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Yadegari F, Farahmand L, Esmaeili R, Zarinfam S, Majidzadeh-A K. Inter-BRCT linker is probably the most intolerant region of the BRCA1 BRCT domain. J Biomol Struct Dyn 2024; 42:5734-5746. [PMID: 37948190 DOI: 10.1080/07391102.2023.2274517] [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: 10/19/2022] [Accepted: 06/15/2023] [Indexed: 11/12/2023]
Abstract
Pathogenic mutations in BRCA1 are associated with an increased risk of hereditary breast, ovarian, and some other cancers; however, the clinical significance of many mutations in this gene remains unknown (Variants of Unknown Significance/VUS). Since mutations in intolerant regions of a protein lead to dysfunction and pathogenicity, identifying these regions helps to predict the clinical importance of VUSs. This study aimed to identify intolerant regions of BRCA1 and understand the possible root of this susceptibility. Intolerant regions appear to carry more pathogenic mutations than expected due to their lower tolerance to missense variations. Therefore, we hypothesized that among the BRCA1 regions, the higher the mutation density, the greater the intolerance. Thus, pathogenic mutation density and regional intolerance scores were calculated to identify BRCA1-intolerant regions. To investigate the pathogenic mechanisms of missense-intolerant regions in BRCA1, transcription activation (TA) experiments and molecular dynamics (MD) simulations were also performed. The results showed that the RING domain, followed by the BRCT domain, has the highest density of pathogenic mutations. In the BRCT domain, a higher density of pathogenic mutations was observed in the inter-BRCT linker. Additionally, scores generated by Missense Tolerance Ratio-3D (MTR3D) and the Missense Tolerance Ratio consensus (MTRX) showed that the inter-BRCT linker is more intolerant than other regions of the BRCT domain. The MD results showed that mutations in the inter-BRCT linker led to cancer susceptibility, likely due to disruption of the interaction between BRCA1 and phosphopeptides. TA laboratory assays further supported the importance of the inter-BRCT linker.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatemeh Yadegari
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Leila Farahmand
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Shiva Zarinfam
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Keivan Majidzadeh-A
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
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Yue W, Li X, Zhan X, Wang L, Ma J, Bi M, Wang Q, Gu X, Xie B, Liu T, Guo H, Zhu X, Song C, Qiao J, Li M. PARP inhibitors suppress tumours via centrosome error-induced senescence independent of DNA damage response. EBioMedicine 2024; 103:105129. [PMID: 38640836 PMCID: PMC11052917 DOI: 10.1016/j.ebiom.2024.105129] [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: 08/10/2023] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Poly(ADP-ribose) polymerase (PARP) inhibitors have emerged as promising chemotherapeutic drugs primarily against BRCA1/2-associated tumours, known as synthetic lethality. However, recent clinical trials reported patients' survival benefits from PARP inhibitor treatments, irrelevant to homologous recombination deficiency. Therefore, revealing the therapeutic mechanism of PARP inhibitors beyond DNA damage repair is urgently needed, which can facilitate precision medicine. METHODS A CRISPR-based knock-in technology was used to establish stable BRCA1 mutant cancer cells. The effects of PARP inhibitors on BRCA1 mutant cancer cells were evaluated by biochemical and cell biological experiments. Finally, we validated its in vivo effects in xenograft and patient-derived xenograft (PDX) tumour mice. FINDINGS In this study, we uncovered that the majority of clinical BRCA1 mutations in breast cancers were in and near the middle of the gene, rather than in essential regions for DNA damage repair. Representative mutations such as R1085I and E1222Q caused transient extra spindle poles during mitosis in cancer cells. PAR, which is synthesized by PARP2 but not PARP1 at mitotic centrosomes, clustered these transient extra poles, independent of DNA damage response. Common PARP inhibitors could effectively suppress PARP2-synthesized PAR and induce cell senescence by abrogating the correction of mitotic extra-pole error. INTERPRETATION Our findings uncover an alternative mechanism by which PARP inhibitors efficiently suppress tumours, thereby pointing to a potential new therapeutic strategy for centrosome error-related tumours. FUNDING Funded by National Natural Science Foundation of China (NSFC) (T2225006, 82272948, 82103106), Beijing Municipal Natural Science Foundation (Key program Z220011), and the National Clinical Key Specialty Construction Program, P. R. China (2023).
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Affiliation(s)
- Wei Yue
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xinyu Li
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xiaolu Zhan
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Lei Wang
- Centre for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China; Peking-Tsinghua Centre for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jihong Ma
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Meiyu Bi
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Qilong Wang
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xiaoyang Gu
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Bingteng Xie
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Tong Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150081, China
| | - Hongyan Guo
- National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xin Zhu
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Chen Song
- Centre for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China; Peking-Tsinghua Centre for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Mo Li
- State Key Laboratory of Female Fertility Promotion, Centre for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, 100191, China; National Clinical Research Centre for Obstetrics and Gynaecology (Peking University Third Hospital), Beijing, 100191, China; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
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Khan MA, Varma AK. In silico and structure-based assessment to classify VUS identified in the α-helical domain of BRCA2. J Biomol Struct Dyn 2023; 41:9879-9889. [PMID: 36404616 DOI: 10.1080/07391102.2022.2148127] [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: 06/16/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays a crucial role in DNA double-strand breaks repair mechanism by homologous recombination. Pathogenic mutations in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer (HBOC). Different missense mutations are identified from a larger cohort of patient populations in the BRCA2. However, most missense mutations are classified as 'Variants of Uncertain Significance' (VUS) due to a lack of data from structural, functional, and clinical assessments. Therefore, this study focused on assessing VUS identified in the α-helical domain of h-BRCA2 using different in silico tools and structure-based molecular dynamics simulation. A total of 286 identified VUS were evaluated using Align-GVGD, PROVEAN and PANTHER servers and 18 variants were predicted to be pathogenic. Further, out of 18 variants analyzed using the ConSurf server, 16 variants were found to be evolutionary conserved. These 16 conserved variants were submitted to PremPS and Dynamut server to assess the effect of the mutation at the protein structure level; 12 mutations were predicted to have a destabilizing effect on the native protein structure. Finally, molecular dynamics simulations revealed 5 variants BRCA2 Cys2646Tyr, Asp2665Val, Trp2619Arg, Trp2619Ser and Tyr2660Cys can alter the folding pattern and need further validation using in vitro, structural and in vivo studies to classify as pathogenic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mudassar Ali Khan
- Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Ashok K Varma
- Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai, Maharashtra, India
- Homi Bhabha National Institute, Mumbai, Maharashtra, India
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Regulation of DNA damage response by trimeric G-proteins. iScience 2023; 26:105973. [PMID: 36756378 PMCID: PMC9900518 DOI: 10.1016/j.isci.2023.105973] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 08/14/2022] [Accepted: 01/10/2023] [Indexed: 01/14/2023] Open
Abstract
Upon sensing DNA double-strand breaks (DSBs), eukaryotic cells either die or repair DSBs via one of the two competing pathways, i.e., non-homologous end-joining (NHEJ) or homologous recombination (HR). We show that cell fate after DSBs hinges on GIV/Girdin, a guanine nucleotide-exchange modulator of heterotrimeric Giα•βγ protein. GIV suppresses HR by binding and sequestering BRCA1, a key coordinator of multiple steps within the HR pathway, away from DSBs; it does so using a C-terminal motif that binds BRCA1's BRCT-modules via both phospho-dependent and -independent mechanisms. Using another non-overlapping C-terminal motif GIV binds and activates Gi and enhances the "free" Gβγ→PI-3-kinase→Akt pathway, which promotes survival and is known to suppress HR, favor NHEJ. Absence of GIV, or loss of either of its C-terminal motifs enhanced cell death upon genotoxic stress. Because GIV selectively binds other BRCT-containing proteins suggests that G-proteins may fine-tune sensing, repair, and survival after diverse types of DNA damage.
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5
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Nepomuceno TC, Dos Santos APP, Fernandes VC, Elias ABR, Gomes TT, Suarez-Kurtz G, Iversen ES, Couch FJ, Monteiro ANA, Carvalho MA. Assessment of small in-frame indels and C-terminal nonsense variants of BRCA1 using a validated functional assay. Sci Rep 2022; 12:16203. [PMID: 36171434 PMCID: PMC9519549 DOI: 10.1038/s41598-022-20500-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 09/14/2022] [Indexed: 11/29/2022] Open
Abstract
BRCA1 (Breast Cancer 1, early onset) is linked to breast and ovarian cancer predisposition. Still, the risks conferred by a significant portion of BRCA1 variants identified in the population remains unknown. Most of these variants of uncertain significance are missense alterations. However, the functional implications of small in-frame deletions and/or insertions (indels) are also difficult to predict. Our group has previously evaluated the functional impact of 347 missense variants using an extensively validated transcriptional activity assay. Here we show a systematic assessment of 30 naturally occurring in-frame indels located at the C-terminal region of BRCA1. We identified positions sensitive and tolerant to alterations, expanding the knowledge of structural determinants of BRCA1 function. We further designed and assessed the impact of four single codon deletions in the tBRCT linker region and six nonsense variants at the C-terminus end of BRCA1. Amino acid substitutions, deletions or insertions in the disordered region do not significantly impact activity and are not likely to constitute pathogenic alleles. On the other hand, a sizeable fraction of in-frame indels at the BRCT domain significantly impact function. We then use a Bayesian integrative statistical model to derive the probability of pathogenicity for each variant. Our data highlights the importance of assessing the impact of small in-frame indels in BRCA1 to improve risk assessment and clinical decisions for carriers.
