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Fernandes VC, Golubeva VA, Di Pietro G, Shields C, Amankwah K, Nepomuceno TC, de Gregoriis G, Abreu RBV, Harro C, Gomes TT, Silva RF, Suarez-Kurtz G, Couch FJ, Iversen ES, Monteiro ANA, Carvalho MA. Impact of amino acid substitutions at secondary structures in the BRCT domains of the tumor suppressor BRCA1: Implications for clinical annotation. J Biol Chem 2019; 294:5980-5992. [PMID: 30765603 DOI: 10.1074/jbc.ra118.005274] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/06/2019] [Indexed: 01/07/2023] Open
Abstract
Genetic testing for BRCA1, a DNA repair protein, can identify carriers of pathogenic variants associated with a substantially increased risk for breast and ovarian cancers. However, an association with increased risk is unclear for a large fraction of BRCA1 variants present in the human population. Most of these variants of uncertain clinical significance lead to amino acid changes in the BRCA1 protein. Functional assays are valuable tools to assess the potential pathogenicity of these variants. Here, we systematically probed the effects of substitutions in the C terminus of BRCA1: the N- and C-terminal borders of its tandem BRCT domain, the BRCT-[N-C] linker region, and the α1 and α'1 helices in BRCT-[N] and -[C]. Using a validated transcriptional assay based on a fusion of the GAL4 DNA-binding domain to the BRCA1 C terminus (amino acids 1396-1863), we assessed the functional impact of 99 missense variants of BRCA1. We include the data obtained for these 99 missense variants in a joint analysis to generate the likelihood of pathogenicity for 347 missense variants in BRCA1 using VarCall, a Bayesian integrative statistical model. The results from this analysis increase our understanding of BRCA1 regions less tolerant to changes, identify functional borders of structural domains, and predict the likelihood of pathogenicity for 98% of all BRCA1 missense variants in this region recorded in the population. This knowledge will be critical for improving risk assessment and clinical treatment of carriers of BRCA1 variants.
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Affiliation(s)
- Vanessa C Fernandes
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Volha A Golubeva
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Giuliano Di Pietro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612; the Universidade Federal de Sergipe, Campus São Cristóvão, Brazil 49100-000
| | - Cara Shields
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Kwabena Amankwah
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Thales C Nepomuceno
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050; the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Giuliana de Gregoriis
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Renata B V Abreu
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Carly Harro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612; the Department of Cell Biology, Microbiology, College of Arts and Sciences, University of South Florida Cancer Biology Ph.D. Program, Tampa, Florida 33612
| | - Thiago T Gomes
- the Instituto Federal do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Ricceli F Silva
- the Instituto Federal do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Guilherme Suarez-Kurtz
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Fergus J Couch
- the Department of Laboratory Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Edwin S Iversen
- the Department of Statistics, Duke University, Durham, North Carolina 27710
| | - Alvaro N A Monteiro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612.
| | - Marcelo A Carvalho
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050.
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