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Morak M, Pineda M, Martins A, Gaildrat P, Tubeuf H, Drouet A, Gómez C, Dámaso E, Schaefer K, Steinke-Lange V, Koehler U, Laner A, Hauchard J, Chauris K, Holinski-Feder E, Capellá G. Splicing analyses for variants in MMR genes: best practice recommendations from the European Mismatch Repair Working Group. Eur J Hum Genet 2022; 30:1051-1059. [PMID: 35676339 PMCID: PMC9437034 DOI: 10.1038/s41431-022-01106-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 03/20/2022] [Accepted: 04/11/2022] [Indexed: 11/09/2022] Open
Abstract
Over 20% of the DNA mismatch repair (MMR) germline variants in suspected Lynch syndrome patients are classified as variants of uncertain significance (VUS). Well-established functional assays are pivotal for assessing the biological impact of these variants and provide relevant evidence for clinical classification. In our collaborative European Mismatch Repair Working Group (EMMR-WG) we compared three different experimental approaches for evaluating the effect of seven variants on mRNA splicing in MMR genes: (i) RT-PCR of full-length transcripts (FLT), (ii) RT-PCR of targeted transcript sections (TTS), both from patient biological samples and (iii) minigene splicing assays. An overall good concordance was observed between splicing patterns in TTS, FLT and minigene analyses for all variants. The FLT analysis depicted a higher number of different isoforms and mitigated PCR-bias towards shorter isoforms. TTS analyses may miss aberrant isoforms and minigene assays may under/overestimate the severity of certain splicing defects. The interpretation of the experimental findings must be cautious to adequately discriminate abnormal events from physiological complex alternative splicing patterns. A consensus strategy for investigating the impact of MMR variants on splicing was defined. First, RNA should be obtained from patient's cell cultures (such as fresh lymphocyte cultures) incubated with/without a nonsense-mediated decay inhibitor. Second, FLT RT-PCR analysis is recommended to oversee all generated isoforms. Third, TTS analysis and minigene assays are useful independent approaches for verifying and clarifying FLT results. The use of several methodologies is likely to increase the strength of the experimental evidence which contributes to improve variant interpretation.
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Affiliation(s)
- Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | | | - Hélène Tubeuf
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Aurélie Drouet
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Carolina Gómez
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Kerstin Schaefer
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany
| | - Verena Steinke-Lange
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany.,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Udo Koehler
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Andreas Laner
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany
| | - Julie Hauchard
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Karine Chauris
- Inserm U1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Munich, Germany. .,MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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2
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Fanconi Anaemia, Childhood Cancer and the BRCA Genes. Genes (Basel) 2021; 12:genes12101520. [PMID: 34680915 PMCID: PMC8535386 DOI: 10.3390/genes12101520] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/18/2022] Open
Abstract
Fanconi anaemia (FA) is an inherited chromosomal instability disorder characterised by congenital and developmental abnormalities and a strong cancer predisposition. In less than 5% of cases FA can be caused by bi-allelic pathogenic variants (PGVs) in BRCA2/FANCD1 and in very rare cases by bi-allelic PGVs in BRCA1/FANCS. The rarity of FA-like presentation due to PGVs in BRCA2 and even more due to PGVs in BRCA1 supports a fundamental role of the encoded proteins for normal development and prevention of malignant transformation. While FA caused by BRCA1/2 PGVs is strongly associated with distinct spectra of embryonal childhood cancers and AML with BRCA2-PGVs, and also early epithelial cancers with BRCA1 PGVs, germline variants in the BRCA1/2 genes have also been identified in non-FA childhood malignancies, and thereby implying the possibility of a role of BRCA PGVs also for non-syndromic cancer predisposition in children. We provide a concise review of aspects of the clinical and genetic features of BRCA1/2-associated FA with a focus on associated malignancies, and review novel aspects of the role of germline BRCA2 and BRCA1 PGVs occurring in non-FA childhood cancer and discuss aspects of clinical and biological implications.
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Missense Variants of Uncertain Significance: A Powerful Genetic Tool for Function Discovery with Clinical Implications. Cancers (Basel) 2021; 13:cancers13153719. [PMID: 34359619 PMCID: PMC8345083 DOI: 10.3390/cancers13153719] [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: 06/08/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Variants of uncertain significance in the breast cancer susceptibility gene BRCA2 represent 50–80% of the results from genetic testing. These mutations may lead to the dysfunction of the gene, thus conferring breast cancer predisposition; however, because they are rare and their impact on the function is not easy to predict, their classification into benign or pathogenic variants remains a challenge. By focusing on three specific rare missense variants identified in breast cancer patients, in this review, we discuss how the functional evaluation of this type of variants can be used to reveal novel activities of BRCA2. Based on these findings, we suggest additional functional tests that might be required for accurate variant classification and how their characterization may be leveraged to find novel clinical strategies for patients bearing these mutations. Abstract The breast cancer susceptibility gene BRCA2 encodes a multifunctional protein required for the accurate repair of DNA double-strand breaks and replicative DNA lesions. In addition, BRCA2 exhibits emerging important roles in mitosis. As a result, mutations in BRCA2 may affect chromosomal integrity in multiple ways. However, many of the BRCA2 mutations found in breast cancer patients and their families are single amino acid substitutions, sometimes unique, and their relevance in cancer risk remains difficult to assess. In this review, we focus on three recent reports that investigated variants of uncertain significance (VUS) located in the N-terminal region of BRCA2. In this framework, we make the case for how the functional evaluation of VUS can be a powerful genetic tool not only for revealing novel aspects of BRCA2 function but also for re-evaluating cancer risk. We argue that other functions beyond homologous recombination deficiency or “BRCAness” may influence cancer risk. We hope our discussion will help the reader appreciate the potential of these functional studies in the prevention and diagnostics of inherited breast and ovarian cancer. Moreover, these novel aspects in BRCA2 function might help find new therapeutic strategies.
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Julien M, Ghouil R, Petitalot A, Caputo SM, Carreira A, Zinn-Justin S. Intrinsic Disorder and Phosphorylation in BRCA2 Facilitate Tight Regulation of Multiple Conserved Binding Events. Biomolecules 2021; 11:1060. [PMID: 34356684 PMCID: PMC8301801 DOI: 10.3390/biom11071060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/26/2022] Open
Abstract
The maintenance of genome integrity in the cell is an essential process for the accurate transmission of the genetic material. BRCA2 participates in this process at several levels, including DNA repair by homologous recombination, protection of stalled replication forks, and cell division. These activities are regulated and coordinated via cell-cycle dependent modifications. Pathogenic variants in BRCA2 cause genome instability and are associated with breast and/or ovarian cancers. BRCA2 is a very large protein of 3418 amino acids. Most well-characterized variants causing a strong predisposition to cancer are mutated in the C-terminal 700 residues DNA binding domain of BRCA2. The rest of the BRCA2 protein is predicted to be disordered. Interactions involving intrinsically disordered regions (IDRs) remain difficult to identify both using bioinformatics tools and performing experimental assays. However, the lack of well-structured binding sites provides unique functional opportunities for BRCA2 to bind to a large set of partners in a tightly regulated manner. We here summarize the predictive and experimental arguments that support the presence of disorder in BRCA2. We describe how BRCA2 IDRs mediate self-assembly and binding to partners during DNA double-strand break repair, mitosis, and meiosis. We highlight how phosphorylation by DNA repair and cell-cycle kinases regulate these interactions. We finally discuss the impact of cancer-associated variants on the function of BRCA2 IDRs and more generally on genome stability and cancer risk.
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Affiliation(s)
- Manon Julien
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Rania Ghouil
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Ambre Petitalot
- Service de Génétique, Unité de Génétique Constitutionnelle, Institut Curie, 75005 Paris, France; (A.P.); (S.M.C.)
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
| | - Sandrine M. Caputo
- Service de Génétique, Unité de Génétique Constitutionnelle, Institut Curie, 75005 Paris, France; (A.P.); (S.M.C.)
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
| | - Aura Carreira
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
- Institut Curie, Paris Sciences Lettres Research University, 75005 Paris, France
- Unité Intégrité du Génome, ARN et Cancer, Institut Curie, CNRS UMR3348, 91405 Orsay, France
| | - Sophie Zinn-Justin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91190 Gif-sur-Yvette, France; (M.J.); (R.G.)