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Affiliation(s)
- Thales C Nepomuceno
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil.,Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Ana P P Dos Santos
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Vanessa C Fernandes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Anna B R Elias
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Thiago T Gomes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Guilherme Suarez-Kurtz
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil
| | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, NC, 27708, USA
| | | | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA.
| | - Marcelo A Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, 20230-130, Brazil. .,Laboratório de Genética Molecular, Instituto Federal Do Rio de Janeiro, Rua Senador Furtado, Campus Rio de Janeiro121, Rio de Janeiro, RJ, 20270-021, Brazil.
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6
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Insights into the Possible Molecular Mechanisms of Resistance to PARP Inhibitors. Cancers (Basel) 2022; 14:cancers14112804. [PMID: 35681784 PMCID: PMC9179506 DOI: 10.3390/cancers14112804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The increasingly wide use of PARP inhibitors in breast, ovarian, pancreatic, and prostate cancers harbouring a pathogenic variant in BRCA1 or BRCA2 has highlighted the problem of resistance to therapy. This review summarises the complex interactions between PARP1, cell cycle regulation, response to stress replication, homologous recombination, and other DNA damage repair pathways in the setting of BRCA1/2 mutated cancers that could explain the development of primary or secondary resistance to PARP inhibitors. Abstract PARP1 enzyme plays an important role in DNA damage recognition and signalling. PARP inhibitors are approved in breast, ovarian, pancreatic, and prostate cancers harbouring a pathogenic variant in BRCA1 or BRCA2, where PARP1 inhibition results mainly in synthetic lethality in cells with impaired homologous recombination. However, the increasingly wide use of PARP inhibitors in clinical practice has highlighted the problem of resistance to therapy. Several different mechanisms of resistance have been proposed, although only the acquisition of secondary mutations in BRCA1/2 has been clinically proved. The aim of this review is to outline the key molecular findings that could explain the development of primary or secondary resistance to PARP inhibitors, analysing the complex interactions between PARP1, cell cycle regulation, PI3K/AKT signalling, response to stress replication, homologous recombination, and other DNA damage repair pathways in the setting of BRCA1/2 mutated cancers.
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7
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Khan MA, Siddiqui MQ, Kuligina E, Varma AK. Evaluation of conformational transitions of h-BRCA2 functional domain and unclassified variant Arg2502Cys using multimodal approach. Int J Biol Macromol 2022; 209:716-724. [PMID: 35413318 DOI: 10.1016/j.ijbiomac.2022.04.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022]
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein plays an essential role in the repair mechanism of DNA double-strand breaks and interstrand cross-links by Homologous recombination. Germline mutations identified in the BRCA2 gene confer an increased risk of hereditary breast and ovarian cancer. Missense mutations are identified all over the gene, including the DNA binding region of BRCA2 that interacts with FANCD2. However, the majority of these missense mutations are classified as 'Variants of Uncertain Significance' due to a lack of structural, functional and clinical correlations. Therefore, multi-disciplinary in-silico, in-vitro and biophysical approaches have been explored to characterize an unclassified missense mutation, BRCA2 Arg2502Cys, identified from a case-control study. Circular-dichroism and Fluorescence spectroscopy show that the Arg2502Cys mutation in hBRCA2 (residues 2350-2545) decreases the α-helical/β-sheet propensity of the wild-type protein and perturb the tertiary structure conformation. Molecular dynamics simulations revealed alteration in the intramolecular H-bonds, overall compactness and stability of the hydrophobic core were observed in the mutant protein. Principle component analysis indicated that Arg2502Cys mutant exhibited comparatively large conformational transitions and periodic fluctuation. Therefore, to our conclusion, BRCA2 Arg2502Cys mutant perturbed the structural integrity and conformational dynamics of BRCA2.
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Affiliation(s)
- Mudassar Ali Khan
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - M Quadir Siddiqui
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Present address: Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Ekaterina Kuligina
- N.N. Petrov Institute of Oncology, Laboratory of Molecular Oncology, RU-197758, Pesochny-2, St.-Petersburg, Russia
| | - Ashok K Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, Maharashtra 410210, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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8
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Saravanan R, Raja K, Shanthi D. GC-MS Analysis, Molecular Docking and Pharmacokinetic Properties of Phytocompounds from Solanum torvum Unripe Fruits and Its Effect on Breast Cancer Target Protein. Appl Biochem Biotechnol 2021; 194:529-555. [PMID: 34643844 PMCID: PMC8760204 DOI: 10.1007/s12010-021-03698-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/04/2021] [Indexed: 01/22/2023]
Abstract
This study was designed to identify phytocompounds from the aqueous extract of Solanum torvum unripe fruits using GC–MS analysis against breast cancer. For this, the identified phytocompounds were subjected to perform molecular docking studies to find the effects on breast cancer target protein. Pharmacokinetic properties were also tested for the identified phytocompounds to evaluate the ADMET properties. Molecular docking studies were done using docking software PyRx, and pharmacokinetic properties of phytocompounds were evaluated using SwissADME. From the results, ten best compounds were identified from GC–MS analysis against breast cancer target protein. Of which, three compounds showed very good binding affinity with breast cancer target protein. They are ergost-25-ene-3,6-dione,5,12-dihydroxy-,(5.alpha.,12.beta.) (− 7.3 kcal/mol), aspidospermidin-17-ol,1-acetyl-16-methoxy (− 6.7 kcal/mol) and 2-(3,4-dichlorophenyl)-4-[[2-[1-methyl-2-pyrrolidinyl]ethyl amino]-6-[trichloromethyl]-s-triazine (− 6.7 kcal/mol). Further, docking study was performed for the synthetic drug doxorubicin to compare the efficiency of phytocompounds. The binding affinity of ergost-25-ene-3,6-dione,5,12-dihydroxy-,(5.alpha.,12.beta.) is higher than the synthetic drug doxorubicin (− 7.2 kcal/mol), and the binding affinity of other compounds is also very near to the drug. Hence, the present study concludes that the phytocompounds from the aqueous extract of Solanum torvum unripe fruits have the potential ability to treat breast cancer.
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Affiliation(s)
- R Saravanan
- Post Graduate and Research Department of Zoology, Dr. Ambedkar Government Arts College, Vyasarpadi, Chennai, 600 039, Tamil Nadu, India.
| | - K Raja
- Post Graduate and Research Department of Zoology, Dr. Ambedkar Government Arts College, Vyasarpadi, Chennai, 600 039, Tamil Nadu, India
| | - D Shanthi
- Post Graduate and Research Department of Zoology, Dr. Ambedkar Government Arts College, Vyasarpadi, Chennai, 600 039, Tamil Nadu, India
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9
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Abd El-hafeez AA, Sun N, Chakraborty A, Ear J, Roy S, Chamarthi P, Rajapakse N, Das S, Luker KE, Hazra TK, Luker GD, Ghosh P. Regulation of DNA damage response by trimeric G-protein Signaling.. [DOI: 10.1101/2021.07.21.452842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractUpon sensing DNA double-strand breaks (DSBs), eukaryotic cells either die or repair DSBs via one of two competing pathways, i.e., non-homologous end-joining (NHEJ) or homologous recombination (HR). We show that cell fate after DNA damage hinges on the guanine nucleotide-exchange modulator of heterotrimeric G-protein, Giα•βγ, GIV/Girdin. GIV suppresses HR by binding and sequestering BRCA1, a key coordinator of multiple steps within the HR pathway, away from DSBs; it does so using a C-terminal motif that binds BRCA1’s BRCT-modules via both phospho-dependent and -independent mechanisms. GIV promotes NHEJ, and binds and activates Gi and enhances the ‘free’ Gβγ→PI-3-kinase→Akt pathway, thus revealing the enigmatic origin of prosurvival Akt signals during dsDNA repair. Absence of GIV, or the loss of either of its two functions impaired DNA repair, and induced cell death when challenged with numerous cytotoxic agents. That GIV selectively binds few other BRCT-containing proteins suggests convergent signaling such that heterotrimeric G-proteins may finetune sensing, repair, and outcome after DNA damage.GRAPHIC ABSTRACTHIGHLIGHTSNon-receptor G protein modulator, GIV/Girdin binds BRCA1Binding occurs in both canonical and non-canonical modesGIV sequesters BRCA1 away from dsDNA breaks, suppresses HRActivation of Gi by GIV enhances Akt signals, favors NHEJIN BRIEFIn this work, the authors show that heterotrimeric G protein signaling that is triggered by non-receptor GEF, GIV/Girdin, in response to double-stranded DNA breaks is critical for decisive signaling events which favor non-homologous end-joining (NHEJ) and inhibit homologous recombination (HR).
