1
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Zhong AX, Chen Y, Chen PL. BRCA1 the Versatile Defender: Molecular to Environmental Perspectives. Int J Mol Sci 2023; 24:14276. [PMID: 37762577 PMCID: PMC10532398 DOI: 10.3390/ijms241814276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The evolving history of BRCA1 research demonstrates the profound interconnectedness of a single protein within the web of crucial functions in human cells. Mutations in BRCA1, a tumor suppressor gene, have been linked to heightened breast and ovarian cancer risks. However, despite decades of extensive research, the mechanisms underlying BRCA1's contribution to tissue-specific tumor development remain elusive. Nevertheless, much of the BRCA1 protein's structure, function, and interactions has been elucidated. Individual regions of BRCA1 interact with numerous proteins to play roles in ubiquitination, transcription, cell checkpoints, and DNA damage repair. At a cellular scale, these BRCA1 functions coordinate tumor suppression, R-loop prevention, and cellular differentiation, all of which may contribute to BRCA1's role in cancer tissue specificity. As research on BRCA1 and breast cancer continues to evolve, it will become increasingly evident that modern materials such as Bisphenol A should be examined for their relationship with DNA stability, cancer incidence, and chemotherapy. Overall, this review offers a comprehensive understanding of BRCA1's many roles at a molecular, cellular, organismal, and environmental scale. We hope that the knowledge gathered here highlights both the necessity of BRCA1 research and the potential for novel strategies to prevent and treat cancer in individuals carrying BRCA1 mutations.
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Affiliation(s)
- Amy X. Zhong
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Yumay Chen
- Department of Medicine, Division of Endocrinology, University of California, Irvine, CA 92697, USA;
| | - Phang-Lang Chen
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
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2
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Kim DM, Feilotter HE, Davey SK. BRCA1 Variant Assessment Using a Simple Analytic Assay. J Appl Lab Med 2022; 7:674-688. [PMID: 35021209 DOI: 10.1093/jalm/jfab163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/04/2021] [Indexed: 11/14/2022]
Abstract
BACKGROUND We previously developed a biological assay to accurately predict BRCA1 (BRCA1 DNA repair associated) mutation status, based on gene expression profiles of Epstein-Barr virus-transformed lymphoblastoid cell lines. The original work was done using whole genome expression microarrays, and nearest shrunken centroids analysis. While these approaches are appropriate for model building, they are difficult to implement clinically, where more targeted testing and analysis are required for time and cost savings. METHODS Here, we describe adaptation of the original predictor to use the NanoString nCounter platform for testing, with analysis based on the k-top scoring pairs (k-TSP) method. RESULTS Assessing gene expression using the nCounter platform on a set of lymphoblastoid cell lines yielded 93.8% agreement with the microarray-derived data, and 87.5% overall correct classification of BRCA1 carriers and controls. Using the original gene expression microarray data used to develop our predictor with nearest shrunken centroids, we rebuilt a classifier based on the k-TSP method. This classifier relies on the relative expression of 10 pairs of genes, compared to the original 43 identified by nearest shrunken centroids (NSC), and was 96.2% concordant with the original training set prediction, with a 94.3% overall correct classification of BRCA1 carriers and controls. CONCLUSIONS The k-TSP classifier was shown to accurately predict BRCA1 status using data generated on the nCounter platform and is feasible for initiating a clinical validation.
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Affiliation(s)
- Daniel M Kim
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Harriet E Feilotter
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
| | - Scott K Davey
- Department of Pathology and Molecular Medicine, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Division of Cancer Biology and Genetics, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada.,Departments of Oncology and Biomedical and Molecular Sciences, Queen's University Cancer Research Institute, Queen's University, Kingston, ON, Canada
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3
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Drenner K, Basu GD, Goodman LJ, Ozols AA, LoBello JR, Royce T, Gordon MS, Borazanci EH, Steinbach MA, Trent J, Sharma S. The value of comprehensive genomic sequencing to maximize the identification of clinically actionable alterations in advanced cancer patients: a case series. Oncotarget 2021; 12:1836-1847. [PMID: 34504655 PMCID: PMC8416559 DOI: 10.18632/oncotarget.28046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
PURPOSE We present seven cases of advanced cancer patients who initially underwent tumor testing utilizing smaller, panel-based tests, followed by a variety of therapeutic treatments which ultimately resulted in progression of their disease. These cases demonstrate the value of utilizing WES/RNA seq and characterization following disease progression in these patients and the determination of clinically targetable alterations as well as acquired resistance mutations. MATERIALS AND METHODS All patients are part of an IRB approved observational study. WES and RNA sequencing were performed, using GEM ExTra® on tumor and blood samples obtained during routine clinical care. To accurately determine somatic versus germline alterations the test was performed with paired normal testing from peripheral blood. RESULTS The presented cases demonstrate the clinical impact of actionable findings uncovered using GEM ExTra® in patients with advanced disease who failed many rounds of treatment. Unique alterations were identified resulting in newly identified potential targeted therapies, mechanisms of resistance, and variation in the genomic characterization of the primary versus the metastatic tumor. CONCLUSIONS Taken together our results demonstrate that GEM ExTra® maximizes detection of actionable mutations, thus allowing for appropriate treatment selection for patients harboring both common and rare genomic alterations.
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Affiliation(s)
- Kevin Drenner
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA
- These authors contributed equally to this work
| | - Gargi D. Basu
- Ashion Analytics, LLC, Phoenix, AZ 85004, USA
- These authors contributed equally to this work
| | | | | | | | | | | | | | | | - Jeffrey Trent
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA
| | - Sunil Sharma
- Translational Genomic Research Institute (Tgen), Phoenix, AZ 85004, USA
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4
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Zhang Y, Park JY, Zhang F, Olson SH, Orlow I, Li Y, Kurtz RC, Ladanyi M, Chen J, Toland AE, Zhang L, Andreassen PR. The p.Ser64Leu and p.Pro104Leu missense variants of PALB2 identified in familial pancreatic cancer patients compromise the DNA damage response. Hum Mutat 2020; 42:150-163. [PMID: 33169439 DOI: 10.1002/humu.24133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 09/17/2020] [Accepted: 11/01/2020] [Indexed: 11/12/2022]
Abstract
PALB2 has been identified as a breast and pancreatic cancer susceptibility gene. Utilizing a targeted sequencing approach, we discovered two novel germline missense PALB2 variants c.191C>T and c.311C>T, encoding p.Ser64Leu and p.Pro104Leu, respectively, in individuals in a pancreatic cancer registry. No missense PALB2 variants from familial pancreatic cancer patients, and few PALB2 variants overall, have been functionally characterized. Given the known role of PALB2, we tested the impact of p.Ser64Leu and p.Pro104Leu variants on DNA damage responses. Neither p.Ser64Leu nor p.Pro104Leu have clear effects on interactions with BRCA1 and KEAP1, which are mediated by adjacent motifs in PALB2. However, both variants are associated with defective recruitment of PALB2, and the RAD51 recombinase downstream, to DNA damage foci. Furthermore, p.Ser64Leu and p.Pro104Leu both largely compromise DNA double-strand break-initiated homologous recombination, and confer increased cellular sensitivity to ionizing radiation (IR) and the poly (ADP-ribose) polymerase (PARP) inhibitor Olaparib. Taken together, our results represent the first demonstration of functionally deleterious PALB2 missense variants associated with familial pancreatic cancer and of deleterious variants in the N-terminus outside of the coiled-coil domain. Furthermore, our results suggest the possibility of personalized treatments, using IR or PARP inhibitor, of pancreatic and other cancers that carry a deleterious PALB2 variant.
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Affiliation(s)
- Yue Zhang
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Peking Union Medical College Hospital, Chinese Academy of Medical Sciences - Peking Union Medical College, Beijing, China
| | - Jung-Young Park
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert C Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jie Chen
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences - Peking Union Medical College, Beijing, China
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA.,Division of Human Genetics, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles (UCLA), Los Angeles, California, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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5
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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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6
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Boonen RACM, Vreeswijk MPG, van Attikum H. Functional Characterization of PALB2 Variants of Uncertain Significance: Toward Cancer Risk and Therapy Response Prediction. Front Mol Biosci 2020; 7:169. [PMID: 33195396 PMCID: PMC7525363 DOI: 10.3389/fmolb.2020.00169] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years it has become clear that pathogenic variants in PALB2 are associated with a high risk for breast, ovarian and pancreatic cancer. However, the clinical relevance of variants of uncertain significance (VUS) in PALB2, which are increasingly identified through clinical genetic testing, is unclear. Here we review recent advances in the functional characterization of VUS in PALB2. A combination of assays has been used to assess the impact of PALB2 VUS on its function in DNA repair by homologous recombination, cell cycle regulation and the control of cellular levels of reactive oxygen species (ROS). We discuss the outcome of this comprehensive analysis of PALB2 VUS, which showed that VUS in PALB2’s Coiled-Coil (CC) domain can impair the interaction with BRCA1, whereas VUS in its WD40 domain affect PALB2 protein stability. Accordingly, the CC and WD40 domains of PALB2 represent hotspots for variants that impair PALB2 protein function. We also provide a future perspective on the high-throughput analysis of VUS in PALB2, as well as the functional characterization of variants that affect PALB2 RNA splicing. Finally, we discuss how results from these functional assays can be valuable for predicting cancer risk and responsiveness to cancer therapy, such as treatment with PARP inhibitor- or platinum-based chemotherapy.
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Affiliation(s)
- Rick A C M Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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7
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Variants of uncertain significance in the era of high-throughput genome sequencing: a lesson from breast and ovary cancers. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:46. [PMID: 32127026 PMCID: PMC7055088 DOI: 10.1186/s13046-020-01554-6] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 02/26/2020] [Indexed: 02/06/2023]
Abstract
The promising expectations about personalized medicine have opened the path to routine large-scale sequencing and increased the importance of genetic counseling for hereditary cancers, among which hereditary breast and ovary cancers (HBOC) have a major impact. High-throughput sequencing, or Next-Generation Sequencing (NGS), has improved cancer patient management, ameliorating diagnosis and treatment decisions. In addition to its undeniable clinical utility, NGS is also unveiling a large number of variants that we are still not able to clearly define and classify, the variants of uncertain significance (VUS), which account for about 40% of total variants. At present, VUS use in the clinical context is challenging. Medical reports may omit this kind of data and, even when included, they limit the clinical utility of genetic information. This has prompted the scientific community to seek easily applicable tests to accurately classify VUS and increase the amount of usable information from NGS data. In this review, we will focus on NGS and classification systems for VUS investigation, with particular attention on HBOC-related genes and in vitro functional tests developed for ameliorating and accelerating variant classification in cancer.
