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Klein J, Allister AB, Schmidt G, Otto A, Heinecke K, Bax-Knoche J, Beger C, Becker S, Bartels S, Ripperger T, Bohne J, Dörk T, Schlegelberger B, Hofmann W, Steinemann D. A Novel Alu Element Insertion in ATM Induces Exon Skipping in Suspected HBOC Patients. Hum Mutat 2023. [DOI: 10.1155/2023/6623515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
The vast majority of patients at risk of hereditary breast and/or ovarian cancer (HBOC) syndrome remain without a molecular diagnosis after routine genetic testing. One type of genomic alteration that is commonly missed by diagnostic pipelines is mobile element insertions (MEIs). Here, we reanalyzed multigene panel data from suspected HBOC patients using the MEI detection tool Mobster. A novel Alu element insertion in ATM intron 54 (ATM:c.8010+30_8010+31insAluYa5) was identified as a potential contributing factor in seven patients. Transcript analysis of patient-derived RNA from three heterozygous carriers revealed exon 54 skipping in 38% of total ATM transcripts. To manifest the direct association between the Alu element insertion and the aberrant splice pattern, HEK293T and MCF7 cells were transfected with wild-type or Alu element-carrying minigene constructs. On average, 77% of plasmid-derived transcripts lacked exon 54 in the presence of the Alu element insertion compared to only 4.7% of transcripts expressed by the wild-type minigene. These results strongly suggest ATM:c.8010+30_8010+31insAluYa5 as the main driver of ATM exon 54 skipping. Since this exon loss is predicted to cause a frameshift and a premature stop codon, mutant transcripts are unlikely to translate into functional proteins. Based on its estimated frequency of up to 0.05% in control populations, we propose to consider ATM:c.8010+30_8010+31insAluYa5 in suspected HBOC patients and to clarify its role in carcinogenesis through future epidemiological and functional analyses. Generally, the implementation of MEI detection tools in diagnostic sequencing pipelines could increase the diagnostic yield, as MEIs are likely underestimated contributors to genetic diseases.
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Affiliation(s)
- Janin Klein
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | - Gunnar Schmidt
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Annette Otto
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Kai Heinecke
- MVZ Labor Krone GbR, Bad Salzuflen, Bielefeld, Germany
| | | | - Carmela Beger
- MVZ Labor Krone GbR, Bad Salzuflen, Bielefeld, Germany
| | - Sarah Becker
- MVZ Labor Krone GbR, Bad Salzuflen, Bielefeld, Germany
| | - Stephan Bartels
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jens Bohne
- Department of Virology, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Department of Gynaecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | | | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
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2
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Bilyalov A, Nikolaev S, Shigapova L, Khatkov I, Danishevich A, Zhukova L, Smolin S, Titova M, Lisica T, Bodunova N, Shagimardanova E, Gusev O. Application of Multigene Panels Testing for Hereditary Cancer Syndromes. BIOLOGY 2022; 11:biology11101461. [PMID: 36290365 PMCID: PMC9598138 DOI: 10.3390/biology11101461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Approximately 5-10% of all cancers are associated with hereditary cancer predisposition syndromes (HCPS). Early identification of HCPS is facilitated by widespread use of next-generation sequencing (NGS) and brings significant benefits to both the patient and their relatives. This study aims to evaluate the landscape of genetic variants in patients with personal and/or family history of cancer using NGS-based multigene panel testing. MATERIALS AND METHODS The study cohort included 1117 probands from Russia: 1060 (94.9%) patients with clinical signs of HCPS and 57 (5.1%) healthy individuals with family history of cancer. NGS analysis of 76 HCPS genes was performed using a custom Roche NimbleGen enrichment panel. RESULTS Pathogenic/likely pathogenic variants were identified in 378 of 1117 individuals (33.8%). The predominant number (59.8%) of genetic variants was identified in BRCA1/BRCA2 genes. CHEK2 was the second most commonly altered gene with a total of 28 (7.4%) variants, and 124 (32.8%) genetic variants were found in other 35 cancer-associated genes with variable penetrance. CONCLUSIONS Multigene panel testing allows for a differential diagnosis and identification of high-risk group for oncological diseases. Our results demonstrate that inclusion of non-coding gene regions into HCPS gene panels is highly important for the identification of rare spliceogenic variants with high penetrance.
