigenes of the breast cancer genes BRCA1 and BRCA2 are useful tools to functionally test DNA variants. In this work, we have constructed a 7-exon BRCA2 minigene (exons 14 to 20) where we mapped critical splicing regulatory sequences and tested 52 selected variants of exons 17 and 18 detected in breast cancer patients. We finely located three DNA segments on both exons that presumably contain splicing enhancer sequences. We observed that a total of 30 variants of any type disrupted the splicing patterns and, given the severity of their outcomes, we classified 20 of them as pathogenic or likely pathogenic. We also showed that a wide range of splicing elements were affected including canonical and novel 5’ and 3’ splice sites, the polypyrimidine tract and enhancer and silencer sequences. We concluded that splicing aberrations are frequent in Hereditary Breast and Ovarian Cancer and that minigenes are valuable tools to functionally classify DNA variants of any human disease gene under the splicing viewpoint.
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58
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Smith LD, Leme de Calais F, Raponi M, Mellone M, Buratti E, Blaydes JP, Baralle D. Novel splice-switching oligonucleotide promotes BRCA1 aberrant splicing and susceptibility to PARP inhibitor action. Int J Cancer 2017; 140:1564-1570. [PMID: 27997688 DOI: 10.1002/ijc.30574] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 11/10/2016] [Accepted: 12/05/2016] [Indexed: 01/02/2023]
Abstract
Tumors carrying hereditary mutations in BRCA1, which attenuate the BRCA1 DNA damage repair pathway, are more susceptible to dual treatment with PARP inhibitors and DNA damaging therapeutics. Conversely, breast cancer tumors with nonmutated functional BRCA1 are less sensitive to PARP inhibition. We describe a method that triggers susceptibility to PARP inhibition in BRCA1-functional tumor cells. BRCA1 exon 11 is a key for the function of BRCA1 in DNA damage repair. Analysis of the BRCA1 exon 11 splicing mechanism identified a key region within this exon which, when deleted, induced exon 11 skipping. An RNA splice-switching oligonucleotide (SSO) developed to target this region was shown to artificially stimulate skipping of exon 11 in endogenous BRCA1 pre-mRNA. SSO transfection rendered wild-type BRCA1 expressing cell lines more susceptible to PARP inhibitor treatment, as demonstrated by a reduction in cell survival at all SSO concentrations tested. Combined SSO and PARP inhibitor treatment increased γH2AX expression indicating that SSO-dependent skipping of BRCA1 exon 11 was able to promote DSBs and therefore synthetic lethality. In conclusion, this SSO provides a new potential therapeutic strategy for targeting BRCA1-functional breast cancer by enhancing the effect of PARP inhibitors.
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Affiliation(s)
- Lindsay D Smith
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK.,Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Flávia Leme de Calais
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Michela Raponi
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Massimiliano Mellone
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano, 99 34149, Trieste, Italy
| | - Jeremy P Blaydes
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
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59
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Nielsen FC, van Overeem Hansen T, Sørensen CS. Hereditary breast and ovarian cancer: new genes in confined pathways. Nat Rev Cancer 2016; 16:599-612. [PMID: 27515922 DOI: 10.1038/nrc.2016.72] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic abnormalities in the DNA repair genes BRCA1 and BRCA2 predispose to hereditary breast and ovarian cancer (HBOC). However, only approximately 25% of cases of HBOC can be ascribed to BRCA1 and BRCA2 mutations. Recently, exome sequencing has uncovered substantial locus heterogeneity among affected families without BRCA1 or BRCA2 mutations. The new pathogenic variants are rare, posing challenges to estimation of risk attribution through patient cohorts. In this Review article, we examine HBOC genes, focusing on their role in genome maintenance, the possibilities for functional testing of putative causal variants and the clinical application of new HBOC genes in cancer risk management and treatment decision-making.