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Abstract
PURPOSE OF REVIEW To summarize recently discovered PARP inhibitor resistance mechanisms and highlight the clinical relevance of these findings to date. RECENT FINDINGS A predominant mechanism of acquired PARP inhibitor resistance in homologous recombination-deficient cancers is the acquisition of homologous recombination proficiency as a consequence of secondary genetic or epigenetic events, such as secondary mutations in BRCA1 or BRCA2, or reversal of BRCA1 promoter methylation that restores homologous recombination and leads to PARP inhibitor resistance. Multiple other potential mechanisms of acquired resistance to PARP inhibitors including loss of DNA end resection inhibition (53BP1/REV7/RIF1/Sheldin) or DNA replication fork protection (PTIP/EZH2), but also increased drug efflux or induction of a reversible senescent or mesenchymal cell state have been described in ovarian cancer models. However, only few of these mechanisms have been identified in clinical samples. SUMMARY Multiple adaptive responses following PARP inhibitor treatment have been identified. Further research is needed to better understand what role these mechanisms play for clinical PARP inhibitor resistance and how these mechanisms may render ovarian cancer cells susceptible to subsequent novel combination therapies.
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Petrosino M, Novak L, Pasquo A, Chiaraluce R, Turina P, Capriotti E, Consalvi V. Analysis and Interpretation of the Impact of Missense Variants in Cancer. Int J Mol Sci 2021; 22:ijms22115416. [PMID: 34063805 PMCID: PMC8196604 DOI: 10.3390/ijms22115416] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/17/2021] [Indexed: 01/10/2023] Open
Abstract
Large scale genome sequencing allowed the identification of a massive number of genetic variations, whose impact on human health is still unknown. In this review we analyze, by an in silico-based strategy, the impact of missense variants on cancer-related genes, whose effect on protein stability and function was experimentally determined. We collected a set of 164 variants from 11 proteins to analyze the impact of missense mutations at structural and functional levels, and to assess the performance of state-of-the-art methods (FoldX and Meta-SNP) for predicting protein stability change and pathogenicity. The result of our analysis shows that a combination of experimental data on protein stability and in silico pathogenicity predictions allowed the identification of a subset of variants with a high probability of having a deleterious phenotypic effect, as confirmed by the significant enrichment of the subset in variants annotated in the COSMIC database as putative cancer-driving variants. Our analysis suggests that the integration of experimental and computational approaches may contribute to evaluate the risk for complex disorders and develop more effective treatment strategies.
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Affiliation(s)
- Maria Petrosino
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Leonore Novak
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Alessandra Pasquo
- ENEA CR Frascati, Diagnostics and Metrology Laboratory FSN-TECFIS-DIM, 00044 Frascati, Italy;
| | - Roberta Chiaraluce
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
| | - Paola Turina
- Dipartimento di Farmacia e Biotecnologie (FaBiT), University of Bologna, 40126 Bologna, Italy;
| | - Emidio Capriotti
- Dipartimento di Farmacia e Biotecnologie (FaBiT), University of Bologna, 40126 Bologna, Italy;
- Correspondence: (E.C.); (V.C.)
| | - Valerio Consalvi
- Dipartimento Scienze Biochimiche “A. Rossi Fanelli”, Sapienza University of Rome, 00185 Roma, Italy; (M.P.); (L.N.); (R.C.)
- Correspondence: (E.C.); (V.C.)
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12
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Zhang J, Yan Z, Wang Y, Wang Y, Guo X, Jing J, Dong X, Dong S, Liu X, Yu X, Wu C. Cancer-associated 53BP1 mutations induce DNA damage repair defects. Cancer Lett 2020; 501:43-54. [PMID: 33359708 DOI: 10.1016/j.canlet.2020.12.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/29/2022]
Abstract
TP53 binding protein 1 (53BP1) plays an important role in DNA damage repair and maintaining genomic stability. However, the mutations of 53BP1 in human cancers have not been systematically examined. Here, we have analyzed 541 somatic mutations of 53BP1 across 34 types of human cancer from databases of The Cancer Genome Atlas, International Cancer Genome Consortium and Catalogue of Somatic Mutations in Cancer. Among these cancer-associated 53BP1 mutations, truncation mutations disrupt the nuclear localization of 53BP1 thus abolish its biological functions in DNA damage repair. Moreover, with biochemical analyses and structural modeling, we have examined the detailed molecular mechanism by which missense mutations in the key domains causes the DNA damage repair defects. Taken together, our results reveal the functional defects of a set of cancer-associated 53BP1 mutations.
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Affiliation(s)
- Jiajia Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Zhenzhen Yan
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Yukun Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Yaguang Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xin Guo
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Ju Jing
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xiangnan Dong
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Shasha Dong
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xiuhua Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China.
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.
| | - Chen Wu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China.
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13
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Le Page C, Amuzu S, Rahimi K, Gotlieb W, Ragoussis J, Tonin PN. Lessons learned from understanding chemotherapy resistance in epithelial tubo-ovarian carcinoma from BRCA1and BRCA2mutation carriers. Semin Cancer Biol 2020; 77:110-126. [PMID: 32827632 DOI: 10.1016/j.semcancer.2020.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 02/07/2023]
Abstract
BRCA1 and BRCA2 are multi-functional proteins and key factors for maintaining genomic stability through their roles in DNA double strand break repair by homologous recombination, rescuing stalled or damaged DNA replication forks, and regulation of cell cycle DNA damage checkpoints. Impairment of any of these critical roles results in genomic instability, a phenotypic hallmark of many cancers including breast and epithelial ovarian carcinomas (EOC). Damaging, usually loss of function germline and somatic variants in BRCA1 and BRCA2, are important drivers of the development, progression, and management of high-grade serous tubo-ovarian carcinoma (HGSOC). However, mutations in these genes render patients particularly sensitive to platinum-based chemotherapy, and to the more innovative targeted therapies with poly-(ADP-ribose) polymerase inhibitors (PARPis) that are targeted to BRCA1/BRCA2 mutation carriers. Here, we reviewed the literature on the responsiveness of BRCA1/2-associated HGSOC to platinum-based chemotherapy and PARPis, and propose mechanisms underlying the frequent development of resistance to these therapeutic agents.
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Affiliation(s)
- Cécile Le Page
- McGill Research Institute of the McGill University Health Center, Montreal, QC, Canada.
| | - Setor Amuzu
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Kurosh Rahimi
- Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Walter Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University, Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
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14
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Krais JJ, Johnson N. BRCA1 Mutations in Cancer: Coordinating Deficiencies in Homologous Recombination with Tumorigenesis. Cancer Res 2020; 80:4601-4609. [PMID: 32747362 PMCID: PMC7641968 DOI: 10.1158/0008-5472.can-20-1830] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/15/2020] [Accepted: 07/29/2020] [Indexed: 01/08/2023]
Abstract
Cancers that arise from BRCA1 germline mutations are deficient for homologous recombination (HR) DNA repair and are sensitive to DNA-damaging agents such as platinum and PARP inhibitors. In vertebrate organisms, knockout of critical HR genes including BRCA1 and BRCA2 is lethal because HR is required for genome replication. Thus, cancers must develop strategies to cope with loss of HR activity. Furthermore, as established tumors respond to chemotherapy selection pressure, additional genetic adaptations transition cancers to an HR-proficient state. In this review, we discuss biological mechanisms that influence the ability of BRCA1-mutant cancers to perform HR. Furthermore, we consider how the HR status fluctuates throughout the cancer life course, from tumor initiation to the development of therapy refractory disease.
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Affiliation(s)
- John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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15
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Lee EK, Matulonis UA. PARP Inhibitor Resistance Mechanisms and Implications for Post-Progression Combination Therapies. Cancers (Basel) 2020; 12:E2054. [PMID: 32722408 PMCID: PMC7465003 DOI: 10.3390/cancers12082054] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022] Open
Abstract
The use of PARP inhibitors (PARPi) is growing widely as FDA approvals have shifted its use from the recurrence setting to the frontline setting. In parallel, the population developing PARPi resistance is increasing. Here we review the role of PARP, DNA damage repair, and synthetic lethality. We discuss mechanisms of resistance to PARP inhibition and how this informs on novel combinations to re-sensitize cancer cells to PARPi.
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Affiliation(s)
- Elizabeth K. Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA;
| | - Ursula A. Matulonis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA;
- Division of Gynecologic Oncology, Dana-Farber Cancer Institute, Boston, MA 02215-5450, USA
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16
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Liu W, Palovcak A, Li F, Zafar A, Yuan F, Zhang Y. Fanconi anemia pathway as a prospective target for cancer intervention. Cell Biosci 2020; 10:39. [PMID: 32190289 PMCID: PMC7075017 DOI: 10.1186/s13578-020-00401-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fanconi anemia (FA) is a recessive genetic disorder caused by biallelic mutations in at least one of 22 FA genes. Beyond its pathological presentation of bone marrow failure and congenital abnormalities, FA is associated with chromosomal abnormality and genomic instability, and thus represents a genetic vulnerability for cancer predisposition. The cancer relevance of the FA pathway is further established with the pervasive occurrence of FA gene alterations in somatic cancers and observations of FA pathway activation-associated chemotherapy resistance. In this article we describe the role of the FA pathway in canonical interstrand crosslink (ICL) repair and possible contributions of FA gene alterations to cancer development. We also discuss the perspectives and potential of targeting the FA pathway for cancer intervention.