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8
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Boonen RACM, Rodrigue A, Stoepker C, Wiegant WW, Vroling B, Sharma M, Rother MB, Celosse N, Vreeswijk MPG, Couch F, Simard J, Devilee P, Masson JY, van Attikum H. Functional analysis of genetic variants in the high-risk breast cancer susceptibility gene PALB2. Nat Commun 2019; 10:5296. [PMID: 31757951 PMCID: PMC6876638 DOI: 10.1038/s41467-019-13194-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/25/2019] [Indexed: 12/16/2022] Open
Abstract
Heterozygous carriers of germ-line loss-of-function variants in the DNA repair gene PALB2 are at a highly increased lifetime risk for developing breast cancer. While truncating variants in PALB2 are known to increase cancer risk, the interpretation of missense variants of uncertain significance (VUS) is in its infancy. Here we describe the development of a relatively fast and easy cDNA-based system for the semi high-throughput functional analysis of 48 VUS in human PALB2. By assessing the ability of PALB2 VUS to rescue the DNA repair and checkpoint defects in Palb2 knockout mouse embryonic stem (mES) cells, we identify various VUS in PALB2 that impair its function. Three VUS in the coiled-coil domain of PALB2 abrogate the interaction with BRCA1, whereas several VUS in the WD40 domain dramatically reduce protein stability. Thus, our functional assays identify damaging VUS in PALB2 that may increase cancer risk. PALB2 is an established breast cancer risk gene but the pathogenicity of many variants remains uncharacterised. Here, the authors present a cDNA-based system for the functional analysis of PALB2 variants of unknown significance.
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Affiliation(s)
- Rick A C M Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Amélie Rodrigue
- CHU de Québec-Université Laval Research Center, Oncology Division, Québec City, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Chantal Stoepker
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Wouter W Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Bas Vroling
- Bio-Prodict, Nijmegen, 6511 AA, The Netherlands
| | - Milan Sharma
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Magdalena B Rother
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Nandi Celosse
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jacques Simard
- CHU de Québec-Université Laval Research Center, Oncology Division, Québec City, QC, G1R 3S3, Canada.,CHU de Québec Research Center, Endocrinology and Nephrology Division, Québec City, QC, G1V 4G2, Canada
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands
| | - Jean-Yves Masson
- CHU de Québec-Université Laval Research Center, Oncology Division, Québec City, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, The Netherlands.
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9
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Genetic Testing to Guide Risk-Stratified Screens for Breast Cancer. J Pers Med 2019; 9:jpm9010015. [PMID: 30832243 PMCID: PMC6462925 DOI: 10.3390/jpm9010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 12/14/2022] Open
Abstract
Breast cancer screening modalities and guidelines continue to evolve and are increasingly based on risk factors, including genetic risk and a personal or family history of cancer. Here, we review genetic testing of high-penetrance hereditary breast and ovarian cancer genes, including BRCA1 and BRCA2, for the purpose of identifying high-risk individuals who would benefit from earlier screening and more sensitive methods such as magnetic resonance imaging. We also consider risk-based screening in the general population, including whether every woman should be genetically tested for high-risk genes and the potential use of polygenic risk scores. In addition to enabling early detection, the results of genetic screens of breast cancer susceptibility genes can be utilized to guide decision-making about when to elect prophylactic surgeries that reduce cancer risk and the choice of therapeutic options. Variants of uncertain significance, especially missense variants, are being identified during panel testing for hereditary breast and ovarian cancer. A finding of a variant of uncertain significance does not provide a basis for increased cancer surveillance or prophylactic procedures. Given that variant classification is often challenging, we also consider the role of multifactorial statistical analyses by large consortia and functional tests for this purpose.
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10
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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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11
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Cusin I, Teixeira D, Zahn-Zabal M, Rech de Laval V, Gleizes A, Viassolo V, Chappuis PO, Hutter P, Bairoch A, Gaudet P. A new bioinformatics tool to help assess the significance of BRCA1 variants. Hum Genomics 2018; 12:36. [PMID: 29996917 PMCID: PMC6042458 DOI: 10.1186/s40246-018-0168-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 06/25/2018] [Indexed: 12/23/2022] Open
Abstract
Background Germline pathogenic variants in the breast cancer type 1 susceptibility gene BRCA1 are associated with a 60% lifetime risk for breast and ovarian cancer. This overall risk estimate is for all BRCA1 variants; obviously, not all variants confer the same risk of developing a disease. In cancer patients, loss of BRCA1 function in tumor tissue has been associated with an increased sensitivity to platinum agents and to poly-(ADP-ribose) polymerase (PARP) inhibitors. For clinical management of both at-risk individuals and cancer patients, it would be important that each identified genetic variant be associated with clinical significance. Unfortunately for the vast majority of variants, the clinical impact is unknown. The availability of results from studies assessing the impact of variants on protein function may provide insight of crucial importance. Results and conclusion We have collected, curated, and structured the molecular and cellular phenotypic impact of 3654 distinct BRCA1 variants. The data was modeled in triple format, using the variant as a subject, the studied function as the object, and a predicate describing the relation between the two. Each annotation is supported by a fully traceable evidence. The data was captured using standard ontologies to ensure consistency, and enhance searchability and interoperability. We have assessed the extent to which functional defects at the molecular and cellular levels correlate with the clinical interpretation of variants by ClinVar submitters. Approximately 30% of the ClinVar BRCA1 missense variants have some molecular or cellular assay available in the literature. Pathogenic variants (as assigned by ClinVar) have at least some significant functional defect in 94% of testable cases. For benign variants, 77% of ClinVar benign variants, for which neXtProt Cancer variant portal has data, shows either no or mild experimental functional defects. While this does not provide evidence for clinical interpretation of variants, it may provide some guidance for variants of unknown significance, in the absence of more reliable data. The neXtProt Cancer variant portal (https://www.nextprot.org/portals/breast-cancer) contains over 6300 observations at the molecular and/or cellular level for BRCA1 variants.
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Affiliation(s)
- Isabelle Cusin
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland
| | - Daniel Teixeira
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland
| | - Monique Zahn-Zabal
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland
| | - Valentine Rech de Laval
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Anne Gleizes
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland
| | - Valeria Viassolo
- Oncogenetics and Cancer Prevention Unit, Division of Oncology, University Hospitals of Geneva, 1205, Geneva, Switzerland
| | - Pierre O Chappuis
- Oncogenetics and Cancer Prevention Unit, Division of Oncology, University Hospitals of Geneva, 1205, Geneva, Switzerland.,Division of Genetic Medicine, University Hospitals of Geneva, 1205, Geneva, Switzerland
| | - Pierre Hutter
- Sophia Genetics, Rue du Centre 172, 1025, Saint Sulpice, Switzerland
| | - Amos Bairoch
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pascale Gaudet
- CALIPHO group, SIB Swiss Institute of Bioinformatics, 1211, Geneva 4, Switzerland. .,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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12
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Kim S, Lee E, Jung J, Lee JW, Kim HJ, Kim J, Yoo HJ, Lee HJ, Chae SY, Jeon SM, Son BH, Gong G, Sharan SK, Chang S. microRNA-155 positively regulates glucose metabolism via PIK3R1-FOXO3a-cMYC axis in breast cancer. Oncogene 2018. [PMID: 29527004 PMCID: PMC5978802 DOI: 10.1038/s41388-018-0124-4] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MicroRNA is an endogenous, small RNA controlling multiple target genes and playing roles in various biological processes including tumorigenesis. Here, we addressed the function of miR-155 using LC-MS/MS-based metabolic profiling of miR-155 deficient breast cancer cells. Our results revealed the loss of miR-155 hampers glucose uptake and glycolysis, via the down-regulation of glucose transporters and metabolic enzymes including HK2, PKM2, and LDHA. We showed this is due to the down-regulation of cMYC, controlled through phosphoinositide-3-kinase regulatory subunit alpha (PIK3R1)-PDK1/AKT-FOXO3a pathway. UTR analysis of the PIK3R1 and FOXO3a indicated miR-155 directly represses these genes. A stable expression of miR-155 in patient-derived cells (PDCs) showed activated glucose metabolism whereas a stable inhibition of miR-155 reduced in vivo tumor growth with retarded glucose metabolism. Furthermore, analysis of 50 triple-negative breast cancer (TNBC) specimens and specific uptake value (SUV) of PET images revealed a positive correlation between miR-155 level and glucose usage in human breast tumors via PIK3R1-PDK/AKT-FOXO3a-cMYC axis. Collectively, these data demonstrate the miR-155 is a key regulator of glucose metabolism in breast cancer.
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Affiliation(s)
- Sinae Kim
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Eunji Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Jaeyun Jung
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Jong Won Lee
- Department of Surgery, Asan Medical Center, Seoul, 05505, Korea
| | - Hee Jung Kim
- Department of Surgery, Asan Medical Center, Seoul, 05505, Korea
| | - Jisun Kim
- Department of Surgery, Asan Medical Center, Seoul, 05505, Korea
| | - Hyun Ju Yoo
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Hee Jin Lee
- Department of Pathology, Asan Medical Center, Seoul, 05505, Korea
| | - Sun Young Chae
- Department of Nuclear Medicine, Asan Medical Center, Seoul, 05505, Korea
| | - Sang Min Jeon
- College of Pharmacy and Institute of Pharmaceutical Science and Technology, Ajou University, Suwon, 16499, Korea
| | - Byung Ho Son
- Department of Surgery, Asan Medical Center, Seoul, 05505, Korea
| | - Gyungyup Gong
- Department of Pathology, Asan Medical Center, Seoul, 05505, Korea
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - Suhwan Chang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Seoul, 05505, Korea.
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13
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Chen CC, Feng W, Lim PX, Kass EM, Jasin M. Homology-Directed Repair and the Role of BRCA1, BRCA2, and Related Proteins in Genome Integrity and Cancer. ANNUAL REVIEW OF CANCER BIOLOGY 2018; 2:313-336. [PMID: 30345412 PMCID: PMC6193498 DOI: 10.1146/annurev-cancerbio-030617-050502] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Germ-line and somatic mutations in genes that promote homology-directed repair (HDR), especially BRCA1 and BRCA2, are frequently observed in several cancers, in particular, breast and ovary but also prostate and other cancers. HDR is critical for the error-free repair of DNA double-strand breaks and other lesions, and HDR factors also protect stalled replication forks. As a result, loss of BRCA1 or BRCA2 poses significant risks to genome integrity, leading not only to cancer predisposition but also to sensitivity to DNA-damaging agents, affecting therapeutic approaches. Here we review recent advances in our understanding of BRCA1 and BRCA2, including how they genetically interact with other repair factors, how they protect stalled replication forks, how they affect the response to aldehydes, and how loss of their functions links to mutation signatures. Importantly, given the recent advances with poly(ADP-ribose) polymerase inhibitors (PARPi) for the treatment of HDR-deficient tumors, we discuss mechanisms by which BRCA-deficient tumors acquire resistance to PARPi and other agents.