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Affiliation(s)
- Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
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60
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de la Hoya M, Soukarieh O, López-Perolio I, Vega A, Walker LC, van Ierland Y, Baralle D, Santamariña M, Lattimore V, Wijnen J, Whiley P, Blanco A, Raponi M, Hauke J, Wappenschmidt B, Becker A, Hansen TVO, Behar R, Investigators KC, Niederacher D, Arnold N, Dworniczak B, Steinemann D, Faust U, Rubinstein W, Hulick PJ, Houdayer C, Caputo SM, Castera L, Pesaran T, Chao E, Brewer C, Southey MC, van Asperen CJ, Singer CF, Sullivan J, Poplawski N, Mai P, Peto J, Johnson N, Burwinkel B, Surowy H, Bojesen SE, Flyger H, Lindblom A, Margolin S, Chang-Claude J, Rudolph A, Radice P, Galastri L, Olson JE, Hallberg E, Giles GG, Milne RL, Andrulis IL, Glendon G, Hall P, Czene K, Blows F, Shah M, Wang Q, Dennis J, Michailidou K, McGuffog L, Bolla MK, Antoniou AC, Easton DF, Couch FJ, Tavtigian S, Vreeswijk MP, Parsons M, Meeks HD, Martins A, Goldgar DE, Spurdle AB. Combined genetic and splicing analysis of BRCA1 c.[594-2A>C; 641A>G] highlights the relevance of naturally occurring in-frame transcripts for developing disease gene variant classification algorithms. Hum Mol Genet 2016; 25:2256-2268. [PMID: 27008870 PMCID: PMC5081057 DOI: 10.1093/hmg/ddw094] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/10/2016] [Accepted: 03/17/2016] [Indexed: 12/13/2022] Open
Abstract
A recent analysis using family history weighting and co-observation classification modeling indicated that BRCA1 c.594-2A > C (IVS9-2A > C), previously described to cause exon 10 skipping (a truncating alteration), displays characteristics inconsistent with those of a high risk pathogenic BRCA1 variant. We used large-scale genetic and clinical resources from the ENIGMA, CIMBA and BCAC consortia to assess pathogenicity of c.594-2A > C. The combined odds for causality considering case-control, segregation and breast tumor pathology information was 3.23 × 10-8 Our data indicate that c.594-2A > C is always in cis with c.641A > G. The spliceogenic effect of c.[594-2A > C;641A > G] was characterized using RNA analysis of human samples and splicing minigenes. As expected, c.[594-2A > C; 641A > G] caused exon 10 skipping, albeit not due to c.594-2A > C impairing the acceptor site but rather by c.641A > G modifying exon 10 splicing regulatory element(s). Multiple blood-based RNA assays indicated that the variant allele did not produce detectable levels of full-length transcripts, with a per allele BRCA1 expression profile composed of ≈70-80% truncating transcripts, and ≈20-30% of in-frame Δ9,10 transcripts predicted to encode a BRCA1 protein with tumor suppression function.We confirm that BRCA1c.[594-2A > C;641A > G] should not be considered a high-risk pathogenic variant. Importantly, results from our detailed mRNA analysis suggest that BRCA-associated cancer risk is likely not markedly increased for individuals who carry a truncating variant in BRCA1 exons 9 or 10, or any other BRCA1 allele that permits 20-30% of tumor suppressor function. More generally, our findings highlight the importance of assessing naturally occurring alternative splicing for clinical evaluation of variants in disease-causing genes.
