1
|
Bassi N, Hovland HN, Rasheed K, Jarhelle E, Pedersen N, Mchaina EK, Bakkan SME, Iversen N, Høberg-Vetti H, Haukanes BI, Knappskog PM, Aukrust I, Ognedal E, Van Ghelue M. Functional analyses of rare germline BRCA1 variants by transcriptional activation and homologous recombination repair assays. BMC Cancer 2023; 23:368. [PMID: 37085799 PMCID: PMC10122298 DOI: 10.1186/s12885-023-10790-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 03/30/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Damaging alterations in the BRCA1 gene have been extensively described as one of the main causes of hereditary breast and ovarian cancer (HBOC). BRCA1 alterations can lead to impaired homologous recombination repair (HRR) of double-stranded DNA breaks, a process which involves the RING, BRCT and coiled-coil domains of the BRCA1 protein. In addition, the BRCA1 protein is involved in transcriptional activation (TA) of several genes through its C-terminal BRCT domain. METHODS In this study, we have investigated the effect on HRR and TA of 11 rare BRCA1 missense variants classified as variants of uncertain clinical significance (VUS), located within or in close proximity to the BRCT domain, with the aim of generating additional knowledge to guide the correct classification of these variants. The variants were selected from our previous study "BRCA1 Norway", which is a collection of all BRCA1 variants detected at the four medical genetic departments in Norway. RESULTS All variants, except one, showed a significantly reduced HRR activity compared to the wild type (WT) protein. Two of the variants (p.Ala1708Val and p.Trp1718Ser) also exhibited low TA activity similar to the pathogenic controls. The variant p.Trp1718Ser could be reclassified to likely pathogenic. However, for ten of the variants, the total strength of pathogenic evidence was not sufficient for reclassification according to the CanVIG-UK BRCA1/BRCA2 gene-specific guidelines for variant interpretation. CONCLUSIONS When including the newly achieved functional evidence with other available information, one VUS was reclassified to likely pathogenic. Eight of the investigated variants affected only one of the assessed activities of BRCA1, highlighting the importance of comparing results obtained from several functional assays to better understand the consequences of BRCA1 variants on protein function. This is especially important for multifunctional proteins such as BRCA1.
Collapse
Affiliation(s)
- Nicola Bassi
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
| | - Henrikke Nilsen Hovland
- Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kashif Rasheed
- Department of Medical Biology, University of Tromsø, Tromsø, Norway
- Present address: Institute for Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim, Norway
| | - Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
- Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway
| | - Nikara Pedersen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Eunice Kabanyana Mchaina
- Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | | | - Nina Iversen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Hildegunn Høberg-Vetti
- Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Per Morten Knappskog
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Elisabet Ognedal
- Familial Cancer Center, Haukeland University Hospital, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
- Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway
- Department of Clinical Medicine, University of Tromsø, Tromsø, Norway
| |
Collapse
|
2
|
Biegała Ł, Gajek A, Marczak A, Rogalska A. Olaparib-Resistant BRCA2MUT Ovarian Cancer Cells with Restored BRCA2 Abrogate Olaparib-Induced DNA Damage and G2/M Arrest Controlled by the ATR/CHK1 Pathway for Survival. Cells 2023; 12:cells12071038. [PMID: 37048111 PMCID: PMC10093185 DOI: 10.3390/cells12071038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The PARP inhibitor (PARPi) olaparib is currently the drug of choice for serous ovarian cancer (OC), especially in patients with homologous recombination (HR) repair deficiency associated with deleterious BRCA1/2 mutations. Unfortunately, OC patients who fail to respond to PARPi or relapse after treatment have limited therapeutic options. To elucidate olaparib resistance and enhance the efficacy of olaparib, intracellular factors exploited by OC cells to achieve decreased sensitivity to PARPi were examined. An olaparib-resistant OC cell line, PEO1-OR, was established from BRCA2MUT PEO1 cells. The anticancer activity and action of olaparib combined with inhibitors of the ATR/CHK1 pathway (ceralasertib as ATRi, MK-8776 as CHK1i) in olaparib-sensitive and -resistant OC cell lines were evaluated. Whole-exome sequencing revealed that PEO1-OR cells acquire resistance through subclonal enrichment of BRCA2 secondary mutations that restore functional full-length protein. Moreover, PEO1-OR cells upregulate HR repair-promoting factors (BRCA1, BRCA2, RAD51) and PARP1. Olaparib-inducible activation of the ATR/CHK1 pathway and G2/M arrest is abrogated in olaparib-resistant cells. Drug sensitivity assays revealed that PEO1-OR cells are less sensitive to ATRi and CHK1i agents. Combined treatment is less effective in olaparib-resistant cells considering inhibition of metabolic activity, colony formation, survival, accumulation of DNA double-strand breaks, and chromosomal aberrations. However, synergistic antitumor activity between compounds is achievable in PEO1-OR cells. Collectively, olaparib-resistant cells display co-existing HR repair-related mechanisms that confer resistance to olaparib, which may be effectively utilized to resensitize them to PARPi via combination therapy. Importantly, the addition of ATR/CHK1 pathway inhibitors to olaparib has the potential to overcome acquired resistance to PARPi.