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Affiliation(s)
- Chun-Chin Chen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Elizabeth M Kass
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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14
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BRE/BRCC45 regulates CDC25A stability by recruiting USP7 in response to DNA damage. Nat Commun 2018; 9:537. [PMID: 29416040 PMCID: PMC5803202 DOI: 10.1038/s41467-018-03020-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 01/12/2018] [Indexed: 01/07/2023] Open
Abstract
BRCA2 is essential for maintaining genomic integrity. BRCA2-deficient primary cells are either not viable or exhibit severe proliferation defects. Yet, BRCA2 deficiency contributes to tumorigenesis. It is believed that mutations in genes such as TRP53 allow BRCA2 heterozygous cells to overcome growth arrest when they undergo loss of heterozygosity. Here, we report the use of an insertional mutagenesis screen to identify a role for BRE (Brain and Reproductive organ Expressed, also known as BRCC45), known to be a part of the BRCA1-DNA damage sensing complex, in the survival of BRCA2-deficient mouse ES cells. Cell viability by BRE overexpression is mediated by deregulation of CDC25A phosphatase, a key cell cycle regulator and an oncogene. We show that BRE facilitates deubiquitylation of CDC25A by recruiting ubiquitin-specific-processing protease 7 (USP7) in the presence of DNA damage. Additionally, we uncovered the role of CDC25A in BRCA-mediated tumorigenesis, which can have implications in cancer treatment. Loss of BRCA2 leads to cancer formation. Here, the authors use an insertional mutagenesis approach and identify a multiprotein complex consisting of BRE, USP7 and CDC25A that can support the survival of BRCA2-deficient cells.
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15
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Yoon KA, Kong SY, Lee EJ, Cho JN, Chang S, Lee ES. A Novel Germline Mutation in BRCA1 Causes Exon 20 Skipping in a Korean Family with a History of Breast Cancer. J Breast Cancer 2017; 20:310-313. [PMID: 28970858 PMCID: PMC5620447 DOI: 10.4048/jbc.2017.20.3.310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/18/2017] [Indexed: 01/15/2023] Open
Abstract
Germline mutations in the BRCA1 and BRCA2 genes are strong genetic factors for predispositions to breast, ovarian, and other related cancers. This report describes a family with a history of breast and ovarian cancers that harbored a novel BRCA1 germline mutation. A single nucleotide deletion in intron 20, namely c.5332+4delA, was detected in a 43-year-old patient with breast cancer. This mutation led to the skipping of exon 20, which in turn resulted in the production of a truncated BRCA1 protein that was 1773 amino acids in length. The mother of the proband had died due to ovarian cancer and had harbored the same germline mutation. Ectopically expressed mutant BRCA1 protein interacted with the BARD1 protein, but showed a reduced transcriptional function, as demonstrated by the expression of cyclin B1. This novel germline mutation in the BRCA1 gene caused familial breast and ovarian cancers.
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Affiliation(s)
- Kyong-Ah Yoon
- Department of Biochemistry, College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Sun-Young Kong
- Genetic Counseling Clinic, National Cancer Center Hospital, National Cancer Center, Goyang, Korea.,Department of System Cancer Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Translational Epidemiology Branch, National Cancer Center Research Institute, National Cancer Center, Goyang, Korea
| | - Eun Ji Lee
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jeong Nam Cho
- Center for Breast Cancer, National Cancer Center Hospital, National Cancer Center, Goyang, Korea
| | - Suhwan Chang
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Eun Sook Lee
- Department of System Cancer Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea.,Center for Breast Cancer, National Cancer Center Hospital, National Cancer Center, Goyang, Korea.,Precision Medicine Branch, National Cancer Center Research Institute, National Cancer Center, Goyang, Korea
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16
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Toland AE, Andreassen PR. DNA repair-related functional assays for the classification of BRCA1 and BRCA2 variants: a critical review and needs assessment. J Med Genet 2017; 54:721-731. [PMID: 28866612 DOI: 10.1136/jmedgenet-2017-104707] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/04/2017] [Accepted: 06/27/2017] [Indexed: 01/02/2023]
Abstract
Mutation of BRCA1 and BRCA2 is the most common cause of inherited breast and ovarian cancer. Genetic screens to detect carriers of variants can aid in cancer prevention by identifying individuals with a greater cancer risk and can potentially be used to predict the responsiveness of tumours to therapy. Frequently, classification cannot be performed based on traditional approaches such as segregation analyses, including for many missense variants, which are therefore referred to as variants of uncertain significance (VUS). Functional assays provide an important alternative for classification of BRCA1 and BRCA2 VUS. As reviewed here, both of these tumour suppressors promote the maintenance of genome stability via homologous recombination. Thus, related assays may be particularly relevant to cancer risk. Progress in implementing functional assays to assess missense variants of BRCA1 and BRCA2 is considered here, along with current limitations and the path to more impactful assay systems. While functional assays have been developed to independently evaluate BRCA1 and BRCA2 VUS, high-throughput assays with sufficient sensitivity to characterise the large number of identified variants are lacking. Additionally, because of relatively low conservation of certain domains of BRCA1, and of BRCA2, between humans and rodents, heterologous expression in rodent cells may have limited reliability or capacity to assess variants present throughout either protein. Moving forward, it will be important to perform assays in human cell lines with relevance to particular tumour types, and to strengthen risk predictions based on multifactorial statistical analyses that also include available data on cosegregation and tumour pathology.
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Affiliation(s)
- Amanda Ewart Toland
- Department of Cancer Biology & Genetics and Division of Human Genetics, Department of Internal Medicine, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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17
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Anantha RW, Simhadri S, Foo TK, Miao S, Liu J, Shen Z, Ganesan S, Xia B. Functional and mutational landscapes of BRCA1 for homology-directed repair and therapy resistance. eLife 2017; 6. [PMID: 28398198 PMCID: PMC5432210 DOI: 10.7554/elife.21350] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 04/10/2017] [Indexed: 12/20/2022] Open
Abstract
BRCA1 plays a critical role in homology-directed repair (HDR) of DNA double strand breaks, and the repair defect of BRCA1-mutant cancer cells is being targeted with platinum drugs and poly (ADP-ribose) polymerase (PARP) inhibitors. We have employed relatively simple and sensitive assays to determine the function of BRCA1 variants or mutants in two HDR mechanisms, homologous recombination (HR) and single strand annealing (SSA), and in conferring resistance to cisplatin and olaparib in human cancer cells. Our results define the functionality of the top 22 patient-derived BRCA1 missense variants and the contribution of different domains of BRCA1 and its E3 ubiquitin ligase activity to HDR and drug resistance. Importantly, our results also demonstrate that the BRCA1-PALB2 interaction dictates the choice between HR and SSA. These studies establish functional and mutational landscapes of BRCA1 for HDR and therapy resistance, while revealing novel insights into BRCA1 regulatory mechanisms and HDR pathway choice. DOI:http://dx.doi.org/10.7554/eLife.21350.001 Genes are the instruction manuals of life and contain the information needed to build the proteins that keep cells alive. Over time, genes can accumulate errors or mutations and eventually become faulty, which can lead to diseases like cancer. Sometimes mutations can be passed on through generations and increase the chances of getting cancer. The BRCA1 gene, for example, provides instructions for making a protein that helps to repair or remove damaged DNA and stops cells from growing uncontrollably. When the BRCA1 gene becomes faulty, cells could continue to grow with damaged DNA. This makes it more likely for cancer to develop, especially breast cancer and ovarian cancer. However, not all changes in BRCA1 gene cause the protein to become faulty or lead to cancer. In fact, about 30% of BRCA1 gene changes identified by genetic tests are referred to as ‘variants of uncertain clinical significance’, meaning that it is not clear if these variants are indeed mutations that could affect the clinical outcome of the people that carry them. Software predictions based largely on patient data have categorized many of these variants as not cancer-causing, but the majority still need to be experimentally tested and confirmed. Many studies have tried to determine the effect of selected variants on the BRCA1 protein, but a complete picture remains lacking. Now, Anantha et al. have tested the top 22 common variants in the BRCA1 gene, some of which had known effects and some did not. The study tested how these variants affect the ability of the protein to repair damaged DNA and the efficacy of chemotherapies targeting cancer cells with a DNA repair defect. The experiments revealed that three specific parts of the protein must remain intact in order for the protein to carry out this activity, i.e. mutations that affect these three areas are likely to cause cancer and also make cancer cells vulnerable to these chemotherapies. Anantha et al. also generated a series of 10 artificially shortened BRCA1 proteins, each missing a specific part, to determine the possible effects of other variants in those missing parts. Together the findings reveal previously unknown effects of certain variants that are commonly seen in cancer patients as well new insights into how the BRCA1 protein repairs DNA. The next step will be to assess rarer variants where little data is available. A better understanding of how these variants affect DNA repair and drug response will help to improve the genetic counseling and treatment of patients with breast cancer and ovarian cancer. DOI:http://dx.doi.org/10.7554/eLife.21350.002
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Affiliation(s)
- Rachel W Anantha
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, United States.,Department of Radiation Oncology, Rutgers, The State University of New Jersey, New Brunswick, United States
| | - Srilatha Simhadri
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, United States.,Department of Radiation Oncology, Rutgers, The State University of New Jersey, New Brunswick, United States.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, United States
| | - Tzeh Keong Foo
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, United States.,Department of Radiation Oncology, Rutgers, The State University of New Jersey, New Brunswick, United States
| | - Susanna Miao
- Department of Genetics, School of Arts and Sciences, Rutgers, The State University of New Jersey, Piscataway, United States
| | - Jingmei Liu
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, United States.,Department of Radiation Oncology, Rutgers, The State University of New Jersey, New Brunswick, United States
| | - Zhiyuan Shen
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, United States.,Department of Radiation Oncology, Rutgers, The State University of New Jersey, New Brunswick, United States
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, United States.,Department of Radiation Oncology, Rutgers, The State University of New Jersey, New Brunswick, United States.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, United States
| | - Bing Xia
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, United States
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18
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Nielsen FC, van Overeem Hansen T, Sørensen CS. Hereditary breast and ovarian cancer: new genes in confined pathways. Nat Rev Cancer 2016; 16:599-612. [PMID: 27515922 DOI: 10.1038/nrc.2016.72] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Genetic abnormalities in the DNA repair genes BRCA1 and BRCA2 predispose to hereditary breast and ovarian cancer (HBOC). However, only approximately 25% of cases of HBOC can be ascribed to BRCA1 and BRCA2 mutations. Recently, exome sequencing has uncovered substantial locus heterogeneity among affected families without BRCA1 or BRCA2 mutations. The new pathogenic variants are rare, posing challenges to estimation of risk attribution through patient cohorts. In this Review article, we examine HBOC genes, focusing on their role in genome maintenance, the possibilities for functional testing of putative causal variants and the clinical application of new HBOC genes in cancer risk management and treatment decision-making.
