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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: 2] [Impact Index Per Article: 2.0] [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.
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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
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Soriano-Sexto A, Gallego D, Leal F, Castejón-Fernández N, Navarrete R, Alcaide P, Couce ML, Martín-Hernández E, Quijada-Fraile P, Peña-Quintana L, Yahyaoui R, Correcher P, Ugarte M, Rodríguez-Pombo P, Pérez B. Identification of Clinical Variants beyond the Exome in Inborn Errors of Metabolism. Int J Mol Sci 2022; 23:ijms232112850. [PMID: 36361642 PMCID: PMC9654865 DOI: 10.3390/ijms232112850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/21/2022] [Indexed: 11/24/2022] Open
Abstract
Inborn errors of metabolism (IEM) constitute a huge group of rare diseases affecting 1 in every 1000 newborns. Next-generation sequencing has transformed the diagnosis of IEM, leading to its proposed use as a second-tier technology for confirming cases detected by clinical/biochemical studies or newborn screening. The diagnosis rate is, however, still not 100%. This paper reports the use of a personalized multi-omics (metabolomic, genomic and transcriptomic) pipeline plus functional genomics to aid in the genetic diagnosis of six unsolved cases, with a clinical and/or biochemical diagnosis of galactosemia, mucopolysaccharidosis type I (MPS I), maple syrup urine disease (MSUD), hyperphenylalaninemia (HPA), citrullinemia, or urea cycle deficiency. Eight novel variants in six genes were identified: six (four of them deep intronic) located in GALE, IDUA, PTS, ASS1 and OTC, all affecting the splicing process, and two located in the promoters of IDUA and PTS, thus affecting these genes’ expression. All the new variants were subjected to functional analysis to verify their pathogenic effects. This work underscores how the combination of different omics technologies and functional analysis can solve elusive cases in clinical practice.
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Affiliation(s)
- Alejandro Soriano-Sexto
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Diana Gallego
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Natalia Castejón-Fernández
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Patricia Alcaide
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - María L. Couce
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, University of Santiago de Compostela, CIBERER, MetabERN, 15706 Santiago de Compostela, Spain
| | - Elena Martín-Hernández
- Unidad de Enfermedades Mitocondriales-Metabólicas Hereditarias, Servicio de Pediatría, Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas Hereditarias, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Pilar Quijada-Fraile
- Unidad de Enfermedades Mitocondriales-Metabólicas Hereditarias, Servicio de Pediatría, Centro de Referencia Nacional (CSUR) y Europeo (MetabERN) para Enfermedades Metabólicas Hereditarias, Hospital Universitario 12 de Octubre, 28041 Madrid, Spain
| | - Luis Peña-Quintana
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Complejo Hospitalario Universitario Insular Materno-Infantil (CHUIMI), Universidad de Las Palmas de Gran Canaria, Asociación Canaria para La Investigación Pediátrica, Centro de Investigación Biomédica en Red de la Fisiopatología de la Obesidad y la Nutrición (CIBEROBN) ISCIII, 35016 Gran Canaria, Spain
| | - Raquel Yahyaoui
- Laboratory of Metabolic Disorders and Newborn Screening, Institute of Biomedical Research in Málaga (IBIMA-Plafatorma BIONAND), IBIMA-RARE, Málaga Regional University Hospital, 29010 Málaga, Spain
| | - Patricia Correcher
- Nutrition and Metabolophaties Unit, Hospital Universitario La Fe, 46026 Valencia, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), IdiPAZ, 28049 Madrid, Spain
- Correspondence:
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Valenzuela-Palomo A, Sanoguera-Miralles L, Bueno-Martínez E, Esteban-Sánchez A, Llinares-Burguet I, García-Álvarez A, Pérez-Segura P, Gómez-Barrero S, de la Hoya M, Velasco-Sampedro EA. Splicing Analysis of 16 PALB2 ClinVar Variants by Minigene Assays: Identification of Six Likely Pathogenic Variants. Cancers (Basel) 2022; 14:cancers14184541. [PMID: 36139699 PMCID: PMC9496955 DOI: 10.3390/cancers14184541] [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: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 11/29/2022] Open
Abstract
