1
|
Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Esteban-Sánchez A, Lorca V, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Infante M, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco-Sampedro EA. Systematic Minigene-Based Splicing Analysis and Tentative Clinical Classification of 52 CHEK2 Splice-Site Variants. Clin Chem 2024; 70:319-338. [PMID: 37725924 DOI: 10.1093/clinchem/hvad125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/07/2023] [Indexed: 09/21/2023]
Abstract
BACKGROUND Disrupted pre-mRNA splicing is a frequent deleterious mechanism in hereditary cancer. We aimed to functionally analyze candidate spliceogenic variants of the breast cancer susceptibility gene CHEK2 by splicing reporter minigenes. METHODS A total of 128 CHEK2 splice-site variants identified in the Breast Cancer After Diagnostic Gene Sequencing (BRIDGES) project (https://cordis.europa.eu/project/id/634935) were analyzed with MaxEntScan and subsetted to 52 variants predicted to impact splicing. Three CHEK2 minigenes, which span all 15 exons, were constructed and validated. The 52 selected variants were then genetically engineered into the minigenes and assayed in MCF-7 (human breast adenocarcinoma) cells. RESULTS Of 52 variants, 46 (88.5%) impaired splicing. Some of them led to complex splicing patterns with up to 11 different transcripts. Thirty-four variants induced splicing anomalies without any trace or negligible amounts of the full-length transcript. A total of 89 different transcripts were annotated, which derived from different events: single- or multi-exon skipping, alternative site-usage, mutually exclusive exon inclusion, intron retention or combinations of the abovementioned events. Fifty-nine transcripts were predicted to introduce premature termination codons, 7 kept the original open-reading frame, 5 removed the translation start codon, 6 affected the 5'UTR (Untranslated Region), and 2 included missense variations. Analysis of variant c.684-2A > G revealed the activation of a non-canonical TG-acceptor site and exon 6 sequences critical for its recognition. CONCLUSIONS Incorporation of minigene read-outs into an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme allowed us to classify 32 CHEK2 variants (27 pathogenic/likely pathogenic and 5 likely benign). However, 20 variants (38%) remained of uncertain significance, reflecting in part the complex splicing patterns of this gene.
Collapse
Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Víctor Lorca
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Mar Infante
- Cancer Genetics, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, CB1 8RN, Cambridge, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eladio A Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas-Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| |
Collapse
|
2
|
Walker LC, Hoya MDL, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet 2023; 110:1046-1067. [PMID: 37352859 PMCID: PMC10357475 DOI: 10.1016/j.ajhg.2023.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1, PS3, PP3, BS3, BP4, and BP7. However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. We utilized empirically derived splicing evidence to (1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, (2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and (3) exemplify methodology to calibrate splice prediction tools. We propose repurposing the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely, BP7 may be used to capture RNA results demonstrating no splicing impact for intronic and synonymous variants. We propose that the PS3/BS3 codes are applied only for well-established assays that measure functional impact not directly captured by RNA-splicing assays. We recommend the application of PS1 based on similarity of predicted RNA-splicing effects for a variant under assessment in comparison with a known pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA-assay evidence described aim to help standardize variant pathogenicity classification processes when interpreting splicing-based evidence.
Collapse
Affiliation(s)
- Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | | | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daffodil M Canson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | | | | | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Steven M Harrison
- Ambry Genetics, Aliso Viejo, CA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
3
|
Jasiak A, Koczkowska M, Stukan M, Wydra D, Biernat W, Izycka-Swieszewska E, Buczkowski K, Eccles MR, Walker L, Wasag B, Ratajska M. Analysis of BRCA1 and BRCA2 alternative splicing in predisposition to ovarian cancer. Exp Mol Pathol 2023; 130:104856. [PMID: 36791903 DOI: 10.1016/j.yexmp.2023.104856] [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: 08/08/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND The mRNA splicing is regulated on multiple levels, resulting in the proper distribution of genes' transcripts in each cell and maintaining cell homeostasis. At the same time, the expression of alternative transcripts can change in response to underlying genetic variants, often missed during routine diagnostics. AIM The main aim of this study was to define the frequency of aberrant splicing in BRCA1 and BRCA2 genes in blood RNA extracted from ovarian cancer patients who were previously found negative for the presence of pathogenic alterations in the 25 most commonly analysed ovarian cancer genes, including BRCA1 and BRCA2. MATERIAL AND METHODS Frequency and spectrum of splicing alterations in BRCA1 and BRCA2 genes were analysed in blood RNA from 101 ovarian cancer patients and healthy controls (80 healthy women) using PCR followed by gel electrophoresis and Sanger sequencing. The expression of splicing events was examined using RT-qPCR. RESULTS We did not identify any novel, potentially pathogenic splicing alterations. Nevertheless, we detected six naturally occurring transcripts, named BRCA1ΔE9-10, BRCA1ΔE11, BRCA1ΔE11q, and BRCA2ΔE3, BRCA2ΔE12 and BRCA2ΔE17-18 of which three (BRCA1ΔE11q, BRCA1ΔE11 and BRCA2ΔE3) were significantly higher expressed in the ovarian cancer cohort than in healthy controls (p ≤ 0.0001). CONCLUSIONS This observation indicates that the upregulation of selected naturally occurring transcripts can be stimulated by non-genetic mechanisms and be a potential systemic response to disease progression and/or treatment. However, this hypothesis requires further examination.
Collapse
Affiliation(s)
- Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland.
| | - Magdalena Koczkowska
- 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Stukan
- Department of Gynecologic Oncology, Gdynia Oncology Center, Pomeranian Hospitals, Gdynia, Poland; Department Oncological Propedeutics, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wydra
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdansk, Gdansk, Poland
| | | | - Kamil Buczkowski
- Department of Pathology & Neuropathology, Medical University of Gdansk, Gdansk, Poland
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Logan Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Magdalena Ratajska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand.
| |
Collapse
|
4
|
Walker LC, de la Hoya M, Wiggins GA, Lindy A, Vincent LM, Parsons M, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. APPLICATION OF THE ACMG/AMP FRAMEWORK TO CAPTURE EVIDENCE RELEVANT TO PREDICTED AND OBSERVED IMPACT ON SPLICING: RECOMMENDATIONS FROM THE CLINGEN SVI SPLICING SUBGROUP. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.24.23286431. [PMID: 36865205 PMCID: PMC9980257 DOI: 10.1101/2023.02.24.23286431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1 (null variant in a gene where loss-of-function is the mechanism of disease), PS3 (functional assays show damaging effect on splicing), PP3 (computational evidence supports a splicing effect), BS3 (functional assays show no damaging effect on splicing), BP4 (computational evidence suggests no splicing impact), and BP7 (silent change with no predicted impact on splicing). However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation (SVI) Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. Our study utilised empirically derived splicing evidence to: 1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, 2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and 3) exemplify methodology to calibrate bioinformatic splice prediction tools. We propose repurposing of the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely BP7 may be used to capture RNA results demonstrating no impact on splicing for both intronic and synonymous variants, and for missense variants if protein functional impact has been excluded. Furthermore, we propose that the PS3 and BS3 codes are applied only for well-established assays that measure functional impact that is not directly captured by RNA splicing assays. We recommend the application of PS1 based on similarity of predicted RNA splicing effects for a variant under assessment in comparison to a known Pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA assay evidence described aim to help standardise variant pathogenicity classification processes and result in greater consistency when interpreting splicing-based evidence.
Collapse
|
5
|
Debbabi I, Vacher S, Neuzillet C, Cros J, Revillon F, Petitalot A, Turpin A, Antonio S, Girard E, Dupain C, Kamal M, Hammel P, Bièche I, Masliah-Planchon J, Caputo SM. Identification of a large intra-exonic deletion in BRCA2 exon 18 in a pancreatic ductal adenocarcinoma. Ther Adv Med Oncol 2023; 15:17588359221146132. [PMID: 36700131 PMCID: PMC9869184 DOI: 10.1177/17588359221146132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/30/2022] [Indexed: 01/19/2023] Open
Abstract
By 2030, pancreatic cancer will become the second leading cause of cancer-related deaths in the United States and in Europe. The management of patients with advanced pancreatic cancer relies on chemotherapy and poly (ADP-ribose) polymerase inhibitors for patients who carry BRCA1/2 inactivating alterations. Some variants, such as large insertion/deletions (Indels), inactivating BRCA1/2 and therefore of clinical relevance can be hard to detect by next-generation sequencing techniques. Here we report a 47-year-old patient presenting with pancreatic cancer whose tumour harbours a large somatic intra-exonic deletion of BRCA2 of 141 bp. This BRCA2 deletion, located in the C-terminal domain, can be considered as pathogenic and consequently affect tumorigenesis because it is involved in the interaction between the DSS1 protein and DNA. Thanks to the optimized bioinformatics algorithm, this intermediate size deletion in BRCA2 was identified, enabling personalized patient management via the inclusion of the patients in a clinical trial.
Collapse
Affiliation(s)
- Inès Debbabi
- Department of Genetics, Institut Curie, Paris, France
| | - Sophie Vacher
- Department of Genetics, Institut Curie, Paris, France,PSL Research University, Paris, France
| | - Cindy Neuzillet
- Department of Medical Oncology, Curie Institute, Versailles Saint Quentin University, Paris, France
| | - Jérome Cros
- INSERM UMR1149, Beaujon University Hospital, Paris University, Paris, France,Department of Pathology, Beaujon University, Hospital Paris 7 Diderot University, Paris, France
| | | | - Ambre Petitalot
- Department of Genetics, Institut Curie, Paris, France,PSL Research University, Paris, France
| | - Anthony Turpin
- ULR9020-UMR-S 1277 Canther-Cancer Heterogeneity, Plasticity and Resistance to Therapies, University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France,Medical Oncology Department, CHU Lille, University of Lille, France
| | - Samantha Antonio
- Department of Genetics, Institut Curie, Paris, France,PSL Research University, Paris, France
| | | | - Célia Dupain
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, Paris
| | - Maud Kamal
- Department of Drug Development and Innovation, Institut Curie, PSL Research University, Paris
| | - Pascal Hammel
- Department of Digestive and Medical Oncology, Paris-Saclay University, Hôpital Paul Brousse, Villejuif, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie, Paris, France,Université de Paris, Paris, France
| | | | | |
Collapse
|
6
|
Thomassen M, Mesman RLS, Hansen TVO, Menendez M, Rossing M, Esteban‐Sánchez A, Tudini E, Törngren T, Parsons MT, Pedersen IS, Teo SH, Kruse TA, Møller P, Borg Å, Jensen UB, Christensen LL, Singer CF, Muhr D, Santamarina M, Brandao R, Andresen BS, Feng B, Canson D, Richardson ME, Karam R, Pesaran T, LaDuca H, Conner BR, Abualkheir N, Hoang L, Calléja FMGR, Andrews L, James PA, Bunyan D, Hamblett A, Radice P, Goldgar DE, Walker LC, Engel C, Claes KBM, Macháčková E, Baralle D, Viel A, Wappenschmidt B, Lazaro C, Vega A, Vreeswijk MPG, de la Hoya M, Spurdle AB. Clinical, splicing, and functional analysis to classify BRCA2 exon 3 variants: Application of a points-based ACMG/AMP approach. Hum Mutat 2022; 43:1921-1944. [PMID: 35979650 PMCID: PMC10946542 DOI: 10.1002/humu.24449] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023]
Abstract
Skipping of BRCA2 exon 3 (∆E3) is a naturally occurring splicing event, complicating clinical classification of variants that may alter ∆E3 expression. This study used multiple evidence types to assess pathogenicity of 85 variants in/near BRCA2 exon 3. Bioinformatically predicted spliceogenic variants underwent mRNA splicing analysis using minigenes and/or patient samples. ∆E3 was measured using quantitative analysis. A mouse embryonic stem cell (mESC) based assay was used to determine the impact of 18 variants on mRNA splicing and protein function. For each variant, population frequency, bioinformatic predictions, clinical data, and existing mRNA splicing and functional results were collated. Variant class was assigned using a gene-specific adaptation of ACMG/AMP guidelines, following a recently proposed points-based system. mRNA and mESC analysis combined identified six variants with transcript and/or functional profiles interpreted as loss of function. Cryptic splice site use for acceptor site variants generated a transcript encoding a shorter protein that retains activity. Overall, 69/85 (81%) variants were classified using the points-based approach. Our analysis shows the value of applying gene-specific ACMG/AMP guidelines using a points-based approach and highlights the consideration of cryptic splice site usage to appropriately assign PVS1 code strength.