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Abreu RBV, Gomes TT, Nepomuceno TC, Li X, Fuchshuber-Moraes M, De Gregoriis G, Suarez-Kurtz G, Monteiro ANA, Carvalho MA. Functional Restoration of BRCA1 Nonsense Mutations by Aminoglycoside-Induced Readthrough. Front Pharmacol 2022; 13:935995. [PMID: 35837282 PMCID: PMC9273842 DOI: 10.3389/fphar.2022.935995] [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: 05/04/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
BRCA1 is a major tumor suppressor that functions in the accurate repair of DNA double-strand breaks via homologous recombination (HR). Nonsense mutations in BRCA1 lead to inactive truncated protein products and are associated with high risk of breast and ovarian cancer. These mutations generate premature termination codons (PTCs). Different studies have shown that aminoglycosides can induce PTC suppression by promoting stop codon readthrough and restoring full-length (FL) protein expression. The use of these compounds has been studied in clinical trials for genetic diseases such as cystic fibrosis and Duchenne muscular dystrophy, with encouraging results. Here we show proof-of-concept data demonstrating that the aminoglycoside G418 can induce BRCA1 PTC readthrough and restore FL protein synthesis and function. We first demonstrate that G418 treatment restores BRCA1 FL protein synthesis in HCC1395, a human breast tumor cell line carrying the R1751X mutation. HCC1395 cells treated with G418 also recover HR DNA repair and restore cell cycle checkpoint activation. A set of naturally occurring BRCA1 nonsense variants encoding different PTCs was evaluated in a GFP C-terminal BRCA1 construct model and BRCA1 PTC readthrough levels vary depending on the stop codon context. Because PTC readthrough could generate FL protein carrying pathogenic missense mutations, variants representing the most probable acquired amino acid substitutions in consequence of readthrough were functionally assessed by a validated transcription activation assay. Overall, this is the first study that evaluates the readthrough of PTC variants with clinical relevance in the breast and ovarian cancer-predisposing gene BRCA1.
Collapse
Affiliation(s)
- Renata B. V. Abreu
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Thiago T. Gomes
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Thales C. Nepomuceno
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Xueli Li
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | | | | | | | - Alvaro N. A. Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Marcelo A. Carvalho
- Divisão de Pesquisa Clínica, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
- Instituto Federal do Rio de Janeiro—IFRJ, Rio de Janeiro, Brazil
- *Correspondence: Marcelo A. Carvalho,
| |
Collapse
|
5
|
Alzahrani FA, Ahmed F, Sharma M, Rehan M, Mahfuz M, Baeshen MN, Hawsawi Y, Almatrafi A, Alsagaby SA, Kamal MA, Warsi MK, Choudhry H, Jamal MS. Investigating the pathogenic SNPs in BLM helicase and their biological consequences by computational approach. Sci Rep 2020; 10:12377. [PMID: 32704157 PMCID: PMC7378827 DOI: 10.1038/s41598-020-69033-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/06/2020] [Indexed: 12/15/2022] Open
Abstract
The BLM helicase protein plays a vital role in DNA replication and the maintenance of genomic integrity. Variation in the BLM helicase gene resulted in defects in the DNA repair mechanism and was reported to be associated with Bloom syndrome (BS) and cancer. Despite extensive investigation of helicase proteins in humans, no attempt has previously been made to comprehensively analyse the single nucleotide polymorphism (SNPs) of the BLM gene. In this study, a comprehensive analysis of SNPs on the BLM gene was performed to identify, characterize and validate the pathogenic SNPs using computational approaches. We obtained SNP data from the dbSNP database version 150 and mapped these data to the genomic coordinates of the "NM_000057.3" transcript expressing BLM helicase (P54132). There were 607 SNPs mapped to missense, 29 SNPs mapped to nonsense, and 19 SNPs mapped to 3'-UTR regions. Initially, we used many consensus tools of SIFT, PROVEAN, Condel, and PolyPhen-2, which together increased the accuracy of prediction and identified 18 highly pathogenic non-synonymous SNPs (nsSNPs) out of 607 SNPs. Subsequently, these 18 high-confidence pathogenic nsSNPs were analysed for BLM protein stability, structure-function relationships and disease associations using various bioinformatics tools. These 18 mutants of the BLM protein along with the native protein were further investigated using molecular dynamics simulations to examine the structural consequences of the mutations, which might reveal their malfunction and contribution to disease. In addition, 28 SNPs were predicted as "stop gained" nonsense SNPs and one SNP was predicted as "start lost". Two SNPs in the 3'UTR were found to abolish miRNA binding and thus may enhance the expression of BLM. Interestingly, we found that BLM mRNA overexpression is associated with different types of cancers. Further investigation showed that the dysregulation of BLM is associated with poor overall survival (OS) for lung and gastric cancer patients and hence led to the conclusion that BLM has the potential to be used as an important prognostic marker for the detection of lung and gastric cancer.