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Affiliation(s)
- Finn Cilius Nielsen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark
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19
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Cochran RL, Cidado J, Kim M, Zabransky DJ, Croessmann S, Chu D, Wong HY, Beaver JA, Cravero K, Erlanger B, Parsons H, Heaphy CM, Meeker AK, Lauring J, Park BH. Functional isogenic modeling of BRCA1 alleles reveals distinct carrier phenotypes. Oncotarget 2016; 6:25240-51. [PMID: 26246475 PMCID: PMC4694828 DOI: 10.18632/oncotarget.4595] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 06/01/2015] [Indexed: 12/16/2022] Open
Abstract
Clinical genetic testing of BRCA1 and BRCA2 is commonly performed to identify specific individuals at risk for breast and ovarian cancers who may benefit from prophylactic therapeutic interventions. Unfortunately, it is evident that deleterious BRCA1 alleles demonstrate variable penetrance and that many BRCA1 variants of unknown significance (VUS) exist. In order to further refine hereditary risks that may be associated with specific BRCA1 alleles, we performed gene targeting to establish an isogenic panel of immortalized human breast epithelial cells harboring eight clinically relevant BRCA1 alleles. Interestingly, BRCA1 mutations and VUS had distinct, quantifiable phenotypes relative to isogenic parental BRCA1 wild type cells and controls. Heterozygous cells with known deleterious BRCA1 mutations (185delAG, C61G and R71G) demonstrated consistent phenotypes in radiation sensitivity and genomic instability assays, but showed variability in other assays. Heterozygous BRCA1 VUS cells also demonstrated assay variability, with some VUS demonstrating phenotypes more consistent with deleterious alleles. Taken together, our data suggest that BRCA1 deleterious mutations and VUS can differ in their range of tested phenotypes, suggesting they might impart varying degrees of risk. These results demonstrate that functional isogenic modeling of BRCA1 alleles could aid in classifying BRCA1 mutations and VUS, and determining BRCA allele cancer risk.
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Affiliation(s)
- Rory L Cochran
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Minsoo Kim
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel J Zabransky
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Croessmann
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hong Yuen Wong
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julia A Beaver
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Karen Cravero
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bracha Erlanger
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Heather Parsons
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher M Heaphy
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan K Meeker
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Josh Lauring
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.,The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD, USA
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20
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Jung J, Yeom C, Choi YS, Kim S, Lee E, Park MJ, Kang SW, Kim SB, Chang S. Simultaneous inhibition of multiple oncogenic miRNAs by a multi-potent microRNA sponge. Oncotarget 2016; 6:20370-87. [PMID: 26284487 PMCID: PMC4653011 DOI: 10.18632/oncotarget.4827] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 07/17/2015] [Indexed: 01/10/2023] Open
Abstract
The roles of oncogenic miRNAs are widely recognized in many cancers. Inhibition of single miRNA using antagomiR can efficiently knock-down a specific miRNA. However, the effect is transient and often results in subtle phenotype, as there are other miRNAs contribute to tumorigenesis. Here we report a multi-potent miRNA sponge inhibiting multiple miRNAs simultaneously. As a model system, we targeted miR-21, miR-155 and miR-221/222, known as oncogenic miRNAs in multiple tumors including breast and pancreatic cancers. To achieve efficient knockdown, we generated perfect and bulged-matched miRNA binding sites (MBS) and introduced multiple copies of MBS, ranging from one to five, in the multi-potent miRNA sponge. Luciferase reporter assay showed the multi-potent miRNA sponge efficiently inhibited 4 miRNAs in breast and pancreatic cancer cells. Furthermore, a stable and inducible version of the multi-potent miRNA sponge cell line showed the miRNA sponge efficiently reduces the level of 4 target miRNAs and increase target protein level of these oncogenic miRNAs. Finally, we showed the miRNA sponge sensitize cells to cancer drug and attenuate cell migratory activity. Altogether, our study demonstrates the multi-potent miRNA sponge is a useful tool to examine the functional impact of simultaneous inhibition of multiple miRNAs and proposes a therapeutic potential.
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Affiliation(s)
- Jaeyun Jung
- Department of Biomedical Sciences, University of Ulsan School of Medicine, Seoul 138-736, Korea
| | | | | | - Sinae Kim
- Department of Biomedical Sciences, University of Ulsan School of Medicine, Seoul 138-736, Korea
| | - EunJi Lee
- Department of Biomedical Sciences, University of Ulsan School of Medicine, Seoul 138-736, Korea
| | - Min Ji Park
- Department of Biomedical Sciences, University of Ulsan School of Medicine, Seoul 138-736, Korea
| | - Sang Wook Kang
- Department of Biomedical Sciences, University of Ulsan School of Medicine, Seoul 138-736, Korea
| | - Sung Bae Kim
- Department of Biomedical Sciences, University of Ulsan School of Medicine, Seoul 138-736, Korea.,Asan Medical Center, Seoul 138-736, Korea
| | - Suhwan Chang
- Department of Biomedical Sciences, University of Ulsan School of Medicine, Seoul 138-736, Korea.,Asan Medical Center, Seoul 138-736, Korea
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21
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Prakash R, Zhang Y, Feng W, Jasin M. Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. Cold Spring Harb Perspect Biol 2015; 7:a016600. [PMID: 25833843 DOI: 10.1101/cshperspect.a016600] [Citation(s) in RCA: 572] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks in mammalian cells, the defining step of which is homologous strand exchange directed by the RAD51 protein. The physiological importance of HR is underscored by the observation of genomic instability in HR-deficient cells and, importantly, the association of cancer predisposition and developmental defects with mutations in HR genes. The tumor suppressors BRCA1 and BRCA2, key players at different stages of HR, are frequently mutated in familial breast and ovarian cancers. Other HR proteins, including PALB2 and RAD51 paralogs, have also been identified as tumor suppressors. This review summarizes recent findings on BRCA1, BRCA2, and associated proteins involved in human disease with an emphasis on their molecular roles and interactions.
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Affiliation(s)
- Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Yu Zhang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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22
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Jhuraney A, Velkova A, Johnson RC, Kessing B, Carvalho RS, Whiley P, Spurdle AB, Vreeswijk MPG, Caputo SM, Millot GA, Vega A, Coquelle N, Galli A, Eccles D, Blok MJ, Pal T, van der Luijt RB, Santamariña Pena M, Neuhausen SL, Donenberg T, Machackova E, Thomas S, Vallée M, Couch FJ, Tavtigian SV, Glover JNM, Carvalho MA, Brody LC, Sharan SK, Monteiro AN. BRCA1 Circos: a visualisation resource for functional analysis of missense variants. J Med Genet 2015; 52:224-30. [PMID: 25643705 PMCID: PMC4392196 DOI: 10.1136/jmedgenet-2014-102766] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/29/2014] [Accepted: 12/05/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Inactivating germline mutations in the tumour suppressor gene BRCA1 are associated with a significantly increased risk of developing breast and ovarian cancer. A large number (>1500) of unique BRCA1 variants have been identified in the population and can be classified as pathogenic, non-pathogenic or as variants of unknown significance (VUS). Many VUS are rare missense variants leading to single amino acid changes. Their impact on protein function cannot be directly inferred from sequence information, precluding assessment of their pathogenicity. Thus, functional assays are critical to assess the impact of these VUS on protein activity. BRCA1 is a multifunctional protein and different assays have been used to assess the impact of variants on different biochemical activities and biological processes. METHODS AND RESULTS To facilitate VUS analysis, we have developed a visualisation resource that compiles and displays functional data on all documented BRCA1 missense variants. BRCA1 Circos is a web-based visualisation tool based on the freely available Circos software package. The BRCA1 Circos web tool (http://research.nhgri.nih.gov/bic/circos/) aggregates data from all published BRCA1 missense variants for functional studies, harmonises their results and presents various functionalities to search and interpret individual-level functional information for each BRCA1 missense variant. CONCLUSIONS This research visualisation tool will serve as a quick one-stop publically available reference for all the BRCA1 missense variants that have been functionally assessed. It will facilitate meta-analysis of functional data and improve assessment of pathogenicity of VUS.
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Affiliation(s)
- Ankita Jhuraney
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- University of South Florida Cancer Biology PhD Program, Tampa, Florida, USA
| | - Aneliya Velkova
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Randall C Johnson
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Bailey Kessing
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Renato S Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Phillip Whiley
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandrine M Caputo
- Service de Génétique, Institut Curie, Hôpital René Huguenin, Paris, France
| | - Gael A Millot
- Institut Curie, Université Pierre et Marie Curie, Paris, France
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica, Santiago, Spain
| | - Nicolas Coquelle
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Alvaro Galli
- Instituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | | | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Tuya Pal
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Rob B van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | | | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Simon Thomas
- Salisbury District Hospital, Salisbury, Wiltshire, UK
| | - Maxime Vallée
- International Agency for Research on Cancer, Lyon, France
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, and Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Marcelo A Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Lawrence C Brody
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Shyam K Sharan
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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23
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Protein stability versus function: effects of destabilizing missense mutations on BRCA1 DNA repair activity. Biochem J 2015; 466:613-24. [DOI: 10.1042/bj20141077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The majority of the unstable BRCA1 BRCT domain missense mutations we studied disrupted DNA repair in vivo, but reduced cellular function only weakly correlated with reduced structural stability. The findings have an impact on assessing cancer susceptibility in patients with BRCA1 mutations.
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24
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Kim S, Rhee JK, Yoo HJ, Lee HJ, Lee EJ, Lee JW, Yu JH, Son BH, Gong G, Kim SB, Singh SR, Ahn SH, Chang S. Bioinformatic and metabolomic analysis reveals miR-155 regulates thiamine level in breast cancer. Cancer Lett 2014; 357:488-97. [PMID: 25484137 DOI: 10.1016/j.canlet.2014.11.058] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/26/2014] [Accepted: 11/26/2014] [Indexed: 12/14/2022]
Abstract
microRNA-155 (miR-155) is one of the well-known oncogenic miRNA implicated in various types of tumors. Thiamine, commonly known as vitamin B1, is one of critical cofactors for energy metabolic enzymes including pyruvate dehydrogenase, alpha ketoglutarate dehydrogenase, and transketolase. Here we report a novel role of miR-155 in cancer metabolism through the up-regulation of thiamine in breast cancer cells. A bioinformatic analysis of miRNA array and metabolite-profiling data from NCI-60 cancer cell panel revealed thiamine as a metabolite positively correlated with the miR-155 expression level. We confirmed it in MCF7, MDA-MB-436 and two human primary breast cancer cells by showing reduced thiamine levels upon a knock-down of miR-155. To understand how the miR-155 controls thiamine level, a set of key molecules for thiamine homeostasis were further analyzed after the knockdown of miR-155. The results showed the expression of two thiamine transporter genes (SLC19A2, SLC25A19) as well as thiamine pyrophosphokinase-1 (TPK1) were decreased in both RNA and protein level in miR-155 dependent manner. Finally, we confirm the finding by showing a positive correlation between miR-155 and thiamine level in 71 triple negative breast tumors. Taken altogether, our study demonstrates a role of miR-155 in thiamine homeostasis and suggests a function of this oncogenic miRNA on breast cancer metabolism.
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Affiliation(s)
- Sinae Kim
- Department of Biomedical Sciences, Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea
| | | | | | | | - Eun Ji Lee
- Department of Biomedical Sciences, Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea
| | | | | | | | | | | | - Shree Ram Singh
- Stem Cell Regulation and Animal Aging Section, Basic Research Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | | | - Suhwan Chang
- Department of Biomedical Sciences, Department of Physiology, University of Ulsan College of Medicine, Seoul, South Korea; Asan Medical Center, Seoul, South Korea.