Collapse
Affiliation(s)
- Mads Thomassen
- Department of Clinical GeneticsOdense University HospitalOdence CDenmark
| | - Romy L. S. Mesman
- Department of Human GeneticsLeiden University Medical CenterLeidenthe Netherlands
| | - Thomas V. O. Hansen
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Mireia Menendez
- Hereditary Cancer ProgramCatalan Institute of Oncology, ONCOBELL‐IDIBELL‐IDTP, CIBERONCHospitalet de LlobregatSpain
| | - Maria Rossing
- Center for Genomic Medicine, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Ada Esteban‐Sánchez
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Emma Tudini
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Therese Törngren
- Division of Oncology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | - Inge S. Pedersen
- Molecular Diagnostics, Aalborg University HospitalAalborgDenmark
- Clinical Cancer Research CenterAalborg University HospitalAalborgDenmark
- Department of Clinical MedicineAalborg UniversityAalborgDenmark
| | - Soo H. Teo
- Breast Cancer Research ProgrammeCancer Research MalaysiaSubang JayaSelangorMalaysia
- Department of Surgery, Faculty of MedicineUniversity of MalayaKuala LumpurMalaysia
| | - Torben A. Kruse
- Department of Clinical GeneticsOdense University HospitalOdence CDenmark
| | - Pål Møller
- Department of Tumour BiologyThe Norwegian Radium Hospital, Oslo University HospitalOsloNorway
| | - Åke Borg
- Division of Oncology, Department of Clinical Sciences LundLund UniversityLundSweden
| | - Uffe B. Jensen
- Department of Clinical GeneticsAarhus University HospitalAarhus NDenmark
| | | | - Christian F. Singer
- Department of OB/GYN and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | - Daniela Muhr
- Department of OB/GYN and Comprehensive Cancer CenterMedical University of ViennaViennaAustria
| | - Marta Santamarina
- Fundación Pública Galega de Medicina XenómicaSantiago de CompostelaSpain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGASSantiago de CompostelaSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)MadridSpain
| | - Rita Brandao
- Department of Clinical GeneticsMaastricht University Medical CenterMaastrichtthe Netherlands
| | - Brage S. Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Bing‐Jian Feng
- Department of DermatologyHuntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUtahUSA
| | - Daffodil Canson
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | | | | | | | | | | | | | | | | | - Lesley Andrews
- Hereditary Cancer Clinic, Nelune Comprehensive Cancer Care CentreSydneyNew South WalesAustralia
| | - Paul A. James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer CenterMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneMelbourneVictoriaAustralia
| | - Dave Bunyan
- Human Development and Health, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Amanda Hamblett
- Middlesex Health Shoreline Cancer CenterWestbrookConnecticutUSA
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of ResearchFondazione IRCCS Istituto Nazionale dei Tumori (INT)MilanItaly
| | - David E. Goldgar
- Department of DermatologyHuntsman Cancer Institute, University of Utah School of MedicineSalt Lake CityUtahUSA
| | - Logan C. Walker
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and EpidemiologyUniversity of LeipzigLeipzigGermany
| | | | - Eva Macháčková
- Department of Cancer Epidemiology and GeneticsMasaryk Memorial Cancer InstituteBrnoCzech Republic
| | - Diana Baralle
- Human Development and Health, Faculty of MedicineUniversity of SouthamptonSouthamptonUK
| | - Alessandra Viel
- Division of Functional Onco‐genomics and GeneticsCentro di Riferimento Oncologico di Aviano (CRO), IRCCSAvianoItaly
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer, Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital CologneUniversity of CologneCologneGermany
| | - Conxi Lazaro
- Hereditary Cancer ProgramCatalan Institute of Oncology, ONCOBELL‐IDIBELL‐IDTP, CIBERONCHospitalet de LlobregatSpain
| | - Ana Vega
- Fundación Pública Galega de Medicina XenómicaSantiago de CompostelaSpain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGASSantiago de CompostelaSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)MadridSpain
| | - ENIGMA Consortium
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQueenslandAustralia
| |
Collapse
|
7
|
Fanconi Anaemia, Childhood Cancer and the BRCA Genes. Genes (Basel) 2021; 12:genes12101520. [PMID: 34680915 PMCID: PMC8535386 DOI: 10.3390/genes12101520] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/18/2022] Open
Abstract
Fanconi anaemia (FA) is an inherited chromosomal instability disorder characterised by congenital and developmental abnormalities and a strong cancer predisposition. In less than 5% of cases FA can be caused by bi-allelic pathogenic variants (PGVs) in BRCA2/FANCD1 and in very rare cases by bi-allelic PGVs in BRCA1/FANCS. The rarity of FA-like presentation due to PGVs in BRCA2 and even more due to PGVs in BRCA1 supports a fundamental role of the encoded proteins for normal development and prevention of malignant transformation. While FA caused by BRCA1/2 PGVs is strongly associated with distinct spectra of embryonal childhood cancers and AML with BRCA2-PGVs, and also early epithelial cancers with BRCA1 PGVs, germline variants in the BRCA1/2 genes have also been identified in non-FA childhood malignancies, and thereby implying the possibility of a role of BRCA PGVs also for non-syndromic cancer predisposition in children. We provide a concise review of aspects of the clinical and genetic features of BRCA1/2-associated FA with a focus on associated malignancies, and review novel aspects of the role of germline BRCA2 and BRCA1 PGVs occurring in non-FA childhood cancer and discuss aspects of clinical and biological implications.
Collapse
|
8
|
BRCA1 and BRCA2 whole cDNA analysis in unsolved hereditary breast/ovarian cancer patients. Cancer Genet 2021; 258-259:10-17. [PMID: 34237702 DOI: 10.1016/j.cancergen.2021.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022]
Abstract
Germline pathogenic variants in BRCA1 and BRCA2 genes (BRCA1/2) explain an important fraction of hereditary breast/ovarian cancer (HBOC) cases. Genetic testing generally involves examining coding regions and exon/intron boundaries, thus the frequency of deleterious variants in non-coding regions is unknown. Here we analysed BRCA1/2 whole cDNA in a large cohort of 320 unsolved high-risk HBOC cases in order to identify potential splicing alterations explained by variants in BRCA1/2 deep intronic regions. Whole RNA splicing profiles were analysed by RT-PCR using Sanger sequencing or high-resolution electrophoresis in a QIAxcel instrument. Known predominant BRCA1/2 alternative splicing events were detected, together with two novel events BRCA1 ▼21 and BRCA2 Δ18q_27p. BRCA2 exon 3 skipping was detected in one patient (male) affected with breast cancer, caused by a known Portuguese founder mutation (c.156_157insAluYa5). An altered BRCA2 splicing pattern was detected in three patients, consisting in the up-regulation of ▼20A, Δ22 and ▼20A+Δ22 transcripts. In silico analysis and semi-quantitative data identified the polymorphism BRCA2 c.8755-66T>C as a potential modifier of Δ22 levels. Our findings suggest that mRNA alterations in BRCA1/2 caused by deep intronic variants are rare in Spanish population. However, RNA analysis complements DNA-based strategies allowing the identification of alterations that could go undetected by conventional testing.
Collapse
|
9
|
Nix P, Mundt E, Coffee B, Goossen E, Warf BM, Brown K, Bowles K, Roa B. Interpretation of BRCA2 Splicing Variants: A Case Series of Challenging Variant Interpretations and the Importance of Functional RNA Analysis. Fam Cancer 2021; 21:7-19. [PMID: 33469799 PMCID: PMC8799590 DOI: 10.1007/s10689-020-00224-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022]
Abstract
A substantial proportion of pathogenic variants associated with an increased risk of hereditary cancer are sequence variants affecting RNA splicing. The classification of these variants can be complex when both non-functional and functional transcripts are produced from the variant allele. We present four BRCA2 splice site variants with complex variant interpretations (BRCA2 c.68-3T>G, c.68-2A>G, c.425G>T, c.8331+2T>C). Evidence supporting a pathogenic classification is available for each variant, including in silico models, absence in population databases, and published functional data. However, comprehensive RNA analysis showed that some functional transcript may be produced by each variant. BRCA2 c.68-3T>G results in a partial splice defect. For BRCA2 c.68-2A>G and c.425G>T, aberrant splicing was shown to produce a potentially functional, in-frame transcript. BRCA2 c.8331+2T>C may utilize a functional GC donor in place of the wild-type GT donor. The severity of cancer history for carriers of these variants was also assessed using a history weighting algorithm and was not consistent with pathogenic controls (carriers of known pathogenic variants in BRCA2). Due to the conflicting evidence, our laboratory classifies these BRCA2 variants as variants of uncertain significance. This highlights the importance of evaluating new and existing evidence to ensure accurate variant classification and appropriate patient care.
Collapse
Affiliation(s)
- Paola Nix
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA.
| | - Erin Mundt
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Bradford Coffee
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | | | - Bryan M Warf
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA.,Third Wave Analytics, Inc., San Francisco, CA, USA
| | - Krystal Brown
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Karla Bowles
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Benjamin Roa
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| |
Collapse
|
10
|
Sanoguera-Miralles L, Valenzuela-Palomo A, Bueno-Martínez E, Llovet P, Díez-Gómez B, Caloca MJ, Pérez-Segura P, Fraile-Bethencourt E, Colmena M, Carvalho S, Allen J, Easton DF, Devilee P, Vreeswijk MPG, de la Hoya M, Velasco EA. Comprehensive Functional Characterization and Clinical Interpretation of 20 Splice-Site Variants of the RAD51C Gene. Cancers (Basel) 2020; 12:E3771. [PMID: 33333735 PMCID: PMC7765170 DOI: 10.3390/cancers12123771] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
Hereditary breast and/or ovarian cancer is a highly heterogeneous disease with more than 10 known disease-associated genes. In the framework of the BRIDGES project (Breast Cancer Risk after Diagnostic Gene Sequencing), the RAD51C gene has been sequenced in 60,466 breast cancer patients and 53,461 controls. We aimed at functionally characterizing all the identified genetic variants that are predicted to disrupt the splicing process. Forty RAD51C variants of the intron-exon boundaries were bioinformatically analyzed, 20 of which were selected for splicing functional assays. To test them, a splicing reporter minigene with exons 2 to 8 was designed and constructed. This minigene generated a full-length transcript of the expected size (1062 nucleotides), sequence, and structure (Vector exon V1- RAD51C exons_2-8- Vector exon V2). The 20 candidate variants were genetically engineered into the wild type minigene and functionally assayed in MCF-7 cells. Nineteen variants (95%) impaired splicing, while 18 of them produced severe splicing anomalies. At least 35 transcripts were generated by the mutant minigenes: 16 protein-truncating, 6 in-frame, and 13 minor uncharacterized isoforms. According to ACMG/AMP-based standards, 15 variants could be classified as pathogenic or likely pathogenic variants: c.404G > A, c.405-6T > A, c.571 + 4A > G, c.571 + 5G > A, c.572-1G > T, c.705G > T, c.706-2A > C, c.706-2A > G, c.837 + 2T > C, c.905-3C > G, c.905-2A > C, c.905-2_905-1del, c.965 + 5G > A, c.1026 + 5_1026 + 7del, and c.1026 + 5G > T.
Collapse
Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - Patricia Llovet
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| | - María José Caloca
- Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain;
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
- Knight Cancer Research Building, 2720 S Moody Ave, Portland, OR 97201, USA
| | - Marta Colmena
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (S.C.); (J.A.); (D.F.E.)
| | - Peter Devilee
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Maaike P. G. Vreeswijk
- Leiden University Medical Center, Department of Human Genetics, 2300RC Leiden, The Netherlands; (P.D.); (M.P.G.V.)
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain; (P.L.); (P.P.-S.); (M.C.)
| | - Eladio A. Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain; (L.S.-M.); (A.V.-P.); (E.B.-M.); (B.D.-G.); (E.F.-B.)
| |
Collapse
|
11
|
Nix P, Mundt E, Manley S, Coffee B, Roa B. Reply to R. Karam et al. JCO Precis Oncol 2020; 4:1224-1225. [DOI: 10.1200/po.20.00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Paola Nix
- Paola Nix, PhD; Erin Mundt, MS, CGC; Susan Manley, MS, CGC, MBA; Bradford Coffee, PhD; and Benjamin Roa, PhD, Myriad Genetic Laboratories, Salt Lake City, UT
| | | | - Susan Manley
- Paola Nix, PhD; Erin Mundt, MS, CGC; Susan Manley, MS, CGC, MBA; Bradford Coffee, PhD; and Benjamin Roa, PhD, Myriad Genetic Laboratories, Salt Lake City, UT
| | - Bradford Coffee
- Paola Nix, PhD; Erin Mundt, MS, CGC; Susan Manley, MS, CGC, MBA; Bradford Coffee, PhD; and Benjamin Roa, PhD, Myriad Genetic Laboratories, Salt Lake City, UT
| | - Benjamin Roa
- Paola Nix, PhD; Erin Mundt, MS, CGC; Susan Manley, MS, CGC, MBA; Bradford Coffee, PhD; and Benjamin Roa, PhD, Myriad Genetic Laboratories, Salt Lake City, UT
| |
Collapse
|
12
|
Rivera D, Paudice M, Gismondi V, Anselmi G, Vellone VG, Varesco L. Implementing NGS-based BRCA tumour tissue testing in FFPE ovarian carcinoma specimens: hints from a real-life experience within the framework of expert recommendations. J Clin Pathol 2020; 74:596-603. [PMID: 32895300 DOI: 10.1136/jclinpath-2020-206840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/19/2022]
Abstract
AIMS Next Generation Sequencing (NGS)-based BRCA tumour tissue testing poses several challenges. As a first step of its implementation within a regional health service network, an in-house validation study was compared with published recommendations. METHODS Epithelial ovarian cancer (EOC) formalin-fixed paraffin-embedded specimens stored in the archives of the eight regional pathology units were selected from a consecutive series of patients with known BRCA germline status. Two expert pathologists evaluated tumour cell content for manual macrodissection. DNA extraction, library preparation and NGS analyses were performed blinded to the germinal status. Parameters used in the study were confronted with guidelines for the validation of NGS-based oncology panels and for BRCA tumour tissue testing. RESULTS NGS analyses were successful in 66 of 67 EOC specimens, with good quality metrics and high reproducibility among different runs. In all, 19 BRCA pathogenic variants were identified: 12 were germline and 7 were somatic. A 100% concordance with blood tests was detected for germline variants. A BRCA1 variant showed a controversial classification. In different areas of two early stage EOCs showing somatic variants, intratumour heterogeneity not relevant for test results (variant allele frequency >5%) was observed. Compared with expert recommendations, main limitations of the study were absence of controls with known somatic BRCA status and exclusion from the validation of BRCA copy number variations (CNV). CONCLUSIONS A close collaboration between pathology and genetics units provides advantages in the implementation of BRCA tumour tissue testing. The development of tools for designing and interpreting complex testing in-house validation could improve process quality.