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Affiliation(s)
- Airat Bilyalov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
- Correspondence: ; Tel.: +7-9625-6038-02
| | - Sergey Nikolaev
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Leila Shigapova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Igor Khatkov
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | | | - Ludmila Zhukova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Sergei Smolin
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Marina Titova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Tatyana Lisica
- Centre for Strategic Planning of FMBA of Russia, 119121 Moscow, Russia
| | - Natalia Bodunova
- The Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Oleg Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
- Endocrinology Research Centre, 117036 Moscow, Russia
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3
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Guglielmi C, Scarpitta R, Gambino G, Conti E, Bellè F, Tancredi M, Cervelli T, Falaschi E, Cosini C, Aretini P, Congregati C, Marino M, Patruno M, Pilato B, Spina F, Balestrino L, Tenedini E, Carnevali I, Cortesi L, Tagliafico E, Tibiletti MG, Tommasi S, Ghilli M, Vivanet C, Galli A, Caligo MA. Detection of Germline Variants in 450 Breast/Ovarian Cancer Families with a Multi-Gene Panel Including Coding and Regulatory Regions. Int J Mol Sci 2021; 22:ijms22147693. [PMID: 34299313 PMCID: PMC8305371 DOI: 10.3390/ijms22147693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/24/2022] Open
Abstract
With the progress of sequencing technologies, an ever-increasing number of variants of unknown functional and clinical significance (VUS) have been identified in both coding and non-coding regions of the main Breast Cancer (BC) predisposition genes. The aim of this study is to identify a mutational profile of coding and intron-exon junction regions of 12 moderate penetrance genes (ATM, BRIP1, CDH1, CHEK2, NBN, PALB2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53) in a cohort of 450 Italian patients with Hereditary Breast/Ovarian Cancer Syndrome, wild type for germline mutation in BRCA1/2 genes. The analysis was extended to 5′UTR and 3′UTR of all the genes listed above and to the BRCA1 and BRCA2 known regulatory regions in a subset of 120 patients. The screening was performed through NGS target resequencing on the Illumina platform MiSeq. 8.7% of the patients analyzed is carriers of class 5/4 coding variants in the ATM (3.6%), BRIP1 (1.6%), CHEK2 (1.8%), PALB2 (0.7%), RAD51C (0.4%), RAD51D (0.4%), and TP53 (0.2%) genes, while variants of uncertain pathological significance (VUSs)/class 3 were identified in 9.1% of the samples. In intron-exon junctions and in regulatory regions, variants were detected respectively in 5.1% and in 32.5% of the cases analyzed. The average age of disease onset of 44.4 in non-coding variant carriers is absolutely similar to the average age of disease onset in coding variant carriers for each proband’s group with the same cancer type. Furthermore, there is not a statistically significant difference in the proportion of cases with a tumor onset under age of 40 between the two groups, but the presence of multiple non-coding variants in the same patient may affect the aggressiveness of the tumor and it is worth underlining that 25% of patients with an aggressive tumor are carriers of a PTEN 3′UTR-variant. This data provides initial information on how important it might be to extend mutational screening to the regulatory regions in clinical practice.
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Affiliation(s)
- Chiara Guglielmi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Rosa Scarpitta
- Division of Pathology, University of Pisa, 56126 Pisa, Italy;
| | - Gaetana Gambino
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy;
| | - Eleonora Conti
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Francesca Bellè
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
| | - Mariella Tancredi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Tiziana Cervelli
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
| | - Elisabetta Falaschi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Cinzia Cosini
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Paolo Aretini
- Section of Oncological Genomics, Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
| | - Caterina Congregati
- Division of Internal Medicine, University Hospital of Pisa, 56126 Pisa, Italy;
| | - Marco Marino
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | - Margherita Patruno
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Brunella Pilato
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Francesca Spina
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Luisa Balestrino
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Elena Tenedini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | - Ileana Carnevali
- Ospedale di Circolo ASST Settelaghi, 21100 Varese, Italy; (I.C.); (M.G.T.)
| | - Laura Cortesi
- Department of Oncology, Haematology and Respiratory Diseases, University Hospital of Modena, 41124 Modena, Italy;
| | - Enrico Tagliafico
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | | | - Stefania Tommasi
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Matteo Ghilli
- Breast Cancer Center, University Hospital, 56126 Pisa, Italy;
| | - Caterina Vivanet
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Alvaro Galli
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
- Correspondence: (A.G.); (M.A.C.)
| | - Maria Adelaide Caligo
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
- Correspondence: (A.G.); (M.A.C.)
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Biologic behavior of resected BRCA-mutated pancreatic cancer: Comparison with sporadic pancreatic cancer and other BRCA-related cancers. Pancreatology 2021; 21:544-549. [PMID: 33612442 DOI: 10.1016/j.pan.2021.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/23/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Since margin-negative resection is essential for the cure of pancreatic cancer (PC), early detection of PC is important. Although PC is the third most common cancer associated with BRCA1/2 mutations, clinical research regarding BRCA mutations in resected PC are rare. In this study, we investigated the oncologic characteristics of resected PC with BRCA mutation to suggest management strategies. METHODS We retrospectively reviewed data from 493 patients who were confirmed to be pathogenic BRCA1/2 mutation carriers between January 2007 and December 2019. We investigated the oncologic characteristics of PC patients by comparing them with resected sporadic PC and other BRCA-related cancer groups (breast cancer, ovarian cancer, and others). RESULTS Ten BRCA mutation carriers (2.0%) experienced PC, and PC onset was significantly later than that of BRCA-related breast cancer (age: breast vs. pancreas, 45.0 vs. 53.5 years, p = 0.050). Six patients underwent pancreatectomy and their long-term survival outcomes did not differ from those of sporadic PC patients (disease free survival: BRCA1/2 vs. sporadic, 10.0 months vs. 9.0 months, p = 0.504; overall survival: BRCA1/2 vs. sporadic, 29.0 months vs. 35.0 months, p = 0.520). CONCLUSION BRCA-mutated PC occurs later than BRCA-mutated breast cancer. Active genetic testing to identify BRCA1/2 mutation carriers at the onset of breast cancer and continuous long-term surveillance of these patients can provide opportunities to detect BRCA-mutated PC at a resectable stage.