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25
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Hendriks G, Morolli B, Calléja FMGR, Plomp A, Mesman RLS, Meijers M, Sharan SK, Vreeswijk MPG, Vrieling H. An efficient pipeline for the generation and functional analysis of human BRCA2 variants of uncertain significance. Hum Mutat 2014; 35:1382-91. [PMID: 25146914 DOI: 10.1002/humu.22678] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 08/04/2014] [Indexed: 11/08/2022]
Abstract
The implementation of next-generation sequence analysis of disease-related genes has resulted in an increasing number of genetic variants with an unknown clinical significance. The functional analysis of these so-called "variants of uncertain significance" (VUS) is hampered by the tedious and time-consuming procedures required to generate and test specific sequence variants in genomic DNA. Here, we describe an efficient pipeline for the generation of gene variants in a full-length human gene, BRCA2, using a bacterial artificial chromosome. This method permits the rapid generation of intronic and exonic variants in a complete gene through the use of an exon-replacement strategy based on simple site-directed mutagenesis and an effective positive-negative selection system in E. coli. The functionality of variants can then be assessed through the use of functional assays, such as complementation of gene-deficient mouse-embryonic stem (mES) cells in the case of human BRCA2. Our methodology builds upon an earlier protocol and, through the introduction of a series of major innovations, now represents a practical proposition for the rapid analysis of BRCA2 variants and a blueprint for the analysis of other genes using similar approaches. This method enables rapid generation and reliable classification of VUS in disease-related genes, allowing informed clinical decision-making.
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Affiliation(s)
- Giel Hendriks
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
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26
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BRCA1 haploinsufficiency leads to altered expression of genes involved in cellular proliferation and development. PLoS One 2014; 9:e100068. [PMID: 24950059 PMCID: PMC4064996 DOI: 10.1371/journal.pone.0100068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/22/2014] [Indexed: 01/09/2023] Open
Abstract
The assessment of BRCA1 and BRCA2 coding sequences to identify pathogenic mutations associated with inherited breast/ovarian cancer syndrome has provided a method to identify high-risk individuals, allowing them to seek preventative treatments and strategies. However, the current test is expensive, and cannot differentiate between pathogenic variants and those that may be benign. Focusing only on one of the two BRCA partners, we have developed a biological assay for haploinsufficiency of BRCA1. Using a series of EBV-transformed cell lines, we explored gene expression patterns in cells that were BRCA1 wildtype compared to those that carried (heterozygous) BRCA1 pathogenic mutations. We identified a subset of 43 genes whose combined expression pattern is a sensitive predictor of BRCA1 status. The gene set was disproportionately made up of genes involved in cellular differentiation, lending credence to the hypothesis that single copy loss of BRCA1 function may impact differentiation, rendering cells more susceptible to undergoing malignant processes.
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27
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Christou CM, Hadjisavvas A, Kyratzi M, Flouri C, Neophytou I, Anastasiadou V, Loizidou MA, Kyriacou K. The BRCA1 variant p.Ser36Tyr abrogates BRCA1 protein function and potentially confers a moderate risk of breast cancer. PLoS One 2014; 9:e93400. [PMID: 24695549 PMCID: PMC3973689 DOI: 10.1371/journal.pone.0093400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Abstract
The identification of variants of unknown clinical significance (VUS) in the BRCA1 gene complicates genetic counselling and causes additional anxiety to carriers. In silico approaches currently used for VUS pathogenicity assessment are predictive and often produce conflicting data. Furthermore, functional assays are either domain or function specific, thus they do not examine the entire spectrum of BRCA1 functions and interpretation of individual assay results can be misleading. PolyPhen algorithm predicted that the BRCA1 p.Ser36Tyr VUS identified in the Cypriot population was damaging, whereas Align-GVGD predicted that it was possibly of no significance. In addition the BRCA1 p.Ser36Tyr variant was found to be associated with increased risk (OR = 3.47, 95% CI 1.13-10.67, P = 0.02) in a single case-control series of 1174 cases and 1109 controls. We describe a cellular system for examining the function of exogenous full-length BRCA1 and for classifying VUS. We achieved strong protein expression of full-length BRCA1 in transiently transfected HEK293T cells. The p.Ser36Tyr VUS exhibited low protein expression similar to the known pathogenic variant p.Cys61Gly. Co-precipitation analysis further demonstrated that it has a reduced ability to interact with BARD1. Further, co-precipitation analysis of nuclear and cytosolic extracts as well as immunofluorescence studies showed that a high proportion of the p.Ser36Tyr variant is withheld in the cytoplasm contrary to wild type protein. In addition the ability of p.Ser36Tyr to co-localize with conjugated ubiquitin foci in the nuclei of S-phase synchronized cells following genotoxic stress with hydroxyurea is impaired at more pronounced levels than that of the p.Cys61Gly pathogenic variant. The p.Ser36Tyr variant demonstrates abrogated function, and based on epidemiological, genetic, and clinical data we conclude that the p.Ser36Tyr variant is probably associated with a moderate breast cancer risk.
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Affiliation(s)
- Charita M. Christou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Maria Kyratzi
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
- The University of Cyprus, Department of Biological Sciences, Nicosia, Cyprus
| | - Christina Flouri
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Ioanna Neophytou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Violetta Anastasiadou
- The Cyprus Institute of Neurology and Genetics, Department of Clinical Genetics, Nicosia, Cyprus
| | - Maria A. Loizidou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
- * E-mail:
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28
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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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29
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Abstract
Germline mutations of human breast cancer-associated gene 1 (BRCA1) predispose women to breast and ovarian cancers. In mice, over 20 distinct mutations, including null, hypomorphic, isoform, conditional, and point mutations, have been created to study functions of Brca1 in mammary development and tumorigenesis. Analyses using these mutant mice have yielded an enormous amount of information that greatly facilitates our understanding of the gender- and tissue-specific tumor suppressor functions of BRCA1, as well as enriches our insights into applying these preclinical models of disease to breast cancer research. Here, we review features of these mutant mice and their applications to cancer prevention and therapeutic treatment.
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30
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Shin MH, He Y, Huang J. Embryonic stem cells shed new light on the developmental roles of p53. Cell Biosci 2013; 3:42. [PMID: 24171803 PMCID: PMC3852614 DOI: 10.1186/2045-3701-3-42] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/28/2013] [Indexed: 11/17/2022] Open
Abstract
The viability and subtle developmental defects of p53 knockout mice suggest that p53 does not play major role in development. However, contradictory evidence also exists. This discrepancy mainly results from the lack of molecular and cellular mechanisms and the general fact that p53 activation requires stresses. Recent studies of p53 in mouse and human ES cells and induced pluripotent stem (iPS) cells shed new light on the mechanisms of the developmental roles of p53. This review summarizes these new studies that support the developmental roles of p53, highlights the possible underlying molecular mechanisms, and discusses the potential relationship between the developmental roles and the tumor suppressive function of p53. In summary, the molecular mechanisms underlying the developmental roles of p53 are emerging, and the developmental roles and tumor suppressive function of p53 may be closely related.
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31
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Bouwman P, van der Gulden H, van der Heijden I, Drost R, Klijn CN, Prasetyanti P, Pieterse M, Wientjens E, Seibler J, Hogervorst FBL, Jonkers J. A high-throughput functional complementation assay for classification of BRCA1 missense variants. Cancer Discov 2013; 3:1142-55. [PMID: 23867111 DOI: 10.1158/2159-8290.cd-13-0094] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED Mutations in BRCA1 and BRCA2 account for the majority of hereditary breast and ovarian cancers, and therefore sequence analysis of both genes is routinely conducted in patients with early-onset breast cancer. Besides mutations that clearly abolish protein function or are known to increase cancer risk, a large number of sequence variants of uncertain significance (VUS) have been identified. Although several functional assays for BRCA1 VUSs have been described, thus far it has not been possible to conduct a high-throughput analysis in the context of the full-length protein. We have developed a relatively fast and easy cDNA-based functional assay to classify BRCA1 VUSs based on their ability to functionally complement BRCA1-deficient mouse embryonic stem cells. Using this assay, we have analyzed 74 unclassified BRCA1 missense mutants for which all predicted pathogenic variants are confined to the BRCA1 RING and BRCT domains. SIGNIFICANCE BRCA1 VUSs are frequently found in patients with hereditary breast or ovarian cancer and present a serious problem for clinical geneticists. This article describes the generation, validation, and application of a reliable high-throughput assay for the functional classification of BRCA1 sequence variants of uncertain significance.
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Affiliation(s)
- Peter Bouwman
- 1Division of Molecular Pathology and Cancer Genomics Centre and 2Department of Pathology, The Netherlands Cancer Institute Amsterdam, The Netherlands; and 3TaconicArtemis GmbH, Cologne, Germany
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32
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BRCA1 is a negative modulator of the PRC2 complex. EMBO J 2013; 32:1584-97. [PMID: 23624935 DOI: 10.1038/emboj.2013.95] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 04/03/2013] [Indexed: 01/07/2023] Open
Abstract
The Polycomb-repressive complex 2 (PRC2) is important for maintenance of stem cell pluripotency and suppression of cell differentiation by promoting histone H3 lysine 27 trimethylation (H3K27me3) and transcriptional repression of differentiation genes. Here we show that the tumour-suppressor protein BRCA1 interacts with the Polycomb protein EZH2 in mouse embryonic stem (ES) and human breast cancer cells. The BRCA1-binding region in EZH2 overlaps with the noncoding RNA (ncRNA)-binding domain, and BRCA1 expression inhibits the binding of EZH2 to the HOTAIR ncRNA. Decreased expression of BRCA1 causes genome-wide EZH2 re-targeting and elevates H3K27me3 levels at PRC2 target loci in both mouse ES and human breast cancer cells. BRCA1 deficiency blocks ES cell differentiation and enhances breast cancer migration and invasion in an EZH2-dependent manner. These results reveal that BRCA1 is a key negative modulator of PRC2 and that loss of BRCA1 inhibits ES cell differentiation and enhances an aggressive breast cancer phenotype by affecting PRC2 function.
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33
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Lindor NM, Goldgar DE, Tavtigian SV, Plon SE, Couch FJ. BRCA1/2 sequence variants of uncertain significance: a primer for providers to assist in discussions and in medical management. Oncologist 2013; 18:518-24. [PMID: 23615697 DOI: 10.1634/theoncologist.2012-0452] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION DNA variants of uncertain significance (VUS) are common outcomes of clinical genetic testing for susceptibility to cancer. A statistically rigorous model that provides a pathogenicity score for each variant has been developed to aid in the clinical management of patients undergoing genetic testing. METHODS The information in this article is derived from multiple publications on VUS in BRCA genes, distilled for communicating with clinicians who may encounter VUS in their practice. RESULTS The posterior probability scores for BRCA1 or BRCA2 VUS, calculated from a multifactorial likelihood model, are explained, and links for looking up specific VUS are provided. The International Agency on Cancer Research (IARC) of the World Health Organization has proposed a simple five-tier system for clinical management that is not widely known to clinicians. Classes 1 and 2 in this system are managed as neutral variants, classes 4 and 5 are managed as pathogenic variants, and class 3 variants still have insufficient evidence to move to either end of this scale and, thus, cannot be used in medical management. CONCLUSIONS Development of models that integrate multiple independent lines of evidence has allowed classification of a growing number of VUS in the BRCA1 and BRCA2 genes. The pathogenicity score that is generated by this model maps to the IARC system for clinical management, which will assist clinicians in the medical management of those patients who obtain a VUS result upon testing.