Collapse
Affiliation(s)
- Daniela Rivera
- Hereditary Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | - Michele Paudice
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Univeristy of Genoa, Genova, Liguria, Italy
| | - Viviana Gismondi
- Hereditary Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | - Giorgia Anselmi
- Anatomic Pathology University Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | - Valerio Gaetano Vellone
- Department of Surgical Sciences and Integrated Diagnostics (DISC), Univeristy of Genoa, Genova, Liguria, Italy .,Anatomic Pathology University Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | - Liliana Varesco
- Hereditary Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Liguria, Italy
| | | |
Collapse
|
13
|
Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
Collapse
Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
| |
Collapse
|
14
|
Tubeuf H, Caputo SM, Sullivan T, Rondeaux J, Krieger S, Caux-Moncoutier V, Hauchard J, Castelain G, Fiévet A, Meulemans L, Révillion F, Léoné M, Boutry-Kryza N, Delnatte C, Guillaud-Bataille M, Cleveland L, Reid S, Southon E, Soukarieh O, Drouet A, Di Giacomo D, Vezain M, Bonnet-Dorion F, Bourdon V, Larbre H, Muller D, Pujol P, Vaz F, Audebert-Bellanger S, Colas C, Venat-Bouvet L, Solano AR, Stoppa-Lyonnet D, Houdayer C, Frebourg T, Gaildrat P, Sharan SK, Martins A. Calibration of Pathogenicity Due to Variant-Induced Leaky Splicing Defects by Using BRCA2 Exon 3 as a Model System. Cancer Res 2020; 80:3593-3605. [PMID: 32641407 DOI: 10.1158/0008-5472.can-20-0895] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/14/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
BRCA2 is a clinically actionable gene implicated in breast and ovarian cancer predisposition that has become a high priority target for improving the classification of variants of unknown significance (VUS). Among all BRCA2 VUS, those causing partial/leaky splicing defects are the most challenging to classify because the minimal level of full-length (FL) transcripts required for normal function remains to be established. Here, we explored BRCA2 exon 3 (BRCA2e3) as a model for calibrating variant-induced spliceogenicity and estimating thresholds for BRCA2 haploinsufficiency. In silico predictions, minigene splicing assays, patients' RNA analyses, a mouse embryonic stem cell (mESC) complementation assay and retrieval of patient-related information were combined to determine the minimal requirement of FL BRCA2 transcripts. Of 100 BRCA2e3 variants tested in the minigene assay, 64 were found to be spliceogenic, causing mild to severe RNA defects. Splicing defects were also confirmed in patients' RNA when available. Analysis of a neutral leaky variant (c.231T>G) showed that a reduction of approximately 60% of FL BRCA2 transcripts from a mutant allele does not cause any increase in cancer risk. Moreover, data obtained from mESCs suggest that variants causing a decline in FL BRCA2 with approximately 30% of wild-type are not pathogenic, given that mESCs are fully viable and resistant to DNA-damaging agents in those conditions. In contrast, mESCs producing lower relative amounts of FL BRCA2 exhibited either null or hypomorphic phenotypes. Overall, our findings are likely to have broader implications on the interpretation of BRCA2 variants affecting the splicing pattern of other essential exons. SIGNIFICANCE: These findings demonstrate that BRCA2 tumor suppressor function tolerates substantial reduction in full-length transcripts, helping to determine the pathogenicity of BRCA2 leaky splicing variants, some of which may not increase cancer risk.
Collapse
Affiliation(s)
- Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Julie Rondeaux
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Sophie Krieger
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Laboratory of Cancer Biology and Genetics, Centre François Baclesse, Caen, France - Normandie University, UNICAEN, Caen, France
| | | | - Julie Hauchard
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Gaia Castelain
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alice Fiévet
- Department of Genetics, Institut Curie, Paris, France.,INSERM U830, University Paris Descartes, Paris, France.,Service Génétique des Tumeurs, Gustave Roussy, Villejuif, France
| | - Laëtitia Meulemans
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | | | | | | | | | - Linda Cleveland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Omar Soukarieh
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Aurélie Drouet
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Daniela Di Giacomo
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Myriam Vezain
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Violaine Bourdon
- Department of Genetics, Institut Paoli-Calmettes, Marseille, France
| | - Hélène Larbre
- Laboratoire d'Oncogénétique Moléculaire, Institut Godinot, Reims, France
| | - Danièle Muller
- Unité d'Oncogénétique, Centre Paul Strauss, Strasbourg, France
| | - Pascal Pujol
- Unité d'Oncogénétique, CHU Arnaud de Villeneuve, Montpellier, France
| | - Fátima Vaz
- Breast Cancer Risk Evaluation Clinic, Portuguese Institute of Oncology of Lisbon, Lisbon, Portugal
| | | | - Chrystelle Colas
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | | | - Angela R Solano
- Genotipificacion y Cancer Hereditario, Departmento de Analisis Clinicos, Centro de Educacion Medica e Investigaciones Clinicas (CEMIC), Ciudad Autonoma de Buenos Aires, Argentina
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France.,INSERM U830, University Paris Descartes, Paris, France
| | - Claude Houdayer
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Thierry Frebourg
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland
| | - Alexandra Martins
- Inserm U1245, UNIROUEN, Normandie University, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
| |
Collapse
|
15
|
Sato K, Brandsma I, van Rossum-Fikkert SE, Verkaik N, Oostra AB, Dorsman JC, van Gent DC, Knipscheer P, Kanaar R, Zelensky AN. HSF2BP negatively regulates homologous recombination in DNA interstrand crosslink repair. Nucleic Acids Res 2020; 48:2442-2456. [PMID: 31960047 PMCID: PMC7049687 DOI: 10.1093/nar/gkz1219] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 12/16/2019] [Accepted: 12/20/2019] [Indexed: 02/06/2023] Open
Abstract
The tumor suppressor BRCA2 is essential for homologous recombination (HR), replication fork stability and DNA interstrand crosslink (ICL) repair in vertebrates. We show that ectopic production of HSF2BP, a BRCA2-interacting protein required for meiotic HR during mouse spermatogenesis, in non-germline human cells acutely sensitize them to ICL-inducing agents (mitomycin C and cisplatin) and PARP inhibitors, resulting in a phenotype characteristic of cells from Fanconi anemia (FA) patients. We biochemically recapitulate the suppression of ICL repair and establish that excess HSF2BP compromises HR by triggering the removal of BRCA2 from the ICL site and thereby preventing the loading of RAD51. This establishes ectopic expression of a wild-type meiotic protein in the absence of any other protein-coding mutations as a new mechanism that can lead to an FA-like cellular phenotype. Naturally occurring elevated production of HSF2BP in tumors may be a source of cancer-promoting genomic instability and also a targetable vulnerability.
Collapse
Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Inger Brandsma
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Sari E van Rossum-Fikkert
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Nicole Verkaik
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Anneke B Oostra
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Josephine C Dorsman
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands
| | - Dik C van Gent
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Alex N Zelensky
- Department of Molecular Genetics, Oncode Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| |
Collapse
|
16
|
Wappenschmidt B, Hauke J, Faust U, Niederacher D, Wiesmüller L, Schmidt G, Groß E, Gehrig A, Sutter C, Ramser J, Rump A, Arnold N, Meindl A. Criteria of the German Consortium for Hereditary Breast and Ovarian Cancer for the Classification of Germline Sequence Variants in Risk Genes for Hereditary Breast and Ovarian Cancer. Geburtshilfe Frauenheilkd 2020; 80:410-429. [PMID: 32322110 PMCID: PMC7174002 DOI: 10.1055/a-1110-0909] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/14/2022] Open
Abstract
More than ten years ago, the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) set up a panel of experts (VUS Task Force) which was tasked with reviewing the classifications of genetic variants reported by individual centres of the GC-HBOC to the central database in Leipzig and reclassifying them, where necessary, based on the most recent data. When it evaluates variants, the VUS Task Force must arrive at a consensus. The resulting classifications are recorded in a central database where they serve as a basis for ensuring the consistent evaluation of previously known and newly identified variants in the different centres of the GC-HBOC. The standardised VUS evaluation by the VUS Task Force is a key element of the recall system which has also been set up by the GC-HBOC. The system will be used to pass on information to families monitored and managed by GC-HBOC centres in the event that previously classified variants are reclassified based on new information. The evaluation algorithm of the VUS Task Force was compiled using internationally established assessment methods (IARC, ACMG, ENIGMA) and is presented here together with the underlying evaluation criteria used to arrive at the classification decision using a flow chart. In addition, the characteristics and special features of specific individual risk genes associated with breast and/or ovarian cancer are discussed in separate subsections. The URLs of relevant databases have also been included together with extensive literature references to provide additional information and cover the scope and dynamism of the current state of knowledge on the evaluation of genetic variants. In future, if criteria are updated based on new information, the update will be published on the website of the GC-HBOC (
https://www.konsortium-familiaerer-brustkrebs.de/
).
Collapse
Affiliation(s)
- Barbara Wappenschmidt
- Zentrum familiärer Brust- und Eierstockkrebs, Universitätsklinikum Köln, Köln, Germany
| | - Jan Hauke
- Zentrum familiärer Brust- und Eierstockkrebs, Universitätsklinikum Köln, Köln, Germany
| | - Ulrike Faust
- Institut für Medizinische Genetik und Angewandte Genomik, Universität Tübingen, Tübingen, Germany
| | - Dieter Niederacher
- Klinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - Lisa Wiesmüller
- Frauenklinik, Sektion Gynäkologische Onkologie, Uniklinik Ulm, Ulm, Germany
| | - Gunnar Schmidt
- Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover, Germany
| | - Evi Groß
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Klinikum der Universität München, Campus Großhadern, München, Germany
| | - Andrea Gehrig
- Institut für Humangenetik, Universität Würzburg, Würzburg, Germany
| | - Christian Sutter
- Institut für Humangenetik, Universität Heidelberg, Heidelberg, Germany
| | - Juliane Ramser
- Frauenklinik der Technischen Universität München, Klinikum rechts der Isar, München, Germany
| | - Andreas Rump
- Institut für klinische Genetik, Technische Universität Dresden, Dresden, Germany
| | - Norbert Arnold
- Universitätsklinikum Kiel, Klinik für Gynäkologie und Geburtshilfe, Kiel, Germany.,Institut für Klinische Molekularbiologie, Universitätsklinikum Kiel, Kiel, Germany
| | - Alfons Meindl
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Klinikum der Universität München, Campus Großhadern, München, Germany.,Frauenklinik der Technischen Universität München, Klinikum rechts der Isar, München, Germany
| |
Collapse
|
17
|
Meulemans L, Mesman RLS, Caputo SM, Krieger S, Guillaud-Bataille M, Caux-Moncoutier V, Léone M, Boutry-Kryza N, Sokolowska J, Révillion F, Delnatte C, Tubeuf H, Soukarieh O, Bonnet-Dorion F, Guibert V, Bronner M, Bourdon V, Lizard S, Vilquin P, Privat M, Drouet A, Grout C, Calléja FMGR, Golmard L, Vrieling H, Stoppa-Lyonnet D, Houdayer C, Frebourg T, Vreeswijk MPG, Martins A, Gaildrat P. Skipping Nonsense to Maintain Function: The Paradigm of BRCA2 Exon 12. Cancer Res 2020; 80:1374-1386. [PMID: 32046981 DOI: 10.1158/0008-5472.can-19-2491] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/18/2019] [Accepted: 02/06/2020] [Indexed: 11/16/2022]
Abstract
Germline nonsense and canonical splice site variants identified in disease-causing genes are generally considered as loss-of-function (LoF) alleles and classified as pathogenic. However, a fraction of such variants could maintain function through their impact on RNA splicing. To test this hypothesis, we used the alternatively spliced BRCA2 exon 12 (E12) as a model system because its in-frame skipping leads to a potentially functional protein. All E12 variants corresponding to putative LoF variants or predicted to alter splicing (n = 40) were selected from human variation databases and characterized for their impact on splicing in minigene assays and, when available, in patient lymphoblastoid cell lines. Moreover, a selection of variants was analyzed in a mouse embryonic stem cell-based functional assay. Using these complementary approaches, we demonstrate that a subset of variants, including nonsense variants, induced in-frame E12 skipping through the modification of splice sites or regulatory elements and, consequently, led to an internally deleted but partially functional protein. These data provide evidence, for the first time in a cancer-predisposition gene, that certain presumed null variants can retain function due to their impact on splicing. Further studies are required to estimate cancer risk associated with these hypomorphic variants. More generally, our findings highlight the need to exercise caution in the interpretation of putative LoF variants susceptible to induce in-frame splicing modifications. SIGNIFICANCE: This study presents evidence that certain presumed loss-of-function variants in a cancer predisposition gene can retain function due to their direct impact on RNA splicing.