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Affiliation(s)
- Wenjun Liu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Anna Palovcak
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fang Li
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Alyan Zafar
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fenghua Yuan
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Yanbin Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
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17
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Wang Y, Bernhardy AJ, Nacson J, Krais JJ, Tan YF, Nicolas E, Radke MR, Handorf E, Llop-Guevara A, Balmaña J, Swisher EM, Serra V, Peri S, Johnson N. BRCA1 intronic Alu elements drive gene rearrangements and PARP inhibitor resistance. Nat Commun 2019; 10:5661. [PMID: 31827092 PMCID: PMC6906494 DOI: 10.1038/s41467-019-13530-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/14/2019] [Indexed: 12/28/2022] Open
Abstract
BRCA1 mutant carcinomas are sensitive to PARP inhibitor (PARPi) therapy; however, resistance arises. BRCA1 BRCT domain mutant proteins do not fold correctly and are subject to proteasomal degradation, resulting in PARPi sensitivity. In this study, we show that cell lines and patient-derived tumors, with highly disruptive BRCT domain mutations, have readily detectable BRCA1 protein expression, and are able to proliferate in the presence of PARPi. Peptide analyses reveal that chemo-resistant cancers contain residues encoded by BRCA1 intron 15. Mechanistically, cancers with BRCT domain mutations harbor BRCA1 gene breakpoints within or adjacent to Alu elements in intron 15; producing partial gene duplications, inversions and translocations, and terminating transcription prior to the mutation-containing BRCT domain. BRCA1 BRCT domain-deficient protein isoforms avoid mutation-induced proteasomal degradation, support homology-dependent DNA repair, and promote PARPi resistance. Taken together, Alu-mediated BRCA1 gene rearrangements are responsible for generating hypomorphic proteins, and may represent a biomarker of PARPi resistance.
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Affiliation(s)
- Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Andrea J Bernhardy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Joseph Nacson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, 19111, USA
| | - John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Yin-Fei Tan
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Emmanuelle Nicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Genomics Facility, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Marc R Radke
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Elizabeth Handorf
- Bioinformatics and Statistics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Alba Llop-Guevara
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Suraj Peri
- Bioinformatics and Statistics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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18
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Cao Y, Sun Y, Karimi M, Chen H, Moronfoye O, Shen Y. Predicting pathogenicity of missense variants with weakly supervised regression. Hum Mutat 2019; 40:1579-1592. [PMID: 31144781 PMCID: PMC6744350 DOI: 10.1002/humu.23826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/23/2019] [Accepted: 05/27/2019] [Indexed: 12/27/2022]
Abstract
Quickly growing genetic variation data of unknown clinical significance demand computational methods that can reliably predict clinical phenotypes and deeply unravel molecular mechanisms. On the platform enabled by the Critical Assessment of Genome Interpretation (CAGI), we develop a novel "weakly supervised" regression (WSR) model that not only predicts precise clinical significance (probability of pathogenicity) from inexact training annotations (class of pathogenicity) but also infers underlying molecular mechanisms in a variant-specific manner. Compared to multiclass logistic regression, a representative multiclass classifier, our kernelized WSR improves the performance for the ENIGMA Challenge set from 0.72 to 0.97 in binary area under the receiver operating characteristic curve (AUC) and from 0.64 to 0.80 in ordinal multiclass AUC. WSR model interpretation and protein structural interpretation reach consensus in corroborating the most probable molecular mechanisms by which some pathogenic BRCA1 variants confer clinical significance, namely metal-binding disruption for p.C44F and p.C47Y, protein-binding disruption for p.M18T, and structure destabilization for p.S1715N.
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Affiliation(s)
- Yue Cao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Mostafa Karimi
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Haoran Chen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Oluwaseyi Moronfoye
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, 77843-3128, United States
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19
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Wang Y, Bernhardy AJ, Cruz C, Krais JJ, Nacson J, Nicolas E, Peri S, van der Gulden H, van der Heijden I, O'Brien SW, Zhang Y, Harrell MI, Johnson SF, Candido Dos Reis FJ, Pharoah PDP, Karlan B, Gourley C, Lambrechts D, Chenevix-Trench G, Olsson H, Benitez JJ, Greene MH, Gore M, Nussbaum R, Sadetzki S, Gayther SA, Kjaer SK, D'Andrea AD, Shapiro GI, Wiest DL, Connolly DC, Daly MB, Swisher EM, Bouwman P, Jonkers J, Balmaña J, Serra V, Johnson N. The BRCA1-Δ11q Alternative Splice Isoform Bypasses Germline Mutations and Promotes Therapeutic Resistance to PARP Inhibition and Cisplatin. Cancer Res 2017; 76:2778-90. [PMID: 27197267 DOI: 10.1158/0008-5472.can-16-0186] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/15/2016] [Indexed: 12/19/2022]
Abstract
Breast and ovarian cancer patients harboring BRCA1/2 germline mutations have clinically benefitted from therapy with PARP inhibitor (PARPi) or platinum compounds, but acquired resistance limits clinical impact. In this study, we investigated the impact of mutations on BRCA1 isoform expression and therapeutic response. Cancer cell lines and tumors harboring mutations in exon 11 of BRCA1 express a BRCA1-Δ11q splice variant lacking the majority of exon 11. The introduction of frameshift mutations to exon 11 resulted in nonsense-mediated mRNA decay of full-length, but not the BRCA1-Δ11q isoform. CRISPR/Cas9 gene editing as well as overexpression experiments revealed that the BRCA1-Δ11q protein was capable of promoting partial PARPi and cisplatin resistance relative to full-length BRCA1, both in vitro and in vivo Furthermore, spliceosome inhibitors reduced BRCA1-Δ11q levels and sensitized cells carrying exon 11 mutations to PARPi treatment. Taken together, our results provided evidence that cancer cells employ a strategy to remove deleterious germline BRCA1 mutations through alternative mRNA splicing, giving rise to isoforms that retain residual activity and contribute to therapeutic resistance. Cancer Res; 76(9); 2778-90. ©2016 AACR.
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Affiliation(s)
- Yifan Wang
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Andrea J Bernhardy
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Cristina Cruz
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain. Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - John J Krais
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Joseph Nacson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Emmanuelle Nicolas
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Suraj Peri
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | | | - Shane W O'Brien
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yong Zhang
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Maribel I Harrell
- Department of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, Washington
| | - Shawn F Johnson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Francisco J Candido Dos Reis
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Sao Paulo, Brazil. Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, United Kingdom
| | - Beth Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Charlie Gourley
- University of Edinburgh Cancer Research UK Centre, MRC IGMM, Edinburgh, United Kingdom
| | | | | | - Håkan Olsson
- Departments of Cancer Epidemiology and Oncology, Lund University, Lund, Sweden
| | - Javier J Benitez
- Human Genetics Group and Human Genotyping Unit Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark H Greene
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Martin Gore
- Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Robert Nussbaum
- University of California San Francisco, Cancer Risk Program, San Francisco, California
| | - Siegal Sadetzki
- Gertner Institute for Epidemiology and Health Policy Research, Sheba Medical Center, Tel Hashomer, Israel
| | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Susanne K Kjaer
- Department of Virus, Lifestyle and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. Department of Pediatrics, Children's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts. Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David L Wiest
- Immune Cell Development and Host Defense Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Denise C Connolly
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Mary B Daly
- Risk Assessment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, Washington
| | - Peter Bouwman
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jos Jonkers
- Division of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Neil Johnson
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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20
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Al-Eitan LN, Jamous RI, Khasawneh RH. Candidate Gene Analysis of Breast Cancer in the Jordanian Population of Arab Descent: A Case-Control Study. Cancer Invest 2017; 35:256-270. [PMID: 28272917 DOI: 10.1080/07357907.2017.1289217] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
This study aimed to investigate whether there are specific polymorphisms within six genes (BRCA1, BRCA2, TP53, DAPK1, MMP9 promoter, and TOX3) that are associated with breast cancer among the Jordanian population. Sequenom MassARRAY system was used to genotype 17 single nucleotide polymorphisms (SNPs) within these genes in 230 Jordanian breast cancer patients and 225 healthy individuals. Three SNPs (MMP9 (rs6065912), TOX3 (rs1420546), and DAPK1 (rs11141901) were found to be significantly associated with an increased risk of breast cancer (p < .05). This study is the first to provide evidence that genetic variation in MMP9, TOX3, and DAPK1 genes contribute to the development of breast cancer in the Jordanian population.