- L’Institut de Biologie Intégrative de la Cellule (I2BC), UMR 9198, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
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5
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Raud L, Le Tertre M, Vigneron L, Ka C, Richard G, Callebaut I, Chen JM, Férec C, Le Gac G, Fichou Y. Missense RHD single nucleotide variants induce weakened D antigen expression by altering splicing and/or protein expression. Transfusion 2021; 61:2468-2476. [PMID: 34110623 DOI: 10.1111/trf.16538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 04/09/2021] [Accepted: 04/28/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Although D variant phenotype is known to be due to genetic defects, including rare missense single nucleotide variants (SNVs), within the RHD gene, few studies have addressed the molecular and cellular mechanisms driving this altered expression. We and others showed previously that splicing is commonly disrupted by SNVs in constitutive splice sites and their vicinity. We thus sought to investigate whether rare missense SNVs located in "deep" exonic regions could also impair this mechanism. STUDY DESIGN AND METHODS Forty-six missense SNVs reported within exons 6 and 7 were first selected from the Human RhesusBase. Their respective effect on splicing was assessed by using an in vitro assay. An RhD-negative cell model was further generated by using the CRISPR-Cas9 approach. RhD-mutated proteins were overexpressed in the newly created model, and cell membrane expression of the D antigen was measured by flow cytometry. RESULTS Minigene splicing assay showed that 14 of 46 (30.4%) missense SNVs alter splicing. Very interestingly, further investigation of two missense SNVs, which both affect codon 338 and confer a weak D phenotype, showed various mechanisms: c.1012C>G (p.Leu338Val) disrupts splicing only, while c.1013T>C (p.Leu338Pro) alters only the protein structure, in agreement with in silico prediction tools and 3D protein structure visualization. CONCLUSION Our functional data set suggests that missense SNVs damage quantitatively D antigen expression by, at least, two different mechanisms (splicing alteration and protein destabilization) that may act independently. These data thereby contribute to extend the current knowledge of the molecular mechanisms governing weakened D expression.
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Affiliation(s)
- Loann Raud
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Marlène Le Tertre
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | | | - Chandran Ka
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | - Gaëlle Richard
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Paris, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | - Gérald Le Gac
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France.,Service de Génétique Médicale, CHRU Brest, Brest, France
| | - Yann Fichou
- Univ Brest, Inserm, EFS, UMR1078, GGB, Brest, France.,Laboratory of Excellence GR-Ex, Paris, France
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6
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Oosthuizen J, Kotze MJ, Van Der Merwe N, Myburgh EJ, Bester P, van der Merwe NC. Globally Rare BRCA2 Variants With Founder Haplotypes in the South African Population: Implications for Point-of-Care Testing Based on a Single-Institution BRCA1/2 Next-Generation Sequencing Study. Front Oncol 2021; 10:619469. [PMID: 33643918 PMCID: PMC7908826 DOI: 10.3389/fonc.2020.619469] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
Breast cancer patients historically benefitted from population-based genetic research performed in South Africa, which led to the development of founder-based BRCA1/2 diagnostic tests. With the advent of next-generation sequencing (NGS) technologies, the clinical utility of limited, targeted genetic assays were questioned. The study focused on mining NGS data obtained from an extensive single-institution NGS series (n=763). The aims were to determine (i) the prevalence of the most common recurrent/founder variants in patients referred for NGS directly; and (ii) to explore the data for inferred haplotypes associated with previous and potential new recurrent/founder variants. The identification of additional founder variants was essential for promoting and potentially advancing to rapid founder-based BRCA1/2 point-of-care (POC) technology as a time- and cost-effective alternative. NGS revealed actionable BRCA1/2 variants in 11.1% of patients tested (BRCA1 - 4.7%; BRCA2 - 6.4%), of which 22.4% represented variants currently screened for using first-tier targeted genetic testing. A retrospective investigation into the overall mutation-positive rate for an extended cohort (n=1906), which included first-tier test results, revealed that targeted genetic testing identified 74% of all pathogenic variants. This percentage justified the use of targeted genetic testing as a first-tier assay. Inferred haplotype analysis confirmed the founder status of BRCA2 c.5771_5774del (rs80359535) and c.7934del (rs80359688) and revealed an additional African founder variant (BRCA2 c.582G>A - rs80358810). A risk-benefit analysis using a questionnaire-based survey was performed in parallel to determine genetic professionals' views regarding POC testing. This was done to bridge the clinical implementation gap between haplotype analysis and POC testing as a first-tier screen during risk stratification of breast and ovarian cancer patients. The results reflected high acceptance (94%) of BRCA1/2 POC testing when accompanied by genetic counselling. Establishing the founder status for several recurrent BRCA2 variants across ethnic groups supports unselected use of the BRCA POC assay in all SA breast/ovarian cancer patients by recent local and international public health recommendations. Incorporating POC genotyping into the planned NGS screening algorithm of the Department of Health will ensure optimal use of the country's recourses to adhere to the set standards for optimal care and management for all breast cancer patients.
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Affiliation(s)
- Jaco Oosthuizen
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.,Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Maritha J Kotze
- Department of Pathology, Division of Chemical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.,Division of Chemical Pathology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Nicole Van Der Merwe
- Department of Pathology, Division of Chemical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | | | - Phillip Bester
- Division of Virology, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
| | - Nerina C van der Merwe
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa.,Division of Human Genetics, National Health Laboratory Service, Universitas Hospital, Bloemfontein, South Africa
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7
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Five Italian Families with Two Mutations in BRCA Genes. Genes (Basel) 2020; 11:genes11121451. [PMID: 33287145 PMCID: PMC7761639 DOI: 10.3390/genes11121451] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
Double heterozygosity (DH) in BRCA1 and BRCA2 genes and double mutation (DM) in BRCA1 or BRCA2 are extremely rare events in the general population, and few cases have been reported worldwide so far. Here, we describe five probands, all women, with breast and/or ovarian cancer and their families. Particularly, we identified two probands with DH in the BRCA1/2 genes with a frequency of 0.3% and three probands with DM in the BRCA2 gene with a frequency of 0.5%. The DH BRCA1 c.547+2T>A (IVS8+2T>A)/BRCA2 c.2830A>T (p.Lys944Ter) and BRCA1 c.3752_3755GTCT (p.Ser1253fs)/BRCA2 c.425+2T>C (IVS4+2T>C) have not been described together so far. The DM in BRCA2, c.631G>A (p.Val211Ile) and c.7008-2A>T (IVS13-2A>T), found in three unrelated probands, was previously reported in further unrelated patients. Due to its peculiarity, it is likely that both pathogenic variants descend from a common ancestor and, therefore, are founder mutations. Interestingly, analyzing the tumor types occurring in DH and DM families, we observed ovarian cancer only in DH families, probably due to the presence in DH patients of BRCA1 pathogenic variants, which predispose one more to ovarian cancer onset. Furthermore, male breast cancer and pancreatic cancer ensued in families with DM but not with DH. These data confirm that BRCA2 pathogenic variants have greater penetrance to develop breast cancer in men and are associated with an increased risk of pancreatic cancer.
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8
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Ravenscroft G, Clayton JS, Faiz F, Sivadorai P, Milnes D, Cincotta R, Moon P, Kamien B, Edwards M, Delatycki M, Lamont PJ, Chan SH, Colley A, Ma A, Collins F, Hennington L, Zhao T, McGillivray G, Ghedia S, Chao K, O'Donnell-Luria A, Laing NG, Davis MR. Neurogenetic fetal akinesia and arthrogryposis: genetics, expanding genotype-phenotypes and functional genomics. J Med Genet 2020; 58:609-618. [PMID: 33060286 DOI: 10.1136/jmedgenet-2020-106901] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/16/2020] [Accepted: 07/05/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Fetal akinesia and arthrogryposis are clinically and genetically heterogeneous and have traditionally been refractive to genetic diagnosis. The widespread availability of affordable genome-wide sequencing has facilitated accurate genetic diagnosis and gene discovery in these conditions. METHODS We performed next generation sequencing (NGS) in 190 probands with a diagnosis of arthrogryposis multiplex congenita, distal arthrogryposis, fetal akinesia deformation sequence or multiple pterygium syndrome. This sequencing was a combination of bespoke neurogenetic disease gene panels and whole exome sequencing. Only class 4 and 5 variants were reported, except for two cases where the identified variants of unknown significance (VUS) are most likely to be causative for the observed phenotype. Co-segregation studies and confirmation of variants identified by NGS were performed where possible. Functional genomics was performed as required. RESULTS Of the 190 probands, 81 received an accurate genetic diagnosis. All except two of these cases harboured class 4 and/or 5 variants based on the American College of Medical Genetics and Genomics guidelines. We identified phenotypic expansions associated with CACNA1S, CHRNB1, GMPPB and STAC3. We describe a total of 50 novel variants, including a novel missense variant in the recently identified gene for arthrogryposis with brain malformations-SMPD4. CONCLUSIONS Comprehensive gene panels give a diagnosis for a substantial proportion (42%) of fetal akinesia and arthrogryposis cases, even in an unselected cohort. Recently identified genes account for a relatively large proportion, 32%, of the diagnoses. Diagnostic-research collaboration was critical to the diagnosis and variant interpretation in many cases, facilitated genotype-phenotype expansions and reclassified VUS through functional genomics.