Collapse
Affiliation(s)
- Laëtitia Meulemans
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Romy L S Mesman
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandrine M Caputo
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Sophie Krieger
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Laboratory of Cancer Biology and Genetics, Centre François Baclesse, Caen, France.,Normandie University, UNICAEN, Caen, France
| | | | | | | | | | | | | | | | - Hélène Tubeuf
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Omar Soukarieh
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Virginie Guibert
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Myriam Bronner
- Department of Genetics, Nancy University Hospital, Nancy, France
| | - Violaine Bourdon
- Department of Genetics, Institut Paoli-Calmettes, Marseille, France
| | - Sarab Lizard
- Department of Genetics, Nancy University Hospital, Nancy, France
| | - Paul Vilquin
- Department of Pathology and Oncobiology, Montpellier University Hospital, Montpellier, France
| | - Maud Privat
- University of Clermont Auvergne, Inserm U1240, Clermont Ferrand, France.,Department of Oncogenetics, Centre Jean Perrin, Clermont Ferrand, France
| | - Aurélie Drouet
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Charlotte Grout
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France.,PSL Research University, Paris, France
| | - Harry Vrieling
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France.,Inserm U830, University Paris Descartes, Paris, France
| | - Claude Houdayer
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, Institut Curie, Paris, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - Thierry Frebourg
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexandra Martins
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pascaline Gaildrat
- Normandie Univ, UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.
| |
Collapse
|
18
|
Gay-Bellile M, Privat M, Martins A, Caputo SM, Pebrel-Richard C, Cavaillé M, Viala S, Corsini C, Rodrigues M, Barnich N, Bidet Y, Uhrhammer N, Bignon YJ. Is BRCA2 involved in early onset colorectal cancer risk? Clin Genet 2019; 97:668-669. [PMID: 31875949 PMCID: PMC7078894 DOI: 10.1111/cge.13679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Mathilde Gay-Bellile
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Maud Privat
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Alexandra Martins
- INSERM U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, UNIROUEN, Normandie Université, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | | | - Céline Pebrel-Richard
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Service de Cytogénétique Médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Mathias Cavaillé
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Sandrine Viala
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Carole Corsini
- Département de Génétique Médicale, unité d'oncogénétique clinique, Hôpital Arnaud de Villeneuve, CHRU de Montpellier, France
| | - Michael Rodrigues
- Université Clermont Auvergne, Laboratoire Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Nicolas Barnich
- Université Clermont Auvergne, Laboratoire Microbes Intestin Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Yannick Bidet
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Nancy Uhrhammer
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Yves-Jean Bignon
- Université Clermont Auvergne, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Clermont Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| |
Collapse
|
19
|
Scarpitta R, Zanna I, Aretini P, Gambino G, Scatena C, Mei B, Ghilli M, Rossetti E, Roncella M, Congregati C, Bonci F, Naccarato AG, Palli D, Caligo MA. Germline investigation in male breast cancer of DNA repair genes by next-generation sequencing. Breast Cancer Res Treat 2019; 178:557-564. [PMID: 31512090 DOI: 10.1007/s10549-019-05429-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/29/2019] [Indexed: 02/03/2023]
Abstract
PURPOSE In order to better define the breast cancer (BC) genetic risk factors in men, a germline investigation was carried out on 81 Male BC cases by screening the 24 genes involved in BC predisposition, genome stability maintenance and DNA repair mechanisms by next-generation sequencing. METHODS Germline DNAs were tested in a custom multi-gene panel focused on all coding exons and exon-intron boundaries of 24 selected genes using two amplicon-based assays on PGM-Ion Torrent (ThermoFisher Scientific) and MiSeq (Illumina) platforms. All variants were recorded and classified by using a custom pipeline. RESULTS Clinical pathological data and the family history of 81 Male BC cases were gathered and analysed, revealing the average age of onset to be 61.3 years old and that in 35 cases there was a family history of BC. Our genetic screening allowed us to identify a germline mutation in 22 patients (23%) in 4 genes: BRCA2, BRIP1, MUTYH and PMS2. Moreover, 12 variants of unknown clinical significance (VUS) in 9 genes (BARD1, BRCA1, BRIP1, CHEK2, ERCC1, NBN, PALB2, PMS1, RAD50) were predicted as potentially pathogenic by in silico analysis bringing the mutation detection rate up to 40%. CONCLUSION As expected, a positive family history is a strong predictor of germline BRCA2 mutations in male BC. Understanding the potential pathogenicity of VUS represents an extremely urgent need for the management of BC risk in Male BC cases and their own families.
Collapse
Affiliation(s)
- R Scarpitta
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - I Zanna
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Delle Oblate 4, 50141, Florence, Italy
| | - P Aretini
- Section of Cancer Genomics, Fondazione Pisana per la Scienza, Pisa, Italy
| | - G Gambino
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - C Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - B Mei
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - M Ghilli
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - E Rossetti
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - M Roncella
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - C Congregati
- Division of Internal Medicine, University Hospital, Pisa, Italy
| | - F Bonci
- Unit of Medical Oncology 2, University Hospital, Pisa, Italy
| | - A G Naccarato
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - D Palli
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Delle Oblate 4, 50141, Florence, Italy
| | - M A Caligo
- Section of Genetic Oncology, University Hospital, Pisa, Italy.
| |
Collapse
|
20
|
Montalban G, Bonache S, Moles-Fernández A, Gadea N, Tenés A, Torres-Esquius S, Carrasco E, Balmaña J, Diez O, Gutiérrez-Enríquez S. Incorporation of semi-quantitative analysis of splicing alterations for the clinical interpretation of variants in BRCA1 and BRCA2 genes. Hum Mutat 2019; 40:2296-2317. [PMID: 31343793 DOI: 10.1002/humu.23882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 07/21/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
BRCA1 and BRCA2 (BRCA1/2) genetic variants that disrupt messenger RNA splicing are commonly associated with increased risks of developing breast/ovarian cancer. The majority of splicing studies published to date rely on qualitative methodologies (i.e., Sanger sequencing), but it is necessary to incorporate semi-quantitative or quantitative approaches to accurately interpret the clinical significance of spliceogenic variants. Here, we characterize the splicing impact of 31 BRCA1/2 variants using semi-quantitative capillary electrophoresis of fluorescent amplicons (CE), Sanger sequencing and allele-specific assays. A total of 14 variants were found to disrupt splicing. Allelic-specific assays could be performed for BRCA1 c.302-1G>A and BRCA2 c.516+2T>A, c.1909+1G>A, c.8332-13T>G, c.8332-2A>G, c.8954-2A>T variants, showing a monoallelic contribution to full-length transcript expression that was concordant with semi-quantitative data. The splicing fraction of alternative and aberrant transcripts was also measured by CE, facilitating variant interpretation. Following Evidence-based Network for the Interpretation of Germline Mutant Alleles criteria, we successfully classified eight variants as pathogenic (Class 5), five variants as likely pathogenic (Class 4), and 14 variants as benign (Class 1). We also provide splicing data for four variants classified as uncertain (Class 3), which produced a "leaky" splicing effect or introduced a missense change in the protein sequence, that will require further assessment to determine their clinical significance.
Collapse
Affiliation(s)
- Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Neus Gadea
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Anna Tenés
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Sara Torres-Esquius
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Estela Carrasco
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | | |
Collapse
|
21
|
Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Caloca MJ, Gómez-Barrero S, Velasco EA. Minigene Splicing Assays Identify 12 Spliceogenic Variants of BRCA2 Exons 14 and 15. Front Genet 2019; 10:503. [PMID: 31191615 PMCID: PMC6546720 DOI: 10.3389/fgene.2019.00503] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/07/2019] [Indexed: 12/11/2022] Open
Abstract
A relevant fraction of BRCA2 variants is associated with splicing alterations and with an increased risk of hereditary breast and ovarian cancer (HBOC). In this work, we have carried out a thorough study of variants from BRCA2 exons 14 and 15 reported at mutation databases. A total of 294 variants from exons 14 and 15 and flanking intronic sequences were analyzed with the online splicing tools NNSplice and Human Splicing Finder. Fifty-three out of these 294 variants were selected as candidate splicing variants. All variants but one, were introduced into the minigene MGBR2_ex14-20 (with exons 14–20) by site-directed mutagenesis and assayed in MCF-7 cells. Twelve of the remaining 52 variants (23.1%) impaired splicing at different degrees, yielding from 5 to 100% of aberrant transcripts. Nine variants affected the natural acceptor or donor sites of both exons and three affected putative enhancers or silencers. Fluorescent capillary electrophoresis revealed at least 10 different anomalous transcripts: (E14q5), Δ (E14p10), Δ(E14p246), Δ(E14q256), Δ(E14), Δ(E15p12), Δ(E15p13), Δ(E15p83), Δ(E15) and a 942-nt fragment of unknown structure. All transcripts, except for Δ(E14q256) and Δ(E15p12), are expected to truncate the BRCA2 protein. Nine variants induced severe splicing aberrations with more than 90% of abnormal transcripts. Thus, according to the guidelines of the American College of Medical Genetics and Genomics, eight variants should be classified as pathogenic (c.7008-2A > T, c.7008-1G > A, c.7435+1G > C, c.7436-2A > T, c.7436-2A > G, c.7617+1G > A, c.7617+1G > T, and c.7617+2T > G), one as likely pathogenic (c.7008-3C > G) and three remain as variants of uncertain clinical significance or VUS (c.7177A > G, c.7447A > G and c.7501C > T). In conclusion, functional assays by minigenes constitute a valuable strategy to primarily check the splicing impact of DNA variants and their clinical interpretation. While bioinformatics predictions of splice site variants were accurate, those of enhancer or silencer variants were poor (only 3/23 spliceogenic variants) which showed weak impacts on splicing (∼5–16% of aberrant isoforms). So, the Exonic Splicing Enhancer and Silencer (ESE and ESS, respectively) prediction algorithms require further improvement.
Collapse
Affiliation(s)
- Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - María José Caloca
- Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | | | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| |
Collapse
|
22
|
Wangensteen T, Felde CN, Ahmed D, Mæhle L, Ariansen SL. Diagnostic mRNA splicing assay for variants in BRCA1 and BRCA2 identified two novel pathogenic splicing aberrations. Hered Cancer Clin Pract 2019; 17:14. [PMID: 31143303 PMCID: PMC6532242 DOI: 10.1186/s13053-019-0113-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/16/2019] [Indexed: 12/15/2022] Open
Abstract
Background Pathogenic variants in BRCA1 and BRCA2 cause hereditary breast and ovarian cancer. Screening of these genes has become easily accessible in diagnostic laboratories. Sequencing and copy number analyses are used to detect pathogenic variants, but also lead to identification of variants of unknown clinical significance (VUS). If the effect of a VUS can be clarified, it has direct consequence for the clinical management of the patient and family members. A splicing assay is one of several tools that might help in the classification of VUS. We therefore established mRNA analyses for BRCA1 and BRCA2 in the diagnostic laboratory in 2015. We hereby report the results of mRNA analysis variants in BRCA1 and BRCA2 after three years. Methods Variants predicted to alter splicing and variants within the canonical splice sites were selected for splicing analyses. Splicing assays were performed by reverse transcription-PCR of patient RNA. A biallalic expression analysis was carried out whenever possible. Results Twenty-five variants in BRCA1 and BRCA2 were analyzed by splicing assays; nine showed altered transcripts and 16 showed normal splicing patterns. The two novel pathogenic variants in BRCA1 c.4484 + 3 A > C and c.5407–10G > A were characterized. Conclusions We conclude that mRNA analyses are useful in characterization of variants that may affect splicing. The results can guide classification of variants from unknown clinical significance to pathogenic or benign in a diagnostic laboratory, and thus be of direct clinical importance.