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Affiliation(s)
- Miguel de la Hoya
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - Omar Soukarieh
- Inserm U1079-IRIB, University of Rouen, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Irene López-Perolio
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - Ana Vega
- Fundacion Publica Galega de Medicina Xenómica-SERGAS Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela 15706, Spain
| | - Logan C Walker
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Yvette van Ierland
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton S016 5YA, UK
| | - Marta Santamariña
- CIBERER, Grupo de Medicina Xenómica-USC, Universidade de Santiago de Compostela, Fundacion Galega de Medicina Xenómica (SERGAS), Santiago de Compostela 15706, Spain
| | - Vanessa Lattimore
- Department of Pathology, University of Otago, Christchurch 8140, New Zealand
| | - Juul Wijnen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Philip Whiley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Ana Blanco
- Fundacion Publica Galega de Medicina Xenómica-SERGAS Grupo de Medicina Xenómica-USC, IDIS, CIBERER, Santiago de Compostela 15706, Spain
| | - Michela Raponi
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton S016 5YA, UK
| | - Jan Hauke
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Alexandra Becker
- Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Medical Faculty, University Hosptial Cologne, Cologne 50931, Germany
| | - Thomas V O Hansen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen DK-2100, Denmark
| | - Raquel Behar
- Molecular Oncology Laboratory, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Hospital Clinico San Carlos, Madrid, Spain
| | - KConFaB Investigators
- Peter MacCallum Cancer Center, University of Melbourne, Melbourne, VIC 3002, Australia
| | - Diether Niederacher
- Department of Gynaecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel 24105, Germany
| | - Bernd Dworniczak
- Institute of Human Genetics, University of Münster, Münster 48149, Germany
| | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover 30625, Germany
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University Hospital Tuebingen, Tuebingen 72076, Germany
| | | | - Peter J Hulick
- Center for Medical Genetics, NorthShore University Health System, University of Chicago Pritzker School of Medicine, Evanston, IL 60201, USA
| | - Claude Houdayer
- Service de Génétique, Department de Biologie des Tumeurs, Institut Curie and INSERM U830, Centre de Recherche de l'Institut Curie, Paris, and Universite Paris Descartes, Sorbonne Paris Cite, Paris 75248, France
| | - Sandrine M Caputo
- Service de Génétique, Department de Biologie des Tumeurs, Institut Curie, Paris 75248, France
| | - Laurent Castera
- Centre Francois Baclesse, Laboratoire de Biologie et de Genetique du Cancer, 14076 Caen, Paris 75248, France
| | | | | | - Carole Brewer
- Department of Clinical Genetics, Royal Devon and Exeter Hospital, Exeter, UK
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Christian F Singer
- Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria, Waehringer Guertel 18-20, A 1090 Vienna, Austria
| | - Jan Sullivan
- Genetic Health Service NZ, South Island Hub, Christchurch Hospital, Christchurch 8140, New Zealand
| | - Nicola Poplawski
- Adult Genetics Unit, South Australian Clinical Genetics Service, SA Pathology at the Women's and Children's Hospital, North Adelaide, SA 5067, Australia University Department of Paediatrics, University of Adelaide, North Terrace, Adelaide, SA 5000, Australia
| | - Phuong Mai
- Clinical Genetics Branch, DCEG, NCI, NIH, Bethesda, MD, USA
| | - Julian Peto
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, UK Division of Breast Cancer Research, Institute of Cancer Research, London SW3 6JB, UK
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany Molecular Epidemiology Group, German Cancer Research Center, DKFZ, Heidelberg 69120, Germany
| | - Harald Surowy
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany Molecular Epidemiology Group, German Cancer Research Center, DKFZ, Heidelberg 69120, Germany
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen 2730, Denmark Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev 2730, Denmark Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1165, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730 Denmark
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Sara Margolin
- Department of Oncology Pathology, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Paolo Radice
- Unit of "Molecular bases of genetic risk and genetic testing", Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano 20139, Italy
| | - Laura Galastri
- Associazione Volontari Italiani Sangue (AVIS) comunale di Milano, Milano 20139, Italy
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Graham G Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, VIC 3010, Australia Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Roger L Milne
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, VIC 3010, Australia Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada Department of Molecular Genetics, University of Toronto, M5B 1W8, Canada