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Affiliation(s)
- Gina Ravenscroft
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia .,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Joshua S Clayton
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
| | - Fathimath Faiz
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Padma Sivadorai
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Di Milnes
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Rob Cincotta
- Maternal and Fetal Medicine, Mater Mothers' Hospital, Brisbane, Queensland, Australia
| | - Phillip Moon
- Department of Obstetrics, Redland Hospital, Cleveland, Queensland, Australia
| | - Ben Kamien
- Genetic Services WA, Women and Newborn Heath Service, Subiaco, Western Australia, Australia.,Hunter Genetics, Hunter New England Health, New Lambton, New South Wales, Australia
| | - Matthew Edwards
- Hunter Genetics, Hunter New England Health, New Lambton, New South Wales, Australia
| | - Martin Delatycki
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Phillipa J Lamont
- Neurology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Sophelia Hs Chan
- Paediatric Neurology Division, Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Alison Colley
- Clinical Genetics Services SWSLHD, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Alan Ma
- Department of Clinical Genetics, Children's Hospital Westmead, Sydney, New South Wales, Australia
| | - Felicity Collins
- Clinical Genetics Department, Western Sydney Genetics Program, Children's Hospitalat Westmead, Westmead, New South Wales, Australia
| | - Lucinda Hennington
- Mercy Health, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Austin Health, Melbourne, Victoria, Australia.,Alfred Health, Melbourne, Victoria, Australia
| | - Teresa Zhao
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sondhya Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Katherine Chao
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Anne O'Donnell-Luria
- Center for Mendelian Genomics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, Perth, Western Australia, Australia.,Faculty of Health and Medical Sciences, University of Western Australia, Nedlands, Western Australia, Australia.,PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
| | - Mark R Davis
- PathWest Diagnostic Genomics, Nedlands, Western Australia, Australia
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9
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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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10
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Characterization of splice-altering mutations in inherited predisposition to cancer. Proc Natl Acad Sci U S A 2019; 116:26798-26807. [PMID: 31843900 DOI: 10.1073/pnas.1915608116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mutations responsible for inherited disease may act by disrupting normal transcriptional splicing. Such mutations can be difficult to detect, and their effects difficult to characterize, because many lie deep within exons or introns where they may alter splice enhancers or silencers or introduce new splice acceptors or donors. Multiple mutation-specific and genome-wide approaches have been developed to evaluate these classes of mutations. We introduce a complementary experimental approach, cBROCA, which yields qualitative and quantitative assessments of the effects of genomic mutations on transcriptional splicing of tumor suppressor genes. cBROCA analysis is undertaken by deriving complementary DNA (cDNA) from puromycin-treated patient lymphoblasts, hybridizing the cDNA to the BROCA panel of tumor suppressor genes, and then multiplex sequencing to very high coverage. At each splice junction suggested by split sequencing reads, read depths of test and control samples are compared. Significant Z scores indicate altered transcripts, over and above naturally occurring minor transcripts, and comparisons of read depths indicate relative abundances of mutant and normal transcripts. BROCA analysis of genomic DNA suggested 120 rare mutations from 150 families with cancers of the breast, ovary, uterus, or colon, in >600 informative genotyped relatives. cBROCA analysis of their transcripts revealed a wide variety of consequences of abnormal splicing in tumor suppressor genes, including whole or partial exon skipping, exonification of intronic sequence, loss or gain of exonic and intronic splicing enhancers and silencers, complete intron retention, hypomorphic alleles, and combinations of these alterations. Combined with pedigree analysis, cBROCA sequencing contributes to understanding the clinical consequences of rare inherited mutations.
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11
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Scarpitta R, Zanna I, Aretini P, Gambino G, Scatena C, Mei B, Ghilli M, Rossetti E, Roncella M, Congregati C, Bonci F, Naccarato AG, Palli D, Caligo MA. Germline investigation in male breast cancer of DNA repair genes by next-generation sequencing. Breast Cancer Res Treat 2019; 178:557-564. [PMID: 31512090 DOI: 10.1007/s10549-019-05429-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/29/2019] [Indexed: 02/03/2023]
Abstract
PURPOSE In order to better define the breast cancer (BC) genetic risk factors in men, a germline investigation was carried out on 81 Male BC cases by screening the 24 genes involved in BC predisposition, genome stability maintenance and DNA repair mechanisms by next-generation sequencing. METHODS Germline DNAs were tested in a custom multi-gene panel focused on all coding exons and exon-intron boundaries of 24 selected genes using two amplicon-based assays on PGM-Ion Torrent (ThermoFisher Scientific) and MiSeq (Illumina) platforms. All variants were recorded and classified by using a custom pipeline. RESULTS Clinical pathological data and the family history of 81 Male BC cases were gathered and analysed, revealing the average age of onset to be 61.3 years old and that in 35 cases there was a family history of BC. Our genetic screening allowed us to identify a germline mutation in 22 patients (23%) in 4 genes: BRCA2, BRIP1, MUTYH and PMS2. Moreover, 12 variants of unknown clinical significance (VUS) in 9 genes (BARD1, BRCA1, BRIP1, CHEK2, ERCC1, NBN, PALB2, PMS1, RAD50) were predicted as potentially pathogenic by in silico analysis bringing the mutation detection rate up to 40%. CONCLUSION As expected, a positive family history is a strong predictor of germline BRCA2 mutations in male BC. Understanding the potential pathogenicity of VUS represents an extremely urgent need for the management of BC risk in Male BC cases and their own families.
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Affiliation(s)
- R Scarpitta
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - I Zanna
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Delle Oblate 4, 50141, Florence, Italy
| | - P Aretini
- Section of Cancer Genomics, Fondazione Pisana per la Scienza, Pisa, Italy
| | - G Gambino
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - C Scatena
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - B Mei
- Section of Genetic Oncology, University Hospital, Pisa, Italy
| | - M Ghilli
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - E Rossetti
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - M Roncella
- Breast Cancer Center, University Hospital, Pisa, Italy
| | - C Congregati
- Division of Internal Medicine, University Hospital, Pisa, Italy
| | - F Bonci
- Unit of Medical Oncology 2, University Hospital, Pisa, Italy
| | - A G Naccarato
- Division of Pathology, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - D Palli
- Cancer Risk Factors and Lifestyle Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network (ISPRO), Via Delle Oblate 4, 50141, Florence, Italy
| | - M A Caligo
- Section of Genetic Oncology, University Hospital, Pisa, Italy.
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12
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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: 4.6] [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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13
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Usefulness and Limitations of Comprehensive Characterization of mRNA Splicing Profiles in the Definition of the Clinical Relevance of BRCA1/2 Variants of Uncertain Significance. Cancers (Basel) 2019; 11:cancers11030295. [PMID: 30832263 PMCID: PMC6468917 DOI: 10.3390/cancers11030295] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/12/2022] Open
Abstract
Highly penetrant variants of BRCA1/2 genes are involved in hereditary predisposition to breast and ovarian cancer. The detection of pathogenic BRCA variants has a considerable clinical impact, allowing appropriate cancer-risk management. However, a major drawback is represented by the identification of variants of uncertain significance (VUS). Many VUS potentially affect mRNA splicing, making transcript analysis an essential step for the definition of their pathogenicity. Here, we characterize the impact on splicing of ten BRCA1/2 variants. Aberrant splicing patterns were demonstrated for eight variants whose alternative transcripts were fully characterized. Different events were observed, including exon skipping, intron retention, and usage of de novo and cryptic splice sites. Transcripts with premature stop codons or in-frame loss of functionally important residues were generated. Partial/complete splicing effect and quantitative contribution of different isoforms were assessed, leading to variant classification according to Evidence-based Network for the Interpretation of Mutant Alleles (ENIGMA) consortium guidelines. Two variants could be classified as pathogenic and two as likely benign, while due to a partial splicing effect, six variants remained of uncertain significance. The association with an undefined tumor risk justifies caution in recommending aggressive risk-reduction treatments, but prevents the possibility of receiving personalized therapies with potential beneficial effect. This indicates the need for applying additional approaches for the analysis of variants resistant to classification by gene transcript analyses.
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14
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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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15
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Baert A, Machackova E, Coene I, Cremin C, Turner K, Portigal-Todd C, Asrat MJ, Nuk J, Mindlin A, Young S, MacMillan A, Van Maerken T, Trbusek M, McKinnon W, Wood ME, Foulkes WD, Santamariña M, de la Hoya M, Foretova L, Poppe B, Vral A, Rosseel T, De Leeneer K, Vega A, Claes KBM. Thorough in silico and in vitro cDNA analysis of 21 putative BRCA1 and BRCA2 splice variants and a complex tandem duplication in BRCA2 allowing the identification of activated cryptic splice donor sites in BRCA2 exon 11. Hum Mutat 2018; 39:515-526. [PMID: 29280214 DOI: 10.1002/humu.23390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/03/2017] [Accepted: 12/17/2017] [Indexed: 12/31/2022]
Abstract
For 21 putative BRCA1 and BRCA2 splice site variants, the concordance between mRNA analysis and predictions by in silico programs was evaluated. Aberrant splicing was confirmed for 12 alterations. In silico prediction tools were helpful to determine for which variants cDNA analysis is warranted, however, predictions for variants in the Cartegni consensus region but outside the canonical sites, were less reliable. Learning algorithms like Adaboost and Random Forest outperformed the classical tools. Further validations are warranted prior to implementation of these novel tools in clinical settings. Additionally, we report here for the first time activated cryptic donor sites in the large exon 11 of BRCA2 by evaluating the effect at the cDNA level of a novel tandem duplication (5' breakpoint in intron 4; 3' breakpoint in exon 11) and of a variant disrupting the splice donor site of exon 11 (c.6841+1G > C). Additional sites were predicted, but not activated. These sites warrant further research to increase our knowledge on cis and trans acting factors involved in the conservation of correct transcription of this large exon. This may contribute to adequate design of ASOs (antisense oligonucleotides), an emerging therapy to render cancer cells sensitive to PARP inhibitor and platinum therapies.