Collapse
Affiliation(s)
| | | | - Deeqa Ahmed
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | |
Collapse
|
23
|
Li D, Harlan-Williams LM, Kumaraswamy E, Jensen RA. BRCA1-No Matter How You Splice It. Cancer Res 2019; 79:2091-2098. [PMID: 30992324 PMCID: PMC6497576 DOI: 10.1158/0008-5472.can-18-3190] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/09/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
BRCA1 (breast cancer 1, early onset), a well-known breast cancer susceptibility gene, is a highly alternatively spliced gene. BRCA1 alternative splicing may serve as an alternative regulatory mechanism for the inactivation of the BRCA1 gene in both hereditary and sporadic breast cancers, and other BRCA1-associated cancers. The alternative transcripts of BRCA1 can mimic known functions, possess unique functions compared with the full-length BRCA1 transcript, and in some cases, appear to function in opposition to full-length BRCA1 In this review, we will summarize the functional "naturally occurring" alternative splicing transcripts of BRCA1 and then discuss the latest next-generation sequencing-based detection methods and techniques to detect alternative BRCA1 splicing patterns and their potential use in cancer diagnosis, prognosis, and therapy.
Collapse
Affiliation(s)
- Dan Li
- The University of Kansas Cancer Center, Kansas City, Kansas
| | - Lisa M Harlan-Williams
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Easwari Kumaraswamy
- The University of Kansas Cancer Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
| | - Roy A Jensen
- The University of Kansas Cancer Center, Kansas City, Kansas.
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, Kansas
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| |
Collapse
|
24
|
Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Goina E, Acedo A, Buratti E, Velasco EA. Mis-splicing in breast cancer: identification of pathogenic BRCA2 variants by systematic minigene assays. J Pathol 2019; 248:409-420. [PMID: 30883759 DOI: 10.1002/path.5268] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 02/21/2019] [Accepted: 03/11/2019] [Indexed: 12/21/2022]
Abstract
Splicing disruption is a common mechanism of gene inactivation associated with germline variants of susceptibility genes. To study the role of BRCA2 mis-splicing in hereditary breast/ovarian cancer (HBOC), we performed a comprehensive analysis of variants from BRCA2 exons 2-9, as well as the initial characterization of the regulatory mechanisms of such exons. A pSAD-based minigene with exons 2-9 was constructed and validated in MCF-7 cells, producing the expected transcript (1016-nt/V1-BRCA2_exons_2-9-V2). DNA variants from mutational databases were analyzed by NNSplice and Human Splicing Finder softwares. To refine ESE-variant prediction, we mapped the regulatory regions through a functional strategy whereby 26 exonic microdeletions were introduced into the minigene and tested in MCF-7 cells. Thus, we identified nine spliceogenic ESE-rich intervals where ESE-variants may be located. Combining bioinformatics and microdeletion assays, 83 variants were selected and genetically engineered in the minigene. Fifty-three changes impaired splicing: 28 variants disrupted the canonical sites, four created new ones, 10 abrogated enhancers, eight created silencers and three caused a double-effect. Notably, nine spliceogenic-ESE variants were located within ESE-containing intervals. Capillary electrophoresis and sequencing revealed more than 23 aberrant transcripts, where exon skipping was the most common event. Interestingly, variant c.67G>A triggered the usage of a noncanonical GC-donor 4-nt upstream. Thirty-six variants that induced severe anomalies (>60% aberrant transcripts) were analyzed according to the ACMG guidelines. Thus, 28 variants were classified as pathogenic, five as likely pathogenic and three as variants of uncertain significance. Interestingly, 13 VUS were reclassified as pathogenic or likely pathogenic variants. In conclusion, a large fraction of BRCA2 variants (∼64%) provoked splicing anomalies lending further support to the high prevalence of this disease-mechanism. The low accuracy of ESE-prediction algorithms may be circumvented by functional ESE-mapping that represents an optimal strategy to identify spliceogenic ESE-variants. Finally, systematic functional assays by minigenes depict a valuable tool for the initial characterization of splicing anomalies and the clinical interpretation of variants. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Elisa Goina
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alberto Acedo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Emanuele Buratti
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| |
Collapse
|
25
|
Abstract
Hereditary breast and ovarian carcinomas are frequently caused by germline mutations of the BRCA1 and BRCA2 genes (BRCA1/2 syndromes) and are often less associated with other hereditary syndromes such as Li-Fraumeni and Peutz-Jeghers. The BRCA1/2 proteins have a special role in DNA repair. Therefore, loss of function due to mutation causes an accumulation of mutations in other genes and subsequent tumorigenesis at an early age. BRCA1/2 mutations are irregularly distributed over the length of the genes without hot spots, although special mutations are known. Breast and ovarian cancer occur far more frequently in women with BRCA1/2 germline mutations compared with the general population. Breast cancer occurs increasingly from the age of 30, ovarian cancer in BRCA1 syndrome from the age of 40 and BRCA2 from the age of 50. Suspicion of a BRCA syndrome should be prompted in the case of clustering of breast cancer in 1st degree relatives, in particular at a young age, if breast and ovarian cancer have occurred, and if cases of male breast cancer are known. Breast carcinomas with medullary differentiation seem to predominate in BRCA syndromes, but other carcinoma types may also occur. BRCA germline mutations seem to occur frequently in triple-negative breast carcinomas, whereas an association with ductal carcinoma in situ (DCIS) is rare. Ovarian carcinomas in BRCA syndromes are usually high-grade serous, mucinous carcinomas and borderline tumors are unusual. Pathology plays a special role within the multidisciplinary team in the recognition of patients with hereditary cancer syndromes.
Collapse
|
26
|
Lopez-Perolio I, Leman R, Behar R, Lattimore V, Pearson JF, Castéra L, Martins A, Vaur D, Goardon N, Davy G, Garre P, García-Barberán V, Llovet P, Pérez-Segura P, Díaz-Rubio E, Caldés T, Hruska KS, Hsuan V, Wu S, Pesaran T, Karam R, Vallon-Christersson J, Borg A, Valenzuela-Palomo A, Velasco EA, Southey M, Vreeswijk MPG, Devilee P, Kvist A, Spurdle AB, Walker LC, Krieger S, de la Hoya M. Alternative splicing and ACMG-AMP-2015-based classification of PALB2 genetic variants: an ENIGMA report. J Med Genet 2019; 56:453-460. [PMID: 30890586 PMCID: PMC6591742 DOI: 10.1136/jmedgenet-2018-105834] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/10/2019] [Accepted: 02/06/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND PALB2 monoallelic loss-of-function germ-line variants confer a breast cancer risk comparable to the average BRCA2 pathogenic variant. Recommendations for risk reduction strategies in carriers are similar. Elaborating robust criteria to identify loss-of-function variants in PALB2-without incurring overprediction-is thus of paramount clinical relevance. Towards this aim, we have performed a comprehensive characterisation of alternative splicing in PALB2, analysing its relevance for the classification of truncating and splice site variants according to the 2015 American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines. METHODS Alternative splicing was characterised in RNAs extracted from blood, breast and fimbriae/ovary-related human specimens (n=112). RNAseq, RT-PCR/CE and CloneSeq experiments were performed by five contributing laboratories. Centralised revision/curation was performed to assure high-quality annotations. Additional splicing analyses were performed in PALB2 c.212-1G>A, c.1684+1G>A, c.2748+2T>G, c.3113+5G>A, c.3350+1G>A, c.3350+4A>C and c.3350+5G>A carriers. The impact of the findings on PVS1 status was evaluated for truncating and splice site variant. RESULTS We identified 88 naturally occurring alternative splicing events (81 newly described), including 4 in-frame events predicted relevant to evaluate PVS1 status of splice site variants. We did not identify tissue-specific alternate gene transcripts in breast or ovarian-related samples, supporting the clinical relevance of blood-based splicing studies. CONCLUSIONS PVS1 is not necessarily warranted for splice site variants targeting four PALB2 acceptor sites (exons 2, 5, 7 and 10). As a result, rare variants at these splice sites cannot be assumed pathogenic/likely pathogenic without further evidences. Our study puts a warning in up to five PALB2 genetic variants that are currently reported as pathogenic/likely pathogenic in ClinVar.
Collapse
Affiliation(s)
- Irene Lopez-Perolio
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Raphaël Leman
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Raquel Behar
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Vanessa Lattimore
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Laurent Castéra
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Alexandra Martins
- Inserm U1245 Genomics and Personalized Medecine in Cancer and Neurological Disorders, UNIROUEN, Normandie Université, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Dominique Vaur
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Nicolas Goardon
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Grégoire Davy
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Pilar Garre
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Vanesa García-Barberán
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Patricia Llovet
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eduardo Díaz-Rubio
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | | | | | - Sitao Wu
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Johan Vallon-Christersson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Ake Borg
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | -
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Alberto Valenzuela-Palomo
- Splicing and genetic susceptibility to cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Eladio A Velasco
- Splicing and genetic susceptibility to cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Melissa Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Sophie Krieger
- Laboratory of Clinical Biology and Oncology, Centre François Baclesse, Inserm U1245 Genomics and Personalized Medicine in Cancer and Neurological Disorders, Normandy University, Caen, France
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| |
Collapse
|
27
|
Usefulness and Limitations of Comprehensive Characterization of mRNA Splicing Profiles in the Definition of the Clinical Relevance of BRCA1/2 Variants of Uncertain Significance. Cancers (Basel) 2019; 11:cancers11030295. [PMID: 30832263 PMCID: PMC6468917 DOI: 10.3390/cancers11030295] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Highly penetrant variants of BRCA1/2 genes are involved in hereditary predisposition to breast and ovarian cancer. The detection of pathogenic BRCA variants has a considerable clinical impact, allowing appropriate cancer-risk management. However, a major drawback is represented by the identification of variants of uncertain significance (VUS). Many VUS potentially affect mRNA splicing, making transcript analysis an essential step for the definition of their pathogenicity. Here, we characterize the impact on splicing of ten BRCA1/2 variants. Aberrant splicing patterns were demonstrated for eight variants whose alternative transcripts were fully characterized. Different events were observed, including exon skipping, intron retention, and usage of de novo and cryptic splice sites. Transcripts with premature stop codons or in-frame loss of functionally important residues were generated. Partial/complete splicing effect and quantitative contribution of different isoforms were assessed, leading to variant classification according to Evidence-based Network for the Interpretation of Mutant Alleles (ENIGMA) consortium guidelines. Two variants could be classified as pathogenic and two as likely benign, while due to a partial splicing effect, six variants remained of uncertain significance. The association with an undefined tumor risk justifies caution in recommending aggressive risk-reduction treatments, but prevents the possibility of receiving personalized therapies with potential beneficial effect. This indicates the need for applying additional approaches for the analysis of variants resistant to classification by gene transcript analyses.
Collapse
|
28
|
Brandão RD, Mensaert K, López‐Perolio I, Tserpelis D, Xenakis M, Lattimore V, Walker LC, Kvist A, Vega A, Gutiérrez‐Enríquez S, Díez O, de la Hoya M, Spurdle AB, De Meyer T, Blok MJ. Targeted RNA-seq successfully identifies normal and pathogenic splicing events in breast/ovarian cancer susceptibility and Lynch syndrome genes. Int J Cancer 2019; 145:401-414. [PMID: 30623411 PMCID: PMC6635756 DOI: 10.1002/ijc.32114] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/27/2018] [Accepted: 12/12/2018] [Indexed: 12/21/2022]
Abstract
A subset of genetic variants found through screening of patients with hereditary breast and ovarian cancer syndrome (HBOC) and Lynch syndrome impact RNA splicing. Through target enrichment of the transcriptome, it is possible to perform deep-sequencing and to identify the different and even rare mRNA isoforms. A targeted RNA-seq approach was used to analyse the naturally-occurring splicing events for a panel of 8 breast and/or ovarian cancer susceptibility genes (BRCA1, BRCA2, RAD51C, RAD51D, PTEN, STK11, CDH1, TP53), 3 Lynch syndrome genes (MLH1, MSH2, MSH6) and the fanconi anaemia SLX4 gene, in which monoallelic mutations were found in non-BRCA families. For BRCA1, BRCA2, RAD51C and RAD51D the results were validated by capillary electrophoresis and were compared to a non-targeted RNA-seq approach. We also compared splicing events from lymphoblastoid cell-lines with those from breast and ovarian fimbriae tissues. The potential of targeted RNA-seq to detect pathogenic changes in RNA-splicing was validated by the inclusion of samples with previously well characterized BRCA1/2 genetic variants. In our study, we update the catalogue of normal splicing events for BRCA1/2, provide an extensive catalogue of normal RAD51C and RAD51D alternative splicing, and list splicing events found for eight other genes. Additionally, we show that our approach allowed the identification of aberrant splicing events due to the presence of BRCA1/2 genetic variants and distinguished between complete and partial splicing events. In conclusion, targeted-RNA-seq can be very useful to classify variants based on their putative pathogenic impact on splicing.