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Fiona Blows
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 1683, Nicosia, Cyprus
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Maaike P Vreeswijk
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden 2300, The Netherlands
| | - Michael Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | | | - Alexandra Martins
- Inserm U1079-IRIB, University of Rouen, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
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61
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Vallée MP, Di Sera TL, Nix DA, Paquette AM, Parsons MT, Bell R, Hoffman A, Hogervorst FBL, Goldgar DE, Spurdle AB, Tavtigian SV. Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants. Hum Mutat 2016; 37:627-39. [PMID: 26913838 PMCID: PMC4907813 DOI: 10.1002/humu.22973] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/29/2016] [Indexed: 01/05/2023]
Abstract
Clinical mutation screening of the cancer susceptibility genes BRCA1 and BRCA2 generates many unclassified variants (UVs). Most of these UVs are either rare missense substitutions or nucleotide substitutions near the splice junctions of the protein coding exons. Previously, we developed a quantitative method for evaluation of BRCA gene UVs—the “integrated evaluation”—that combines a sequence analysis‐based prior probability of pathogenicity with patient and/or tumor observational data to arrive at a posterior probability of pathogenicity. One limitation of the sequence analysis‐based prior has been that it evaluates UVs from the perspective of missense substitution severity but not probability to disrupt normal mRNA splicing. Here, we calibrated output from the splice‐site fitness program MaxEntScan to generate spliceogenicity‐based prior probabilities of pathogenicity for BRCA gene variants; these range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. We created a database http://priors.hci.utah.edu/PRIORS/ that provides the combined missense substitution severity and spliceogenicity‐based probability of pathogenicity for BRCA gene single‐nucleotide substitutions. We also updated the BRCA gene Ex‐UV LOVD, available at http://hci‐exlovd.hci.utah.edu, with 77 re‐evaluable variants.
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Affiliation(s)
- Maxime P Vallée
- Department of Molecular Medicine, CHUQ Research Center, Quebec City, Canada
| | - Tonya L Di Sera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - David A Nix
- ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrew M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Russel Bell
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Hoffman
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
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62
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Fackenthal JD, Yoshimatsu T, Zhang B, de Garibay GR, Colombo M, De Vecchi G, Ayoub SC, Lal K, Olopade OI, Vega A, Santamariña M, Blanco A, Wappenschmidt B, Becker A, Houdayer C, Walker LC, López-Perolio I, Thomassen M, Parsons M, Whiley P, Blok MJ, Brandão RD, Tserpelis D, Baralle D, Montalban G, Gutiérrez-Enríquez S, Díez O, Lazaro C, Spurdle AB, Radice P, de la Hoya M. Naturally occurring BRCA2 alternative mRNA splicing events in clinically relevant samples. J Med Genet 2016; 53:548-58. [PMID: 27060066 DOI: 10.1136/jmedgenet-2015-103570] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/10/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND BRCA1 and BRCA2 are the two principal tumour suppressor genes associated with inherited high risk of breast and ovarian cancer. Genetic testing of BRCA1/2 will often reveal one or more sequence variants of uncertain clinical significance, some of which may affect normal splicing patterns and thereby disrupt gene function. mRNA analyses are therefore among the tests used to interpret the clinical significance of some genetic variants. However, these could be confounded by the appearance of naturally occurring alternative transcripts unrelated to germline sequence variation or defects in gene function. To understand which novel splicing events are associated with splicing mutations and which are part of the normal BRCA2 splicing repertoire, a study was undertaken by members of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium to characterise the spectrum of naturally occurring BRCA2 mRNA alternate-splicing events. METHODS mRNA was prepared from several blood and breast tissue-derived cells and cell lines by contributing ENIGMA laboratories. cDNA representing BRCA2 alternate splice sites was amplified and visualised using capillary or agarose gel electrophoresis, followed by sequencing. RESULTS We demonstrate the existence of 24 different BRCA2 mRNA alternate-splicing events in lymphoblastoid cell lines and both breast cancer and non-cancerous breast cell lines. CONCLUSIONS These naturally occurring alternate-splicing events contribute to the array of cDNA fragments that may be seen in assays for mutation-associated splicing defects. Caution must be observed in assigning alternate-splicing events to potential splicing mutations.