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Affiliation(s)
- Laith N Al-Eitan
- a Department of Applied Biological Sciences , Jordan University of Science and Technology , Irbid , Jordan.,b Department of Biotechnology and Genetic Engineering , Jordan University of Science and Technology , Irbid , Jordan
| | - Reem I Jamous
- a Department of Applied Biological Sciences , Jordan University of Science and Technology , Irbid , Jordan.,b Department of Biotechnology and Genetic Engineering , Jordan University of Science and Technology , Irbid , Jordan
| | - Rame H Khasawneh
- c Department of Hematopathology, King Hussein Medical Center (KHMC) , Jordan Royal Medical Services (RMS) , Amman , Jordan
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21
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Thirumal Kumar D, George Priya Doss C. Role of E542 and E545 missense mutations of PIK3CA in breast cancer: a comparative computational approach. J Biomol Struct Dyn 2016; 35:2745-2757. [DOI: 10.1080/07391102.2016.1231082] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- D. Thirumal Kumar
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
| | - C. George Priya Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
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22
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New concepts on BARD1: Regulator of BRCA pathways and beyond. Int J Biochem Cell Biol 2016; 72:1-17. [DOI: 10.1016/j.biocel.2015.12.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 01/09/2023]
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23
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Wu Q, Paul A, Su D, Mehmood S, Foo TK, Ochi T, Bunting EL, Xia B, Robinson CV, Wang B, Blundell TL. Structure of BRCA1-BRCT/Abraxas Complex Reveals Phosphorylation-Dependent BRCT Dimerization at DNA Damage Sites. Mol Cell 2016; 61:434-448. [PMID: 26778126 PMCID: PMC4747905 DOI: 10.1016/j.molcel.2015.12.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/22/2015] [Accepted: 12/09/2015] [Indexed: 01/22/2023]
Abstract
BRCA1 accumulation at DNA damage sites is an important step for its function in the DNA damage response and in DNA repair. BRCA1-BRCT domains bind to proteins containing the phosphorylated serine-proline-x-phenylalanine (pSPxF) motif including Abraxas, Bach1/FancJ, and CtIP. In this study, we demonstrate that ionizing radiation (IR)-induces ATM-dependent phosphorylation of serine 404 (S404) next to the pSPxF motif. Crystal structures of BRCT/Abraxas show that phosphorylation of S404 is important for extensive interactions through the N-terminal sequence outside the pSPxF motif and leads to formation of a stable dimer. Mutation of S404 leads to deficiency in BRCA1 accumulation at DNA damage sites and cellular sensitivity to IR. In addition, two germline mutations of BRCA1 are found to disrupt the dimer interface and dimer formation. Thus, we demonstrate a mechanism involving IR-induced phosphorylation and dimerization of the BRCT/Abraxas complex for regulating Abraxas-mediated recruitment of BRCA1 in response to IR.
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Affiliation(s)
- Qian Wu
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Atanu Paul
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Genes and Development Program, The University of Texas Graduate School of Biomedical Sciences at Houston, 6767 Bertner Avenue, Houston, TX 77030, USA
| | - Dan Su
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Shahid Mehmood
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, OX1 3QZ Oxford, UK
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Takashi Ochi
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Emma L Bunting
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK
| | - Bing Xia
- Department of Radiation Oncology, Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, 195 Little Albany Street, New Brunswick, NJ 08903, USA
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, OX1 3QZ Oxford, UK
| | - Bin Wang
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Genes and Development Program, The University of Texas Graduate School of Biomedical Sciences at Houston, 6767 Bertner Avenue, Houston, TX 77030, USA.
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK.
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Coluccio ML, Gentile F, Das G, Nicastri A, Perri AM, Candeloro P, Perozziello G, Proietti Zaccaria R, Gongora JST, Alrasheed S, Fratalocchi A, Limongi T, Cuda G, Di Fabrizio E. Detection of single amino acid mutation in human breast cancer by disordered plasmonic self-similar chain. SCIENCE ADVANCES 2015; 1:e1500487. [PMID: 26601267 PMCID: PMC4643778 DOI: 10.1126/sciadv.1500487] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/13/2015] [Indexed: 05/15/2023]
Abstract
Control of the architecture and electromagnetic behavior of nanostructures offers the possibility of designing and fabricating sensors that, owing to their intrinsic behavior, provide solutions to new problems in various fields. We show detection of peptides in multicomponent mixtures derived from human samples for early diagnosis of breast cancer. The architecture of sensors is based on a matrix array where pixels constitute a plasmonic device showing a strong electric field enhancement localized in an area of a few square nanometers. The method allows detection of single point mutations in peptides composing the BRCA1 protein. The sensitivity demonstrated falls in the picomolar (10(-12) M) range. The success of this approach is a result of accurate design and fabrication control. The residual roughness introduced by fabrication was taken into account in optical modeling and was a further contributing factor in plasmon localization, increasing the sensitivity and selectivity of the sensors. This methodology developed for breast cancer detection can be considered a general strategy that is applicable to various pathologies and other chemical analytical cases where complex mixtures have to be resolved in their constitutive components.
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Affiliation(s)
- Maria Laura Coluccio
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Francesco Gentile
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
- Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125, Italy
| | - Gobind Das
- Physical Sciences and Engineering (PSE) and Biological and Environment Science and Engineering Divisions (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Annalisa Nicastri
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Angela Mena Perri
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Patrizio Candeloro
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Gerardo Perozziello
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | | | - Juan Sebastian Totero Gongora
- PRIMALIGHT, Electrical Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Salma Alrasheed
- Physical Sciences and Engineering (PSE) and Biological and Environment Science and Engineering Divisions (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Andrea Fratalocchi
- PRIMALIGHT, Electrical Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Tania Limongi
- Physical Sciences and Engineering (PSE) and Biological and Environment Science and Engineering Divisions (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Giovanni Cuda
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
| | - Enzo Di Fabrizio
- Bio-Nanotechnology and Engineering for Medicine (BIONEM), Department of Experimental and Clinical Medicine, University of Magna Graecia Viale Europa, Germaneto, Catanzaro 88100, Italy
- Physical Sciences and Engineering (PSE) and Biological and Environment Science and Engineering Divisions (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
- Corresponding author. E-mail:
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25
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Biunno I, Aceto G, Awadelkarim KD, Morgano A, Elhaj A, Eltayeb EA, Abuidris DO, Elwali NE, Spinelli C, De Blasio P, Rovida E, Mariani-Costantini R. BRCA1 point mutations in premenopausal breast cancer patients from Central Sudan. Fam Cancer 2015; 13:437-44. [PMID: 24729269 DOI: 10.1007/s10689-014-9717-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Premenopausal breast cancer (BC) is one of the most common cancers of women in rural Africa and part of the disease load may be related to hereditary predisposition, including mutations in the BRCA1 gene. However, the BRCA1 mutations associated with BC in Africa are scarcely characterized. We report here 33 BRCA1 point mutations, among which 2 novel missense variants, found in 59 Central Sudanese premenopausal BC patients. The high fractions of mutations with intercontinental and uniquely African distribution (17/33, 51.5 % and 14/33, 42.4 %, respectively) are in agreement with the high genetic diversity expected in an African population. Overall 24/33 variants (72.7 %) resulted neutral; 8/33 of unknown significance (24.3 %, including the 2 novel missense mutations); 1 (3.0 %) overtly deleterious. Notably, in silico studies predict that the novel C-terminal missense variant c.5090G>A (p.Cys1697Tyr) affects phosphopeptide recognition by the BRCA1 BRCT1 domain and may have a pathogenic impact. Genetic variation and frequency of unique or rare mutations of uncertain clinical relevance pose significant challenges to BRCA1 testing in Sudan, as it might happen in other low-resource rural African contexts.
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Affiliation(s)
- Ida Biunno
- Institute for Genetic and Biomedical Research, National Research Council, Via Fantoli 16/15, 20138, Milan, Italy
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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: 561] [Impact Index Per Article: 62.3] [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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27
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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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BRCA genetic screening in Middle Eastern and North African: mutational spectrum and founder BRCA1 mutation (c.798_799delTT) in North African. DISEASE MARKERS 2015; 2015:194293. [PMID: 25814778 PMCID: PMC4359853 DOI: 10.1155/2015/194293] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/16/2015] [Accepted: 01/26/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND The contribution of BRCA1 mutations to both hereditary and sporadic breast and ovarian cancer (HBOC) has not yet been thoroughly investigated in MENA. METHODS To establish the knowledge about BRCA1 mutations and their correlation with the clinical aspect in diagnosed cases of HBOC in MENA populations. A systematic review of studies examining BRCA1 in BC women in Cyprus, Jordan, Egypt, Lebanon, Morocco, Algeria, and Tunisia was conducted. RESULTS Thirteen relevant references were identified, including ten studies which performed DNA sequencing of all BRCA1 exons. For the latter, 31 mutations were detected in 57 of the 547 patients ascertained. Familial history of BC was present in 388 (71%) patients, of whom 50 were mutation carriers. c.798_799delTT was identified in 11 North African families, accounting for 22% of total identified BRCA1 mutations, suggesting a founder allele. A broad spectrum of other mutations including c.68_69delAG, c.181T>G, c.5095C>T, and c.5266dupC, as well as sequence of unclassified variants and polymorphisms, was also detected. CONCLUSION The knowledge of genetic structure of BRCA1 in MENA should contribute to the assessment of the necessity of preventive programs for mutation carriers and clinical management. The high prevalence of BC and the presence of frequent mutations of the BRCA1 gene emphasize the need for improving screening programs and individual testing/counseling.