Collapse
Affiliation(s)
- Rita D. Brandão
- Department of Clinical GeneticsMaastricht University Medical Centre+, GROW‐ School for Oncology and Developmental BiologyMaastrichtThe Netherlands
| | - Klaas Mensaert
- Department of Data Analysis and Mathematical Modelling and Bioinformatics Institute Ghent N2NGhent UniversityGhentBelgium
| | - Irene López‐Perolio
- Molecular Oncology Laboratory CIBERONCHospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Demis Tserpelis
- Department of Clinical GeneticsMaastricht University Medical Centre+, GROW‐ School for Oncology and Developmental BiologyMaastrichtThe Netherlands
| | - Markos Xenakis
- Department of Clinical GeneticsMaastricht University Medical Centre+, GROW‐ School for Oncology and Developmental BiologyMaastrichtThe Netherlands
- Department of Data Science and Knowledge EngineeringMaastricht UniversityMaastrichtThe Netherlands
| | - Vanessa Lattimore
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Logan C. Walker
- Department of Pathology and Biomedical ScienceUniversity of OtagoChristchurchNew Zealand
| | - Anders Kvist
- Division of Oncology and Pathology, Department of Clinical SciencesLund UniversityLundSweden
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica‐Servicio Galgo de SaúdeGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | | | - Orland Díez
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- Area of Clinical and Molecular GeneticsUniversity Hospital of Vall d'HebronBarcelonaSpain
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONCHospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling and Bioinformatics Institute Ghent N2NGhent UniversityGhentBelgium
- CRIG (Cancer Research Institute Ghent)Ghent UniversityGhentBelgium
| | - Marinus J. Blok
- Department of Clinical GeneticsMaastricht University Medical Centre+, GROW‐ School for Oncology and Developmental BiologyMaastrichtThe Netherlands
| |
Collapse
|
29
|
Quantifying BRCA1 and BRCA2 mRNA Isoform Expression Levels in Single Cells. Int J Mol Sci 2019; 20:ijms20030693. [PMID: 30736279 PMCID: PMC6387195 DOI: 10.3390/ijms20030693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/28/2019] [Accepted: 02/05/2019] [Indexed: 12/05/2022] Open
Abstract
BRCA1 and BRCA2 spliceogenic variants are often associated with an elevated risk of breast and ovarian cancers. Analyses of BRCA1 and BRCA2 splicing patterns have traditionally used technologies that sample a population of cells but do not account for the variation that may be present between individual cells. This novel proof of concept study utilises RNA in situ hybridisation to measure the absolute expression of BRCA1 and BRCA2 mRNA splicing events in single lymphoblastoid cells containing known spliceogenic variants (BRCA1c.671-2 A>G or BRCA2c.7988 A>T). We observed a large proportion of cells (>42%) in each sample that did not express mRNA for the targeted gene. Increased levels (average mRNA molecules per cell) of BRCA2 ∆17_18 were observed in the cells containing the known spliceogenic variant BRCA2c.7988 A>T, but cells containing BRCA1c.671-2 A>G were not found to express significantly increased levels of BRCA1 ∆11, as had been shown previously. Instead, we show for each variant carrier sample that a higher proportion of cells expressed the targeted splicing event compared to control cells. These results indicate that BRCA1/2 mRNA is expressed stochastically, suggesting that previously reported results using RT-PCR may have been influenced by the number of cells with BRCA1/2 mRNA expression and may not represent an elevation of constitutive mRNA expression. Detection of mRNA expression in single cells allows for a more comprehensive understanding of how spliceogenic variants influence the expression of mRNA isoforms. However, further research is required to assess the utility of this technology to measure the expression of predicted spliceogenic BRCA1 and BRCA2 variants in a diagnostic setting.
Collapse
|
30
|
Farber-Katz S, Hsuan V, Wu S, Landrith T, Vuong H, Xu D, Li B, Hoo J, Lam S, Nashed S, Toppmeyer D, Gray P, Haynes G, Lu HM, Elliott A, Tippin Davis B, Karam R. Quantitative Analysis of BRCA1 and BRCA2 Germline Splicing Variants Using a Novel RNA-Massively Parallel Sequencing Assay. Front Oncol 2018; 8:286. [PMID: 30101128 PMCID: PMC6072868 DOI: 10.3389/fonc.2018.00286] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/09/2018] [Indexed: 12/27/2022] Open
Abstract
Clinical genetic testing for hereditary breast and ovarian cancer (HBOC) is becoming widespread. However, the interpretation of variants of unknown significance (VUS) in HBOC genes, such as the clinically actionable genes BRCA1 and BRCA2, remain a challenge. Among the variants that are frequently classified as VUS are those with unclear effects on splicing. In order to address this issue we developed a high-throughput RNA-massively parallel sequencing assay—CloneSeq—capable to perform quantitative and qualitative analysis of transcripts in cell lines and HBOC patients. This assay is based on cloning of RT-PCR products followed by massive parallel sequencing of the cloned transcripts. To validate this assay we compared it to the RNA splicing assays recommended by members of the ENIGMA (Evidence-based Network for the Interpretation of Germline Mutant Alleles) consortium. This comparison was performed using well-characterized lymphoblastoid cell lines (LCLs) generated from carriers of the BRCA1 or BRCA2 germline variants that have been previously described to be associated with splicing defects. CloneSeq was able to replicate the ENIGMA results, in addition to providing quantitative characterization of BRCA1 and BRCA2 germline splicing alterations in a high-throughput fashion. Furthermore, CloneSeq was used to analyze blood samples obtained from carriers of BRCA1 or BRCA2 germline sequence variants, including the novel uncharacterized alteration BRCA1 c.5152+5G>T, which was identified in a HBOC family. CloneSeq provided a high-resolution picture of all the transcripts induced by BRCA1 c.5152+5G>T, indicating it results in significant levels of exon skipping. This analysis proved to be important for the classification of BRCA1 c.5152+5G>T as a clinically actionable likely pathogenic variant. Reclassifications such as these are fundamental in order to offer preventive measures, targeted treatment, and pre-symptomatic screening to the correct individuals.
Collapse
Affiliation(s)
- Suzette Farber-Katz
- Translational Genomics Laboratory, Ambry Genetics, Aliso Viejo, CA, United States
| | - Vickie Hsuan
- Translational Genomics Laboratory, Ambry Genetics, Aliso Viejo, CA, United States
| | - Sitao Wu
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA, United States
| | - Tyler Landrith
- Translational Genomics Laboratory, Ambry Genetics, Aliso Viejo, CA, United States
| | - Huy Vuong
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA, United States
| | - Dong Xu
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA, United States
| | - Bing Li
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA, United States
| | - Jayne Hoo
- Department of Research and Development, Ambry Genetics, Aliso Viejo, CA, United States
| | - Stephanie Lam
- Department of Research and Development, Ambry Genetics, Aliso Viejo, CA, United States
| | - Sarah Nashed
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Deborah Toppmeyer
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Phillip Gray
- Department of Research and Development, Ambry Genetics, Aliso Viejo, CA, United States
| | - Ginger Haynes
- Translational Genomics Laboratory, Ambry Genetics, Aliso Viejo, CA, United States
| | - Hsiao-Mei Lu
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA, United States
| | - Aaron Elliott
- Department of Research and Development, Ambry Genetics, Aliso Viejo, CA, United States
| | - Brigette Tippin Davis
- Department of Research and Development, Ambry Genetics, Aliso Viejo, CA, United States
| | - Rachid Karam
- Translational Genomics Laboratory, Ambry Genetics, Aliso Viejo, CA, United States
| |
Collapse
|
31
|
Montalban G, Fraile-Bethencourt E, López-Perolio I, Pérez-Segura P, Infante M, Durán M, Alonso-Cerezo MC, López-Fernández A, Diez O, de la Hoya M, Velasco EA, Gutiérrez-Enríquez S. Characterization of spliceogenic variants located in regions linked to high levels of alternative splicing: BRCA2 c.7976+5G > T as a case study. Hum Mutat 2018; 39:1155-1160. [PMID: 29969168 DOI: 10.1002/humu.23583] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 06/04/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022]
Abstract
Many BRCA1 and BRCA2 (BRCA1/2) genetic variants have been studied at mRNA level and linked to hereditary breast and ovarian cancer due to splicing alteration. In silico tools are reliable when assessing variants located in consensus splice sites, but we may identify variants in complex genomic contexts for which bioinformatics is not precise enough. In this study, we characterize BRCA2 c.7976 + 5G > T variant located in intron 17 which has an atypical donor site (GC). This variant was identified in three unrelated Spanish families and we have detected exon 17 skipping as the predominant transcript occurring in carriers. We have also detected several isoforms (Δ16-18, Δ17,18, Δ18, and ▼17q224 ) at different expression levels among carriers and controls. This study remarks the challenge of interpreting genetic variants when multiple alternative isoforms are present, and that caution must be taken when using in silico tools to identify potential spliceogenic variants located in GC-AG introns.
Collapse
Affiliation(s)
- Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Eugenia Fraile-Bethencourt
- Splicing and genetic susceptibility to cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Irene López-Perolio
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Mar Infante
- Cancer Genetics, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - Mercedes Durán
- Cancer Genetics, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | - María Concepción Alonso-Cerezo
- Genética Clínica. Servicio Análisis Clínicos. Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria Hospital Universitario de la Princesa, Madrid, Spain
| | - Adrià López-Fernández
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain.,Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eladio A Velasco
- Splicing and genetic susceptibility to cancer, Instituto de Biología y Genética Molecular (CSIC-UVa), Valladolid, Spain
| | | |
Collapse
|
32
|
Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Acedo A, Velasco EA. Identification of Eight Spliceogenic Variants in BRCA2 Exon 16 by Minigene Assays. Front Genet 2018; 9:188. [PMID: 29881398 PMCID: PMC5977032 DOI: 10.3389/fgene.2018.00188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/08/2018] [Indexed: 11/17/2022] Open
Abstract
Genetic testing of BRCA1 and BRCA2 identifies a large number of variants of uncertain clinical significance whose functional and clinical interpretations pose a challenge for genetic counseling. Interestingly, a relevant fraction of DNA variants can disrupt the splicing process in cancer susceptibility genes. We have tested more than 200 variants throughout 19 BRCA2 exons mostly by minigene assays, 54% of which displayed aberrant splicing, thus confirming the utility of this assay to check genetic variants in the absence of patient RNA. Our goal was to investigate BRCA2 exon 16 with a view to characterizing spliceogenic variants recorded at the mutational databases. Seventy-two different BIC and UMD variants were analyzed with NNSplice and Human Splicing Finder, 12 of which were selected because they were predicted to disrupt essential splice motifs: canonical splice sites (ss; eight variants) and exonic/intronic splicing enhancers (four variants). These 12 candidate variants were introduced into the BRCA2 minigene with seven exons (14–20) by site-directed mutagenesis and then transfected into MCF-7 cells. Seven variants (six intronic and one missense) induced complete abnormal splicing patterns: c.7618-2A>T, c.7618-2A>G, c.7618-1G>C, c.7618-1G>A, c.7805G>C, c.7805+1G>A, and c.7805+3A>C, as well as a partial anomalous outcome by c.7802A>G. They generated at least 10 different transcripts: Δ16p44 (alternative 3’ss 44-nt downstream; acceptor variants), Δ16 (exon 16-skipping; donor variants), Δ16p55 (alternative 3’ss 55-nt downstream), Δ16q4 (alternative 5’ss 4-nt upstream), Δ16q100 (alternative 5’ss 4-nt upstream), ▾16q20 (alternative 5’ss 20-nt downstream), as well as minor (Δ16p93 and Δ16,17p69) and uncharacterized transcripts of 893 and 954 nucleotides. Isoforms Δ16p44, Δ16, Δ16p55, Δ16q4, Δ16q100, and ▾16q20 introduced premature termination codons which presumably inactivate BRCA2. According to the guidelines the American College of Medical Genetics and Genomics these eight variants could be classified as pathogenic or likely pathogenic whereas the Evidence-based Network for the Interpretation of Germline Mutant Alleles rules suggested seven class 4 and one class 3 variants. In conclusion, our study highlights the relevance of splicing functional assays by hybrid minigenes for the clinical classification of genetic variations. Hence, we provide new data about spliceogenic variants of BRCA2 exon 16 that are directly correlated with breast cancer susceptibility.
Collapse
Affiliation(s)
- Eugenia Fraile-Bethencourt
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Beatriz Díez-Gómez
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| | - Alberto Acedo
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain.,Biome Makers Inc., San Francisco, CA, United States
| | - Eladio A Velasco
- Splicing and Genetic Susceptibility to Cancer, Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas, Universidad de Valladolid, Valladolid, Spain
| |
Collapse
|
33
|
Lattimore VL, Pearson JF, Currie MJ, Spurdle AB, Robinson BA, Walker LC. Investigation of Experimental Factors That Underlie BRCA1/2 mRNA Isoform Expression Variation: Recommendations for Utilizing Targeted RNA Sequencing to Evaluate Potential Spliceogenic Variants. Front Oncol 2018; 8:140. [PMID: 29774201 PMCID: PMC5943536 DOI: 10.3389/fonc.2018.00140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2. The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess BRCA1 and BRCA2 mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study. Capture of the targeted cDNA sequences was carried out using 34 BRCA1 and 28 BRCA2 oligonucleotides from the Illumina Truseq Targeted RNA Expression platform. Our results show that targeted RNA-seq analysis of LCLs overcomes many of the methodology limitations associated with PCR-based assays leading us to make the following observations and recommendations: (1) technical replicates (n > 2) of variant carriers to capture methodology induced variability associated with RNA-seq assays, (2) LCLs can undergo multiple freeze/thaw cycles and can be cultured up to 2 weeks without noticeably influencing isoform expression levels, (3) nonsense-mediated decay inhibitors are essential prior to splicing assays for comprehensive mRNA isoform detection, (4) quantitative assessment of exon:exon junction levels across BRCA1 and BRCA2 can help distinguish between normal and aberrant isoform expression patterns. Experimentally derived recommendations from this study will facilitate the application of targeted RNA-seq platforms for the quantitation of BRCA1 and BRCA2 mRNA aberrations associated with sequence variants of uncertain clinical significance.