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Affiliation(s)
- Annelot Baert
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Ilse Coene
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Carol Cremin
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | | | - Jennifer Nuk
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Sean Young
- BC Cancer Agency, Vancouver, British Columbia, Canada.,Cancer Genetics and Genomics Laboratory, Department of Pathology and Laboratory Medicine, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Andree MacMillan
- Provincial Medical Genetics Program, Eastern Health, St. John's, Newfoundland and Labrador, Canada
| | - Tom Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Martin Trbusek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Wendy McKinnon
- Familial Cancer Program, University of Vermont Medical Center, Burlington, Vermont, United States
| | - Marie E Wood
- Familial Cancer Program, University of Vermont Medical Center, Burlington, Vermont, United States
| | - William D Foulkes
- Cancer Research Program, Research Institute of the McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - Marta Santamariña
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Anne Vral
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kim De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica, CIBERER, IDIS, Santiago de Compostela, Spain
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16
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Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease. Genes (Basel) 2018; 9:genes9010015. [PMID: 29300302 PMCID: PMC5793168 DOI: 10.3390/genes9010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/11/2017] [Accepted: 12/27/2017] [Indexed: 01/12/2023] Open
Abstract
Mutations in the OCRL gene are associated with both Lowe syndrome and Dent-2 disease. Patients with Lowe syndrome present congenital cataracts, mental disabilities and a renal proximal tubulopathy, whereas patients with Dent-2 disease exhibit similar proximal tubule dysfunction but only mild, or no additional clinical defects. It is not yet understood why some OCRL mutations cause the phenotype of Lowe syndrome, while others develop the milder phenotype of Dent-2 disease. Our goal was to gain new insights into the consequences of OCRL exonic mutations on pre-mRNA splicing. Using predictive bioinformatics tools, we selected thirteen missense mutations and one synonymous mutation based on their potential effects on splicing regulatory elements or splice sites. These mutations were analyzed in a minigene splicing assay. Results of the RNA analysis showed that three presumed missense mutations caused alterations in pre-mRNA splicing. Mutation c.741G>T; p.(Trp247Cys) generated splicing silencer sequences and disrupted splicing enhancer motifs that resulted in skipping of exon 9, while mutations c.2581G>A; p.(Ala861Thr) and c.2581G>C; p.(Ala861Pro) abolished a 5′ splice site leading to skipping of exon 23. Mutation c.741G>T represents the first OCRL exonic variant outside the conserved splice site dinucleotides that results in alteration of pre-mRNA splicing. Our results highlight the importance of evaluating the effects of OCRL exonic mutations at the mRNA level.
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17
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Savisaar R, Hurst LD. Both Maintenance and Avoidance of RNA-Binding Protein Interactions Constrain Coding Sequence Evolution. Mol Biol Evol 2017; 34:1110-1126. [PMID: 28138077 PMCID: PMC5400389 DOI: 10.1093/molbev/msx061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
While the principal force directing coding sequence (CDS) evolution is selection on protein function, to ensure correct gene expression CDSs must also maintain interactions with RNA-binding proteins (RBPs). Understanding how our genes are shaped by these RNA-level pressures is necessary for diagnostics and for improving transgenes. However, the evolutionary impact of the need to maintain RBP interactions remains unresolved. Are coding sequences constrained by the need to specify RBP binding motifs? If so, what proportion of mutations are affected? Might sequence evolution also be constrained by the need not to specify motifs that might attract unwanted binding, for instance because it would interfere with exon definition? Here, we have scanned human CDSs for motifs that have been experimentally determined to be recognized by RBPs. We observe two sets of motifs-those that are enriched over nucleotide-controlled null and those that are depleted. Importantly, the depleted set is enriched for motifs recognized by non-CDS binding RBPs. Supporting the functional relevance of our observations, we find that motifs that are more enriched are also slower-evolving. The net effect of this selection to preserve is a reduction in the over-all rate of synonymous evolution of 2-3% in both primates and rodents. Stronger motif depletion, on the other hand, is associated with stronger selection against motif gain in evolution. The challenge faced by our CDSs is therefore not only one of attracting the right RBPs but also of avoiding the wrong ones, all while also evolving under selection pressures related to protein structure.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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18
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Grodecká L, Buratti E, Freiberger T. Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics? Int J Mol Sci 2017; 18:ijms18081668. [PMID: 28758972 PMCID: PMC5578058 DOI: 10.3390/ijms18081668] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023] Open
Abstract
For more than three decades, researchers have known that consensus splice sites alone are not sufficient regulatory elements to provide complex splicing regulation. Other regulators, so-called splicing regulatory elements (SREs) are needed. Most importantly, their sequence variants often underlie the development of various human disorders. However, due to their variable location and high degeneracy, these regulatory sequences are also very difficult to recognize and predict. Many different approaches aiming to identify SREs have been tried, often leading to the development of in silico prediction tools. While these tools were initially expected to be helpful to identify splicing-affecting mutations in genetic diagnostics, we are still quite far from meeting this goal. In fact, most of these tools are not able to accurately discern the SRE-affecting pathological variants from those not affecting splicing. Nonetheless, several recent evaluations have given appealing results (namely for EX-SKIP, ESRseq and Hexplorer predictors). In this review, we aim to summarize the history of the different approaches to SRE prediction, and provide additional validation of these tools based on patients' clinical data. Finally, we evaluate their usefulness for diagnostic settings and discuss the challenges that have yet to be met.
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Affiliation(s)
- Lucie Grodecká
- Centre for Cardiovascular Surgery and Transplantation, Brno 65691, Czech Republic.
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy.
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, Brno 65691, Czech Republic.
- Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic.
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19
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Davy G, Rousselin A, Goardon N, Castéra L, Harter V, Legros A, Muller E, Fouillet R, Brault B, Smirnova AS, Lemoine F, de la Grange P, Guillaud-Bataille M, Caux-Moncoutier V, Houdayer C, Bonnet F, Blanc-Fournier C, Gaildrat P, Frebourg T, Martins A, Vaur D, Krieger S. Detecting splicing patterns in genes involved in hereditary breast and ovarian cancer. Eur J Hum Genet 2017; 25:1147-1154. [PMID: 28905878 DOI: 10.1038/ejhg.2017.116] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/13/2017] [Accepted: 06/13/2017] [Indexed: 12/15/2022] Open
Abstract
Interpretation of variants of unknown significance (VUS) is a major challenge for laboratories performing molecular diagnosis of hereditary breast and ovarian cancer (HBOC), especially considering that many genes are now known to be involved in this syndrome. One important way these VUS can have a functional impact is through their effects on RNA splicing. Here we present a custom RNA-Seq assay plus bioinformatics and biostatistics pipeline to analyse specifically alternative and abnormal splicing junctions in 11 targeted HBOC genes. Our pipeline identified 14 new alternative splices in BRCA1 and BRCA2 in addition to detecting the majority of known alternative spliced transcripts therein. We provide here the first global splicing pattern analysis for the other nine genes, which will enable a comprehensive interpretation of splicing defects caused by VUS in HBOC. Previously known splicing alterations were consistently detected, occasionally with a more complex splicing pattern than expected. We also found that splicing in the 11 genes is similar in blood and breast tissue, supporting the utility and simplicity of blood splicing assays. Our pipeline is ready to be integrated into standard molecular diagnosis for HBOC, but it could equally be adapted for an integrative analysis of any multigene disorder.