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Affiliation(s)
| | - Toshio Yoshimatsu
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Bifeng Zhang
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Giovanna De Vecchi
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Samantha C Ayoub
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Kumar Lal
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Ana Blanco
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Barbara Wappenschmidt
- Medical Faculty, Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University of Cologne and University Hospital Cologne, Germany
| | - Alexandra Becker
- Medical Faculty, Center for Hereditary Breast and Ovarian Cancer, Center for Integrated Oncology (CIO) and Center for Molecular Medicine Cologne (CMMC), University of Cologne and University Hospital Cologne, Germany
| | - Claude Houdayer
- Service de Génétique and INSERM U830, Institut Curie and Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Logan C Walker
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Irene López-Perolio
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense C, Denmark
| | - Michael Parsons
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Phillip Whiley
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Rita D Brandão
- Maastricht Science Programme, Faculty of Humanities and Sciences, Maastricht University, Maastricht, The Netherlands
| | - Demis Tserpelis
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Diana Baralle
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Sara Gutiérrez-Enríquez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Orland Díez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona, Barcelona, Spain Clinical and Molecular Genetics Area, University Hospital Vall d'Hebron, Barcelona, Spain
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, IDIBELL-Catalan Institute of Oncology, Barcelona, Spain
| | | | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milano, Italy
| | - Miguel de la Hoya
- Laboratorio de Oncología Molecular, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
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Tourancheau A, Margaillan G, Rouleau M, Gilbert I, Villeneuve L, Lévesque E, Droit A, Guillemette C. Unravelling the transcriptomic landscape of the major phase II UDP-glucuronosyltransferase drug metabolizing pathway using targeted RNA sequencing. THE PHARMACOGENOMICS JOURNAL 2015; 16:60-70. [PMID: 25869014 DOI: 10.1038/tpj.2015.20] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/21/2014] [Accepted: 02/09/2015] [Indexed: 02/04/2023]
Abstract
A comprehensive view of the human UDP-glucuronosyltransferase (UGT) transcriptome is a prerequisite to the establishment of an individual's UGT metabolic glucuronidation signature. Here, we uncover the transcriptome landscape of the 10 human UGT gene loci in normal and tumoral metabolic tissues by targeted RNA next-generation sequencing. Alignment on the human hg19 reference genome identifies 234 novel exon-exon junctions. We recover all previously known UGT1 and UGT2 enzyme-coding transcripts and identify over 130 structurally and functionally diverse novel UGT variants. We further expose a revised genomic structure of UGT loci and provide a comprehensive repertoire of transcripts for each UGT gene. Data also uncover a remodelling of the UGT transcriptome occurring in a tissue- and tumor-specific manner. The complex alternative splicing program regulating UGT expression and protein functions is likely critical in determining detoxification capacity of an organ and stress-related responses, with significant impact on drug responses and diseases.