Collapse
Affiliation(s)
- Vanessa L Lattimore
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand.,Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Margaret J Currie
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Bridget A Robinson
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.,Canterbury Regional Cancer and Haematology Service, Canterbury District Health Board, Christchurch Hospital, Christchurch, New Zealand
| | - Logan C Walker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| |
Collapse
|
34
|
Colombo M, Lòpez‐Perolio I, Meeks HD, Caleca L, Parsons MT, Li H, De Vecchi G, Tudini E, Foglia C, Mondini P, Manoukian S, Behar R, Garcia EBG, Meindl A, Montagna M, Niederacher D, Schmidt AY, Varesco L, Wappenschmidt B, Bolla MK, Dennis J, Michailidou K, Wang Q, Aittomäki K, Andrulis IL, Anton‐Culver H, Arndt V, Beckmann MW, Beeghly‐Fadel A, Benitez J, Boeckx B, Bogdanova NV, Bojesen SE, Bonanni B, Brauch H, Brenner H, Burwinkel B, Chang‐Claude J, Conroy DM, Couch FJ, Cox A, Cross SS, Czene K, Devilee P, Dörk T, Eriksson M, Fasching PA, Figueroa J, Fletcher O, Flyger H, Gabrielson M, García‐Closas M, Giles GG, González‐Neira A, Guénel P, Haiman CA, Hall P, Hamann U, Hartman M, Hauke J, Hollestelle A, Hopper JL, Jakubowska A, Jung A, Kosma V, Lambrechts D, Le Marchand L, Lindblom A, Lubinski J, Mannermaa A, Margolin S, Miao H, Milne RL, Neuhausen SL, Nevanlinna H, Olson JE, Peterlongo P, Peto J, Pylkäs K, Sawyer EJ, Schmidt MK, Schmutzler RK, Schneeweiss A, Schoemaker MJ, See MH, Southey MC, Swerdlow A, Teo SH, Toland AE, Tomlinson I, Truong T, van Asperen CJ, van den Ouweland AM, van der Kolk LE, Winqvist R, Yannoukakos D, Zheng W, Dunning AM, Easton DF, Henderson A, Hogervorst FB, Izatt L, Offitt K, Side LE, van Rensburg EJ, EMBRACE S, HEBON S, McGuffog L, Antoniou AC, Chenevix‐Trench G, Spurdle AB, Goldgar DE, de la Hoya M, Radice P. The BRCA2 c.68-7T > A variant is not pathogenic: A model for clinical calibration of spliceogenicity. Hum Mutat 2018; 39:729-741. [PMID: 29460995 PMCID: PMC5947288 DOI: 10.1002/humu.23411] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 02/06/2018] [Accepted: 02/10/2018] [Indexed: 12/12/2022]
Abstract
Although the spliceogenic nature of the BRCA2 c.68-7T > A variant has been demonstrated, its association with cancer risk remains controversial. In this study, we accurately quantified by real-time PCR and digital PCR (dPCR), the BRCA2 isoforms retaining or missing exon 3. In addition, the combined odds ratio for causality of the variant was estimated using genetic and clinical data, and its associated cancer risk was estimated by case-control analysis in 83,636 individuals. Co-occurrence in trans with pathogenic BRCA2 variants was assessed in 5,382 families. Exon 3 exclusion rate was 4.5-fold higher in variant carriers (13%) than controls (3%), indicating an exclusion rate for the c.68-7T > A allele of approximately 20%. The posterior probability of pathogenicity was 7.44 × 10-115 . There was neither evidence for increased risk of breast cancer (OR 1.03; 95% CI 0.86-1.24) nor for a deleterious effect of the variant when co-occurring with pathogenic variants. Our data provide for the first time robust evidence of the nonpathogenicity of the BRCA2 c.68-7T > A. Genetic and quantitative transcript analyses together inform the threshold for the ratio between functional and altered BRCA2 isoforms compatible with normal cell function. These findings might be exploited to assess the relevance for cancer risk of other BRCA2 spliceogenic variants.
Collapse
Affiliation(s)
- Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Irene Lòpez‐Perolio
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Huong D. Meeks
- Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Laura Caleca
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Hongyan Li
- Huntsman Cancer InstituteUniversity of UtahSalt Lake CityUtah
| | - Giovanna De Vecchi
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Emma Tudini
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Claudia Foglia
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Patrizia Mondini
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Siranoush Manoukian
- Unit of Medical GeneticsDepartment of Medical Oncology and HematologyFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| | - Raquel Behar
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Encarna B. Gómez Garcia
- Department of Clinical Genetics and GROWSchool for Oncology and Developmental BiologyMUMCMaastrichtThe Netherlands
| | - Alfons Meindl
- Department of Obstetrics and GynecologyUniversity HospitalLMU MunichGermany
| | - Marco Montagna
- Immunology and Molecular Oncology UnitVeneto Institute of Oncology IOV ‐ IRCCSPaduaItaly
| | - Dieter Niederacher
- Department of Gynaecology and ObstetricsUniversity Hospital DüsseldorfHeinrich‐Heine UniversityDuesseldorfGermany
| | - Ane Y. Schmidt
- Center for Genomic MedicineRigshospitaletUniversity of CopenhagenCopenhagenDenmark
| | | | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
| | - Manjeet K. Bolla
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Joe Dennis
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
- Department of Electron Microscopy/Molecular PathologyThe Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Qin Wang
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Kristiina Aittomäki
- Department of Clinical GeneticsHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Irene L. Andrulis
- Fred A. Litwin Center for Cancer GeneticsLunenfeld‐Tanenbaum Research Institute of Mount Sinai HospitalTorontoOntario
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
| | - Hoda Anton‐Culver
- Department of EpidemiologyUniversity of California IrvineIrvineCalifornia
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Matthias W. Beckmann
- Department of Gynaecology and ObstetricsUniversity Hospital Erlangen, Friedrich‐Alexander University Erlangen‐NurembergComprehensive Cancer Center Erlangen‐EMNErlangenGermany
| | - Alicia Beeghly‐Fadel
- Division of EpidemiologyDepartment of MedicineVanderbilt Epidemiology CenterVanderbilt‐Ingram Cancer CenterVanderbilt University School of MedicineNashvilleTennessee
| | - Javier Benitez
- Human Cancer Genetics ProgramSpanish National Cancer Research CentreMadridSpain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER)ValenciaSpain
| | - Bram Boeckx
- VIB Center for Cancer BiologyVIBLeuvenBelgium
- Laboratory for Translational GeneticsDepartment of Human GeneticsUniversity of LeuvenLeuvenBelgium
| | - Natalia V. Bogdanova
- Department of Radiation OncologyHannover Medical SchoolHannoverGermany
- Gynaecology Research UnitHannover Medical SchoolHannoverGermany
- N.N. Alexandrov Research Institute of Oncology and Medical RadiologyMinskBelarus
| | - Stig E. Bojesen
- Copenhagen General Population StudyHerlevand Gentofte HospitalCopenhagen University HospitalHerlevDenmark
- Department of Clinical BiochemistryHerlev and Gentofte HospitalCopenhagen University HospitalHerlevDenmark
- Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Bernardo Bonanni
- Division of Cancer Prevention and GeneticsIstituto Europeo di OncologiaMilanItaly
| | - Hiltrud Brauch
- Dr. Margarete Fischer‐Bosch‐Institute of Clinical PharmacologyStuttgartGermany
- University of TübingenTübingenGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging ResearchGerman Cancer Research Center (DKFZ)HeidelbergGermany
- German Cancer Consortium (DKTK)German Cancer Research Center (DKFZ)HeidelbergGermany
- Division of Preventive OncologyGerman Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT)HeidelbergGermany
| | - Barbara Burwinkel
- Department of Obstetrics and GynecologyUniversity of HeidelbergHeidelbergGermany
- Molecular Epidemiology GroupC080German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Jenny Chang‐Claude
- Division of Cancer EpidemiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Research Group Genetic Cancer EpidemiologyUniversity Cancer Center Hamburg (UCCH)University Medical Center Hamburg‐EppendorfHamburgGermany
| | - Don M. Conroy
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Fergus J. Couch
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterNew York
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA)Department of Oncology and MetabolismUniversity of SheffieldSheffieldUK
| | - Simon S. Cross
- Academic Unit of PathologyDepartment of NeuroscienceUniversity of SheffieldSheffieldUK
| | - Kamila Czene
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Peter Devilee
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Thilo Dörk
- Gynaecology Research UnitHannover Medical SchoolHannoverGermany
| | - Mikael Eriksson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Peter A. Fasching
- Department of Gynaecology and ObstetricsUniversity Hospital Erlangen, Friedrich‐Alexander University Erlangen‐NurembergComprehensive Cancer Center Erlangen‐EMNErlangenGermany
- David Geffen School of MedicineDepartment of Medicine Division of Hematology and OncologyUniversity of California at Los AngelesLos AngelesCalifornia
| | - Jonine Figueroa
- Usher Institute of Population Health Sciences and InformaticsThe University of Edinburgh Medical SchoolEdinburghUK
- Division of Cancer Epidemiology and GeneticsNational Cancer InstituteRockvilleMaryland
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer ResearchLondonUK
| | - Henrik Flyger
- Department of Breast SurgeryHerlev and Gentofte HospitalCopenhagen University HospitalHerlevDenmark
| | - Marike Gabrielson
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | | | - Graham G. Giles
- Cancer Epidemiology & Intelligence DivisionCancer Council VictoriaMelbourneAustralia
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Anna González‐Neira
- Human Cancer Genetics ProgramSpanish National Cancer Research CentreMadridSpain
| | - Pascal Guénel
- Cancer & Environment GroupCenter for Research in Epidemiology and Population Health (CESP)INSERMUniversity Paris‐SudUniversity Paris‐SaclayVillejuifFrance
| | - Christopher A. Haiman
- Department of Preventive MedicineKeck School of MedicineUniversity of Southern CaliforniaLos AngelesCalifornia
| | - Per Hall
- Department of Medical Epidemiology and BiostatisticsKarolinska InstitutetStockholmSweden
| | - Ute Hamann
- Molecular Genetics of Breast CancerDeutsches Krebsforschungszentrum (DKFZ)HeidelbergGermany
| | - Mikael Hartman
- Saw Swee Hock School of Public HealthNational University of SingaporeSingaporeSingapore
- Department of SurgeryNational University Health SystemSingaporeSingapore
| | - Jan Hauke
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Antoinette Hollestelle
- Department of Medical OncologyFamily Cancer ClinicErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - John L. Hopper
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Anna Jakubowska
- Department of Genetics and PathologyPomeranian Medical UniversitySzczecinPoland
| | - Audrey Jung
- Division of Cancer EpidemiologyGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Veli‐Matti Kosma
- Translational Cancer Research AreaUniversity of Eastern FinlandKuopioFinland
- Institute of Clinical MedicinePathology and Forensic MedicineUniversity of Eastern FinlandKuopioFinland
- Imaging CenterDepartment of Clinical PathologyKuopio University HospitalKuopioFinland
| | - Diether Lambrechts
- VIB Center for Cancer BiologyVIBLeuvenBelgium
- Laboratory for Translational GeneticsDepartment of Human GeneticsUniversity of LeuvenLeuvenBelgium
| | - Loid Le Marchand
- Epidemiology ProgramUniversity of Hawaii Cancer CenterHonoluluHawaii
| | - Annika Lindblom
- Department of Molecular Medicine and SurgeryKarolinska InstitutetStockholmSweden
| | - Jan Lubinski
- Department of Genetics and PathologyPomeranian Medical UniversitySzczecinPoland
| | - Arto Mannermaa
- Translational Cancer Research AreaUniversity of Eastern FinlandKuopioFinland
- Institute of Clinical MedicinePathology and Forensic MedicineUniversity of Eastern FinlandKuopioFinland
- Imaging CenterDepartment of Clinical PathologyKuopio University HospitalKuopioFinland
| | - Sara Margolin
- Department of Clinical Science and Education SödersjukhusetKarolinska InstitutetStockholmSweden
| | - Hui Miao
- Saw Swee Hock School of Public HealthNational University of SingaporeSingaporeSingapore
| | - Roger L. Milne
- Cancer Epidemiology & Intelligence DivisionCancer Council VictoriaMelbourneAustralia
- Centre for Epidemiology and BiostatisticsMelbourne School of Population and Global healthThe University of MelbourneMelbourneAustralia
| | - Susan L. Neuhausen
- Department of Population SciencesBeckman Research Institute of City of HopeDuarteCalifornia
| | - Heli Nevanlinna
- Department of Obstetrics and GynecologyHelsinki University HospitalUniversity of HelsinkiHelsinkiFinland
| | - Janet E. Olson
- Department of Health Sciences ResearchMayo ClinicRochesterNew York
| | - Paolo Peterlongo
- IFOMThe FIRC (Italian Foundation for Cancer Research) Institute of Molecular OncologyMilanItaly
| | - Julian Peto
- Department of Non‐Communicable Disease EpidemiologyLondon School of Hygiene and Tropical MedicineLondonUK
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor BiologyCancer and Translational Medicine Research UnitBiocenter OuluUniversity of OuluOuluFinland
- Laboratory of Cancer Genetics and Tumor BiologyNorthern Finland Laboratory Centre OuluOuluFinland
| | | | - Marjanka K. Schmidt
- Division of Molecular PathologyThe Netherlands Cancer Institute – Antoni van Leeuwenhoek HospitalAmsterdamThe Netherlands
- Division of Psychosocial Research and EpidemiologyThe Netherlands Cancer Institute – Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Rita K. Schmutzler