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Affiliation(s)
- Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, Arizona 85259, USA.
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34
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Shyam K Sharan KB, Sharan SK. Manipulating the Mouse Genome Using Recombineering. ADVANCES IN GENETICS 2013; 2. [PMID: 31404315 DOI: 10.4172/2169-0111.1000108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetically engineered mouse models are indispensable for understanding the biological function of genes, understanding the genetic basis of human diseases and for preclinical testing of novel therapies. Generation of such mouse models has been possible because of our ability to manipulate the mouse genome. Recombineering is a highly efficient recombination-based method of genetic engineering that has revolutionized our ability to generate mouse models. Since recombineering technology is not dependent on the availability of restriction enzyme recognition sites, it allows us to modify the genome with great precision. It requires homology arms as short as 40 bases for recombination, which makes it relatively easy to generate targeting constructs to insert, change or delete either a single nucleotide or a DNA fragment several kb in size; insert selectable markers, reporter genes or add epitope tags to any gene of interest. In this review, we focus on the development of recombineering technology and its application in the generation of transgenic and knockout or knock-in mouse models. High throughput generation of gene targeting vectors, used to construct knockout alleles in mouse embryonic stem cells, is now feasible because of this technology. The challenge now is to use the "designer" mice to develop novel therapies to prevent, cure or effectively manage some the most debilitating human diseases.
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Affiliation(s)
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland 21702
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35
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Towler WI, Zhang J, Ransburgh DJR, Toland AE, Ishioka C, Chiba N, Parvin JD. Analysis of BRCA1 variants in double-strand break repair by homologous recombination and single-strand annealing. Hum Mutat 2012; 34:439-45. [PMID: 23161852 DOI: 10.1002/humu.22251] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/24/2012] [Indexed: 01/13/2023]
Abstract
Missense substitutions of uncertain clinical significance in the BRCA1 gene are a vexing problem in genetic counseling for women who have a family history of breast cancer. In this study, we evaluated the functions of 29 missense substitutions of BRCA1 in two DNA repair pathways. Repair of double-strand breaks by homology-directed recombination (HDR) had been previously analyzed for 16 of these BRCA1 variants, and 13 more variants were analyzed in this study. All 29 variants were also analyzed for function in double-strand break repair by the single-strand annealing (SSA) pathway. We found that among the pathogenic mutations in BRCA1, all were defective for DNA repair by either pathway. The HDR assay was accurate because all pathogenic mutants were defective for HDR, and all nonpathogenic variants were fully functional for HDR. Repair by SSA accurately identified pathogenic mutants, but several nonpathogenic variants were scored as defective or partially defective. These results indicated that specific amino acid residues of the BRCA1 protein have different effects in the two related DNA repair pathways, and these results validate the HDR assay as highly correlative with BRCA1-associated breast cancer.
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Affiliation(s)
- William I Towler
- Department of Biomedical Informatics and the Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
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36
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Bouwman P, Jonkers J. The effects of deregulated DNA damage signalling on cancer chemotherapy response and resistance. Nat Rev Cancer 2012; 12:587-98. [PMID: 22918414 DOI: 10.1038/nrc3342] [Citation(s) in RCA: 457] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tumours with specific DNA repair defects can be completely dependent on back-up DNA repair pathways for their survival. This dependence can be exploited therapeutically to induce synthetic lethality in tumour cells. For instance, homologous recombination (HR)-deficient tumours can be effectively targeted by DNA double-strand break-inducing agents. However, not all HR-defective tumours respond equally well to this type of therapy. Tumour cells may acquire resistance by invoking biochemical mechanisms that reduce drug action or by acquiring additional alterations in DNA damage response pathways. A thorough understanding of these processes is important for predicting treatment response and for the development of novel treatment strategies that prevent the emergence of therapy-resistant tumours.
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Affiliation(s)
- Peter Bouwman
- Division of Molecular Pathology and Cancer Systems Biology Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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37
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Millot GA, Carvalho MA, Caputo SM, Vreeswijk MPG, Brown MA, Webb M, Rouleau E, Neuhausen SL, Hansen TVO, Galli A, Brandão RD, Blok MJ, Velkova A, Couch FJ, Monteiro ANA. A guide for functional analysis of BRCA1 variants of uncertain significance. Hum Mutat 2012; 33:1526-37. [PMID: 22753008 DOI: 10.1002/humu.22150] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 12/12/2022]
Abstract
Germline mutations in the tumor suppressor gene BRCA1 confer an estimated lifetime risk of 56-80% for breast cancer and 15-60% for ovarian cancer. Since the mid 1990s when BRCA1 was identified, genetic testing has revealed over 1,500 unique germline variants. However, for a significant number of these variants, the effect on protein function is unknown making it difficult to infer the consequences on risks of breast and ovarian cancers. Thus, many individuals undergoing genetic testing for BRCA1 mutations receive test results reporting a variant of uncertain clinical significance (VUS), leading to issues in risk assessment, counseling, and preventive care. Here, we describe functional assays for BRCA1 to directly or indirectly assess the impact of a variant on protein conformation or function and how these results can be used to complement genetic data to classify a VUS as to its clinical significance. Importantly, these methods may provide a framework for genome-wide pathogenicity assignment.
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Affiliation(s)
- Gaël A Millot
- Institut Curie, CNRS, UMR 3244 Université Pierre et Marie Curie, Paris, France
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38
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Biswas K, Das R, Eggington JM, Qiao H, North SL, Stauffer S, Burkett SS, Martin BK, Southon E, Sizemore SC, Pruss D, Bowles KR, Roa BB, Hunter N, Tessarollo L, Wenstrup RJ, Byrd RA, Sharan SK. Functional evaluation of BRCA2 variants mapping to the PALB2-binding and C-terminal DNA-binding domains using a mouse ES cell-based assay. Hum Mol Genet 2012; 21:3993-4006. [PMID: 22678057 DOI: 10.1093/hmg/dds222] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-nucleotide substitutions and small in-frame insertions or deletions identified in human breast cancer susceptibility genes BRCA1 and BRCA2 are frequently classified as variants of unknown clinical significance (VUS) due to the availability of very limited information about their functional consequences. Such variants can most reliably be classified as pathogenic or non-pathogenic based on the data of their co-segregation with breast cancer in affected families and/or their co-occurrence with a pathogenic mutation. Biological assays that examine the effect of variants on protein function can provide important information that can be used in conjunction with available familial data to determine the pathogenicity of VUS. In this report, we have used a previously described mouse embryonic stem (mES) cell-based functional assay to characterize eight BRCA2 VUS that affect highly conserved amino acid residues and map to the N-terminal PALB2-binding or the C-terminal DNA-binding domains. For several of these variants, very limited co-segregation information is available, making it difficult to determine their pathogenicity. Based on their ability to rescue the lethality of Brca2-deficient mES cells and their effect on sensitivity to DNA-damaging agents, homologous recombination and genomic integrity, we have classified these variants as pathogenic or non-pathogenic. In addition, we have used homology-based modeling as a predictive tool to assess the effect of some of these variants on the structural integrity of the C-terminal DNA-binding domain and also generated a knock-in mouse model to analyze the physiological significance of a residue reported to be essential for the interaction of BRCA2 with meiosis-specific recombinase, DMC1.
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Affiliation(s)
- Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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39
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Gauthier M, Maury Y, Peschanski M, Martinat C. Human pluripotent stem cells for genetic disease modeling and drug screening. Regen Med 2012; 6:607-22. [PMID: 21916596 DOI: 10.2217/rme.11.46] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Considerable hope surrounds the use of disease-specific pluripotent stem cells, which can differentiate into any cell type, as starting materials to generate models of human disease that will allow exploration of pathological mechanisms and the search for new treatments. Disease-specific human embryonic stem cells have provided a useful source for studying certain disease states. However, reprogramming of human somatic cells that use readily accessible tissue, such as skin or blood, to generate embryonic-like induced pluripotent stem cells has opened new perspectives for modeling and understanding a larger number of human pathologies. Here, we examine the challenges in creating a disease model from human pluripotent stem cells, and describe their use to model both cell-autonomous and non-cell-autonomous mechanisms, the need for adequate control experiments and the genetic limitations of human induced pluripotent stem cells. Progress in these areas will substantially accelerate effective application of disease-specific human pluripotent stem cells for drug screening.
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40
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Epigenetic control of an oncogenic microRNA, miR-155, by BRCA1. Oncotarget 2012; 3:5-6. [PMID: 22403740 PMCID: PMC3292886 DOI: 10.18632/oncotarget.433] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 01/23/2012] [Indexed: 11/25/2022] Open
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41
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Abstract
The proteins encoded by the two major breast cancer susceptibility genes, BRCA1 and BRCA2, work in a common pathway of genome protection. However, the two proteins work at different stages in the DNA damage response (DDR) and in DNA repair. BRCA1 is a pleiotropic DDR protein that functions in both checkpoint activation and DNA repair, whereas BRCA2 is a mediator of the core mechanism of homologous recombination. The links between the two proteins are not well understood, but they must exist to explain the marked similarity of human cancer susceptibility that arises with germline mutations in these genes. As discussed here, the proteins work in concert to protect the genome from double-strand DNA damage during DNA replication.
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Affiliation(s)
- Rohini Roy
- Molecular Biology Program and Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
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42
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Drost R, Bouwman P, Rottenberg S, Boon U, Schut E, Klarenbeek S, Klijn C, van der Heijden I, van der Gulden H, Wientjens E, Pieterse M, Catteau A, Green P, Solomon E, Morris JR, Jonkers J. BRCA1 RING function is essential for tumor suppression but dispensable for therapy resistance. Cancer Cell 2011; 20:797-809. [PMID: 22172724 DOI: 10.1016/j.ccr.2011.11.014] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 10/20/2011] [Accepted: 11/17/2011] [Indexed: 12/30/2022]
Abstract
Hereditary breast cancers are frequently caused by germline BRCA1 mutations. The BRCA1(C61G) mutation in the BRCA1 RING domain is a common pathogenic missense variant, which reduces BRCA1/BARD1 heterodimerization and abrogates its ubiquitin ligase activity. To investigate the role of BRCA1 RING function in tumor suppression and therapy response, we introduced the Brca1(C61G) mutation in a conditional mouse model for BRCA1-associated breast cancer. In contrast to BRCA1-deficient mammary carcinomas, tumors carrying the Brca1(C61G) mutation responded poorly to platinum drugs and PARP inhibition and rapidly developed resistance while retaining the Brca1(C61G) mutation. These findings point to hypomorphic activity of the BRCA1-C61G protein that, although unable to prevent tumor development, affects response to therapy.