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Affiliation(s)
- A Tourancheau
- Pharmacogenomics Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - G Margaillan
- Pharmacogenomics Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - M Rouleau
- Pharmacogenomics Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - I Gilbert
- Pharmacogenomics Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - L Villeneuve
- Pharmacogenomics Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada
| | - E Lévesque
- Pharmacogenomics Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center, Québec, QC, Canada.,Faculty of Medicine, Laval University, Québec, QC, Canada
| | - A Droit
- Faculty of Medicine, Laval University, Québec, QC, Canada
| | - C Guillemette
- Pharmacogenomics Laboratory, Centre Hospitalier Universitaire (CHU) de Québec Research Center, Québec, QC, Canada.,Faculty of Pharmacy, Laval University, Québec, QC, Canada.,Canada Research Chair in Pharmacogenomics, Pharmacogenomics Laboratory, CHU de Quebec Research Center, Quebec, QC, Canada
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64
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Romero A, García-García F, López-Perolio I, Ruiz de Garibay G, García-Sáenz JA, Garre P, Ayllón P, Benito E, Dopazo J, Díaz-Rubio E, Caldés T, de la Hoya M. BRCA1 Alternative splicing landscape in breast tissue samples. BMC Cancer 2015; 15:219. [PMID: 25884417 PMCID: PMC4393587 DOI: 10.1186/s12885-015-1145-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/27/2015] [Indexed: 11/23/2022] Open
Abstract
Background BRCA1 is a key protein in cell network, involved in DNA repair pathways and cell cycle. Recently, the ENIGMA consortium has reported a high number of alternative splicing (AS) events at this locus in blood-derived samples. However, BRCA1 splicing pattern in breast tissue samples is unknown. Here, we provide an accurate description of BRCA1 splicing events distribution in breast tissue samples. Methods BRCA1 splicing events were scanned in 70 breast tumor samples, 4 breast samples from healthy individuals and in 72 blood-derived samples by capillary electrophoresis (capillary EP). Molecular subtype was identified in all tumor samples. Splicing events were considered predominant if their relative expression level was at least the 10% of the full-length reference signal. Results 54 BRCA1 AS events were identified, 27 of them were annotated as predominant in at least one sample. Δ5q, Δ13, Δ9, Δ5 and ▼1aA were significantly more frequently annotated as predominant in breast tumor samples than in blood-derived samples. Predominant splicing events were, on average, more frequent in tumor samples than in normal breast tissue samples (P = 0.010). Similarly, likely inactivating splicing events (PTC-NMDs, Non-Coding, Δ5 and Δ18) were more frequently annotated as predominant in tumor than in normal breast samples (P = 0.020), whereas there were no significant differences for other splicing events (No-Fs) frequency distribution between tumor and normal breast samples (P = 0.689). Conclusions Our results complement recent findings by the ENIGMA consortium, demonstrating that BRCA1 AS, despite its tremendous complexity, is similar in breast and blood samples, with no evidences for tissue specific AS events. Further on, we conclude that somatic inactivation of BRCA1 through spliciogenic mutations is, at best, a rare mechanism in breast carcinogenesis, albeit our data detects an excess of likely inactivating AS events in breast tumor samples. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1145-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Atocha Romero
- Molecular Oncology Laboratoy, Instituto de Investigación Sanitaria San Carlos. Center affiliated to the Red Temática de Investigación Cooperativa (RD12/0036/006), Instituto Carlos III, Spanish Ministry of Economy and Competitivy, 28040, Madrid, Spain. .,Medical Oncology Department, Hospital Puerta de Hierro, Madrid, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain.
| | - Francisco García-García
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain.
| | - Irene López-Perolio
- Molecular Oncology Laboratoy, Instituto de Investigación Sanitaria San Carlos. Center affiliated to the Red Temática de Investigación Cooperativa (RD12/0036/006), Instituto Carlos III, Spanish Ministry of Economy and Competitivy, 28040, Madrid, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain.
| | - Gorka Ruiz de Garibay
- Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain.
| | - José A García-Sáenz
- Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain. .,Medical Oncology Department. Hospital Clínico San Carlos. Department of Medicine. Faculty of Medicine, Universidad Complutense Madrid, Madrid, Spain.
| | - Pilar Garre
- Molecular Oncology Laboratoy, Instituto de Investigación Sanitaria San Carlos. Center affiliated to the Red Temática de Investigación Cooperativa (RD12/0036/006), Instituto Carlos III, Spanish Ministry of Economy and Competitivy, 28040, Madrid, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain.
| | - Patricia Ayllón
- Molecular Oncology Laboratoy, Instituto de Investigación Sanitaria San Carlos. Center affiliated to the Red Temática de Investigación Cooperativa (RD12/0036/006), Instituto Carlos III, Spanish Ministry of Economy and Competitivy, 28040, Madrid, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain.
| | - Esperanza Benito
- Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain. .,Plastic Surgery Department, Hospital Clínico San Carlos, Madrid, Spain.