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Affiliation(s)
- Grégoire Davy
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Antoine Rousselin
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Nicolas Goardon
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Laurent Castéra
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Valentin Harter
- Cancéropôle Nord-Ouest Data Processing Centre, CLCC François Baclesse, Caen, France
| | - Angelina Legros
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France
| | - Etienne Muller
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Robin Fouillet
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France
| | - Baptiste Brault
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Anna S Smirnova
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Fréderic Lemoine
- GenoSplice Technology, iPEPS-ICM, Pitié-Salpétrière Hospital, Paris, France
| | | | | | | | - Claude Houdayer
- Department of Genetics, Institut Curie, Paris, France.,Inserm U830, Paris, France.,Université Paris-Descartes, Sorbonne Paris Cité, Paris, France
| | - Françoise Bonnet
- Laboratory of Molecular Genetics, Institut Bergonié, Bordeaux, France
| | - Cécile Blanc-Fournier
- Department of Pathology, CLCC François Baclesse, Caen, France.,Tumorothèque de Caen Basse-Normandie, Caen, France
| | - Pascaline Gaildrat
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Thierry Frebourg
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.,Department of Genetics, University Hospital, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Alexandra Martins
- Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Dominique Vaur
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France
| | - Sophie Krieger
- Department of Cancer Biology and Genetics, CLCC François Baclesse, Normandy Centre for Genomic and Personalized Medicine, Caen, France.,Inserm U1079-IRIB, Normandy Centre for Genomic and Personalized Medicine, University of Rouen, Rouen, France.,University of Caen Normandy, Caen, France
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20
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Systematic analysis of splicing defects in selected primary immunodeficiencies-related genes. Clin Immunol 2017; 180:33-44. [DOI: 10.1016/j.clim.2017.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/03/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022]
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21
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Aljohi HA, Liu W, Lin Q, Yu J, Hu S. ISVASE: identification of sequence variant associated with splicing event using RNA-seq data. BMC Bioinformatics 2017; 18:320. [PMID: 28659141 PMCID: PMC5490186 DOI: 10.1186/s12859-017-1732-7] [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: 12/21/2016] [Accepted: 06/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Exon recognition and splicing precisely and efficiently by spliceosome is the key to generate mature mRNAs. About one third or a half of disease-related mutations affect RNA splicing. Software PVAAS has been developed to identify variants associated with aberrant splicing by directly using RNA-seq data. However, it bases on the assumption that annotated splicing site is normal splicing, which is not true in fact. RESULTS We develop the ISVASE, a tool for specifically identifying sequence variants associated with splicing events (SVASE) by using RNA-seq data. Comparing with PVAAS, our tool has several advantages, such as multi-pass stringent rule-dependent filters and statistical filters, only using split-reads, independent sequence variant identification in each part of splicing (junction), sequence variant detection for both of known and novel splicing event, additional exon-exon junction shift event detection if known splicing events provided, splicing signal evaluation, known DNA mutation and/or RNA editing data supported, higher precision and consistency, and short running time. Using a realistic RNA-seq dataset, we performed a case study to illustrate the functionality and effectiveness of our method. Moreover, the output of SVASEs can be used for downstream analysis such as splicing regulatory element study and sequence variant functional analysis. CONCLUSIONS ISVASE is useful for researchers interested in sequence variants (DNA mutation and/or RNA editing) associated with splicing events. The package is freely available at https://sourceforge.net/projects/isvase/ .
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Affiliation(s)
- Hasan Awad Aljohi
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh, 11442, Saudi Arabia
| | - Wanfei Liu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh, 11442, Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.,Current address: Grail Scientific Co. Ltd., Room 26-1, Build A, Meilong Jiayuan, NO. 80 South Nanjing Street, Heping District, Shenyang, Liaoning, 110000, China
| | - Qiang Lin
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh, 11442, Saudi Arabia.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Jun Yu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh, 11442, Saudi Arabia. .,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Songnian Hu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology and Chinese Academy of Sciences, Prince Turki Road, Riyadh, 11442, Saudi Arabia. .,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
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22
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Meyer S, Stevens A, Paredes R, Schneider M, Walker MJ, Williamson AJK, Gonzalez-Sanchez MB, Smetsers S, Dalal V, Teng HY, White DJ, Taylor S, Muter J, Pierce A, de Leonibus C, Rockx DAP, Rooimans MA, Spooncer E, Stauffer S, Biswas K, Godthelp B, Dorsman J, Clayton PE, Sharan SK, Whetton AD. Acquired cross-linker resistance associated with a novel spliced BRCA2 protein variant for molecular phenotyping of BRCA2 disruption. Cell Death Dis 2017; 8:e2875. [PMID: 28617445 PMCID: PMC5520920 DOI: 10.1038/cddis.2017.264] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/29/2017] [Accepted: 05/05/2017] [Indexed: 12/25/2022]
Abstract
BRCA2 encodes a protein with a fundamental role in homologous recombination that is essential for normal development. Carrier status of mutations in BRCA2 is associated with familial breast and ovarian cancer, while bi-allelic BRCA2 mutations can cause Fanconi anemia (FA), a cancer predisposition syndrome with cellular cross-linker hypersensitivity. Cancers associated with BRCA2 mutations can acquire chemo-resistance on relapse. We modeled acquired cross-linker resistance with an FA-derived BRCA2-mutated acute myeloid leukemia (AML) platform. Associated with acquired cross-linker resistance was the expression of a functional BRCA2 protein variant lacking exon 5 and exon 7 (BRCA2ΔE5+7), implying a role for BRCA2 splicing for acquired chemo-resistance. Integrated network analysis of transcriptomic and proteomic differences for phenotyping of BRCA2 disruption infers impact on transcription and chromatin remodeling in addition to the DNA damage response. The striking overlap with transcriptional profiles of FA patient hematopoiesis and BRCA mutation associated ovarian cancer helps define and explicate the ‘BRCAness’ profile.
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Affiliation(s)
- Stefan Meyer
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric and Adolescent Oncology, Royal Manchester Children's Hospital, Manchester, UK.,Young Oncology Unit, Christie Hospital, Manchester, UK
| | - Adam Stevens
- Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric Endocrinology, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK
| | - Roberto Paredes
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Marion Schneider
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Michael J Walker
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Andrew J K Williamson
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Maria-Belen Gonzalez-Sanchez
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Stephanie Smetsers
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Vineet Dalal
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Hsiang Ying Teng
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Daniel J White
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Sam Taylor
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Joanne Muter
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Andrew Pierce
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Chiara de Leonibus
- Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric Endocrinology, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK
| | - Davy A P Rockx
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Martin A Rooimans
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Elaine Spooncer
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Stacey Stauffer
- Mouse Cancer Genetics Program; Center for Cancer Research; Frederick National Laboratory for Cancer Research; National Cancer Institute, Frederick, MD, USA
| | - Kajal Biswas
- Mouse Cancer Genetics Program; Center for Cancer Research; Frederick National Laboratory for Cancer Research; National Cancer Institute, Frederick, MD, USA
| | - Barbara Godthelp
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Josephine Dorsman
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Peter E Clayton
- Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric Endocrinology, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK
| | - Shyam K Sharan
- Mouse Cancer Genetics Program; Center for Cancer Research; Frederick National Laboratory for Cancer Research; National Cancer Institute, Frederick, MD, USA
| | - Anthony D Whetton
- Stem Cell &Leukaemia Proteomics Laboratory, Manchester Cancer Research Centre, Division of Molecular and Clinical Cancer Sciences, Faculty of Biology, Medicine &Health, University of Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK.,Stoller Biomarker Discovery Centre, University of Manchester, Manchester, UK
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23
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Savisaar R, Hurst LD. Estimating the prevalence of functional exonic splice regulatory information. Hum Genet 2017; 136:1059-1078. [PMID: 28405812 PMCID: PMC5602102 DOI: 10.1007/s00439-017-1798-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/04/2017] [Indexed: 12/14/2022]
Abstract
In addition to coding information, human exons contain sequences necessary for correct splicing. These elements are known to be under purifying selection and their disruption can cause disease. However, the density of functional exonic splicing information remains profoundly uncertain. Several groups have experimentally investigated how mutations at different exonic positions affect splicing. They have found splice information to be distributed widely in exons, with one estimate putting the proportion of splicing-relevant nucleotides at >90%. These results suggest that splicing could place a major pressure on exon evolution. However, analyses of sequence conservation have concluded that the need to preserve splice regulatory signals only slightly constrains exon evolution, with a resulting decrease in the average human rate of synonymous evolution of only 1–4%. Why do these two lines of research come to such different conclusions? Among other reasons, we suggest that the methods are measuring different things: one assays the density of sites that affect splicing, the other the density of sites whose effects on splicing are visible to selection. In addition, the experimental methods typically consider short exons, thereby enriching for nucleotides close to the splice junction, such sites being enriched for splice-control elements. By contrast, in part owing to correction for nucleotide composition biases and to the assumption that constraint only operates on exon ends, the conservation-based methods can be overly conservative.