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5
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Pirim D, Kaya N, Yıldırım EU, Sag SO, Temel SG. Characterization and in silico analyses of the BRCA1/2 variants identified in individuals with personal and/or family history of BRCA-related cancers. Int J Biol Macromol 2020; 162:1166-1177. [PMID: 32599251 DOI: 10.1016/j.ijbiomac.2020.06.222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/05/2020] [Accepted: 06/24/2020] [Indexed: 12/17/2022]
Abstract
Pathogenic variants in the coding regions of the BRCA1/2 lead dysfunctional or nonfunctional BRCA proteins however the contribution of non-coding BRCA1/2 variants to BRCA-related disease risk has not been fully elucidated. Thus, we characterized the functional impact of both coding and non-coding BRCA1/2 variants identified in individuals with personal and/or family history of BRCA-related cancers. The data were produced by resequencing the exons and exon-intron junctions of the BRCA1/2 in 125 individuals and were comprehensively analyzed by using bioinformatics tools and databases. A total of 96 variants (59 coding and 37 non-coding) including 7 novel variants were identified and analyzed for their functional importance. We identified 11 missense variants that potentially affect protein function; 22 variants were likely to alter different types of posttranslational modifications. Also, multiple non-coding BRCA1/2 variants were found to reside in the critical regulatory regions that have the potential to act as eQTLs and affect alternative splicing. The results of our study shed light on the possible contributions of not only coding variants but also non-coding BRCA1/2 variants in BRCRA-related cancers. Further investigation is required to fully understand their potential associations with phenotypes which may ultimately lead their utilization on cancer management as a biomarker.
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Affiliation(s)
- Dilek Pirim
- Bursa Uludag University, Department of Molecular Biology and Genetics, Bursa, Turkey; Bursa Uludag University, Institute of Health Sciences, Department of Translational Medicine, Bursa, Turkey.
| | - Niyazi Kaya
- Bursa Uludag University, Institute of Natural and Applied Sciences, Department of Molecular Biology and Genetics, Bursa, Turkey
| | - Elif Uz Yıldırım
- Bursa Uludag University, Department of Molecular Biology and Genetics, Bursa, Turkey; Bursa Uludag University, Institute of Health Sciences, Department of Translational Medicine, Bursa, Turkey
| | - Sebnem Ozemri Sag
- Bursa Uludag University, Faculty of Medicine, Department of Medical Genetics, Bursa, Turkey
| | - Sehime Gulsun Temel
- Bursa Uludag University, Faculty of Medicine, Department of Medical Genetics, Bursa, Turkey; Bursa Uludag University, Institute of Health Sciences, Department of Translational Medicine, Bursa, Turkey; Bursa Uludag University, Faculty of Medicine, Department of Histology and Embryology, Bursa, Turkey.
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6
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Santana dos Santos E, Lallemand F, Petitalot A, Caputo SM, Rouleau E. HRness in Breast and Ovarian Cancers. Int J Mol Sci 2020; 21:E3850. [PMID: 32481735 PMCID: PMC7312125 DOI: 10.3390/ijms21113850] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian and breast cancers are currently defined by the main pathways involved in the tumorigenesis. The majority are carcinomas, originating from epithelial cells that are in constant division and subjected to cyclical variations of the estrogen stimulus during the female hormonal cycle, therefore being vulnerable to DNA damage. A portion of breast and ovarian carcinomas arises in the context of DNA repair defects, in which genetic instability is the backdrop for cancer initiation and progression. For these tumors, DNA repair deficiency is now increasingly recognized as a target for therapeutics. In hereditary breast/ovarian cancers (HBOC), tumors with BRCA1/2 mutations present an impairment of DNA repair by homologous recombination (HR). For many years, BRCA1/2 mutations were only screened on germline DNA, but now they are also searched at the tumor level to personalize treatment. The reason of the inactivation of this pathway remains uncertain for most cases, even in the presence of a HR-deficient signature. Evidence indicates that identifying the mechanism of HR inactivation should improve both genetic counseling and therapeutic response, since they can be useful as new biomarkers of response.
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Affiliation(s)
- Elizabeth Santana dos Santos
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800 Villejuif, France;
- Department of Clinical Oncology, A.C. Camargo Cancer Center, São Paulo 01509-010, Brazil
| | - François Lallemand
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Ambre Petitalot
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Sandrine M. Caputo
- Department of Genetics, Institut Curie, 75005 Paris, France; (F.L.); (A.P.); (S.M.C.)