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29
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Wu Q, Jubb H, Blundell TL. Phosphopeptide interactions with BRCA1 BRCT domains: More than just a motif. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:143-148. [PMID: 25701377 PMCID: PMC4728184 DOI: 10.1016/j.pbiomolbio.2015.02.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 01/05/2015] [Accepted: 02/10/2015] [Indexed: 01/15/2023]
Abstract
BRCA1 BRCT domains function as phosphoprotein-binding modules for recognition of the phosphorylated protein-sequence motif pSXXF. While the motif interaction interface provides strong anchor points for binding, protein regions outside the motif have recently been found to be important for binding affinity. In this review, we compare the available structural data for BRCA1 BRCT domains in complex with phosphopeptides in order to gain a more complete understanding of the interaction between phosphopeptides and BRCA1-BRCT domains.
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Affiliation(s)
- Qian Wu
- Department of Biochemistry, 80 Tennis Court Road, University of Cambridge, CB2 1GA, Cambridge, United Kingdom.
| | - Harry Jubb
- Department of Biochemistry, 80 Tennis Court Road, University of Cambridge, CB2 1GA, Cambridge, United Kingdom
| | - Tom L Blundell
- Department of Biochemistry, 80 Tennis Court Road, University of Cambridge, CB2 1GA, Cambridge, United Kingdom
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30
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Vikrant, Kumar R, Siddiqui Q, Singh N, Waghmare SK, Varma AK. Mislocalization of BRCA1-complex due to ABRAXAS Arg361Gln mutation. J Biomol Struct Dyn 2014; 33:1291-301. [DOI: 10.1080/07391102.2014.945484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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31
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Perozziello G, Candeloro P, Gentile F, Nicastri A, Perri A, Coluccio ML, Adamo A, Pardeo F, Catalano R, Parrotta E, Espinosa HD, Cuda G, Di Fabrizio E. Microfluidics & nanotechnology: towards fully integrated analytical devices for the detection of cancer biomarkers. RSC Adv 2014. [DOI: 10.1039/c4ra10486b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this paper, we describe an innovative modular microfluidic platform allowing filtering, concentration and analysis of peptides from a complex mixture.
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Affiliation(s)
- G. Perozziello
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
- Department of Mechanical Engineering
- NorthWestern University
| | - P. Candeloro
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - F. Gentile
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - A. Nicastri
- Proteomics lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - A. Perri
- Proteomics lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - M. L. Coluccio
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - A. Adamo
- Department of Chemical Engineering
- Massachusetts Institute of Technology (MIT)
- Cambridge, USA
| | - F. Pardeo
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - R. Catalano
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - E. Parrotta
- Proteomics lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - H. D. Espinosa
- Department of Mechanical Engineering
- NorthWestern University
- Evanston, USA
| | - G. Cuda
- Proteomics lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
| | - E. Di Fabrizio
- BioNEM lab
- Department of Experimental and Clinical Medicine, University “Magna Graecia” of Catanzaro
- Catanzaro, Italy
- King Abdullah University of Science and Technology (KAUST)
- Thuwal, Kingdom of Saudi Arabia
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32
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Chakraborty A, Katarkar A, Chaudhuri K, Mukhopadhyay A, Basak J. Detection of a novel mutation in exon 20 of the BRCA1 gene. Cell Mol Biol Lett 2013; 18:631-8. [PMID: 24297685 PMCID: PMC6275959 DOI: 10.2478/s11658-013-0110-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 11/27/2013] [Indexed: 11/20/2022] Open
Abstract
Hereditary breast cancer constitutes 5-10% of all breast cancer cases. Inherited mutations in the BRCA1 and BRCA2 tumor-suppressor genes account for the majority of hereditary breast cancer cases. The BRCA1 C-terminal region (BRCT) has a functional duplicated globular domain, which helps with DNA damage repair and cell cycle checkpoint protein control. More than 100 distinct BRCA1 missense variants with structural and functional effects have been documented within the BRCT domain. Interpreting the results of mutation screening of tumor-suppressor genes that can have high-risk susceptibility mutations is increasingly important in clinical practice. This study includes a novel mutation, p.His1746 Pro (c.5237A>C), which was found in BRCA1 exon 20 of a breast cancer patient. In silico analysis suggests that this mutation could alter the stability and orientation of the BRCT domain and the differential binding of the BACH1 substrate.
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Affiliation(s)
- Abhijit Chakraborty
- Department of Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute (NCRI), Kolkata, India
| | - Atul Katarkar
- Molecular & Human Genetics Division, Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Keya Chaudhuri
- Molecular & Human Genetics Division, Indian Institute of Chemical Biology (IICB), Kolkata, India
| | - Ashis Mukhopadhyay
- Department of Oncology, Netaji Subhas Chandra Bose Cancer Research Institute (NCRI), Kolkata, India
| | - Jayasri Basak
- Department of Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute (NCRI), Kolkata, India
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33
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Vikrant, Nakhwa P, Badgujar DC, Kumar R, Rathore KKS, Varma AK. Structural and functional characterization of the MERIT40 to understand its role in DNA repair. J Biomol Struct Dyn 2013; 32:2017-32. [PMID: 24125081 DOI: 10.1080/07391102.2013.843473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
MERIT40 (MEdiator of RAP80 Interaction and Targeting 40) is a novel associate of the BRCA1-complex and plays an essential role in DNA damage repair. It is the least characterized protein of BRCA1-complex and mainly responsible for maintaining the complex integrity. However, its structural and functional aspects of regulating the complex stability still remain elusive. Here, we carried out a comprehensive examination of MERIT40 biophysical properties and identified its novel interacting partner which would help to understand its role in BRCA1-complex. The recombinant protein was purified by affinity chromatography and unfolding pathway was determined using spectroscopic and calorimetric methods. Molecular model was generated using combinatorial approaches of modeling, and monomer-monomer docking was carried out to identify dimeric interface. Disordered region of MERIT40 was hatchet using trypsin and chymotrypsin to illustrate the existence of stable domain whose function was speculated through DALI search. Our findings suggest that MERIT40 forms a dimer in a concentration-independent manner. Its central region shows remarkable stability towards the protease digestion and has structural similarity with vWA-like region, a domain mainly present in complement activation factors. MERIT40 undergoes a three-state unfolding transition pathway with a dimeric intermediate. It interacts with adaptor molecule of BRCA1-complex, called ABRAXAS, thus help in extending the bridging interaction among various members which further stabilizes the whole complex. The results presented in this paper provide first-hand information on structural and folding behavior of MERIT40. These findings will help in elucidating the role of protein-protein interactions in stabilization of BRCA1-complex.
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Affiliation(s)
- Vikrant
- a Tata Memorial Centre, Advanced Centre for Treatment, Research and Education in Cancer , Kharghar, Navi Mumbai , Maharashtra 410 210 , India
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34
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Stabilization of mutant BRCA1 protein confers PARP inhibitor and platinum resistance. Proc Natl Acad Sci U S A 2013; 110:17041-6. [PMID: 24085845 DOI: 10.1073/pnas.1305170110] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Breast Cancer Type 1 Susceptibility Protein (BRCA1)-deficient cells have compromised DNA repair and are sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. Despite initial responses, the development of resistance limits clinical efficacy. Mutations in the BRCA C-terminal (BRCT) domain of BRCA1 frequently create protein products unable to fold that are subject to protease-mediated degradation. Here, we show HSP90-mediated stabilization of a BRCT domain mutant BRCA1 protein under PARP inhibitor selection pressure. The stabilized mutant BRCA1 protein interacted with PALB2-BRCA2-RAD51, was essential for RAD51 focus formation, and conferred PARP inhibitor as well as cisplatin resistance. Treatment of resistant cells with the HSP90 inhibitor 17-dimethylaminoethylamino-17-demethoxygeldanamycin reduced mutant BRCA1 protein levels and restored their sensitivity to PARP inhibition. Resistant cells also acquired a TP53BP1 mutation that facilitated DNA end resection in the absence of a BRCA1 protein capable of binding CtIP. Finally, concomitant increased mutant BRCA1 and decreased 53BP1 protein expression occur in clinical samples of BRCA1-mutated recurrent ovarian carcinomas that have developed resistance to platinum. These results provide evidence for a two-event mechanism by which BRCA1-mutant tumors acquire anticancer therapy resistance.