PALB2 loss-of-function variants are associated with significant increased risk of breast cancer as well as other types of tumors. Likewise, splicing disruptions are a common mechanism of disease susceptibility. Indeed, we previously showed, by minigene assays, that 35 out of 42 PALB2 variants impaired splicing. Taking advantage of one of these constructs (mgPALB2_ex1-3), we proceeded to analyze other variants at exons 1 to 3 reported at the ClinVar database. Thirty-one variants were bioinformatically analyzed with MaxEntScan and SpliceAI. Then, 16 variants were selected for subsequent RNA assays. We identified a total of 12 spliceogenic variants, 11 of which did not produce any trace of the expected minigene full-length transcript. Interestingly, variant c.49-1G > A mimicked previous outcomes in patient RNA (transcript ∆(E2p6)), supporting the reproducibility of the minigene approach. A total of eight variant-induced transcripts were characterized, three of which (∆(E1q17), ∆(E3p11), and ∆(E3)) were predicted to introduce a premature termination codon and to undergo nonsense-mediated decay, and five (▼(E1q9), ∆(E2p6), ∆(E2), ▼(E3q48)-a, and ▼(E3q48)-b) maintained the reading frame. According to an ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme, which integrates mgPALB2 data, six PALB2 variants were classified as pathogenic/likely pathogenic, five as VUS, and five as likely benign. Furthermore, five ±1,2 variants were catalogued as VUS because they produced significant proportions of in-frame transcripts of unknown impact on protein function.
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Affiliation(s)
- Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 Valladolid, Spain
| | - Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biología y Genética Molecular, Consejo Superior de Investigaciones Científicas (CSIC-UVa), 47003 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 (CSIC-UVa), 47003 Valladolid, Spain
| | - Ada Esteban-Sánchez
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 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 (CSIC-UVa), 47003 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 (CSIC-UVa), 47003 Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 Madrid, Spain
| | - Susana Gómez-Barrero
- Facultad de Ciencias de la Salud, Universidad Alfonso X “El Sabio”, Avda. de la Universidad 1, Villanueva de la Cañada, 28691 Madrid, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040 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 (CSIC-UVa), 47003 Valladolid, Spain
- Correspondence:
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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: 10] [Impact Index Per Article: 2.0] [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.
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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.)
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Implications of CLSPN Variants in Cellular Function and Susceptibility to Cancer. Cancers (Basel) 2020; 12:cancers12092396. [PMID: 32847043 PMCID: PMC7565888 DOI: 10.3390/cancers12092396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/05/2020] [Accepted: 08/20/2020] [Indexed: 11/28/2022] Open
Abstract
Claspin is a multifunctional protein that participates in physiological processes essential for cell homeostasis that are often defective in cancer, namely due to genetic changes. It is conceivable that Claspin gene (CLSPN) alterations may contribute to cancer development. Therefore, CLSPN germline alterations were characterized in sporadic and familial breast cancer and glioma samples, as well as in six cancer cell lines. Their association to cancer susceptibility and functional impact were investigated. Eight variants were identified (c.-68C>T, c.17G>A, c.1574A>G, c.2230T>C, c.2028+16G>A, c.3595-3597del, and c.3839C>T). CLSPN c.1574A>G (p.Asn525Ser) was significantly associated with breast cancer and was shown to cause partial exon skipping and decreased Claspin expression and Chk1 activation in a minigene splicing assay and in signalling experiments, respectively. CLSPN c.2028+16G>A was significantly associated with familial breast cancer and glioma, whereas c.2230T>C (p.Ser744Pro), was exclusively detected in breast cancer and glioma patients, but not in healthy controls. The remaining variants lacked a significant association with cancer. Nevertheless, the c.-68C>T promoter variant increased transcriptional activity in a luciferase assay. In conclusion, some of the CLSPN variants identified in the present study appear to modulate Claspin’s function by altering CLSPN transcription and RNA processing, as well as Chk1 activation.
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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: 23] [Impact Index Per Article: 3.8] [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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7
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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, ENIGMA Consortium, 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: 1.9] [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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8
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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: 1.6] [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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