- PSL Research University, 75005 Paris, France
| | - Etienne Rouleau
- Department of Medical Biology and Pathology, Gustave Roussy, Cancer Genetics Laboratory, Gustave Roussy, 94800 Villejuif, France;
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7
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Høberg-Vetti H, Ognedal E, Buisson A, Vamre TBA, Ariansen S, Hoover JM, Eide GE, Houge G, Fiskerstrand T, Haukanes BI, Bjorvatn C, Knappskog PM. The intronic BRCA1 c.5407-25T>A variant causing partly skipping of exon 23-a likely pathogenic variant with reduced penetrance? Eur J Hum Genet 2020; 28:1078-1086. [PMID: 32203205 PMCID: PMC7382492 DOI: 10.1038/s41431-020-0612-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 11/16/2022] Open
Abstract
Rare sequence variants in the non-coding part of the BRCA genes are often reported as variants of uncertain significance (VUS), which leave patients and doctors in a challenging position. The aim of this study was to determine the pathogenicity of the BRCA1 c.5407-25T>A variant found in 20 families from Norway, France and United States with suspected hereditary breast and ovarian cancer. This was done by combining clinical and family information with allele frequency data, and assessment of the variant’s effect on mRNA splicing. Mean age at breast (n = 12) and ovarian (n = 11) cancer diagnosis in female carriers was 49.9 and 60.4 years, respectively. The mean Manchester score in the 20 families was 16.4. The allele frequency of BRCA1 c.5407-25T>A was 1/64,566 in non-Finnish Europeans (gnomAD database v2.1.1). We found the variant in 1/400 anonymous Norwegian blood donors and 0/784 in-house exomes. Sequencing of patient-derived cDNA from blood, normal breast and ovarian tissue showed that BRCA1 c.5407-25T>A leads to skipping of exon 23, resulting in frameshift and protein truncation: p.(Gly1803GlnfsTer11). Western blot analysis of transiently expressed BRCA1 proteins in HeLa cells showed a reduced amount of the truncated protein compared with wild type. Noteworthily, we found that a small amount of full-length transcript was also generated from the c.5407-25T>A allele, potentially explaining the intermediate cancer burden in families carrying this variant. In summary, our results show that BRCA1 c.5407-25T>A leads to partial skipping of exon 23, and could represent a likely pathogenic variant with reduced penetrance.
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Affiliation(s)
- Hildegunn Høberg-Vetti
- Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway. .,Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway. .,Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Elisabet Ognedal
- Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway.,Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | | | | | - Sarah Ariansen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Geir Egil Eide
- Centre for Clinical Research, Haukeland University Hospital, Bergen, Norway.,Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Torunn Fiskerstrand
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Cathrine Bjorvatn
- Western Norway Familial Cancer Center, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Research and Development, Haukeland University Hospital, Bergen, Norway
| | - Per Morten Knappskog
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
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8
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Shirley BC, Mucaki EJ, Rogan PK. Pan-cancer repository of validated natural and cryptic mRNA splicing mutations. F1000Res 2019; 7:1908. [PMID: 31275557 DOI: 10.12688/f1000research.17204.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/30/2018] [Indexed: 12/26/2022] Open
Abstract
We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. An algorithm was developed to classify variants into splicing molecular phenotypes that integrates germline heterozygosity, degree of information change and impact on expression. The classification thresholds were calibrated against the ClinVar clinical database phenotypic assignments. Variants are partitioned into allele-specific alternative splicing, likely aberrant and aberrant splicing phenotypes. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon "Validated Splicing Mutations" either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website. The website provides additional information, such as a visual representation of supporting RNAseq results, gene expression in the corresponding normal tissues, and splicing molecular phenotypes.
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Affiliation(s)
| | - Eliseos J Mucaki
- Biochemistry, University of Western Ontario, London, Ontario, N6A 2C1, Canada
| | - Peter K Rogan
- CytoGnomix Inc., London, Ontario, N5X 3X5, Canada.,Biochemistry, University of Western Ontario, London, Ontario, N6A 2C1, Canada.,Computer Science, University of Western Ontario, London, Ontario, N6A 2C1, Canada.,Oncology, University of Western Ontario, London, Ontario, N6A 2C1, Canada
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9
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Gabrieli T, Sharim H, Fridman D, Arbib N, Michaeli Y, Ebenstein Y. Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH). Nucleic Acids Res 2019; 46:e87. [PMID: 29788371 PMCID: PMC6101500 DOI: 10.1093/nar/gky411] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 05/04/2018] [Indexed: 12/15/2022] Open
Abstract
Next generation sequencing (NGS) is challenged by structural and copy number variations larger than the typical read length of several hundred bases. Third-generation sequencing platforms such as single-molecule real-time (SMRT) and nanopore sequencing provide longer reads and are able to characterize variations that are undetected in NGS data. Nevertheless, these technologies suffer from inherent low throughput which prohibits deep sequencing at reasonable cost without target enrichment. Here, we optimized Cas9-Assisted Targeting of CHromosome segments (CATCH) for nanopore sequencing of the breast cancer gene BRCA1. A 200 kb target containing the 80 kb BRCA1 gene body and its flanking regions was isolated intact from primary human peripheral blood cells, allowing long-range amplification and long-read nanopore sequencing. The target was enriched 237-fold and sequenced at up to 70× coverage on a single flow-cell. Overall performance and single-nucleotide polymorphism (SNP) calling were directly compared to Illumina sequencing of the same enriched sample, highlighting the benefits of CATCH for targeted sequencing. The CATCH enrichment scheme only requires knowledge of the target flanking sequence for Cas9 cleavage while providing contiguous data across both coding and non-coding sequence and holds promise for characterization of complex disease-related or highly variable genomic regions.
