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Lavoro A, Scalisi A, Candido S, Zanghì GN, Rizzo R, Gattuso G, Caruso G, Libra M, Falzone L. Identification of the most common BRCA alterations through analysis of germline mutation databases: Is droplet digital PCR an additional strategy for the assessment of such alterations in breast and ovarian cancer families? Int J Oncol 2022; 60:58. [PMID: 35383859 PMCID: PMC8997337 DOI: 10.3892/ijo.2022.5349] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Abstract
Breast and ovarian cancer represent two of the most common tumor types in females worldwide. Over the years, several non‑modifiable and modifiable risk factors have been associated with the onset and progression of these tumors, including age, reproductive factors, ethnicity, socioeconomic status and lifestyle factors, as well as family history and genetic factors. Of note, BRCA1 and BRCA2 are two tumor suppressor genes with a key role in DNA repair processes, whose mutations may induce genomic instability and increase the risk of cancer development. Specifically, females with a family history of breast or ovarian cancer harboring BRCA1/2 germline mutations have a 60‑70% increased risk of developing breast cancer and a 15‑40% increased risk for ovarian cancer. Different databases have collected the most frequent germline mutations affecting BRCA1/2. Through the analysis of such databases, it is possible to identify frequent hotspot mutations that may be analyzed with next‑generation sequencing (NGS) and novel innovative strategies. In this context, NGS remains the gold standard method for the assessment of BRCA1/2 mutations, while novel techniques, including droplet digital PCR (ddPCR), may improve the sensitivity to identify such mutations in the hereditary forms of breast and ovarian cancer. On these bases, the present study aimed to provide an update of the current knowledge on the frequency of BRCA1/2 mutations and cancer susceptibility, focusing on the diagnostic potential of the most recent methods, such as ddPCR.
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Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Aurora Scalisi
- Italian League Against Cancer, Section of Catania, I‑95122 Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Guido Nicola Zanghì
- Department of General Surgery and Medical‑Surgical Specialties, Policlinico‑Vittorio Emanuele Hospital, University of Catania, I‑95123 Catania, Italy
| | - Roberta Rizzo
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Caruso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Luca Falzone
- Epidemiology and Biostatistics Unit, National Cancer Institute IRCCS Fondazione 'G. Pascale', I‑80131 Naples, Italy
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Choudhary RK, Siddiqui MQ, Gadewal N, Kumar NS, Kuligina ES, Varma AK. Biophysical evaluation to categorize pathogenicity of cancer-predisposing mutations identified in the BARD1 BRCT domain. RSC Adv 2018; 8:34056-34068. [PMID: 35548793 PMCID: PMC9086705 DOI: 10.1039/c8ra06524a] [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: 08/02/2018] [Accepted: 09/17/2018] [Indexed: 11/21/2022] Open
Abstract
The BRCT domain of BARD1 (BARD1 BRCT) is involved in many cellular processes such as DNA damage repair (DDR) and cell-cycle checkpoint regulation. BARD1 BRCT performs tumor suppressor function by recruiting BRCA1 at DNA damage site via interactions with other DNA damage repair (DDR) proteins. Considering the importance of the BRCT domain in genomic integrity, we decided to evaluate reported mutations of BARD1 BRCT Cys645Arg, Val695Leu, and Ser761Asn for their pathogenicity. To explore the effect of the mutation on the structure and function, BARD1 BRCT wild-type proteins and the mutant proteins were studied using different biochemical, biophysical and in silico techniques. Comparative fluorescence, circular dichroism (CD) spectroscopy and limited proteolysis studies demonstrate the well-folded structural conformation of wild-type and mutant proteins. However, thermal and chemical denaturation studies revealed similarity in the folding pattern of BARD1 BRCT wild-type and Cys645Arg mutant proteins, whereas there was a significant loss in the thermodynamic stability of Val695Leu and Ser761Asn mutants. Molecular dynamics (MD) simulation studies on wild-type and mutant protein structures indicate the loss in structural integrity of mutants compared with the wild-type protein.