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Affiliation(s)
- Rosina Savisaar
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
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24
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Detailed molecular characterization of a novel IDS exonic mutation associated with multiple pseudoexon activation. J Mol Med (Berl) 2016; 95:299-309. [PMID: 27837218 DOI: 10.1007/s00109-016-1484-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/12/2016] [Accepted: 11/01/2016] [Indexed: 12/21/2022]
Abstract
Mutations affecting splicing underlie the development of many human genetic diseases, but rather rarely through mechanisms of pseudoexon activation. Here, we describe a novel c.1092T>A mutation in the iduronate-2-sulfatase (IDS) gene detected in a patient with significantly decreased IDS activity and a clinical diagnosis of mild mucopolysaccharidosis II form. The mutation created an exonic de novo acceptor splice site and resulted in a complex splicing pattern with multiple pseudoexon activation in the patient's fibroblasts. Using an extensive series of minigene splicing experiments, we showed that the competition itself between the de novo and authentic splice site led to the bypass of the authentic one. This event then resulted in activation of several cryptic acceptor and donor sites in the upstream intron. As this was an unexpected and previously unreported mechanism of aberrant pseudoexon inclusion, we systematically analysed and disproved that the patient's mutation induced any relevant change in surrounding splicing regulatory elements. Interestingly, all pseudoexons included in the mature transcripts overlapped with the IDS alternative terminal exon 7b suggesting that this sequence represents a key element in the IDS pre-mRNA architecture. These findings extend the spectrum of mechanisms enabling pseudoexon activation and underscore the complexity of mutation-induced splicing aberrations. KEY MESSAGE Novel exonic IDS gene mutation leads to a complex splicing pattern. Mutation activates multiple pseudoexons through a previously unreported mechanism. Multiple cryptic splice site (ss) activation results from a bypass of authentic ss. Authentic ss bypass is due to a competition between de novo and authentic ss.
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25
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Vallée MP, Di Sera TL, Nix DA, Paquette AM, Parsons MT, Bell R, Hoffman A, Hogervorst FBL, Goldgar DE, Spurdle AB, Tavtigian SV. Adding In Silico Assessment of Potential Splice Aberration to the Integrated Evaluation of BRCA Gene Unclassified Variants. Hum Mutat 2016; 37:627-39. [PMID: 26913838 PMCID: PMC4907813 DOI: 10.1002/humu.22973] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 01/29/2016] [Indexed: 01/05/2023]
Abstract
Clinical mutation screening of the cancer susceptibility genes BRCA1 and BRCA2 generates many unclassified variants (UVs). Most of these UVs are either rare missense substitutions or nucleotide substitutions near the splice junctions of the protein coding exons. Previously, we developed a quantitative method for evaluation of BRCA gene UVs—the “integrated evaluation”—that combines a sequence analysis‐based prior probability of pathogenicity with patient and/or tumor observational data to arrive at a posterior probability of pathogenicity. One limitation of the sequence analysis‐based prior has been that it evaluates UVs from the perspective of missense substitution severity but not probability to disrupt normal mRNA splicing. Here, we calibrated output from the splice‐site fitness program MaxEntScan to generate spliceogenicity‐based prior probabilities of pathogenicity for BRCA gene variants; these range from 0.97 for variants with high probability to damage a donor or acceptor to 0.02 for exonic variants that do not impact a splice junction and are unlikely to create a de novo donor. We created a database http://priors.hci.utah.edu/PRIORS/ that provides the combined missense substitution severity and spliceogenicity‐based probability of pathogenicity for BRCA gene single‐nucleotide substitutions. We also updated the BRCA gene Ex‐UV LOVD, available at http://hci‐exlovd.hci.utah.edu, with 77 re‐evaluable variants.
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Affiliation(s)
- Maxime P Vallée
- Department of Molecular Medicine, CHUQ Research Center, Quebec City, Canada
| | - Tonya L Di Sera
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - David A Nix
- ARUP Laboratories, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrew M Paquette
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Russel Bell
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Andrea Hoffman
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | | | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
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26
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Chaudhary AK, Girisha KM, Bashyam MD. A novel EDARADD 5'-splice site mutation resulting in activation of two alternate cryptic 5'-splice sites causes autosomal recessive Hypohidrotic Ectodermal Dysplasia. Am J Med Genet A 2016; 170:1639-41. [PMID: 26991760 DOI: 10.1002/ajmg.a.37607] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 02/19/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Ajay K Chaudhary
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | - Murali D Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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27
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Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools. PLoS Genet 2016; 12:e1005756. [PMID: 26761715 PMCID: PMC4711968 DOI: 10.1371/journal.pgen.1005756] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 12/01/2015] [Indexed: 01/01/2023] Open
Abstract
The identification of a causal mutation is essential for molecular diagnosis and clinical management of many genetic disorders. However, even if next-generation exome sequencing has greatly improved the detection of nucleotide changes, the biological interpretation of most exonic variants remains challenging. Moreover, particular attention is typically given to protein-coding changes often neglecting the potential impact of exonic variants on RNA splicing. Here, we used the exon 10 of MLH1, a gene implicated in hereditary cancer, as a model system to assess the prevalence of RNA splicing mutations among all single-nucleotide variants identified in a given exon. We performed comprehensive minigene assays and analyzed patient's RNA when available. Our study revealed a staggering number of splicing mutations in MLH1 exon 10 (77% of the 22 analyzed variants), including mutations directly affecting splice sites and, particularly, mutations altering potential splicing regulatory elements (ESRs). We then used this thoroughly characterized dataset, together with experimental data derived from previous studies on BRCA1, BRCA2, CFTR and NF1, to evaluate the predictive power of 3 in silico approaches recently described as promising tools for pinpointing ESR-mutations. Our results indicate that ΔtESRseq and ΔHZEI-based approaches not only discriminate which variants affect splicing, but also predict the direction and severity of the induced splicing defects. In contrast, the ΔΨ-based approach did not show a compelling predictive power. Our data indicates that exonic splicing mutations are more prevalent than currently appreciated and that they can now be predicted by using bioinformatics methods. These findings have implications for all genetically-caused diseases.
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28
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Identification of Promotor and Exonic Variations, and Functional Characterization of a Splice Site Mutation in Indian Patients with Unconjugated Hyperbilirubinemia. PLoS One 2015; 10:e0145967. [PMID: 26716871 PMCID: PMC4696816 DOI: 10.1371/journal.pone.0145967] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/10/2015] [Indexed: 01/07/2023] Open
Abstract
Background Mild unconjugated hyperbilirubinemia (UH), due to reduced activity of the enzyme uridine diphosphoglucuronate-glucuronosyltransferase family, polypeptide 1 (UGT1A1), is a common clinical condition. Most cases are caused by presence in homozygous form of an A(TA)7TAA nucleotide sequence instead of the usual A(TA)6TAA sequence in promoter region of the UGT1A1 gene. In some cases, other genetic variations have been identified which differ between populations. There is need for more data on such genetic variations from India. Methods DNA from subjects with unexplained persistent or recurrent UH was tested for the presence of TA promoter insertions. In addition, all five exons and splicing site regions of UGT1A1 gene were sequenced. Several bioinformatics tools were used to determine the biological significance of the observed genetic changes. Functional analysis was done to look for effect of a splice site mutation in UGT1A1. Results Of 71 subjects with UH (68 male; median age [range], 26 [16–63] years; serum bilirubin 56 [26–219] μM/L, predominantly unconjugated) studied, 65 (91.5%) subjects were homozygous for A(TA)7TAA allele, five (7.0%) were heterozygous, and one (1.4%) lacked this change. Fifteen subjects with UH had missense exonic single nucleotide changes (14 heterozygous, 1 homozygous), including one subject with a novel nucleotide change (p.Thr205Asn). Bioinformatics tools predicted some of these variations (p.Arg108Cys, p.Ile159Thr and p.Glu463Val) to be deleterious. Functional characterization of an exonic variation (c.1084G>A) located at a splice site revealed that it results in frameshift deletion of 31 nucleotides and premature truncation of the protein. Conclusion Our study revealed several single nucleotide variations in UGT1A1 gene in Indian subjects with UH. Functional characterization of a splice site variation indicated that it leads to disordered splicing. These variations may explain UH in subjects who lacked homozygous A(TA)7TAA promoter alleles.
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29
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Kergourlay V, Raï G, Blandin G, Salgado D, Béroud C, Lévy N, Krahn M, Bartoli M. Identification of Splicing Defects Caused by Mutations in the Dysferlin Gene. Hum Mutat 2014; 35:1532-41. [DOI: 10.1002/humu.22710] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 10/03/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Virginie Kergourlay
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
| | - Ghadi Raï
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
| | - Gaëlle Blandin
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
| | - David Salgado
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
| | - Christophe Béroud
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
- Département de Génétique Médicale et de Biologie Cellulaire; AP-HM, Hôpital d'Enfants de la Timone; Marseille 13385 France
| | - Nicolas Lévy
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
- Département de Génétique Médicale et de Biologie Cellulaire; AP-HM, Hôpital d'Enfants de la Timone; Marseille 13385 France
| | - Martin Krahn
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
- Département de Génétique Médicale et de Biologie Cellulaire; AP-HM, Hôpital d'Enfants de la Timone; Marseille 13385 France
| | - Marc Bartoli
- Aix Marseille Université; GMGF; Marseille 13385 France
- Inserm, UMR_S 910; Marseille 13385 France
- Département de Génétique Médicale et de Biologie Cellulaire; AP-HM, Hôpital d'Enfants de la Timone; Marseille 13385 France
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Van Neste L, Van Criekinge W. We are all individuals... bioinformatics in the personalized medicine era. Cell Oncol (Dordr) 2014; 38:29-37. [PMID: 25204962 DOI: 10.1007/s13402-014-0195-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 12/16/2022] Open
Abstract
The medical landscape is evolving at a rapid pace, creating the opportunity for more personalized patient treatment and shifting the way healthcare is approached and thought about. With the availability of (epi)genome-wide, transcriptomic and proteogenomic profiling techniques detailed characterization of a disease at the level of the individual is now possible, offering the opportunity for truly tailored approaches for treatment and patient care. While improvements are still expected, the techniques and the basic analytical tools have reached a state that these can be efficiently deployed in both routine research and clinical practice. Still, some major challenges remain. Notably, holistic approaches, integrating data from several sources, e.g. genomic and epigenomic, will increase the understanding of the underlying biological concepts and provide insight into the causes, effects and effective solutions. However, creating and validating such a knowledge base, potentially for different levels of expertise, and integrating several data points into meaningful information is not trivial.