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Affiliation(s)
- Tslil Gabrieli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hila Sharim
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dena Fridman
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nissim Arbib
- Department of Obstetrics and Gynecology, Meir Hospital, Kfar Saba, Israel & Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Michaeli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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10
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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.
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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
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11
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Morgan RD, Burghel GJ, Flaum N, Bulman M, Clamp AR, Hasan J, Mitchell CL, Schlecht H, Woodward ER, Lallo FI, Crosbie EJ, Edmondson RJ, Wallace AJ, Jayson GC, Evans DGR. Prevalence of germline pathogenic BRCA1/2 variants in sequential epithelial ovarian cancer cases. J Med Genet 2019; 56:301-307. [DOI: 10.1136/jmedgenet-2018-105792] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/14/2018] [Accepted: 01/05/2019] [Indexed: 12/29/2022]
Abstract
IntroductionPoly(ADP-ribose) polymerase inhibitors significantly improve progression-free survival in platinum-sensitive high-grade serous and endometrioid ovarian carcinoma, with greatest benefits observed in women with a pathogenic BRCA1/2 variant. Consequently, the demand for germline BRCA1/2 testing in ovarian cancer has increased substantially, leading to the screening of unselected populations of patients. We aimed to determine the prevalence of pathogenic germline BRCA1/2 variants in women diagnosed with epithelial ovarian cancer, categorised according to the established risk factors for hereditary breast and ovarian cancer syndrome and the Manchester BRCA Score, to inform risk stratification.MethodsA cohort of sequential epithelial ovarian cancer cases recruited between June 2013 and September 2018 underwent germline BRCA1/2 testing by next-generation sequencing and multiplex ligation-dependent probe amplification.ResultsFive hundred and fifty-seven patients were screened. Of these, 18% had inherited a pathogenic BRCA1/2 variant. The prevalence of pathogenic BRCA1/2 variants was >10% in women diagnosed with ovarian cancer earlier than 60 years of age (21%) and those diagnosed later than 60 years of age with a family history of breast and/or ovarian cancer (17%) or a medical history of breast cancer (34%). The prevalence of pathogenic BRCA1/2 variants was also >10% in women with a Manchester BRCA Score of ≥15 points (14%).DiscussionOur study suggests that age at diagnosis, family history of breast and/or ovarian cancer, medical history of breast cancer or a Manchester BRCA Score of ≥15 points are associated with a >10% prevalence of germline pathogenic BRCA1/2 variants in epithelial ovarian cancer.
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12
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Shirley BC, Mucaki EJ, Rogan PK. Pan-cancer repository of validated natural and cryptic mRNA splicing mutations. F1000Res 2018; 7:1908. [PMID: 31275557 PMCID: PMC6544075 DOI: 10.12688/f1000research.17204.3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 11/20/2022] Open
Abstract
We present a major public resource of mRNA splicing mutations validated according to multiple lines of evidence of abnormal gene expression. Likely mutations present in all tumor types reported in the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) were identified based on the comparative strengths of splice sites in tumor versus normal genomes, and then validated by respectively comparing counts of splice junction spanning and abundance of transcript reads in RNA-Seq data from matched tissues and tumors lacking these mutations. The comprehensive resource features 341,486 of these validated mutations, the majority of which (69.9%) are not present in the Single Nucleotide Polymorphism Database (dbSNP 150). There are 131,347 unique mutations which weaken or abolish natural splice sites, and 222,071 mutations which strengthen cryptic splice sites (11,932 affect both simultaneously). 28,812 novel or rare flagged variants (with <1% population frequency in dbSNP) were observed in multiple tumor tissue types. An algorithm was developed to classify variants into splicing molecular phenotypes that integrates germline heterozygosity, degree of information change and impact on expression. The classification thresholds were calibrated against the ClinVar clinical database phenotypic assignments. Variants are partitioned into allele-specific alternative splicing, likely aberrant and aberrant splicing phenotypes. Single variants or chromosome ranges can be queried using a Global Alliance for Genomics and Health (GA4GH)-compliant, web-based Beacon "Validated Splicing Mutations" either separately or in aggregate alongside other Beacons through the public Beacon Network, as well as through our website. The website provides additional information, such as a visual representation of supporting RNAseq results, gene expression in the corresponding normal tissues, and splicing molecular phenotypes.