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain. .,Functional Genomics Node, INB, CIPF, Valencia, Spain. .,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Valencia, Spain.
| | - Eduardo Díaz-Rubio
- Molecular Oncology Laboratoy, Instituto de Investigación Sanitaria San Carlos. Center affiliated to the Red Temática de Investigación Cooperativa (RD12/0036/006), Instituto Carlos III, Spanish Ministry of Economy and Competitivy, 28040, Madrid, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain. .,Medical Oncology Department. Hospital Clínico San Carlos. Department of Medicine. Faculty of Medicine, Universidad Complutense Madrid, Madrid, Spain.
| | - Trinidad Caldés
- Molecular Oncology Laboratoy, Instituto de Investigación Sanitaria San Carlos. Center affiliated to the Red Temática de Investigación Cooperativa (RD12/0036/006), Instituto Carlos III, Spanish Ministry of Economy and Competitivy, 28040, Madrid, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain.
| | - Miguel de la Hoya
- Molecular Oncology Laboratoy, Instituto de Investigación Sanitaria San Carlos. Center affiliated to the Red Temática de Investigación Cooperativa (RD12/0036/006), Instituto Carlos III, Spanish Ministry of Economy and Competitivy, 28040, Madrid, Spain. .,Breast Cancer and Systems Biology Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Instituto Carlos III, Spanish Ministry of Economy and Competitivy, Barcelona, 08908, Spain.
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Ahlborn LB, Dandanell M, Steffensen AY, Jønson L, Nielsen FC, Hansen TVO. Splicing analysis of 14 BRCA1 missense variants classifies nine variants as pathogenic. Breast Cancer Res Treat 2015; 150:289-98. [PMID: 25724305 PMCID: PMC4368840 DOI: 10.1007/s10549-015-3313-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/15/2015] [Indexed: 01/23/2023]
Abstract
Pathogenic germline mutations in the BRCA1 gene predispose carriers to early onset breast and ovarian cancer. Clinical genetic screening of BRCA1 often reveals variants with uncertain clinical significance, complicating patient and family management. Therefore, functional examinations are urgently needed to classify whether these uncertain variants are pathogenic or benign. In this study, we investigated 14 BRCA1 variants by in silico splicing analysis and mini-gene splicing assay. All 14 alterations were missense variants located within the BRCT domain of BRCA1 and had previously been examined by functional analysis at the protein level. Results from a validated mini-gene splicing assay indicated that nine BRCA1 variants resulted in splicing aberrations leading to truncated transcripts and thus can be considered pathogenic (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5072C>T/p.Thr1691Ile, c.5074G>C/p.Asp1692His, c.5074G>A/p.Asp1692Asn, c.5074G>T/p.Asp1692Tyr, c.5332G>A/p.Asp1778Asn, c.5332G>T/p.Asp1778Tyr, and c.5408G>C/p.Gly1803Ala), whereas five BRCA1 variants had no effect on splicing (c.4985T>C/p.Phe1662Ser, c.5072C>A/p.Thr1691Lys, c.5153G>C/p.Trp1718Ser, c.5154G>T/p.Trp1718Cys, and c.5333A>G/p.Asp1778Gly). Eight of the variants having an effect on splicing (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5074G>C/p.Asp1692His, c.5074G>A/p.Asp1692Asn, c.5074G>T/p.Asp1692Tyr, c.5332G>A/p.Asp1778Asn, c.5332G>T/p.Asp1778Tyr, and c.5408G>C/p.Gly1803Ala) were previously determined to have no or an uncertain effect on the protein level, whereas one variant (c.5072C>T/p.Thr1691Ile) were shown to have a strong effect on the protein level as well. In conclusion, our study emphasizes that in silico splicing prediction and mini-gene splicing analysis are important for the classification of BRCA1 missense variants located close to exon/intron boundaries.
