1
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Christowitz C, Olivier DW, Schneider JW, Kotze MJ, Engelbrecht AM. Incorporating functional genomics into the pathology-supported genetic testing framework implemented in South Africa: A future view of precision medicine for breast carcinomas. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2024; 793:108492. [PMID: 38631437 DOI: 10.1016/j.mrrev.2024.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/25/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024]
Abstract
A pathology-supported genetic testing (PSGT) framework was established in South Africa to improve access to precision medicine for patients with breast carcinomas. Nevertheless, the frequent identification of variants of uncertain significance (VUSs) with the use of genome-scale next-generation sequencing has created a bottleneck in the return of results to patients. This review highlights the importance of incorporating functional genomics into the PSGT framework as a proposed initiative. Here, we explore various model systems and experimental methods available for conducting functional studies in South Africa to enhance both variant classification and clinical interpretation. We emphasize the distinct advantages of using in vitro, in vivo, and translational ex vivo models to improve the effectiveness of precision oncology. Moreover, we highlight the relevance of methodologies such as protein modelling and structural bioinformatics, multi-omics, metabolic activity assays, flow cytometry, cell migration and invasion assays, tube-formation assays, multiplex assays of variant effect, and database mining and machine learning models. The selection of the appropriate experimental approach largely depends on the molecular mechanism of the gene under investigation and the predicted functional effect of the VUS. However, before making final decisions regarding the pathogenicity of VUSs, it is essential to assess the functional evidence and clinical outcomes under current variant interpretation guidelines. The inclusion of a functional genomics infrastructure within the PSGT framework will significantly advance the reclassification of VUSs and enhance the precision medicine pipeline for patients with breast carcinomas in South Africa.
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Affiliation(s)
- Claudia Christowitz
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Daniel W Olivier
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Johann W Schneider
- Division of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Anna-Mart Engelbrecht
- Department of Physiological Sciences, Faculty of Science, Stellenbosch University, Stellenbosch 7600, South Africa; Department of Global Health, African Cancer Institute, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
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2
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Mishra AP, Hartford SA, Sahu S, Klarmann K, Chittela RK, Biswas K, Jeon AB, Martin BK, Burkett S, Southon E, Reid S, Albaugh ME, Karim B, Tessarollo L, Keller JR, Sharan SK. BRCA2-DSS1 interaction is dispensable for RAD51 recruitment at replication-induced and meiotic DNA double strand breaks. Nat Commun 2022; 13:1751. [PMID: 35365640 PMCID: PMC8975877 DOI: 10.1038/s41467-022-29409-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 03/14/2022] [Indexed: 12/31/2022] Open
Abstract
The interaction between tumor suppressor BRCA2 and DSS1 is essential for RAD51 recruitment and repair of DNA double stand breaks (DSBs) by homologous recombination (HR). We have generated mice with a leucine to proline substitution at position 2431 of BRCA2, which disrupts this interaction. Although a significant number of mutant mice die during embryogenesis, some homozygous and hemizygous mutant mice undergo normal postnatal development. Despite lack of radiation induced RAD51 foci formation and a severe HR defect in somatic cells, mutant mice are fertile and exhibit normal RAD51 recruitment during meiosis. We hypothesize that the presence of homologous chromosomes in close proximity during early prophase I may compensate for the defect in BRCA2-DSS1 interaction. We show the restoration of RAD51 foci in mutant cells when Topoisomerase I inhibitor-induced single strand breaks are converted into DSBs during DNA replication. We also partially rescue the HR defect by tethering the donor DNA to the site of DSBs using streptavidin-fused Cas9. Our findings demonstrate that the BRCA2-DSS1 complex is dispensable for RAD51 loading when the homologous DNA is close to the DSB. Mishra et al. have generated mice with a single amino acid substitution in BRCA2, which disrupts its interaction with DSS1 resulting in a severe HR defect. They show the interaction to be dispensable for HR at replication induced and meiotic DSBs.
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Affiliation(s)
- Arun Prakash Mishra
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Suzanne A Hartford
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Regeneron Pharmaceuticals, Inc, Tarrytown, NY, USA
| | - Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Kimberly Klarmann
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, NCI, Frederick, MD, USA
| | - Rajani Kant Chittela
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Applied Genomics Section, Bhabha Atomic Research Center, Trombay, Mumbai, India
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Albert B Jeon
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Betty K Martin
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Laboratory Animal Sciences Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sandra Burkett
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Mary E Albaugh
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Laboratory Animal Sciences Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Baktiar Karim
- Molecular Histopathology Laboratory, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Jonathan R Keller
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.,Basic Science Program, Leidos Biomedical Research, Inc. Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.