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Affiliation(s)
| | - Eliseos J Mucaki
- Biochemistry, University of Western Ontario, London, Ontario, N6A 2C1, Canada
| | - Peter K Rogan
- CytoGnomix Inc., London, Ontario, N5X 3X5, Canada.,Biochemistry, University of Western Ontario, London, Ontario, N6A 2C1, Canada.,Computer Science, University of Western Ontario, London, Ontario, N6A 2C1, Canada.,Oncology, University of Western Ontario, London, Ontario, N6A 2C1, Canada
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13
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Burke LJ, Sevcik J, Gambino G, Tudini E, Mucaki EJ, Shirley BC, Whiley P, Parsons MT, De Leeneer K, Gutiérrez‐Enríquez S, Santamariña M, Caputo SM, Santana dos Santos E, Soukupova J, Janatova M, Zemankova P, Lhotova K, Stolarova L, Borecka M, Moles‐Fernández A, Manoukian S, Bonanni B, Edwards SL, Blok MJ, van Overeem Hansen T, Rossing M, Diez O, Vega A, Claes KB, Goldgar DE, Rouleau E, Radice P, Peterlongo P, Rogan PK, Caligo M, Spurdle AB, Brown MA. BRCA1 and BRCA2 5' noncoding region variants identified in breast cancer patients alter promoter activity and protein binding. Hum Mutat 2018; 39:2025-2039. [PMID: 30204945 PMCID: PMC6282814 DOI: 10.1002/humu.23652] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 09/01/2018] [Accepted: 09/07/2018] [Indexed: 12/13/2022]
Abstract
The widespread use of next generation sequencing for clinical testing is detecting an escalating number of variants in noncoding regions of the genome. The clinical significance of the majority of these variants is currently unknown, which presents a significant clinical challenge. We have screened over 6,000 early-onset and/or familial breast cancer (BC) cases collected by the ENIGMA consortium for sequence variants in the 5' noncoding regions of BC susceptibility genes BRCA1 and BRCA2, and identified 141 rare variants with global minor allele frequency < 0.01, 76 of which have not been reported previously. Bioinformatic analysis identified a set of 21 variants most likely to impact transcriptional regulation, and luciferase reporter assays detected altered promoter activity for four of these variants. Electrophoretic mobility shift assays demonstrated that three of these altered the binding of proteins to the respective BRCA1 or BRCA2 promoter regions, including NFYA binding to BRCA1:c.-287C>T and PAX5 binding to BRCA2:c.-296C>T. Clinical classification of variants affecting promoter activity, using existing prediction models, found no evidence to suggest that these variants confer a high risk of disease. Further studies are required to determine if such variation may be associated with a moderate or low risk of BC.
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Affiliation(s)
- Leslie J. Burke
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
| | - Jan Sevcik
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Gaetana Gambino
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
- Section of Molecular GeneticsDepartment of Laboratory MedicineUniversity Hospital of PisaPisaItaly
| | - Emma Tudini
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Eliseos J. Mucaki
- University of Western Ontario, Department of BiochemistrySchulich School of Medicine and DentistryLondonOntarioCanada
| | | | - Phillip Whiley
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Michael T. Parsons
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kim De Leeneer
- Center for Medical GeneticsGhent University Hospitaland Cancer Research Institute Ghent (CRIG)Ghent UniversityGhentBelgium
| | | | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica‐SERGASGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | - Sandrine M. Caputo
- Service de GénétiqueDepartment de Biologie des TumeursInstitut CurieParisFrance
| | - Elizabeth Santana dos Santos
- Service de GénétiqueDepartment de Biologie des TumeursInstitut CurieParisFrance
- Department of oncologyCenter for Translational OncologyCancer Institute of the State of São Paulo ‐ ICESPSão PauloBrazil
- A.C.Camargo Cancer CenterSão PauloBrazil
| | - Jana Soukupova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Marketa Janatova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Petra Zemankova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Klara Lhotova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Lenka Stolarova
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Mariana Borecka
- Institute of Biochemistry and Experimental Oncology, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | | | - 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
| | - Bernardo Bonanni
- Division of Cancer Prevention and GeneticsIstituto Europeo di OncologiaMilanItaly
| | - ENIGMA Consortium
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
| | - Stacey L. Edwards
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Marinus J. Blok
- Department of Clinical GeneticsMaastricht University Medical CentreMaastrichtThe Netherlands
| | | | - Maria Rossing
- Center for Genomic MedicineCopenhagen University Hospital, RigshospitaletCopenhagenDenmark
| | - Orland Diez
- Oncogenetics GroupVall d'Hebron Institute of Oncology (VHIO)BarcelonaSpain
- Area of Clinical and Molecular GeneticsUniversity Hospital Vall d'Hebron (UHVH)BarcelonaSpain
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica‐SERGASGrupo de Medicina Xenómica‐USC, CIBERER, IDISSantiago de CompostelaSpain
| | - Kathleen B.M. Claes
- Center for Medical GeneticsGhent University Hospitaland Cancer Research Institute Ghent (CRIG)Ghent UniversityGhentBelgium
| | | | | | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic TestingDepartment of ResearchFondazione IRCCS Istituto Nazionale dei Tumori di MilanoMilanItaly
| | | | - Peter K. Rogan
- University of Western Ontario, Department of BiochemistrySchulich School of Medicine and DentistryLondonOntarioCanada
- CytoGnomix Inc.LondonOntarioCanada
| | - Maria Caligo
- Section of Molecular GeneticsDepartment of Laboratory MedicineUniversity Hospital of PisaPisaItaly
| | - Amanda B. Spurdle
- Department of Genetics and Computational BiologyQIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Melissa A. Brown
- School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneAustralia
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14