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35
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Laraqui A, Uhrhammer N, Lahlou-Amine I, El Rhaffouli H, El Baghdadi J, Dehayni M, Moussaoui RD, Ichou M, Sbitti Y, Al Bouzidi A, Amzazi S, Bignon YJ. Mutation screening of the BRCA1 gene in early onset and familial breast/ovarian cancer in Moroccan population. Int J Med Sci 2013; 10:60-7. [PMID: 23289006 PMCID: PMC3534878 DOI: 10.7150/ijms.5014] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Accepted: 10/15/2012] [Indexed: 12/19/2022] Open
Abstract
Worldwide variation in the distribution of BRCA mutations is well recognised, and for the Moroccan population no comprehensive studies about BRCA mutation spectra or frequencies have been published. We therefore performed mutation analysis of the BRCA1 gene in 121 Moroccan women diagnosed with breast cancer. All cases completed epidemiology and family history questionnaires and provided a DNA sample for BRCA testing. Mutation analysis was performed by direct DNA sequencing of all coding exons and flanking intron sequences of the BRCA1 gene. 31.6 % (6/19) of familial cases and 1 % (1/102) of early-onset sporadic (< 45 years)were found to be associated with BRCA1 mutations. The pathogenic mutations included two frame-shift mutations (c.798_799delTT, c.1016dupA), one missense mutation (c.5095C>T),and one nonsense mutation (c.4942A>T). The c.798_799delTT mutation was also observed in Algerian and Tunisian BC families, suggesting the first non-Jewish founder mutation to be described in Northern Africa. In addition, ten different unclassified variants were detected in BRCA1, none of which were predicted to affect splicing. Most unclassified variants were placed in Align-GVGD classes suggesting neutrality. c.5117G>C involves a highly conserved amino acid suggestive of interfering with function (Align-GVGD class C55), but has been observed in conjunction with a deleterious mutation in a Tunisian family. These findings reflect the genetic heterogeneity of the Moroccan population and are relevant to genetic counselling and clinical management. The role of BRCA2 in BC is also under study.
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Affiliation(s)
- Abdelilah Laraqui
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Rabat, Maroc
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36
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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: 96] [Impact Index Per Article: 8.0] [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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37
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Yuan Z, Kumar EA, Campbell SJ, Palermo NY, Kizhake S, Glover JNM, Natarajan A. Exploiting the P-1 pocket of BRCT domains toward a structure guided inhibitor design. ACS Med Chem Lett 2011; 2:764-767. [PMID: 22046493 DOI: 10.1021/ml200147a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Breast cancer gene 1 carboxy terminus (BRCT) domains are found in a number of proteins that are important for DNA damage response (DDR). The BRCT domains bind phosphorylated proteins and these protein-protein interactions are essential for DDR and DNA repair. High affinity domain specific inhibitors are needed to facilitate the dissection of the protein-protein interactions in the DDR signaling. The BRCT domains of BRCA1 bind phosphorylated protein through a pSXXF consensus recognition motif. We identified a hydrophobic pocket at the P-1 position of the pSXXF binding site. Here we conducted a structure-guided synthesis of peptide analogs with hydrophobic functional groups at the P-1 position. Evaluation of these led to the identification of a peptide mimic 15 with a inhibitory constant (K(i)) of 40 nM for BRCT(BRCA1). Analysis of the TopBP1 and MDC1 BRCT domains suggests a similar approach is viable to design high affinity inhibitors.
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Affiliation(s)
| | | | - Stephen J. Campbell
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | | | | | - J. N. Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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38
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Thanassoulas A, Nomikos M, Theodoridou M, Stavros P, Mastellos D, Nounesis G. Thermal and chemical denaturation of the BRCT functional module of human 53BP1. Int J Biol Macromol 2011; 49:297-304. [DOI: 10.1016/j.ijbiomac.2011.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 04/29/2011] [Accepted: 05/03/2011] [Indexed: 12/17/2022]
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39
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Dever SM, Golding SE, Rosenberg E, Adams BR, Idowu MO, Quillin JM, Valerie N, Xu B, Povirk LF, Valerie K. Mutations in the BRCT binding site of BRCA1 result in hyper-recombination. Aging (Albany NY) 2011; 3:515-32. [PMID: 21666281 PMCID: PMC3156602 DOI: 10.18632/aging.100325] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We introduced a K1702M mutation in the BRCA1 BRCT domain known to prevent the binding of proteins harboring pS-X-X-F motifs such as Abraxas-RAP80, BRIP1, and CtIP. Surprisingly, rather than impairing homologous recombination repair (HRR), expression of K1702M resulted in hyper-recombination coinciding with an accumulation of cells in S-G2 and no effect on nonhomologous end-joining. These cells also showed increased RAD51 and RPA nuclear staining. More pronounced effects were seen with a naturally occurring BRCT mutant (M1775R) that also produced elevated levels of ssDNA, in part co-localizing with RPA, in line with excessive DNA resection. M1775R induced unusual, thread-like promyelocytic leukemia (PML) nuclear bodies and clustered RPA foci rather than the typical juxtaposed RPA-PML foci seen with wild-type BRCA1. Interestingly, K1702M hyper-recombination diminished with a second mutation in the BRCA1 RING domain (I26A) known to reduce BRCA1 ubiquitin-ligase activity. Thesein vitro findings correlated with elevated nuclear RAD51 and RPA staining of breast cancer tissue from a patient with the M1775R mutation. Altogether, the disruption of BRCA1 (BRCT)-pS-X-X-F protein binding results in ubiquitination-dependent hyper-recombination via excessive DNA resection and the appearance of atypical PML-NBs. Thus, certain BRCA1 mutations that cause hyper-recombination instead of reduced DSB repair might lead to breast cancer.
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Affiliation(s)
- Seth M Dever
- Department of Radiation Oncology, Virginia Commonwealth University, Richmond, 23298, USA
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40
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di Masi A, Gullotta F, Cappadonna V, Leboffe L, Ascenzi P. Cancer predisposing mutations in BRCT domains. IUBMB Life 2011; 63:503-12. [DOI: 10.1002/iub.472] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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41
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Coquelle N, Green R, Glover JNM. Impact of BRCA1 BRCT domain missense substitutions on phosphopeptide recognition. Biochemistry 2011; 50:4579-89. [PMID: 21473589 PMCID: PMC3100782 DOI: 10.1021/bi2003795] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The BRCA1 BRCT domain binds pSer-x-x-Phe motifs in partner proteins to regulate the cellular response to DNA damage. Approximately 120 distinct missense variants have been identified in the BRCA1 BRCT through breast cancer screening, and several of these have been linked to an increased cancer risk. Here we probe the structures and peptide-binding activities of variants that affect the BRCA1 BRCT phosphopeptide-binding groove. The results obtained from the G1656D and T1700A variants illustrate the role of Ser1655 in pSer recognition. Mutations at Arg1699 (R1699W and R1699Q) significantly reduce peptide binding through loss of contacts to the main chain of the Phe(+3) residue and, in the case of R1699W, to a destabilization of the BRCT fold. The R1835P and E1836K variants do not dramatically reduce peptide binding, in spite of the fact that these mutations significantly alter the structure of the walls of the Phe(+3) pocket.
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Affiliation(s)
- Nicolas Coquelle
- Department of Biochemistry, School of Medicine, University of Alberta, Edmonton, AB, Canada
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42
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Abstract
BRCA1 is a well-established tumor suppressor gene, which is frequently mutated in familial breast and ovarian cancers. The gene product of BRCA1 functions in a number of cellular pathways that maintain genomic stability, including DNA damage-induced cell cycle checkpoint activation, DNA damage repair, protein ubiquitination, chromatin remodeling, as well as transcriptional regulation and apoptosis. In this review, we discuss recent advances regarding our understanding of the role of BRCA1 in tumor suppression and DNA damage response, including DNA damage-induced cell cycle checkpoint activation and DNA damage repair.
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Affiliation(s)
- Jiaxue Wu
- Division of Molecular Medicine and Genetics, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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43
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Borg A, Haile RW, Malone KE, Capanu M, Diep A, Törngren T, Teraoka S, Begg CB, Thomas DC, Concannon P, Mellemkjaer L, Bernstein L, Tellhed L, Xue S, Olson ER, Liang X, Dolle J, Børresen-Dale AL, Bernstein JL. Characterization of BRCA1 and BRCA2 deleterious mutations and variants of unknown clinical significance in unilateral and bilateral breast cancer: the WECARE study. Hum Mutat 2010; 31:E1200-40. [PMID: 20104584 DOI: 10.1002/humu.21202] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BRCA1 and BRCA2 screening in women at high-risk of breast cancer results in the identification of both unambiguously defined deleterious mutations and sequence variants of unknown clinical significance (VUS). We examined a population-based sample of young women with contralateral breast cancer (CBC, n=705) or unilateral breast cancer (UBC, n=1398). We identified 470 unique sequence variants, of which 113 were deleterious mutations. The remaining 357 VUS comprised 185 unique missense changes, 60% were observed only once, while 3% occurred with a frequency of >10%. Deleterious mutations occurred three times more often in women with CBC (15.3%) than in women with UBC (5.2%), whereas combined, VUS were observed in similar frequencies in women with CBC and UBC. A protein alignment algorithm defined 16 rare VUS, occurring at highly conserved residues and/or conferring a considerable biochemical difference, the majority located in the BRCA2 DNA-binding domain. We confirm a multiplicity of BRCA1 and BRCA2 VUS that occur at a wide range of allele frequencies. Although some VUS inflict chemical differences at conserved residues, suggesting a deleterious effect, the majority are not associated with an increased risk of CBC.
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Affiliation(s)
- Ake Borg
- Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden.
