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Biswas K, Mitrophanov AY, Sahu S, Sullivan T, Southon E, Nousome D, Reid S, Narula S, Smolen J, Sengupta T, Riedel-Topper M, Kapoor M, Babbar A, Stauffer S, Cleveland L, Tandon M, Malys T, Sharan SK. Sequencing-based functional assays for classification of BRCA2 variants in mouse ESCs. CELL REPORTS METHODS 2023; 3:100628. [PMID: 37922907 PMCID: PMC10694496 DOI: 10.1016/j.crmeth.2023.100628] [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: 07/25/2023] [Revised: 09/12/2023] [Accepted: 10/12/2023] [Indexed: 11/07/2023]
Abstract
Sequencing of genes, such as BRCA1 and BRCA2, is recommended for individuals with a personal or family history of early onset and/or bilateral breast and/or ovarian cancer or a history of male breast cancer. Such sequencing efforts have resulted in the identification of more than 17,000 BRCA2 variants. The functional significance of most variants remains unknown; consequently, they are called variants of uncertain clinical significance (VUSs). We have previously developed mouse embryonic stem cell (mESC)-based assays for functional classification of BRCA2 variants. We now developed a next-generation sequencing (NGS)-based approach for functional evaluation of BRCA2 variants using pools of mESCs expressing 10-25 BRCA2 variants from a given exon. We use this approach for functional evaluation of 223 variants listed in ClinVar. Our functional classification of BRCA2 variants is concordant with the classification reported in ClinVar or those reported by other orthogonal assays.
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Affiliation(s)
- Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Alexander Y Mitrophanov
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Sounak Sahu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; Leidos Biomed Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Darryl Nousome
- Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sakshi Narula
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Julia Smolen
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Trisha Sengupta
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Maximilian Riedel-Topper
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Medha Kapoor
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Anav Babbar
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Stacey Stauffer
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Linda Cleveland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Mayank Tandon
- Biomedical Informatics and Data Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Tyler Malys
- Statistical Consulting and Scientific Programming, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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Chevrier S, Richard C, Collot T, Mananet H, Arnould L, Boidot R. An Algorithm Combining Patient Performance Status, Second Hit Analysis, PROVEAN and Dann Prediction Tools Could Foretell Sensitization to PARP Inhibitors in Digestive, Skin, Ovarian and Breast Cancers. Cancers (Basel) 2021; 13:cancers13133113. [PMID: 34206535 PMCID: PMC8268870 DOI: 10.3390/cancers13133113] [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: 04/30/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary PARP inhibitors, a family of targeted cancer therapeutics, have been shown to be efficient in patients with some deficiencies in the homologous recombination machinery. However, a quick and reliable identification of patients who would benefit from such therapies remains a challenge. In particular, patients with tumors carrying variants of unknown significance (VUS) in homologous recombination genes do not currently benefit from PARP inhibitor treatments. In this study, we present an algorithm that may allow classification of these variants with regard to their impact on tumor responsiveness to PARP inhibitors. If validated on a larger patient sample, our algorithm would allow patients with tumors potentially responsive to PARP inhibitors to benefit from this therapy. Abstract PARP inhibitors yield interesting outcomes for patients with ovarian tumors harboring BRCA1 or BRCA2 mutation, but also with other tumors with homologous repair (HR) deficiency. About 40% of variants are variants of unknown significance (VUS), blocking the use of PARP inhibitors. In this study, we analyzed NGS data from 78 metastatic patients treated with PARP inhibitors. We tested NGS data and in silico predictions to classify VUS as potentially benign or deleterious. Among 41 patients treated with olaparib, three had tumors harboring benign and 26 pathogenic variants, while 12 had VUS. Progression-Free Survival (PFS) analysis showed that benign variants did not respond to olaparib whereas pathogenic variants were associated with a median PFS of 190 days. Surprisingly, median PFS of patients with VUS-carrying tumors suggested that some of them may be sensitive to PARP inhibitors. By testing different in silico predictions and variant allelic frequency, we obtained an algorithm predicting VUS sensitivity to PARP inhibitors for patients with a Performance Status below 3. Our work suggests that VUS in HR genes could be predicted as benign or deleterious, which may increase the number of patients eligible for PARP inhibitor treatment. Further studies in a larger sample are warranted to validate our prediction algorithm.
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Affiliation(s)
- Sandy Chevrier
- Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France; (S.C.); (C.R.); (L.A.)
| | - Corentin Richard
- Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France; (S.C.); (C.R.); (L.A.)
| | - Thomas Collot
- Department of Medical Oncology, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France;
| | - Hugo Mananet
- Platform of Transfer in Cancer Biology, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France;
| | - Laurent Arnould
- Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France; (S.C.); (C.R.); (L.A.)
| | - Romain Boidot
- Department of Biology and Pathology of Tumors, Georges-François Leclerc Cancer Center-UNICANCER, 21079 Dijon, France; (S.C.); (C.R.); (L.A.)
- UMR CNRS 6302, University of Burgundy, 21079 Dijon, France
- Correspondence: ; Tel.: +33-3-80-73-77-67; Fax: +33-3-80-73-77-82
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Biswas K, Lipton GB, Stauffer S, Sullivan T, Cleveland L, Southon E, Reid S, Magidson V, Iversen ES, Sharan SK. A computational model for classification of BRCA2 variants using mouse embryonic stem cell-based functional assays. NPJ Genom Med 2020; 5:52. [PMID: 33293522 PMCID: PMC7722754 DOI: 10.1038/s41525-020-00158-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/29/2020] [Indexed: 12/12/2022] Open
Abstract
Sequencing-based genetic tests to identify individuals at increased risk of hereditary breast and ovarian cancers have resulted in the identification of more than 40,000 sequence variants of BRCA1 and BRCA2. A majority of these variants are considered to be variants of uncertain significance (VUS) because their impact on disease risk remains unknown, largely due to lack of sufficient familial linkage and epidemiological data. Several assays have been developed to examine the effect of VUS on protein function, which can be used to assess their impact on cancer susceptibility. In this study, we report the functional characterization of 88 BRCA2 variants, including several previously uncharacterized variants, using a well-established mouse embryonic stem cell (mESC)-based assay. We have examined their ability to rescue the lethality of Brca2 null mESC as well as sensitivity to six DNA damaging agents including ionizing radiation and a PARP inhibitor. We have also examined the impact of BRCA2 variants on splicing. In addition, we have developed a computational model to determine the probability of impact on function of the variants that can be used for risk assessment. In contrast to the previous VarCall models that are based on a single functional assay, we have developed a new platform to analyze the data from multiple functional assays separately and in combination. We have validated our VarCall models using 12 known pathogenic and 10 neutral variants and demonstrated their usefulness in determining the pathogenicity of BRCA2 variants that are listed as VUS or as variants with conflicting functional interpretation.
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Affiliation(s)
- Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Gary B Lipton
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA
| | - Stacey Stauffer
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Teresa Sullivan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Linda Cleveland
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Eileen Southon
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Susan Reid
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Valentin Magidson
- Optical Microscopy and Analysis Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA.
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
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