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Affiliation(s)
- Rajan Kumar Choudhary
- Advanced Centre for Treatment, Research and Education in CancerKhargharNavi MumbaiMaharashtra 410 210India+91-22-2740 5085+91-22-2740 5112,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, The Hebrew University of JerusalemJerusalem 91904Israel
| | - M. Quadir Siddiqui
- Advanced Centre for Treatment, Research and Education in CancerKhargharNavi MumbaiMaharashtra 410 210India+91-22-2740 5085+91-22-2740 5112,University of Nebraska Medical CentreOmahaNEUSA
| | - Nikhil Gadewal
- Advanced Centre for Treatment, Research and Education in CancerKhargharNavi MumbaiMaharashtra 410 210India+91-22-2740 5085+91-22-2740 5112
| | - Nachimuthu Senthil Kumar
- Department of Biotechnology, Mizoram University (A Central University)Aizawl – 796 004MizoramIndia
| | - Ekaterina S. Kuligina
- Laboratory of Molecular Oncology, Department of Tumor Growth Biology, N.N. Petrov Institute of OncologyRU-197758, Pesochny-2St.-PetersburgRussia
| | - Ashok K. Varma
- Advanced Centre for Treatment, Research and Education in CancerKhargharNavi MumbaiMaharashtra 410 210India+91-22-2740 5085+91-22-2740 5112,Homi Bhabha National Institute, Training School ComplexAnushaktinagarMumbai - 400 094India
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3
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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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Choudhary RK, Vikrant, Siddiqui QM, Thapa PS, Raikundalia S, Gadewal N, Kumar NS, Hosur M, Varma AK. Multimodal approach to explore the pathogenicity of BARD1, ARG 658 CYS, and ILE 738 VAL mutants. J Biomol Struct Dyn 2015; 34:1533-44. [DOI: 10.1080/07391102.2015.1082149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Rajan Kumar Choudhary
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410 210, Maharashtra, India
| | - Vikrant
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410 210, Maharashtra, India
| | - Quadir M. Siddiqui
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410 210, Maharashtra, India
| | - Pankaj S. Thapa
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410 210, Maharashtra, India
| | - Sweta Raikundalia
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410 210, Maharashtra, India
| | - Nikhil Gadewal
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410 210, Maharashtra, India
| | - Nachimuthu Senthil Kumar
- Department of Biotechnology, Mizoram University (A Central University), Aizawl 796 004, Mizoram, India
| | - M.V. Hosur
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410 210, Maharashtra, India
| | - Ashok K. Varma
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410 210, Maharashtra, India
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Stavros P, Malecki PH, Theodoridou M, Rypniewski W, Vorgias CE, Nounesis G. The stability of the TIM-barrel domain of a psychrophilic chitinase. Biochem Biophys Rep 2015; 3:108-116. [PMID: 29124173 PMCID: PMC5668695 DOI: 10.1016/j.bbrep.2015.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/24/2015] [Accepted: 07/28/2015] [Indexed: 11/22/2022] Open
Abstract
Chitinase 60 from the psychrophilic bacterium Moritella marina (MmChi60) is a four-domain protein whose structure revealed flexible hinge regions between the domains, yielding conformations in solution that range from fully extended to compact. The catalytic domain is a shallow-grooved TIM-barrel. Heat-induced denaturation experiments of the wild-type and mutants resulting from the deletions of the two-Ig-like domains and the chitin binding domain reveal calorimetric profiles that are consistent with non-collaborative thermal unfolding of the individual domains, a property that must be associated to the “hinge-regions”. The calorimetric measurements of the (β/α)8 catalytic domain reveal that the thermal unfolding is a slow-relaxation transition exhibiting a stable, partially structured intermediate state. Circular dichroism provides evidence that the intermediate exhibits features of a molten globule i.e., loss of tertiary structure while maintaining the secondary structural elements of the native. GdnHCl-induced denaturation studies of the TIM-barrel demonstrate an extraordinarily high resistance to the denaturant. Slow-relaxation kinetics characterize the unfolding with equilibration times exceeding six days, a property that is for the first time observed for a psychrophilic TIM barrel. On the other hand, the thermodynamic stability is ΔG=6.75±1.3 kcal/mol, considerably lower than for structural-insertions-containing barrels. The mutant E153Q used for the crystallographic studies of MmChi60 complexes with NAG ligands has a much lower stability than the wild-type. We use heat-induced and chemical denaturation to study MmChi60. The impact of “hinge” regions upon the DSC calorimetric profiles is explored. CD is used to characterize the thermal unfolding intermediate of the catalytic domain. The thermodynamic stability of the TIM-barrel is measured via chemical denaturation. High-resistance to denaturants is evidenced for the psychrophilic (β/α)8 domain.
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Affiliation(s)
- Philemon Stavros
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
- Physics Department, National and Kapodistrian University of Athens, 157 01 Zografou, Greece
| | - Piotr H. Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Maria Theodoridou
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Constantinos E. Vorgias
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 157 01 Zografou, Greece
| | - George Nounesis
- Biomolecular Physics Laboratory, INRASTES, National Centre for Scientific Research “Demokritos”, 153 10 Aghia Paraskevi, Greece
- Corresponding author.