Collapse
Affiliation(s)
- Faisal A Alzahrani
- Department of Biochemistry, Faculty of Science, Stem Cells Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Aston Medical Research Institute, Aston Medical School, Aston University, Birmingham, B4 7ET, UK
| | - Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia.
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia.
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, India
| | - Mohd Rehan
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Maryam Mahfuz
- Department of Computer Science, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Mohammed N Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Yousef Hawsawi
- Department of Genetics, Research Center, King Faisal Specialist Hospital, and Research Center, MBC-03, PO Box 3354, Riyadh, 11211, Saudi Arabia
| | - Ahmed Almatrafi
- Department of Biology, Faculty of Science, University of Taibah, Medinah, Saudi Arabia
| | - Suliman Abdallah Alsagaby
- Department of Medical Laboratories, Central Biosciences Research Laboratories, College of Science in Al Zulfi, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Mohammad Azhar Kamal
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Mohiuddin Khan Warsi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 21589, Saudi Arabia
- University of Jeddah Centre for Scientific and Medical Research (UJ-CSMR), University of Jeddah, Jeddah, 21589, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Sarwar Jamal
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
- Integrative Biosciences Center, Wayne State University, Detroit, MI, 48202, USA.
| |
Collapse
|
6
|
Bouwman P, van der Heijden I, van der Gulden H, de Bruijn R, Braspenning ME, Moghadasi S, Wessels LFA, Vreeswijk MPG, Jonkers J. Functional Categorization of BRCA1 Variants of Uncertain Clinical Significance in Homologous Recombination Repair Complementation Assays. Clin Cancer Res 2020; 26:4559-4568. [PMID: 32546644 DOI: 10.1158/1078-0432.ccr-20-0255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/29/2020] [Accepted: 06/12/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Because BRCA1 is a high-risk breast/ovarian cancer susceptibility gene, BRCA1 sequence variants of uncertain clinical significance (VUS) complicate genetic counseling. As most VUS are rare, reliable classification based on clinical and genetic data is often impossible. However, all pathogenic BRCA1 variants analyzed result in defective homologous recombination DNA repair (HRR). Thus, BRCA1 VUS may be categorized based on their functional impact on this pathway. EXPERIMENTAL DESIGN Two hundred thirty-eight BRCA1 VUS-comprising most BRCA1 VUS known in the Netherlands and Belgium-were tested for their ability to complement Brca1-deficient mouse embryonic stem cells in HRR, using cisplatin and olaparib sensitivity assays and a direct repeat GFP (DR-GFP) HRR assay. Assays were validated using 25 known benign and 25 known pathogenic BRCA1 variants. For assessment of pathogenicity by a multifactorial likelihood analysis method, we collected clinical and genetic data for functionally deleterious VUS and VUS occurring in three or more families. RESULTS All three assays showed 100% sensitivity and specificity (95% confidence interval, 83%-100%). Out of 238 VUS, 45 showed functional defects, 26 of which were deleterious in all three assays. For 13 of these 26 variants, we could calculate the probability of pathogenicity using clinical and genetic data, resulting in the identification of 7 (likely) pathogenic variants. CONCLUSIONS We have functionally categorized 238 BRCA1 VUS using three different HRR-related assays. Classification based on clinical and genetic data alone for a subset of these variants confirmed the high sensitivity and specificity of our functional assays.