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Affiliation(s)
- Lise B. Ahlborn
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Mette Dandanell
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Ane Y. Steffensen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Finn C. Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Thomas v. O. Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
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Gambino G, Tancredi M, Falaschi E, Aretini P, Caligo MA. Characterization of three alternative transcripts of the BRCA1 gene in patients with breast cancer and a family history of breast and/or ovarian cancer who tested negative for pathogenic mutations. Int J Mol Med 2015; 35:950-6. [PMID: 25683334 PMCID: PMC4356434 DOI: 10.3892/ijmm.2015.2103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 01/28/2015] [Indexed: 12/24/2022] Open
Abstract
The study of BRCA1 and BRCA2 genes and their alterations has been essential to the understanding of the development of familial breast and ovarian cancers. Many of the variants identified have an unknown pathogenic significance. These include variants which determine alternative mRNA splicing, identified in the intronic regions and those are capable of destroying the splicing ability. The aim of this study was to detect BRCA1/BRCA2 aberrant transcripts resulting from alternative splicing, in women with a known family history and/or early onset of breast and/or ovarian cancer, tested wild-type for BRCA1 and BRCA2. The identification and characterization of aberrant transcripts through the analysis of mRNA levels in blood lymphocytes may help us to recognize families otherwise misclassified as wild-type BRCA1 and BRCA2. Blood samples were collected from 13 women that had a family history of breast and/or ovarian cancer and tested negative for pathogenic mutations in the BRCA1 and BRCA2 genes. Total RNA was analyzed for the presence of BRCA1 and BRCA2 naturally occuring and pathological transcripts using RT-PCR. In 2 out of the 13 samples, 2 alternative transcripts of the BRCA1 gene were identified. These were probably pathogenic as they lacked exon 17 and exon 15, respectively, giving rise to a truncated protein. In addition to these, we identified the Δ17–19 transcript in 1 patient, which gives rise to a protein with an in-frame deletion of 69 amino acids. In conclusion, this study on alternative transcripts of the BRCA1 and BRCA2 genes revealed the presence of isoforms (prevalence of 15%) in blood samples from women with breast and ovarian cancer that were probably pathogenic, that were not detected by conventional methods of mutation screening based on direct sequencing of all coding regions, intron-exons junctions and MLPA analysis.
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Affiliation(s)
- Gaetana Gambino
- Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa 56126, Italy
| | - Mariella Tancredi
- Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa 56126, Italy
| | - Elisabetta Falaschi
- Section of Genetic Oncology, Santa Chiara University Hospital, Pisa 56126, Italy
| | - Paolo Aretini
- Fondazione Pisana per la Scienza - ONLUS, Pisa 56126, Italy
| | - Maria Adelaide Caligo
- Department of Translational Research and New Technologies in Medicine, University of Pisa, Pisa 56126, Italy
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67
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Rosenthal E, Bowles K, Pruss D, van Kan A, Vail P, McElroy H, Wenstrup R. Exceptions to the rule: Case studies in the prediction of pathogenicity for genetic variants in hereditary cancer genes. Clin Genet 2015; 88:533-41. [DOI: 10.1111/cge.12560] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 11/28/2022]
Affiliation(s)
| | - K.R. Bowles
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - D. Pruss
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - A. van Kan
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - P.J. Vail
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - H. McElroy
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
| | - R.J. Wenstrup
- Myriad Genetic Laboratories, Inc. Salt Lake City UT USA
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68
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Thompson B, Martins A, Spurdle A. A review of mismatch repair gene transcripts: issues for interpretation of mRNA splicing assays. Clin Genet 2014; 87:100-8. [DOI: 10.1111/cge.12450] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/17/2014] [Accepted: 06/24/2014] [Indexed: 12/21/2022]
Affiliation(s)
- B.A. Thompson
- Department of Genetics and Computational Biology; QIMR Berghofer Medical Research Institute; Brisbane Australia
- School of Medicine; University of Queensland; Brisbane Australia
| | - A. Martins
- Inserm U1079; University of Rouen, Institute for Research and Innovation in Biomedicine; Rouen France
| | - A.B. Spurdle
- Department of Genetics and Computational Biology; QIMR Berghofer Medical Research Institute; Brisbane Australia
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