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3
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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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4
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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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Andreassen PR, Seo J, Wiek C, Hanenberg H. Understanding BRCA2 Function as a Tumor Suppressor Based on Domain-Specific Activities in DNA Damage Responses. Genes (Basel) 2021; 12:genes12071034. [PMID: 34356050 PMCID: PMC8307705 DOI: 10.3390/genes12071034] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 01/14/2023] Open
Abstract
BRCA2 is an essential genome stability gene that has various functions in cells, including roles in homologous recombination, G2 checkpoint control, protection of stalled replication forks, and promotion of cellular resistance to numerous types of DNA damage. Heterozygous mutation of BRCA2 is associated with an increased risk of developing cancers of the breast, ovaries, pancreas, and other sites, thus BRCA2 acts as a classic tumor suppressor gene. However, understanding BRCA2 function as a tumor suppressor is severely limited by the fact that ~70% of the encoded protein has not been tested or assigned a function in the cellular DNA damage response. Remarkably, even the specific role(s) of many known domains in BRCA2 are not well characterized, predominantly because stable expression of the very large BRCA2 protein in cells, for experimental purposes, is challenging. Here, we review what is known about these domains and the assay systems that are available to study the cellular roles of BRCA2 domains in DNA damage responses. We also list criteria for better testing systems because, ultimately, functional assays for assessing the impact of germline and acquired mutations identified in genetic screens are important for guiding cancer prevention measures and for tailored cancer treatments.
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Affiliation(s)
- Paul R. Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-(513)-636-0499
| | - Joonbae Seo
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.W.); (H.H.)
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.W.); (H.H.)
- Department of Pediatrics III, Children’s Hospital, University of Duisburg-Essen, 45122 Essen, Germany
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6
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Radulovic I, Kuechler A, Schündeln MM, Paulussen M, von Neuhoff N, Reinhardt D, Hanenberg H. A homozygous nonsense mutation early in exon 5 of BRCA2 is associated with very severe Fanconi anemia. Eur J Med Genet 2021; 64:104260. [PMID: 34118472 DOI: 10.1016/j.ejmg.2021.104260] [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: 11/11/2020] [Revised: 03/24/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
Fanconi anemia (FA) due to biallelic mutations in the BRCA2 gene is very rare and associated with an extremely high risk of early-onset of aggressive childhood malignancies, predominantly brain tumors, leukemia, and nephroblastoma. Here, we present a consanguineous family with three affected children of the D1 subtype of FA and describe the clinical consequences of the earliest known biallelic nonsense/stop-gain germ-line mutation in BRCA2, exon 5 c.469A>T, that leads to a premature stop of translation, p.Lys157*. The three patients were born with severe intrauterine growth restrictions and different degrees of congenital malformations. Altogether, they developed eight distinct malignancies and died within their first three years of life. Treatment with a reduced chemotherapy regimen was only performed in patient 2 for his first tumor, a nephroblastoma, which the patient tolerated well for eight months, until he developed myelodysplastic syndrome (MDS) and then acute myeloid leukemia (AML). Finally, the third patient experienced a hepatoblastoma, an unclassified brain tumor and MDS in parallel and died in her second year of life. Our report re-emphasizes the aggressiveness and fatality of the FA-D1 children with biallelic BRCA2 nonsense mutations, that are both located before exon 11, which contains binding domains for the RAD51 recombinase.
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Affiliation(s)
- Ivana Radulovic
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Michael M Schündeln
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Michael Paulussen
- Vestische Kinder- & Jugendklinik Datteln, Witten/Herdecke University, 45711 Datteln, Germany
| | - Nils von Neuhoff
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Dirk Reinhardt
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Helmut Hanenberg
- Department of Pediatrics III, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany; Department of Otorhinolaryngology & Head/Neck Surgery, University Hospital Düsseldorf, Heinrich Heine University, 40225 Düsseldorf, Germany.
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7
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Nix P, Mundt E, Coffee B, Goossen E, Warf BM, Brown K, Bowles K, Roa B. Interpretation of BRCA2 Splicing Variants: A Case Series of Challenging Variant Interpretations and the Importance of Functional RNA Analysis. Fam Cancer 2021; 21:7-19. [PMID: 33469799 PMCID: PMC8799590 DOI: 10.1007/s10689-020-00224-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 12/15/2020] [Indexed: 11/13/2022]
Abstract
A substantial proportion of pathogenic variants associated with an increased risk of hereditary cancer are sequence variants affecting RNA splicing. The classification of these variants can be complex when both non-functional and functional transcripts are produced from the variant allele. We present four BRCA2 splice site variants with complex variant interpretations (BRCA2 c.68-3T>G, c.68-2A>G, c.425G>T, c.8331+2T>C). Evidence supporting a pathogenic classification is available for each variant, including in silico models, absence in population databases, and published functional data. However, comprehensive RNA analysis showed that some functional transcript may be produced by each variant. BRCA2 c.68-3T>G results in a partial splice defect. For BRCA2 c.68-2A>G and c.425G>T, aberrant splicing was shown to produce a potentially functional, in-frame transcript. BRCA2 c.8331+2T>C may utilize a functional GC donor in place of the wild-type GT donor. The severity of cancer history for carriers of these variants was also assessed using a history weighting algorithm and was not consistent with pathogenic controls (carriers of known pathogenic variants in BRCA2). Due to the conflicting evidence, our laboratory classifies these BRCA2 variants as variants of uncertain significance. This highlights the importance of evaluating new and existing evidence to ensure accurate variant classification and appropriate patient care.