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Affiliation(s)
- Rinske Drost
- Division of Molecular Biology, The Netherlands Cancer Institute, Amsterdam
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43
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Lindor NM, Guidugli L, Wang X, Vallée MP, Monteiro ANA, Tavtigian S, Goldgar DE, Couch FJ. A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Hum Mutat 2011; 33:8-21. [PMID: 21990134 DOI: 10.1002/humu.21627] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 09/26/2011] [Indexed: 01/23/2023]
Abstract
Clinical mutation screening of the BRCA1 and BRCA2 genes for the presence of germline inactivating mutations is used to identify individuals at elevated risk of breast and ovarian cancer. Variants identified during screening are usually classified as pathogenic (increased risk of cancer) or not pathogenic (no increased risk of cancer). However, a significant proportion of genetic tests yields variants of uncertain significance (VUS) that have undefined risk of cancer. Individuals carrying these VUS cannot benefit from individualized cancer risk assessment. Recently, a quantitative "posterior probability model" for assessing the clinical relevance of VUS in BRCA1 or BRCA2, which integrates multiple forms of genetic evidence has been developed. Here, we provide a detailed review of this model. We describe the components of the model and explain how these can be combined to calculate a posterior probability of pathogenicity for each VUS. We explain how the model can be applied to public data and provide tables that list the VUS that have been classified as not pathogenic or pathogenic using this method. While we use BRCA1 and BRCA2 VUS as examples, the method can be used as a framework for classification of the pathogenicity of VUS in other cancer genes.
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Affiliation(s)
- Noralane M Lindor
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota 55905, USA
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44
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Maxwell CA, Benítez J, Gómez-Baldó L, Osorio A, Bonifaci N, Fernández-Ramires R, Costes SV, Guinó E, Chen H, Evans GJR, Mohan P, Català I, Petit A, Aguilar H, Villanueva A, Aytes A, Serra-Musach J, Rennert G, Lejbkowicz F, Peterlongo P, Manoukian S, Peissel B, Ripamonti CB, Bonanni B, Viel A, Allavena A, Bernard L, Radice P, Friedman E, Kaufman B, Laitman Y, Dubrovsky M, Milgrom R, Jakubowska A, Cybulski C, Gorski B, Jaworska K, Durda K, Sukiennicki G, Lubiński J, Shugart YY, Domchek SM, Letrero R, Weber BL, Hogervorst FBL, Rookus MA, Collee JM, Devilee P, Ligtenberg MJ, van der Luijt RB, Aalfs CM, Waisfisz Q, Wijnen J, van Roozendaal CEP, Easton DF, Peock S, Cook M, Oliver C, Frost D, Harrington P, Evans DG, Lalloo F, Eeles R, Izatt L, Chu C, Eccles D, Douglas F, Brewer C, Nevanlinna H, Heikkinen T, Couch FJ, Lindor NM, Wang X, Godwin AK, Caligo MA, Lombardi G, Loman N, Karlsson P, Ehrencrona H, von Wachenfeldt A, Bjork Barkardottir R, Hamann U, Rashid MU, Lasa A, Caldés T, Andrés R, Schmitt M, Assmann V, Stevens K, Offit K, Curado J, Tilgner H, Guigó R, Aiza G, Brunet J, Castellsagué J, Martrat G, Urruticoechea A, Blanco I, Tihomirova L, Goldgar DE, Buys S, John EM, Miron A, Southey M, Daly MB, Schmutzler RK, Wappenschmidt B, Meindl A, Arnold N, Deissler H, Varon-Mateeva R, Sutter C, Niederacher D, Imyamitov E, Sinilnikova OM, Stoppa-Lyonne D, Mazoyer S, Verny-Pierre C, Castera L, de Pauw A, Bignon YJ, Uhrhammer N, Peyrat JP, Vennin P, Fert Ferrer S, Collonge-Rame MA, Mortemousque I, Spurdle AB, Beesley J, Chen X, Healey S, Barcellos-Hoff MH, Vidal M, Gruber SB, Lázaro C, Capellá G, McGuffog L, Nathanson KL, Antoniou AC, Chenevix-Trench G, Fleisch MC, Moreno V, Pujana MA. Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer. PLoS Biol 2011; 9:e1001199. [PMID: 22110403 PMCID: PMC3217025 DOI: 10.1371/journal.pbio.1001199] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 10/10/2011] [Indexed: 12/24/2022] Open
Abstract
Differentiated mammary epithelium shows apicobasal polarity, and loss of tissue organization is an early hallmark of breast carcinogenesis. In BRCA1 mutation carriers, accumulation of stem and progenitor cells in normal breast tissue and increased risk of developing tumors of basal-like type suggest that BRCA1 regulates stem/progenitor cell proliferation and differentiation. However, the function of BRCA1 in this process and its link to carcinogenesis remain unknown. Here we depict a molecular mechanism involving BRCA1 and RHAMM that regulates apicobasal polarity and, when perturbed, may increase risk of breast cancer. Starting from complementary genetic analyses across families and populations, we identified common genetic variation at the low-penetrance susceptibility HMMR locus (encoding for RHAMM) that modifies breast cancer risk among BRCA1, but probably not BRCA2, mutation carriers: n = 7,584, weighted hazard ratio ((w)HR) = 1.09 (95% CI 1.02-1.16), p(trend) = 0.017; and n = 3,965, (w)HR = 1.04 (95% CI 0.94-1.16), p(trend) = 0.43; respectively. Subsequently, studies of MCF10A apicobasal polarization revealed a central role for BRCA1 and RHAMM, together with AURKA and TPX2, in essential reorganization of microtubules. Mechanistically, reorganization is facilitated by BRCA1 and impaired by AURKA, which is regulated by negative feedback involving RHAMM and TPX2. Taken together, our data provide fundamental insight into apicobasal polarization through BRCA1 function, which may explain the expanded cell subsets and characteristic tumor type accompanying BRCA1 mutation, while also linking this process to sporadic breast cancer through perturbation of HMMR/RHAMM.
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Affiliation(s)
- Christopher A. Maxwell
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Javier Benítez
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Biomedical Research Centre Network for Rare Diseases, Spain
| | - Laia Gómez-Baldó
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
| | - Ana Osorio
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Biomedical Research Centre Network for Rare Diseases, Spain
| | - Núria Bonifaci
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Ricardo Fernández-Ramires
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre, Madrid, Spain
- Biomedical Research Centre Network for Rare Diseases, Spain
| | - Sylvain V. Costes
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Elisabet Guinó
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Helen Chen
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Gareth J. R. Evans
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Pooja Mohan
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Isabel Català
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Anna Petit
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Helena Aguilar
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Alberto Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Alvaro Aytes
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Jordi Serra-Musach
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Gad Rennert
- CHS National Cancer Control Center, Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Flavio Lejbkowicz
- CHS National Cancer Control Center, Department of Community Medicine and Epidemiology, Carmel Medical Center and B. Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Paolo Peterlongo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, and IFOM Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Carla B. Ripamonti
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, and IFOM Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Alessandra Viel
- Division of Experimental Oncology 1, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - Anna Allavena
- Department of Genetics, Biology and Biochemistry, University of Turin, Turin, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia, and Consortium for Genomics Technology (Cogentech), Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori, and IFOM Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Bella Kaufman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Maya Dubrovsky
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Roni Milgrom
- The Susanne Levy Gertner Oncogenetics Unit, Institute of Human Genetics, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Anna Jakubowska
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Cezary Cybulski
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Bohdan Gorski
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Durda
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Grzegorz Sukiennicki
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- International Hereditary Cancer Centre, Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Yin Yao Shugart
- Unit of Statistical Genetics, Division of Intramural Research Program, National Institute of Mental Health, National Institute of Health, Bethesda, Maryland, United States of America
| | - Susan M. Domchek
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Richard Letrero
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Barbara L. Weber
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Frans B. L. Hogervorst
- Family Cancer Clinic, Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Matti A. Rookus
- Department of Epidemiology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - J. Margriet Collee
- Department of Clinical Genetics, Rotterdam Family Cancer Clinic, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Peter Devilee
- Department of Genetic Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Rob B. van der Luijt
- Department of Clinical Molecular Genetics, Utrecht University Medical Center, Utrecht, the Netherlands
| | - Cora M. Aalfs
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, the Netherlands
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Juul Wijnen
- Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - HEBON
- Hereditary Breast and Ovarian Cancer Group, the Netherlands
| | - EMBRACE
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Susan Peock
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Margaret Cook
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Clare Oliver
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | | | - D. Gareth Evans
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Fiona Lalloo
- Genetic Medicine, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom
| | - Rosalind Eeles
- The Oncogenetics Team, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, United Kingdom
| | - Louise Izatt
- Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Carol Chu
- Yorkshire Regional Genetics Service, St. James's Hospital, Leeds, United Kingdom
| | - Diana Eccles
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | - Fiona Douglas
- Institute of Human Genetics, Centre for Life, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, United Kingdom
| | - Carole Brewer
- Department of Clinical Genetics, Royal Devon & Exeter Hospital, Exeter, United Kingdom
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Tuomas Heikkinen
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Noralane M. Lindor
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Maria A. Caligo
- Section of Genetic Oncology, Department of Oncology, University of Pisa, and Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Grazia Lombardi
- Section of Genetic Oncology, Department of Oncology, University of Pisa, and Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Niklas Loman
- Department of Oncology, Lund University Hospital, Lund, Sweden
| | - Per Karlsson
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Hans Ehrencrona
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - SWE-BRCA
- Swedish Breast Cancer Study, Sweden
| | | | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Muhammad U. Rashid
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum, Heidelberg, Germany, and Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Adriana Lasa
- Genetic Service, Hospital de la Santa Creu i Sant Pau, Barcelona, Catalonia, Spain
| | - Trinidad Caldés
- Molecular Oncology Laboratory, Hospital Clínico San Carlos, Madrid, Spain
| | - Raquel Andrés
- Medical Oncology Division, Hospital Clínico de Zaragoza, Zaragoza, Spain
| | - Michael Schmitt
- Department of Internal Medicine III, University of Rostock, Rostock, Germany
| | - Volker Assmann
- Center for Experimental Medicine, Institute of Tumor Biology, University Hospital Hamburg–Eppendorf, Hamburg, Germany
| | - Kristen Stevens
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - João Curado
- Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG), Biomedical Research Park of Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Hagen Tilgner
- Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG), Biomedical Research Park of Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics Group, Centre for Genomic Regulation (CRG), Biomedical Research Park of Barcelona (PRBB), Barcelona, Catalonia, Spain
| | - Gemma Aiza
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Joan Brunet