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Montalban G, Bonache S, Moles-Fernández A, Gisbert-Beamud A, Tenés A, Bach V, Carrasco E, López-Fernández A, Stjepanovic N, Balmaña J, Diez O, Gutiérrez-Enríquez S. Screening of BRCA1/2 deep intronic regions by targeted gene sequencing identifies the first germline BRCA1 variant causing pseudoexon activation in a patient with breast/ovarian cancer. J Med Genet 2018; 56:63-74. [PMID: 30472649 DOI: 10.1136/jmedgenet-2018-105606] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/16/2018] [Accepted: 10/28/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Genetic analysis of BRCA1 and BRCA2 for the diagnosis of hereditary breast and ovarian cancer (HBOC) is commonly restricted to coding regions and exon-intron boundaries. Although germline pathogenic variants in these regions explain about ~20% of HBOC cases, there is still an important fraction that remains undiagnosed. We have screened BRCA1/2 deep intronic regions to identify potential spliceogenic variants that could explain part of the missing HBOC susceptibility. METHODS We analysed BRCA1/2 deep intronic regions by targeted gene sequencing in 192 high-risk HBOC families testing negative for BRCA1/2 during conventional analysis. Rare variants (MAF <0.005) predicted to create/activate splice sites were selected for further characterisation in patient RNA. The splicing outcome was analysed by RT-PCR and Sanger sequencing, and allelic imbalance was also determined when heterozygous exonic loci were present. RESULTS A novel transcript was detected in BRCA1 c.4185+4105C>T variant carrier. This variant promotes the inclusion of a pseudoexon in mature mRNA, generating an aberrant transcript predicted to encode for a non-functional protein. Quantitative and allele-specific assays determined haploinsufficiency in the variant carrier, supporting a pathogenic effect for this variant. Genotyping of 1030 HBOC cases and 327 controls did not identify additional carriers in Spanish population. CONCLUSION Screening of BRCA1/2 intronic regions has identified the first BRCA1 deep intronic variant associated with HBOC by pseudoexon activation. Although the frequency of deleterious variants in these regions appears to be low, our study highlights the importance of studying non-coding regions and performing comprehensive RNA assays to complement genetic diagnosis.
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Affiliation(s)
- Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | | | | | - Anna Tenés
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Vanessa Bach
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Estela Carrasco
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Adrià López-Fernández
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain
| | - Neda Stjepanovic
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain.,Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain.,Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institut d'Oncologia, Barcelona, Spain.,Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
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15
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Non-Coding Variants in BRCA1 and BRCA2 Genes: Potential Impact on Breast and Ovarian Cancer Predisposition. Cancers (Basel) 2018; 10:cancers10110453. [PMID: 30453575 PMCID: PMC6266896 DOI: 10.3390/cancers10110453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/04/2018] [Accepted: 11/12/2018] [Indexed: 12/21/2022] Open
Abstract
BRCA1 and BRCA2 are major breast cancer susceptibility genes whose pathogenic variants are associated with a significant increase in the risk of breast and ovarian cancers. Current genetic screening is generally limited to BRCA1/2 exons and intron/exon boundaries. Most identified pathogenic variants cause the partial or complete loss of function of the protein. However, it is becoming increasingly clear that variants in these regions only account for a small proportion of cancer risk. The role of variants in non-coding regions beyond splice donor and acceptor sites, including those that have no qualitative effect on the protein, has not been thoroughly investigated. The key transcriptional regulatory elements of BRCA1 and BRCA2 are housed in gene promoters, untranslated regions, introns, and long-range elements. Within these sequences, germline and somatic variants have been described, but the clinical significance of the majority is currently unknown and it remains a significant clinical challenge. This review summarizes the available data on the impact of variants on non-coding regions of BRCA1/2 genes and their role on breast and ovarian cancer predisposition.
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16
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Petitalot A, Dardillac E, Jacquet E, Nhiri N, Guirouilh-Barbat J, Julien P, Bouazzaoui I, Bonte D, Feunteun J, Schnell JA, Lafitte P, Aude JC, Noguès C, Rouleau E, Lidereau R, Lopez BS, Zinn-Justin S, Caputo SM. Combining Homologous Recombination and Phosphopeptide-binding Data to Predict the Impact of BRCA1 BRCT Variants on Cancer Risk. Mol Cancer Res 2018; 17:54-69. [PMID: 30257991 DOI: 10.1158/1541-7786.mcr-17-0357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 02/07/2018] [Accepted: 09/11/2018] [Indexed: 11/16/2022]
Abstract
BRCA1 mutations have been identified that increase the risk of developing hereditary breast and ovarian cancers. Genetic screening is now offered to patients with a family history of cancer, to adapt their treatment and the management of their relatives. However, a large number of BRCA1 variants of uncertain significance (VUS) are detected. To better understand the significance of these variants, a high-throughput structural and functional analysis was performed on a large set of BRCA1 VUS. Information on both cellular localization and homology-directed DNA repair (HR) capacity was obtained for 78 BRCT missense variants in the UMD-BRCA1 database and measurement of the structural stability and phosphopeptide-binding capacities was performed for 42 mutated BRCT domains. This extensive and systematic analysis revealed that most characterized causal variants affect BRCT-domain solubility in bacteria and all impair BRCA1 HR activity in cells. Furthermore, binding to a set of 5 different phosphopeptides was tested: all causal variants showed phosphopeptide-binding defects and no neutral variant showed such defects. A classification is presented on the basis of mutated BRCT domain solubility, phosphopeptide-binding properties, and VUS HR capacity. These data suggest that HR-defective variants, which present, in addition, BRCT domains either insoluble in bacteria or defective for phosphopeptide binding, lead to an increased cancer risk. Furthermore, the data suggest that variants with a WT HR activity and whose BRCT domains bind with a WT affinity to the 5 phosphopeptides are neutral. The case of variants with WT HR activity and defective phosphopeptide binding should be further characterized, as this last functional defect might be sufficient per se to lead to tumorigenesis. IMPLICATIONS: The analysis of the current study on BRCA1 structural and functional defects on cancer risk and classification presented may improve clinical interpretation and therapeutic selection.