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Affiliation(s)
- Paola Nix
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA.
| | - Erin Mundt
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Bradford Coffee
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | | | - Bryan M Warf
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA.,Third Wave Analytics, Inc., San Francisco, CA, USA
| | - Krystal Brown
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Karla Bowles
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Benjamin Roa
- Myriad Genetics, Inc., 320 Wakara Way, Salt Lake City, UT, USA
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8
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Ming Z, Zou Z, Cai K, Xu YI, Chen X, Yi W, Luo J, Luo Z. ARG1 functions as a tumor suppressor in breast cancer. Acta Biochim Biophys Sin (Shanghai) 2020; 52:1257-1264. [PMID: 33128544 DOI: 10.1093/abbs/gmaa116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/15/2020] [Accepted: 08/26/2020] [Indexed: 12/18/2022] Open
Abstract
Arginase I (ARG1) is a cytosolic enzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea. The association of ARG1 with cancer has mostly been focused on the ARG1 released by tumor-associated myeloid cells in tumor microenvironment. However, the role of ARG1 expressed in cancer cells is unclear. Here, we showed that the expression of ARG1 in human breast cancer (BC) is related to a good prognosis in BC patients. Overexpression of ARG1 suppresses BC cell proliferation and migration in vitro and xenograft tumor growth and development in mouse models. Furthermore, ARG1 expression down-regulates the expression of p-AKT, leading to the de-activation of AKT signal pathway in BC cells. Thus, our results established that in contrast to the role of ARG1 released from tumor-associated myeloid cells in tumor microenvironment that promotes tumor immune escape, ARG1 expressed in BC cells suppresses AKT signaling pathway and functions as a tumor suppressor.
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Affiliation(s)
- Zhengnan Ming
- Molecular Biology Research Centre, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha 410078, China
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zizheng Zou
- Molecular Biology Research Centre, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Kaimei Cai
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Y i Xu
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xueyan Chen
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Junli Luo
- The Hunan Provincial Key Lab of Precision Diagnosis and Treatment for Gastrointestinal Tumor, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhiyong Luo
- Molecular Biology Research Centre, Hunan Province Key Laboratory of Basic and Applied Hematology, Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Xiangya School of Medicine, Central South University, Changsha 410078, China
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9
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Bypass of premature stop codons and generation of functional BRCA2 by exon skipping. J Hum Genet 2020; 65:805-809. [PMID: 32393813 DOI: 10.1038/s10038-020-0768-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/08/2020] [Accepted: 04/21/2020] [Indexed: 11/08/2022]
Abstract
A pathogenic mutation in BRCA2 significantly increases the risk of breast and ovarian cancers making it imperative to examine the functional consequences of variants of uncertain clinical significance. Variants that are predicted to result in a truncated protein are unambiguously classified as pathogenic. We have previously shown how a pathogenic splice site variant known to generate a premature termination codon (PTC) in exon 9 and a nonsense mutation at exon 7, can generate functional BRCA2 by skipping exons 4-7 and restoring the reading frame. Using a well-established mouse embryonic stem cell-based assay, we functionally characterize here one splice site mutation and 11 pathogenic BRCA2 variants that are either nonsense mutation or generate PTC in different exons ranging from exons 4 to 7. Our study shows that five variants can restore the open reading frame by exon skipping and generate a functional protein. This suggests further need to exercise prudence when classifying clearly pathogenic variants.
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10
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Monteiro AN, Bouwman P, Kousholt AN, Eccles DM, Millot GA, Masson JY, Schmidt MK, Sharan SK, Scully R, Wiesmüller L, Couch F, Vreeswijk MPG. Variants of uncertain clinical significance in hereditary breast and ovarian cancer genes: best practices in functional analysis for clinical annotation. J Med Genet 2020; 57:509-518. [PMID: 32152249 DOI: 10.1136/jmedgenet-2019-106368] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/28/2019] [Accepted: 12/01/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Alvaro N Monteiro
- Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Peter Bouwman
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arne N Kousholt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Diana M Eccles
- Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, UK
| | - Gael A Millot
- Hub-DBC, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Marjanka K Schmidt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Shyam K Sharan
- National Cancer Institute at Frederick, Frederick, Maryland, USA
| | - Ralph Scully
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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11
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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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