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | - Joan Castellsagué
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | - Griselda Martrat
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Ander Urruticoechea
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
| | - Ignacio Blanco
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | | | - David E. Goldgar
- Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - Saundra Buys
- Department of Internal Medicine, Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, California, United States of America
| | - Alexander Miron
- Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Melissa Southey
- Centre for Molecular, Environmental, Genetic and Analytic (MEGA) Epidemiology, Melbourne School of Population Health, The University of Melbourne, Victoria, Australia
| | - Mary B. Daly
- Division of Population Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - BCFR
- Breast Cancer Family Registry, United States of America
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer and Center of Integrated Oncology, University of Cologne, Cologne, Germany
| | - Barbara Wappenschmidt
- Center for Familial Breast and Ovarian Cancer and Center of Integrated Oncology, University of Cologne, Cologne, Germany
| | - Alfons Meindl
- Department of Obstetrics and Gynaecology, Klinikum rechts der Isar, Technical University, Munich, Germany
| | - Norbert Arnold
- Division of Oncology, Department of Gynaecology and Obstetrics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Helmut Deissler
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | | | - Christian Sutter
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Dieter Niederacher
- Division of Molecular Genetics, Department of Gynaecology and Obstetrics, Clinical Center University of Düsseldorf, Düsseldorf, Germany
| | - Evgeny Imyamitov
- N. N. Petrov Institute of Oncology, Saint-Petersburg, Russian Federation
| | - Olga M. Sinilnikova
- Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Centre Hospitalier Universitaire de Lyon, Centre Léon Bérard, Lyon, France
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Dominique Stoppa-Lyonne
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Sylvie Mazoyer
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Carole Verny-Pierre
- Equipe labellisée LIGUE 2008, UMR5201 CNRS, Centre Léon Bérard, Université de Lyon, Lyon, France
| | - Laurent Castera
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Antoine de Pauw
- INSERM U509, Service de Génétique Oncologique, Institut Curie, Université Paris-Descartes, Paris, France
| | - Yves-Jean Bignon
- Département d'Oncogénétique, Centre Jean Perrin, Université de Clermont-Ferrand, Clermont-Ferrand, France
| | - Nancy Uhrhammer
- Département d'Oncogénétique, Centre Jean Perrin, Université de Clermont-Ferrand, Clermont-Ferrand, France
| | - Jean-Philippe Peyrat
- Laboratoire d'Oncologie Moléculaire Humaine, Centre Oscar Lambret, Lille, France
| | - Philippe Vennin
- Consultation d'Oncogénétique, Centre Oscar Lambret, Lille, France
| | - Sandra Fert Ferrer
- Laboratoire de Génétique Chromosomique, Hôtel Dieu Centre Hospitalier, Chambéry, France
| | - Marie-Agnès Collonge-Rame
- Service de Génétique-Histologie-Biologie du Développement et de la Reproduction, Centre Hospitalier Universitaire de Besançon, Besançon, France
| | | | - GEMO Study Collaborators
- GEMO Study (Genetics Network “Groupe Génétique et Cancer”), Fédération Nationale des Centres de Lutte Contre le Cancer, France
| | | | | | - Xiaoqing Chen
- Queensland Institute of Medical Research, Brisbane, Australia
| | - Sue Healey
- Queensland Institute of Medical Research, Brisbane, Australia
| | - kConFab
- The Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer, Peter MacCallum Cancer Institute, East Melbourne, Australia
| | - Mary Helen Barcellos-Hoff
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephen B. Gruber
- Department of Internal Medicine, Epidemiology, Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Conxi Lázaro
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | - Gabriel Capellá
- Genetic Counseling and Hereditary Cancer Programme, Catalan Institute of Oncology, IDIBELL and Girona Biomedical Research Institute (IdIBGi), Catalonia, Spain
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Katherine L. Nathanson
- Abramson Cancer Center, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | | | - Markus C. Fleisch
- Department of Obstetrics and Gynaecologie, Heinrich-Heine-University, Duesseldorf, Germany
| | - Víctor Moreno
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
| | - Miguel Angel Pujana
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Catalonia, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health, Spain
- Biomarkers and Susceptibility Unit, Catalan Institute of Oncology, IDIBELL, L'Hospitalet, Catalonia, Spain
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Maury Y, Gauthier M, Peschanski M, Martinat C. Human pluripotent stem cells for disease modelling and drug screening. Bioessays 2011; 34:61-71. [PMID: 22038777 DOI: 10.1002/bies.201100071] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Considerable hope surrounds the use of disease-specific pluripotent stem cells to generate models of human disease allowing exploration of pathological mechanisms and search for new treatments. Disease-specific human embryonic stem cells were the first to provide a useful source for studying certain disease states. The recent demonstration that human somatic cells, derived from readily accessible tissue such as skin or blood, can be converted to embryonic-like induced pluripotent stem cells (hiPSCs) has opened new perspectives for modelling and understanding a larger number of human pathologies. In this review, we examine the opportunities and challenges for the use of disease-specific pluripotent stem cells in disease modelling and drug screening. Progress in these areas will substantially accelerate effective application of disease-specific human pluripotent stem cells for drug screening.
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Millot GA, Berger A, Lejour V, Boulé JB, Bobo C, Cullin C, Lopes J, Stoppa-Lyonnet D, Nicolas A. Assessment of human Nter and Cter BRCA1 mutations using growth and localization assays in yeast. Hum Mutat 2011; 32:1470-80. [PMID: 21922593 DOI: 10.1002/humu.21608] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 08/18/2011] [Indexed: 11/05/2022]
Abstract
A large number of missense mutations have been identified within the tumor suppressor gene BRCA1. Most of them, called "variants of unknown significance" (VUS), cannot be classified as pathogenic or neutral by genetic methods, which complicates their cancer risk assessment. Functional assays have been developed to circumvent this uncertainty. They aim to determine how VUS impact the BRCA1 protein structure or function, thereby giving an indication of their potential to cause cancer. So far, three relevant assays have been designed in yeast and used on large sets of variants. However, they are limited to variants mapped in restricted domains of BRCA1. One of them, the small colony phenotype (SCP) assay, monitors the BRCA1-dependent growth of yeast colonies that increases with pathogenic but not neutral mutations positioned in the Cter region. Here, we extend this assay to the Nter part of BRCA1. We also designed a new assay, called the "yeast localization phenotype (YLP) assay," based on the accumulation of BRCA1 in a single inclusion body in the yeast nucleus. This phenotype is altered by variants positioned both in the Nter and Cter regions. Together, these assays provide new perspectives for the functional assessment of BRCA1 mutations in yeast.
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Affiliation(s)
- Gaël A Millot
- Institut Curie, Centre de Recherche, 26 rue d'Ulm, Paris, France.
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Chang S, Wang RH, Akagi K, Kim KA, Martin BK, Cavallone L, Haines DC, Basik M, Mai P, Poggi E, Isaacs C, Looi LM, Mun KS, Greene MH, Byers SW, Teo SH, Deng CX, Sharan SK. Tumor suppressor BRCA1 epigenetically controls oncogenic microRNA-155. Nat Med 2011; 17:1275-82. [PMID: 21946536 DOI: 10.1038/nm.2459] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 08/03/2011] [Indexed: 12/13/2022]
Abstract
BRCA1, a well-known tumor suppressor with multiple interacting partners, is predicted to have diverse biological functions. However, so far its only well-established role is in the repair of damaged DNA and cell cycle regulation. In this regard, the etiopathological study of low-penetrant variants of BRCA1 provides an opportunity to uncover its other physiologically important functions. Using this rationale, we studied the R1699Q variant of BRCA1, a potentially moderate-risk variant, and found that it does not impair DNA damage repair but abrogates the repression of microRNA-155 (miR-155), a bona fide oncomir. Mechanistically, we found that BRCA1 epigenetically represses miR-155 expression via its association with HDAC2, which deacetylates histones H2A and H3 on the miR-155 promoter. We show that overexpression of miR-155 accelerates but the knockdown of miR-155 attenuates the growth of tumor cell lines in vivo. Our findings demonstrate a new mode of tumor suppression by BRCA1 and suggest that miR-155 is a potential therapeutic target for BRCA1-deficient tumors.
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Affiliation(s)
- Suhwan Chang
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, USA
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Cantor SB, Guillemette S. Hereditary breast cancer and the BRCA1-associated FANCJ/BACH1/BRIP1. Future Oncol 2011; 7:253-61. [PMID: 21345144 DOI: 10.2217/fon.10.191] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
It is clear that FANCJ, also known as BACH1 or BRIP1, is an essential tumor suppressor gene based on the identification of clinically relevant mutations not only in breast cancer, but also the childhood cancer syndrome, Fanconi anemia. This conclusion is further supported by the direct and functional interaction between FANCJ and the hereditary breast cancer-associated gene product BRCA1. In the absence of the FANCJ DNA helicase or its interaction with BRCA1, cells have defects in several aspects of the DNA damage response. In particular, the BRCA1-FANCJ interaction is essential for promoting error-free repair, checkpoint control and for limiting DNA damage tolerance. As the number of FANCJ clinical mutations and affected patients accumulate, it will be critical to understand whether the associated tumors resemble BRCA-associated tumors. If so, FANCJ patients could also benefit from new therapies that selectively sensitize DNA repair-defective tumors and spare healthy cells. In this article, we summarize the breast cancer-associated FANCJ mutations and discuss functional outcomes for DNA repair and tumor suppression.
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Affiliation(s)
- Sharon B Cantor
- Department of Cancer Biology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA.
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A new assay for functional screening of BRCA2 linker region mutations identifies variants that alter chemoresistance to cisplatin. Exp Cell Res 2011; 317:2099-109. [PMID: 21741379 DOI: 10.1016/j.yexcr.2011.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 06/20/2011] [Accepted: 06/21/2011] [Indexed: 11/21/2022]
Abstract
Variants of unknown significance (VUS) complicate the assignment of risk to new DNA sequence variants found in at-risk populations. This study focused on the poorly studied linker region of the cancer-associated BRCA2 protein encoded by exons twelve through fourteen of BRCA2. To develop a new method to characterize VUS in this region of BRCA2, we first chose to study 4 reported VUS occurring on evolutionarily conserved residues within the linker region. To determine if these VUS represent neutral changes or if they impact the function of the BRCA2 protein, we stably transfected expression plasmids encoding wild-type or each mutant peptide into T47D breast cancer cells, which are wild-type for BRCA2. Four mutant peptide expressing cell lines and a wild-type linker region expressing cell line next were studied by challenging transfected cell lines with the DNA crosslinking compound cisplatin (10μM) for 5days. Expression of the wild-type linker region and certain mutant linker peptides (N2452D and I2285V) decreased apoptosis (as demonstrated by cell death detection assay) in transfected cell lines, indicating that the linker region peptide directly or indirectly affects the DNA damage repair pathway. By determining the cell survival and assaying the apoptotic index of treated cell lines, one could potentially use this screen to determine that a particular VUS has a functional impact on BRCA2 function, and hence is of functional significance. We conclude that this method is useful for screening the effect of linker region VUS on BRCA2 function, and to identify mutations for further testing. We also conclude that mutations in the linker region may have heretofore unappreciated roles in BRCA2 function.
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