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44
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Guidugli L, Rugani C, Lombardi G, Aretini P, Galli A, Caligo MA. A recombination-based method to characterize human BRCA1 missense variants. Breast Cancer Res Treat 2010; 125:265-72. [DOI: 10.1007/s10549-010-1112-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 07/30/2010] [Indexed: 01/03/2023]
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45
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Lee MS, Green R, Marsillac SM, Coquelle N, Williams RS, Yeung T, Foo D, Hau DD, Hui B, Monteiro ANA, Glover JNM. Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. Cancer Res 2010; 70:4880-90. [PMID: 20516115 DOI: 10.1158/0008-5472.can-09-4563] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Genetic screening of the breast and ovarian cancer susceptibility gene BRCA1 has uncovered a large number of variants of uncertain clinical significance. Here, we use biochemical and cell-based transcriptional assays to assess the structural and functional defects associated with a large set of 117 distinct BRCA1 missense variants within the essential BRCT domain of the BRCA1 protein that have been documented in individuals with a family history of breast or ovarian cancer. In the first method, we used limited proteolysis to assess the protein folding stability of each of the mutants compared with the wild-type. In the second method, we used a phosphopeptide pull-down assay to assess the ability of each of the variants to specifically interact with a peptide containing a pSer-X-X-Phe motif, a known functional target of the BRCA1 BRCT domain. Finally, we used transcriptional assays to assess the ability of each BRCT variant to act as a transcriptional activation domain in human cells. Through a correlation of the assay results with available family history and clinical data, we define limits to predict the disease risk associated with each variant. Forty-two of the variants show little effect on function and are likely to represent variants with little or no clinical significance; 50 display a clear functional effect and are likely to represent pathogenic variants; and the remaining 25 variants display intermediate activities. The excellent agreement between the structure/function effects of these mutations and available clinical data supports the notion that functional and structure information can be useful in the development of models to assess cancer risk.
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Affiliation(s)
- Megan S Lee
- Department of Biochemistry, School of Systems Molecular Medicine, University of Alberta, Edmonton, Alberta, Canada
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46
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Campbell SJ, Edwards RA, Glover JM. Comparison of the Structures and Peptide Binding Specificities of the BRCT Domains of MDC1 and BRCA1. Structure 2010; 18:167-76. [DOI: 10.1016/j.str.2009.12.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2009] [Revised: 11/18/2009] [Accepted: 12/02/2009] [Indexed: 12/30/2022]
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47
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Drikos I, Nounesis G, Vorgias CE. Characterization of cancer-linked BRCA1-BRCT missense variants and their interaction with phosphoprotein targets. Proteins 2009; 77:464-76. [PMID: 19452558 DOI: 10.1002/prot.22460] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The breast cancer tumor suppressor protein BRCA1 is involved in DNA repair and cell cycle control. Mutations at the two C-terminal tandem (BRCT) repeats of BRCA1 detected in breast tumor patients were identified either to lower the stability of the BRCT domain and/or to disrupt the interaction of BRCT with phoshpopeptides. The aim of this study was to analyze five BRCT pathogenic mutations for their effect on structural integrity and protein stability. For this purpose, the five cancer-associated BRCT mutants: V1696L, M1775K, M1783T, V1809F, and P1812A were cloned in suitable prokaryotic protein production vectors, and the recombinant proteins were purified in soluble and stable form for further biophysical studies. The biophysical analysis of the secondary structure and the thermodynamic stability of the wild-type, wt, and the five mutants of the BRCT domain were performed by Circular Dichroism Spectroscopy (CD) and Differential Scanning Microcalorimetry (DSC), respectively. The binding capacity of the wt and mutant BRCT with (pBACH1/BRIP1) and pCtIP were measured by Isothermal Titration Calorimetry (ITC). The experimental results demonstrated that the five mutations of the BRCT domain: (i) affected the thermal unfolding temperature as well as the unfolding enthalpy of the domain, to a varying degree depending upon the induced destabilization and (ii) altered and/or abolished their affinity to synthetic pBACH1/BRIP1 and pCtIP phosphopeptides by affecting the structural integrity of the BRCT active sites. The presented experimental results are one step towards the elucidation of the effect of various missense mutations on the structure and function of BRCA1-BRCT.
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Affiliation(s)
- Ioannis Drikos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis-Zographou, 15701 Athens, Hellas
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48
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Edwards RA, Lee MS, Tsutakawa SE, Williams RS, Tainer JA, Glover JNM. The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50. Biochemistry 2008; 47:11446-56. [PMID: 18842000 PMCID: PMC2654182 DOI: 10.1021/bi801115g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 08/20/2008] [Indexed: 12/19/2022]
Abstract
The BARD1 N-terminal RING domain binds BRCA1 while the BARD1 C-terminal ankyrin and tandem BRCT repeat domains bind CstF-50 to modulate mRNA processing and RNAP II stability in response to DNA damage. Here we characterize the BARD1 structural biochemistry responsible for CstF-50 binding. The crystal structure of the BARD1 BRCT domain uncovers a degenerate phosphopeptide binding pocket lacking the key arginine required for phosphopeptide interactions in other BRCT proteins. Small angle X-ray scattering together with limited proteolysis results indicates that ankyrin and BRCT domains are linked by a flexible tether and do not adopt a fixed orientation relative to one another. Protein pull-down experiments utilizing a series of purified BARD1 deletion mutants indicate that interactions between the CstF-50 WD-40 domain and BARD1 involve the ankyrin-BRCT linker but do not require ankyrin or BRCT domains. The structural plasticity imparted by the ANK-BRCT linker helps to explain the regulated assembly of different protein BARD1 complexes with distinct functions in DNA damage signaling including BARD1-dependent induction of apoptosis plus p53 stabilization and interactions. BARD1 architecture and plasticity imparted by the ANK-BRCT linker are suitable to allow the BARD1 C-terminus to act as a hub with multiple binding sites to integrate diverse DNA damage signals directly to RNA polymerase.
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Affiliation(s)
| | | | | | | | | | - J. N. Mark Glover
- Address correspondence to this author. Tel: (780) 492-2136. Fax: (780) 492-0886. E-mail:
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49
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Couch FJ, Rasmussen LJ, Hofstra R, Monteiro ANA, Greenblatt MS, de Wind N. Assessment of functional effects of unclassified genetic variants. Hum Mutat 2008; 29:1314-26. [PMID: 18951449 PMCID: PMC2771414 DOI: 10.1002/humu.20899] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Inherited predisposition to disease is often linked to reduced activity of a disease associated gene product. Thus, quantitation of the influence of inherited variants on gene function can potentially be used to predict the disease relevance of these variants. While many disease genes have been extensively characterized at the functional level, few assays based on functional properties of the encoded proteins have been established for the purpose of predicting the contribution of rare inherited variants to disease. Much of the difficulty in establishing predictive functional assays stems from the technical complexity of the assays. However, perhaps the most challenging aspect of functional assay development for clinical testing purposes is the absolute requirement for validation of the sensitivity and specificity of the assays and the determination of positive predictive values (PPVs) and negative predictive values (NPVs) of the assays relative to a "gold standard" measure of disease predisposition. In this commentary, we provide examples of some of the functional assays under development for several cancer predisposition genes (BRCA1, BRCA2, CDKN2A, and mismatch repair [MMR] genes MLH1, MSH2, MSH6, and PMS2) and present a detailed review of the issues associated with functional assay development. We conclude that validation is paramount for all assays that will be used for clinical interpretation of inherited variants of any gene, but note that in certain circumstances information derived from incompletely validated assays may be valuable for classification of variants for clinical purposes when used to supplement data derived from other sources.
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Affiliation(s)
- Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905, USA.
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50
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Carvalho M, Pino MA, Karchin R, Beddor J, Godinho-Netto M, Mesquita RD, Rodarte RS, Vaz DC, Monteiro VA, Manoukian S, Colombo M, Ripamonti CB, Rosenquist R, Suthers G, Borg A, Radice P, Grist SA, Monteiro ANA, Billack B. Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1. Mutat Res 2008; 660:1-11. [PMID: 18992264 DOI: 10.1016/j.mrfmmm.2008.09.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 08/12/2008] [Accepted: 09/27/2008] [Indexed: 12/19/2022]
Abstract
Germline mutations that inactivate BRCA1 are responsible for breast and ovarian cancer susceptibility. One possible outcome of genetic testing for BRCA1 is the finding of a genetic variant of uncertain significance for which there is no information regarding its cancer association. This outcome leads to problems in risk assessment, counseling and preventive care. The purpose of the present study was to functionally evaluate seven unclassified variants of BRCA1 including a genomic deletion that leads to the in-frame loss of exons 16/17 (Delta exons 16/17) in the mRNA, an insertion that leads to a frameshift and an extended carboxy-terminus (5673insC), and five missense variants (K1487R, S1613C, M1652I, Q1826H and V1833M). We analyzed the variants using a functional assay based on the transcription activation property of BRCA1 combined with supervised learning computational models. Functional analysis indicated that variants S1613C, Q1826H, and M1652I are likely to be neutral, whereas variants V1833M, Delta exons 16/17, and 5673insC are likely to represent deleterious variants. In agreement with the functional analysis, the results of the computational analysis also indicated that the latter three variants are likely to be deleterious. Taken together, a combined approach of functional and bioinformatics analysis, plus structural modeling, can be utilized to obtain valuable information pertaining to the effect of a rare variant on the structure and function of BRCA1. Such information can, in turn, aid in the classification of BRCA1 variants for which there is a lack of genetic information needed to provide reliable risk assessment.
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Affiliation(s)
- Marcelo Carvalho
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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