- Center for Hereditary Breast and Ovarian CancerUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology (CIO)Medical FacultyUniversity Hospital of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)University of CologneCologneGermany
| | - Andreas Schneeweiss
- Department of Obstetrics and GynecologyUniversity of HeidelbergHeidelbergGermany
- National Center for Tumor DiseasesUniversity of HeidelbergHeidelbergGermany
| | | | - Mee Hoong See
- Breast Cancer Research UnitCancer Research InstituteUniversity Malaya Medical CentreKuala LumpurMalaysia
| | | | - Anthony Swerdlow
- Division of Genetics and EpidemiologyThe Institute of Cancer ResearchLondonUK
- Division of Breast Cancer ResearchThe Institute of Cancer ResearchLondonUK
| | - Soo H. Teo
- Breast Cancer Research UnitCancer Research InstituteUniversity Malaya Medical CentreKuala LumpurMalaysia
- Cancer Research MalaysiaSubang JayaSelangorMalaysia
| | - Amanda E. Toland
- Department of Molecular VirologyImmunology and Medical GeneticsComprehensive Cancer CenterThe Ohio State UniversityColumbusOhio
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford NIHR Biomedical Research CentreUniversity of OxfordOxfordUK
| | - Thérèse Truong
- Cancer & Environment GroupCenter for Research in Epidemiology and Population Health (CESP)INSERMUniversity Paris‐SudUniversity Paris‐SaclayVillejuifFrance
| | | | | | - Lizet E. van der Kolk
- Family Cancer ClinicThe Netherlands Cancer Institute ‐ Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor BiologyCancer and Translational Medicine Research UnitBiocenter OuluUniversity of OuluOuluFinland
- Laboratory of Cancer Genetics and Tumor BiologyNorthern Finland Laboratory Centre OuluOuluFinland
| | - Drakoulis Yannoukakos
- Molecular Diagnostics LaboratoryINRASTESNational Centre for Scientific Research “Demokritos”AthensGreece
| | - Wei Zheng
- Division of EpidemiologyDepartment of MedicineVanderbilt Epidemiology CenterVanderbilt‐Ingram Cancer CenterVanderbilt University School of MedicineNashvilleTennessee
| | | | - Alison M. Dunning
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Douglas F. Easton
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
- Centre for Cancer Genetic EpidemiologyDepartment of OncologyUniversity of CambridgeCambridgeUK
| | - Alex Henderson
- Institute of Genetic MedicineCentre for LifeNewcastle Upon Tyne Hospitals NHS TrustNewcastle upon TyneUK
| | - Frans B.L. Hogervorst
- Family Cancer ClinicThe Netherlands Cancer Institute ‐ Antoni van Leeuwenhoek hospitalAmsterdamThe Netherlands
| | - Louise Izatt
- Clinical GeneticsGuy's and St. Thomas’ NHS Foundation TrustLondonUK
| | - Kenneth Offitt
- Clinical Genetics Research LaboratoryDept. of MedicineCancer Biology and GeneticsMemorial Sloan‐Kettering Cancer CenterNew YorkNew York
| | - Lucy E. Side
- Wessex Clinical Genetics ServiceMailpoint 627, Princess Anne Hospital, Coxford Road, Southampton, SO16 5YA
| | | | - Study EMBRACE
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeStrangeways Research LaboratoryWorts CausewayCambridgeUK
| | - Study HEBON
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON)Coordinating center: Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Lesley McGuffog
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Antonis C. Antoniou
- Centre for Cancer Genetic EpidemiologyDepartment of Public Health and Primary CareUniversity of CambridgeCambridgeUK
| | - Georgia Chenevix‐Trench
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbane, QLD 4006Australia
| | | | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONCHospital Clinico San CarlosIdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos)MadridSpain
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT)MilanItaly
| |
Collapse
|
35
|
Baert A, Machackova E, Coene I, Cremin C, Turner K, Portigal-Todd C, Asrat MJ, Nuk J, Mindlin A, Young S, MacMillan A, Van Maerken T, Trbusek M, McKinnon W, Wood ME, Foulkes WD, Santamariña M, de la Hoya M, Foretova L, Poppe B, Vral A, Rosseel T, De Leeneer K, Vega A, Claes KBM. Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2 allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11. Hum Mutat 2018; 39:515-526. [PMID: 29280214 DOI: 10.1002/humu.23390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/03/2017] [Accepted: 12/17/2017] [Indexed: 12/31/2022]
Abstract
For 21 putative BRCA1 and BRCA2 splice site variants, the concordance between mRNA analysis and predictions by in silico programs was evaluated. Aberrant splicing was confirmed for 12 alterations. In silico prediction tools were helpful to determine for which variants cDNA analysis is warranted, however, predictions for variants in the Cartegni consensus region but outside the canonical sites, were less reliable. Learning algorithms like Adaboost and Random Forest outperformed the classical tools. Further validations are warranted prior to implementation of these novel tools in clinical settings. Additionally, we report here for the first time activated cryptic donor sites in the large exon 11 of BRCA2 by evaluating the effect at the cDNA level of a novel tandem duplication (5' breakpoint in intron 4; 3' breakpoint in exon 11) and of a variant disrupting the splice donor site of exon 11 (c.6841+1G > C). Additional sites were predicted, but not activated. These sites warrant further research to increase our knowledge on cis and trans acting factors involved in the conservation of correct transcription of this large exon. This may contribute to adequate design of ASOs (antisense oligonucleotides), an emerging therapy to render cancer cells sensitive to PARP inhibitor and platinum therapies.
Collapse
Affiliation(s)
- Annelot Baert
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ilse Coene
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Carol Cremin
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | | | - Jennifer Nuk
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Sean Young
- BC Cancer Agency, Vancouver, British Columbia, Canada.,Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andree MacMillan
- Provincial Medical Genetics Program, Eastern Health, St. John's, Newfoundland and Labrador, Canada
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin Trbusek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Wendy McKinnon
- Familial Cancer Program, University of Vermont Medical Center, Burlington, Vermont, United States
| | - Marie E Wood
- Familial Cancer Program, University of Vermont Medical Center, Burlington, Vermont, United States
| | - William D Foulkes
- Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Anne Vral
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
| | | |
Collapse
|
36
|
Jarhelle E, Riise Stensland HMF, Mæhle L, Van Ghelue M. Characterization of BRCA1 and BRCA2 variants found in a Norwegian breast or ovarian cancer cohort. Fam Cancer 2017; 16:1-16. [PMID: 27495310 DOI: 10.1007/s10689-016-9916-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Germline mutations in BRCA1 and BRCA2 cause hereditary breast and ovarian cancer. Molecular screening of these two genes in patients with a family history of breast or ovarian cancer has revealed pathogenic variants as well as genetic variants of unknown significance (VUS). These VUS may cause a challenge in the genetic counseling process regarding clinical management of the patient and the family. We investigated 32 variants previously detected in 33 samples from patients with a family history of breast or ovarian cancer. cDNA was analyzed for alternative transcripts and selected missense variants located in the BRCT domains of BRCA1 were assessed for their trans-activation ability. Although an extensive cDNA analysis was done, only three of the 32 variants appeared to affect the splice-process (BRCA1 c.213-5T>A, BRCA1 c.5434C>G and BRCA2 c.68-7T>A). In addition, two variants located in the BRCT domains of BRCA1 (c.5075A>C p.Asp1692Ala and c.5513T>G p.Val1838Gly) were shown to abolish the BRCT domain trans-activation ability, whereas BRCA1 c.5125G>A p.Gly1709Arg exhibited equal trans-activation capability as the WT domain. These functional studies may offer further insights into the pathogenicity of certain identified variants; however, this assay is only applicable for a subset of missense variants.
Collapse
Affiliation(s)
- Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway
| | - Hilde Monica Frostad Riise Stensland
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway. .,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway. .,Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway.
| |
Collapse
|
37
|
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: 32] [Impact Index Per Article: 4.6] [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.
Collapse
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
| |
Collapse
|
38
|
Meyer S, Stevens A, Paredes R, Schneider M, Walker MJ, Williamson AJK, Gonzalez-Sanchez MB, Smetsers S, Dalal V, Teng HY, White DJ, Taylor S, Muter J, Pierce A, de Leonibus C, Rockx DAP, Rooimans MA, Spooncer E, Stauffer S, Biswas K, Godthelp B, Dorsman J, Clayton PE, Sharan SK, Whetton AD. Acquired cross-linker resistance associated with a novel spliced BRCA2 protein variant for molecular phenotyping of BRCA2 disruption. Cell Death Dis 2017; 8:e2875. [PMID: 28617445 PMCID: PMC5520920 DOI: 10.1038/cddis.2017.264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/29/2017] [Accepted: 05/05/2017] [Indexed: 12/25/2022]
Abstract
BRCA2 encodes a protein with a fundamental role in homologous recombination that is essential for normal development. Carrier status of mutations in BRCA2 is associated with familial breast and ovarian cancer, while bi-allelic BRCA2 mutations can cause Fanconi anemia (FA), a cancer predisposition syndrome with cellular cross-linker hypersensitivity. Cancers associated with BRCA2 mutations can acquire chemo-resistance on relapse. We modeled acquired cross-linker resistance with an FA-derived BRCA2-mutated acute myeloid leukemia (AML) platform. Associated with acquired cross-linker resistance was the expression of a functional BRCA2 protein variant lacking exon 5 and exon 7 (BRCA2ΔE5+7), implying a role for BRCA2 splicing for acquired chemo-resistance. Integrated network analysis of transcriptomic and proteomic differences for phenotyping of BRCA2 disruption infers impact on transcription and chromatin remodeling in addition to the DNA damage response. The striking overlap with transcriptional profiles of FA patient hematopoiesis and BRCA mutation associated ovarian cancer helps define and explicate the ‘BRCAness’ profile.
Collapse
Affiliation(s)
- Stefan Meyer
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric and Adolescent Oncology, Royal Manchester Children's Hospital, Manchester, UK.,Young Oncology Unit, Christie Hospital, Manchester, UK
| | - Adam Stevens
- Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric Endocrinology, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK
| | - Roberto Paredes
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Marion Schneider
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Michael J Walker
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Andrew J K Williamson
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Maria-Belen Gonzalez-Sanchez
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Stephanie Smetsers
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Vineet Dalal
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Hsiang Ying Teng
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Daniel J White
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Sam Taylor
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Joanne Muter
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Andrew Pierce
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Chiara de Leonibus
- Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric Endocrinology, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK
| | - Davy A P Rockx
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Martin A Rooimans
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Elaine Spooncer
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Stacey Stauffer
- Mouse Cancer Genetics Program; Center for Cancer Research; Frederick National Laboratory for Cancer Research; National Cancer Institute, Frederick, MD, USA
| | - Kajal Biswas
- Mouse Cancer Genetics Program; Center for Cancer Research; Frederick National Laboratory for Cancer Research; National Cancer Institute, Frederick, MD, USA
| | - Barbara Godthelp
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Josephine Dorsman
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Peter E Clayton
- Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric Endocrinology, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK
| | - Shyam K Sharan
- Mouse Cancer Genetics Program; Center for Cancer Research; Frederick National Laboratory for Cancer Research; National Cancer Institute, Frederick, MD, USA
| | - Anthony D Whetton
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK.,Stoller Biomarker Discovery Centre, University of Manchester, Manchester, UK
| |
Collapse
|
39
|
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: 38] [Impact Index Per Article: 5.4] [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.
Collapse
|
40
|
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: 248] [Impact Index Per Article: 31.0] [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.
Collapse
Affiliation(s)
- Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | | |
Collapse
|