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Affiliation(s)
- Leander Van Neste
- Department of Pathology, School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands,
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Šípek A, Grodecká L, Baxová A, Cibulková P, Dvořáková M, Mazurová S, Magner M, Zeman J, Honzík T, Freiberger T. NovelFBN1gene mutation and maternal germinal mosaicism as the cause of neonatal form of Marfan syndrome. Am J Med Genet A 2014; 164A:1559-64. [DOI: 10.1002/ajmg.a.36480] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/06/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Antonín Šípek
- Institute of Biology and Medical Genetics, First Faculty of Medicine; Charles University in Prague and General University Hospital; Prague Czech Republic
| | - Lucie Grodecká
- Molecular Genetics Laboratory; Centre for Cardiovascular Surgery and Transplantation; Brno Czech Republic
- Central European Institute of Technology; Masaryk University; Brno Czech Republic
| | - Alice Baxová
- Institute of Biology and Medical Genetics, First Faculty of Medicine; Charles University in Prague and General University Hospital; Prague Czech Republic
| | - Petra Cibulková
- AGEL Research and Training Institute-Nový Jičín Branch; AGEL Laboratories; Nový Jičín Czech Republic
| | - Magdaléna Dvořáková
- AGEL Research and Training Institute-Nový Jičín Branch; AGEL Laboratories; Nový Jičín Czech Republic
| | - Stella Mazurová
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine; Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Martin Magner
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine; Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Jiří Zeman
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine; Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Tomáš Honzík
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine; Charles University in Prague and General University Hospital in Prague; Prague Czech Republic
| | - Tomáš Freiberger
- Molecular Genetics Laboratory; Centre for Cardiovascular Surgery and Transplantation; Brno Czech Republic
- Central European Institute of Technology; Masaryk University; Brno Czech Republic
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Grodecká L, Lockerová P, Ravčuková B, Buratti E, Baralle FE, Dušek L, Freiberger T. Exon first nucleotide mutations in splicing: evaluation of in silico prediction tools. PLoS One 2014; 9:e89570. [PMID: 24586880 PMCID: PMC3931810 DOI: 10.1371/journal.pone.0089570] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 01/21/2014] [Indexed: 12/20/2022] Open
Abstract
Mutations in the first nucleotide of exons (E+1) mostly affect pre-mRNA splicing when found in AG-dependent 3′ splice sites, whereas AG-independent splice sites are more resistant. The AG-dependency, however, may be difficult to assess just from primary sequence data as it depends on the quality of the polypyrimidine tract. For this reason, in silico prediction tools are commonly used to score 3′ splice sites. In this study, we have assessed the ability of sequence features and in silico prediction tools to discriminate between the splicing-affecting and non-affecting E+1 variants. For this purpose, we newly tested 16 substitutions in vitro and derived other variants from literature. Surprisingly, we found that in the presence of the substituting nucleotide, the quality of the polypyrimidine tract alone was not conclusive about its splicing fate. Rather, it was the identity of the substituting nucleotide that markedly influenced it. Among the computational tools tested, the best performance was achieved using the Maximum Entropy Model and Position-Specific Scoring Matrix. As a result of this study, we have now established preliminary discriminative cut-off values showing sensitivity up to 95% and specificity up to 90%. This is expected to improve our ability to detect splicing-affecting variants in a clinical genetic setting.
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Affiliation(s)
- Lucie Grodecká
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavla Lockerová
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Barbora Ravčuková
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Ladislav Dušek
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Clinical Immunology and Allergology, St. Anne’s University Hospital and Masaryk University, Brno, Czech Republic
- * E-mail:
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Multifactorial likelihood assessment of BRCA1 and BRCA2 missense variants confirms that BRCA1:c.122A>G(p.His41Arg) is a pathogenic mutation. PLoS One 2014; 9:e86836. [PMID: 24489791 PMCID: PMC3904950 DOI: 10.1371/journal.pone.0086836] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/13/2013] [Indexed: 11/22/2022] Open
Abstract
Rare exonic, non-truncating variants in known cancer susceptibility genes such as BRCA1 and BRCA2 are problematic for genetic counseling and clinical management of relevant families. This study used multifactorial likelihood analysis and/or bioinformatically-directed mRNA assays to assess pathogenicity of 19 BRCA1 or BRCA2 variants identified following patient referral to clinical genetic services. Two variants were considered to be pathogenic (Class 5). BRCA1:c.4484G> C(p.Arg1495Thr) was shown to result in aberrant mRNA transcripts predicted to encode truncated proteins. The BRCA1:c.122A>G(p.His41Arg) RING-domain variant was found from multifactorial likelihood analysis to have a posterior probability of pathogenicity of 0.995, a result consistent with existing protein functional assay data indicating lost BARD1 binding and ubiquitin ligase activity. Of the remaining variants, seven were determined to be not clinically significant (Class 1), nine were likely not pathogenic (Class 2), and one was uncertain (Class 3).These results have implications for genetic counseling and medical management of families carrying these specific variants. They also provide additional multifactorial likelihood variant classifications as reference to evaluate the sensitivity and specificity of bioinformatic prediction tools and/or functional assay data in future studies.
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Bashyam M, Chaudhary A, Kiran M, Reddy V, Nagarajaram H, Dalal A, Bashyam L, Suri D, Gupta A, Gupta N, Kabra M, Puri R, RamaDevi R, Kapoor S, Danda S. Molecular analyses of novelASAH1mutations causing Farber lipogranulomatosis: analyses of exonic splicing enhancer inactivating mutation. Clin Genet 2013; 86:530-8. [DOI: 10.1111/cge.12316] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/23/2013] [Accepted: 10/24/2013] [Indexed: 11/28/2022]
Affiliation(s)
- M.D. Bashyam
- Laboratory of Molecular Oncology; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - A.K. Chaudhary
- Laboratory of Molecular Oncology; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - M. Kiran
- Laboratory of Computational Biology; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - V. Reddy
- Laboratory of Computational Biology; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - H.A. Nagarajaram
- Laboratory of Computational Biology; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - A. Dalal
- Diagnostics Division; Centre for DNA Fingerprinting and Diagnostics; Hyderabad India
| | - L. Bashyam
- School of Life Sciences; University of Hyderabad; Hyderabad India
| | - D. Suri
- Department of Pediatrics; Post Graduate Institute of Medical Education and Research; Chandigarh India
| | - A. Gupta
- Department of Pediatrics; Post Graduate Institute of Medical Education and Research; Chandigarh India
| | - N. Gupta
- Department of Pediatrics; All India Institute of Medical Sciences; New Delhi India
| | - M. Kabra
- Department of Pediatrics; All India Institute of Medical Sciences; New Delhi India
| | - R.D. Puri
- Deparment of Genetic Medicine; Sir Ganga Ram Hospital; Delhi India
| | | | - S. Kapoor
- Division of Genetics; Lok Nayak Hospital & Maulana Azad Medical College; New Delhi India
| | - S. Danda
- Department of Clinical Genetics; Christian Medical College and Hospital; Vellore India
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Bloom AJ, Martinez M, Chen LS, Bierut LJ, Murphy SE, Goate A. CYP2B6 non-coding variation associated with smoking cessation is also associated with differences in allelic expression, splicing, and nicotine metabolism independent of common amino-acid changes. PLoS One 2013; 8:e79700. [PMID: 24260284 PMCID: PMC3829832 DOI: 10.1371/journal.pone.0079700] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 10/04/2013] [Indexed: 11/23/2022] Open
Abstract
The Cytochrome P450 2B6 (CYP2B6) enzyme makes a small contribution to hepatic nicotine metabolism relative to CYP2A6, but CYP2B6 is the primary enzyme responsible for metabolism of the smoking cessation drug bupropion. Using CYP2A6 genotype as a covariate, we find that a non-coding polymorphism in CYP2B6 previously associated with smoking cessation (rs8109525) is also significantly associated with nicotine metabolism. The association is independent of the well-studied non-synonymous variants rs3211371, rs3745274, and rs2279343 (CYP2B6*5 and *6). Expression studies demonstrate that rs8109525 is also associated with differences in CYP2B6 mRNA expression in liver biopsy samples. Splicing assays demonstrate that specific splice forms of CYP2B6 are associated with haplotypes defined by variants including rs3745274 and rs8109525. These results indicate differences in mRNA expression and splicing as potential molecular mechanisms by which non-coding variation in CYP2B6 may affect enzymatic activity leading to differences in metabolism and smoking cessation.