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Carvalho RS, Fernandes VC, Nepomuceno TC, Rodrigues DC, Woods NT, Suarez-Kurtz G, Chammas R, Monteiro AN, Carvalho MA. Characterization of LGALS3 (galectin-3) as a player in DNA damage response. Cancer Biol Ther 2014; 15:840-50. [PMID: 24755837 DOI: 10.4161/cbt.28873] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
DNA damage repair (DDR) is an orchestrated process encompassing the injury detection to its complete resolution. DNA double-strand break lesions are repaired mainly by two distinct mechanisms: the error-free homologous recombination (HR) and the error-prone non-homologous end-joining. Galectin-3 (GAL3) is the unique member of the chimeric galectins subfamily and is reported to be involved in several cancer development and progression related events. Recently our group described a putative protein interaction between GAL3 and BARD1, the main partner of breast and ovarian cancer susceptibility gene product BRCA1, both involved in HR pathway. In this report we characterized GAL3/BARD1 protein interaction and evaluated the role of GAL3 in DDR pathways using GAL3 silenced human cells exposed to different DNA damage agents. In the absence of GAL3 we observed a delayed DDR response activation, as well as a decrease in the G 2/M cell cycle checkpoint arrest associated with HR pathway. Moreover, using a TAP-MS approach we also determined the protein interaction network of GAL3.
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Affiliation(s)
- Renato S Carvalho
- Instituto de Biofísica Carlos Chagas Filho; Universidade Federal do Rio de Janeiro; Rio de Janeiro, Brazil; Cancer Epidemiology Program; H. Lee Moffitt Cancer Center & Research Institute; Tampa, FL USA
| | | | | | - Deivid C Rodrigues
- Instituto de Biofísica Carlos Chagas Filho; Universidade Federal do Rio de Janeiro; Rio de Janeiro, Brazil
| | - Nicholas T Woods
- Cancer Epidemiology Program; H. Lee Moffitt Cancer Center & Research Institute; Tampa, FL USA
| | | | - Roger Chammas
- Faculdade de Medicina; Universidade de São Paulo; São Paulo, Brazil
| | - Alvaro N Monteiro
- Cancer Epidemiology Program; H. Lee Moffitt Cancer Center & Research Institute; Tampa, FL USA
| | - Marcelo A Carvalho
- Instituto Federal do Rio de Janeiro (IFRJ); Rio de Janeiro, Brazil; Programa de Farmacologia; Instituto Nacional de Câncer; Rio de Janeiro, Brazil
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1 0 6. Cancer Biomark 2012. [DOI: 10.1201/b14318-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Ghai R, Falconer RJ, Collins BM. Applications of isothermal titration calorimetry in pure and applied research--survey of the literature from 2010. J Mol Recognit 2012; 25:32-52. [PMID: 22213449 DOI: 10.1002/jmr.1167] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Isothermal titration calorimetry (ITC) is a biophysical technique for measuring the formation and dissociation of molecular complexes and has become an invaluable tool in many branches of science from cell biology to food chemistry. By measuring the heat absorbed or released during bond formation, ITC provides accurate, rapid, and label-free measurement of the thermodynamics of molecular interactions. In this review, we survey the recent literature reporting the use of ITC and have highlighted a number of interesting studies that provide a flavour of the diverse systems to which ITC can be applied. These include measurements of protein-protein and protein-membrane interactions required for macromolecular assembly, analysis of enzyme kinetics, experimental validation of molecular dynamics simulations, and even in manufacturing applications such as food science. Some highlights include studies of the biological complex formed by Staphylococcus aureus enterotoxin C3 and the murine T-cell receptor, the mechanism of membrane association of the Parkinson's disease-associated protein α-synuclein, and the role of non-specific tannin-protein interactions in the quality of different beverages. Recent developments in automation are overcoming limitations on throughput imposed by previous manual procedures and promise to greatly extend usefulness of ITC in the future. We also attempt to impart some practical advice for getting the most out of ITC data for those researchers less familiar with the method.
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Affiliation(s)
- Rajesh Ghai
- Institute for Molecular Bioscience (IMB), University of Queensland, St. Lucia, Queensland, 4072, Australia
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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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10
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Abstract
BRCA1 C-terminal (BRCT) domains are integral signaling modules in the DNA damage response (DDR). Aside from their established roles as phospho-peptide binding modules, BRCT domains have been implicated in phosphorylation-independent protein interactions, DNA binding and poly(ADP-ribose) (PAR) binding. These numerous functions can be attributed to the diversity in BRCT domain structure and architecture, where domains can exist as isolated single domains or assemble into higher order homo- or hetero- domain complexes. In this review, we incorporate recent structural and biochemical studies to demonstrate how structural features allow single and tandem BRCT domains to attain a high degree of functional diversity.
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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: 39] [Impact Index Per Article: 3.0] [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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