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Affiliation(s)
- Ambre Petitalot
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France.,Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Elodie Dardillac
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Josée Guirouilh-Barbat
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Patrick Julien
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Isslam Bouazzaoui
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dorine Bonte
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France
| | - Jean Feunteun
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France
| | - Jeff A Schnell
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Lafitte
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Jean-Christophe Aude
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Catherine Noguès
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Etienne Rouleau
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Rosette Lidereau
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Bernard S Lopez
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Sophie Zinn-Justin
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France.
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17
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Fraile-Bethencourt E, Valenzuela-Palomo A, Díez-Gómez B, Infante M, Durán M, Marcos G, Lastra E, Gómez-Barrero S, Velasco EA. Genetic dissection of the BRCA2 promoter and transcriptional impact of DNA variants. Breast Cancer Res Treat 2018; 171:53-63. [PMID: 29766361 DOI: 10.1007/s10549-018-4826-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/16/2018] [Indexed: 11/28/2022]
Abstract
PURPOSE Promoter mutations may affect transcription and can be associated with human diseases. However, the promoters of the breast cancer (BC) genes are not regularly screened. Our goal was to investigate the BRCA2 promoter in order to study a possible correlation between impaired transcription and disease. METHODS The proximal and core promoter of the BRCA2 gene was sequenced in 95 high-risk BC patients. A BRCA2-promoter insert [- 938 to + 312 from the transcription start site (TSS)] was generated and cloned into the firefly luciferase vector pGL4.10. Promoter variants and deletions were introduced by site-directed mutagenesis and quantified by Dual-Luciferase assays and semi-quantitative RT-PCR. RESULTS Three different variants were detected in high-risk BC patients: rs3092989, rs206118, and rs563971900. Functional mapping of 13 overlapping deletions revealed four down-regulating segments (TSS positions): -59_-10del/µdel3 (16% of activity of the wild-type construct), -104_-55del/µdel4 (62%), -239_-190del/µdel7 (39%), -464_-415/µdel12 (78%), suggesting the presence therein of putative transcriptional activator motifs. Additionally, six microdeletions rendered luciferase overexpression: +32_+81del/µdel1 (356%), -14_+36del/µdel2 (180%), -194_-145del/µdel6 (154%), -284_-235del/µdel8 (168%), -329_-280del/µdel9 (111%), and -509_-460del/µdel13 (139%), which is indicative of repressor elements. Functional assays of 15 promoter variants (including those detected in patients) showed that ten of them significantly altered expression with seven up-regulating (113-163%) and three down-regulating (rs551887850_G, rs570548398_T, rs55880202_T; 72-83%) SNPs. Eight of them were located in an ENCODE-DNase Hypersensitive Cluster (TSS - 185 to + 105) where most active transcriptional motifs are known to be placed. CONCLUSIONS BRCA2 expression is highly sensitive to promoter variations as most of them induced relevant changes. Moreover, we mapped critical regions of the BRCA2 promoter that may constitute potential targets for regulatory variants. Three SNPs moderately decreased luciferase activity, but confirmation of its potential pathogenicity requires further analysis. These data reinforce the need to screen the promoter regions of breast cancer genes with a view to discovering novel deleterious mutations.
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Affiliation(s)
- Eugenia Fraile-Bethencourt
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Alberto Valenzuela-Palomo
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Beatriz Díez-Gómez
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Mar Infante
- Cancer Genetics, Instituto de Biología y Genética Molecular (UVa-CSIC), Valladolid, Spain
| | - Mercedes Durán
- Cancer Genetics, Instituto de Biología y Genética Molecular (UVa-CSIC), Valladolid, Spain
| | - Germán Marcos
- Servicio de Oncología, Hospital Río Hortega, Valladolid, Spain
| | - Enrique Lastra
- Servicio de Oncología, Hospital Universitario de Burgos, Burgos, Spain
| | | | - Eladio A Velasco
- Grupo de Splicing y Cáncer, Instituto de Biología y Genética Molecular (IBGM), Consejo Superior de Investigaciones Científicas (CSIC-UVa), Sanz y Forés 3, 47003, Valladolid, Spain.
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