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Affiliation(s)
- A. Joseph Bloom
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| | - Maribel Martinez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sharon E. Murphy
- Department of Biochemistry Molecular Biology and BioPhysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alison Goate
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, United States of America
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Di Giacomo D, Gaildrat P, Abuli A, Abdat J, Frébourg T, Tosi M, Martins A. Functional analysis of a large set of BRCA2 exon 7 variants highlights the predictive value of hexamer scores in detecting alterations of exonic splicing regulatory elements. Hum Mutat 2013; 34:1547-57. [PMID: 23983145 DOI: 10.1002/humu.22428] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 08/14/2013] [Indexed: 11/06/2022]
Abstract
Exonic variants can alter pre-mRNA splicing either by changing splice sites or by modifying splicing regulatory elements. Often these effects are difficult to predict and are only detected by performing RNA analyses. Here, we analyzed, in a minigene assay, 26 variants identified in the exon 7 of BRCA2, a cancer predisposition gene. Our results revealed eight new exon skipping mutations in this exon: one directly altering the 5' splice site and seven affecting potential regulatory elements. This brings the number of splicing regulatory mutations detected in BRCA2 exon 7 to a total of 11, a remarkably high number considering the total number of variants reported in this exon (n = 36), all tested in our minigene assay. We then exploited this large set of splicing data to test the predictive value of splicing regulator hexamers' scores recently established by Ke et al. (). Comparisons of hexamer-based predictions with our experimental data revealed high sensitivity in detecting variants that increased exon skipping, an important feature for prescreening variants before RNA analysis. In conclusion, hexamer scores represent a promising tool for predicting the biological consequences of exonic variants and may have important applications for the interpretation of variants detected by high-throughput sequencing.
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Affiliation(s)
- Daniela Di Giacomo
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France; Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, Italy
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RNA splicing: a new player in the DNA damage response. Int J Cell Biol 2013; 2013:153634. [PMID: 24159334 PMCID: PMC3789447 DOI: 10.1155/2013/153634] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 12/16/2022] Open
Abstract
It is widely accepted that tumorigenesis is a multistep process characterized by the sequential accumulation of genetic alterations. However, the molecular basis of genomic instability in cancer is still partially understood. The observation that hereditary cancers are often characterized by mutations in DNA repair and checkpoint genes suggests that accumulation of DNA damage is a major contributor to the oncogenic transformation. It is therefore of great interest to identify all the cellular pathways that contribute to the response to DNA damage. Recently, RNA processing has emerged as a novel pathway that may contribute to the maintenance of genome stability. In this review, we illustrate several different mechanisms through which pre-mRNA splicing and genomic stability can influence each other. We specifically focus on the role of splicing factors in the DNA damage response and describe how, in turn, activation of the DDR can influence the activity of splicing factors.
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Walker LC, Whiley PJ, Houdayer C, Hansen TVO, Vega A, Santamarina M, Blanco A, Fachal L, Southey MC, Lafferty A, Colombo M, De Vecchi G, Radice P, Spurdle AB. Evaluation of a 5-Tier Scheme Proposed for Classification of Sequence Variants Using Bioinformatic and Splicing Assay Data: Inter-Reviewer Variability and Promotion of Minimum Reporting Guidelines. Hum Mutat 2013; 34:1424-31. [DOI: 10.1002/humu.22388] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 07/12/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Logan C. Walker
- Department of Pathology; University of Otago; Christchurch; New Zealand
| | | | - Claude Houdayer
- Service de Génétique, INSERM U830, Institut Curie et Université Paris Descartes; Sorbonne Paris Cité; Paris; France
| | - Thomas V. O. Hansen
- Center for Genomic Medicine; Copenhagen University Hospital; Rigshospitalet; Copenhagen; Denmark
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC; CIBERER, IDIS; Santiago de Compostela; Spain
| | - Marta Santamarina
- Grupo de Medicina Xenómica -USC, University of Santiago de Compostela; CIBERER; IDIS; Santiago de Compostela; Spain
| | - Ana Blanco
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC; CIBERER, IDIS; Santiago de Compostela; Spain
| | - Laura Fachal
- Fundación Pública Galega de Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC; CIBERER, IDIS; Santiago de Compostela; Spain
| | - Melissa C. Southey
- Epidemiology Laboratory, Department of Pathology; The University of Melbourne; Melbourne; Victoria; Australia
| | | | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine; Fondazione IRCCS Istituto Nazionale dei Tumouri (INT); Milan; Italy
| | - Giovanna De Vecchi
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine; Fondazione IRCCS Istituto Nazionale dei Tumouri (INT); Milan; Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine; Fondazione IRCCS Istituto Nazionale dei Tumouri (INT); Milan; Italy
| | - Amanda B. Spurdle
- Molecular Cancer Epidemiology Laboratory, Genetics and Computational Biology Division; Queensland Institute of Medical Research; Herston; Queensland; Australia
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A compensatory effect upon splicing results in normal function of the CYP2A6*14 allele. Pharmacogenet Genomics 2013; 23:107-16. [PMID: 23292114 DOI: 10.1097/fpc.0b013e32835caf7d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A synonymous variant in the first exon of CYP2A6, rs1137115 (51G>A), defines the common reference allele CYP2A6*1A, and is associated with lower mRNA expression and slower in-vivo nicotine metabolism. Another common allele, CYP2A6*14, differs from CYP2A6*1A by a single variant, rs28399435 (86G>A, S29N). However, CYP2A6*14 shows in-vivo activity comparable with that of full-function alleles, and significantly higher than CYP2A6*1A. rs1137115A is predicted to create an exonic splicing suppressor site overlapping an exonic splicing enhancer (ESE) site in the first exon of CYP2A6, whereas rs28399435A is predicted to strengthen another adjacent ESE, potentially compensating for rs1137115A. Using an allelic expression assay to assess cDNAs produced from rs1137115 heterozygous liver biopsy samples, lower expression of the CYP2A6*1A allele is confirmed while CYP2A6*14 expression is found to be indistinguishable from that of rs1137115G alleles. Quantitative PCR assays to determine the relative abundance of spliced and unspliced or partially spliced CYP2A6 mRNAs in liver biopsy samples show that *1A/*1A homozygotes have a significantly lower ratio, due to both a reduction in spliced forms and an increase in unspliced or partially spliced CYP2A6. These results show the importance of common genetic variants that effect exonic splicing suppressor and ESEs to explain human variation regarding clinically-relevant phenotypes.
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Comparative in vitro and in silico analyses of variants in splicing regions of BRCA1 and BRCA2 genes and characterization of novel pathogenic mutations. PLoS One 2013; 8:e57173. [PMID: 23451180 PMCID: PMC3579815 DOI: 10.1371/journal.pone.0057173] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 01/18/2013] [Indexed: 12/15/2022] Open
Abstract
Several unclassified variants (UVs) have been identified in splicing regions of disease-associated genes and their characterization as pathogenic mutations or benign polymorphisms is crucial for the understanding of their role in disease development. In this study, 24 UVs located at BRCA1 and BRCA2 splice sites were characterized by transcripts analysis. These results were used to evaluate the ability of nine bioinformatics programs in predicting genetic variants causing aberrant splicing (spliceogenic variants) and the nature of aberrant transcripts. Eleven variants in BRCA1 and 8 in BRCA2, including 8 not previously characterized at transcript level, were ascertained to affect mRNA splicing. Of these, 16 led to the synthesis of aberrant transcripts containing premature termination codons (PTCs), 2 to the up-regulation of naturally occurring alternative transcripts containing PTCs, and one to an in-frame deletion within the region coding for the DNA binding domain of BRCA2, causing the loss of the ability to bind the partner protein DSS1 and ssDNA. For each computational program, we evaluated the rate of non-informative analyses, i.e. those that did not recognize the natural splice sites in the wild-type sequence, and the rate of false positive predictions, i.e., variants incorrectly classified as spliceogenic, as a measure of their specificity, under conditions setting sensitivity of predictions to 100%. The programs that performed better were Human Splicing Finder and Automated Splice Site Analyses, both exhibiting 100% informativeness and specificity. For 10 mutations the activation of cryptic splice sites was observed, but we were unable to derive simple criteria to select, among the different cryptic sites predicted by the bioinformatics analyses, those actually used. Consistent with previous reports, our study provides evidences that in silico tools can be used for selecting splice site variants for in vitro analyses. However, the latter remain mandatory for the characterization of the nature of aberrant transcripts.
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