Collapse
Affiliation(s)
- Peter Bouwman
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Ingrid van der Heijden
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hanneke van der Gulden
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Roebi de Bruijn
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Oncode Institute and Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Merel E Braspenning
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Setareh Moghadasi
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lodewyk F A Wessels
- Oncode Institute and Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Maaike P G Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jos Jonkers
- Oncode Institute and Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| |
Collapse
|
7
|
Kour A, Sambyal V, Guleria K, Singh NR, Uppal MS, Manjari M, Sudan M. Screening of BRCA1 variants c.190T>C, 1307delT, g.5331G>A and c.2612C>T in breast cancer patients from North India. Genet Mol Biol 2020; 43:e20190014. [PMID: 32453341 PMCID: PMC7250277 DOI: 10.1590/1678-4685-gmb-2019-0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/22/2019] [Indexed: 12/01/2022] Open
Abstract
The polymorphic variants of BRCA1, which lead to amino acid
substitutions, have a known pathogenic role in breast cancer. The present study
investigated in North Indian breast cancer patients the association of risk with
four reported pathogenic variants of BRCA1: c.190T>C
(p.Cys64Arg), 1307delT, g.5331G>A (p.G1738R) and c.2612C>T (p.Pro871Leu).
Genotyping was done by PCR-RFLP method in 255 clinically confirmed breast cancer
patients and 255 age and gender matched healthy individuals. For c.190T>C,
1307delT and g.5331G>A, all the patients and controls had the wild-type
genotype indicating no association with breast cancer risk. For c.2612C>T
polymorphism, the frequency of the CC, CT, and TT genotypes was 14.5 vs 15.7%,
59.6 vs 53.7% and 25.9 vs 30.6% in breast cancer patients and controls
respectively. The frequency of heterozygotes (CT genotype) was higher in cases
than controls but the difference was not statistically significant. Genetic
model analysis showed no association of the four analyzed BRCA1
variants with breast cancer risk with any model. The studied variants were not
associated with the risk of breast cancer in Punjab, North west India,
suggesting a need for further screening of other BRCA1
variants. It is the first reported study on these 4 variants from India.
Collapse
Affiliation(s)
- Akeen Kour
- Guru Nanak Dev University, Department of Human Genetics, Human Cytogenetics Laboratory, Amritsar, Punjab, India
| | - Vasudha Sambyal
- Guru Nanak Dev University, Department of Human Genetics, Human Cytogenetics Laboratory, Amritsar, Punjab, India
| | - Kamlesh Guleria
- Guru Nanak Dev University, Department of Human Genetics, Human Cytogenetics Laboratory, Amritsar, Punjab, India
| | - Neeti Rajan Singh
- Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah,Department of Surgery, Amritsar, Punjab, India
| | - Manjit Singh Uppal
- Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah,Department of Surgery, Amritsar, Punjab, India
| | - Mridu Manjari
- Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah,Department of Pathology, Amritsar, Punjab, India
| | - Meena Sudan
- Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Department of Radiotherapy, Amritsar, Punjab, India
| |
Collapse
|
8
|
Cervelli T, Lodovichi S, Bellè F, Galli A. Yeast-based assays for the functional characterization of cancer-associated variants of human DNA repair genes. MICROBIAL CELL 2020; 7:162-174. [PMID: 32656256 PMCID: PMC7328678 DOI: 10.15698/mic2020.07.721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Technological advances are continuously revealing new genetic variants that are often difficult to interpret. As one of the most genetically tractable model organisms, yeast can have a central role in determining the consequences of human genetic variation. DNA repair gene mutations are associated with many types of cancers, therefore the evaluation of the functional impact of these mutations is crucial for risk assessment and for determining therapeutic strategies. Owing to the evolutionary conservation of DNA repair pathways between human cells and the yeast Saccharomyces cerevisiae, several functional assays have been developed. Here, we describe assays for variants of human genes belonging to the major DNA repair pathways divided in functional assays for human genes with yeast orthologues and human genes lacking a yeast orthologue. Human genes with orthologues can be studied by introducing the correspondent human mutations directly in the yeast gene or expressing the human gene carrying the mutations; while the only possible approach for human genes without a yeast orthologue is the heterologous expression. The common principle of these approaches is that the mutated gene determines a phenotypic alteration that can vary according to the gene studied and the domain of the protein. Here, we show how the versatility of yeast can help in classifying cancer-associated variants.
Collapse
Affiliation(s)
- Tiziana Cervelli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Samuele Lodovichi
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Francesca Bellè
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| |
Collapse
|
9
|
Yadegari F, Farahmand L, Esmaeili R, Samadi T, Majidzadeh K. Functional investigation of the BRCA1 Val1714Gly and Asp1733Gly variants by computational tools and yeast transcription activation assay. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2020; 8:113-118. [PMID: 31998812 PMCID: PMC6802689 DOI: 10.22099/mbrc.2019.33971.1414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mutations in the BRCA1 gene are known to be a major cause of hereditary breast cancer. However, characterizing the point mutations associated with cancer in BRCA1 is challenging because the functional impact of most of them is still unknown. Nowadays, a variety of methods are employed to identify cancer-associated mutations in BRCA1. This study is aimed to assess the functional effects of two mutations, Asp1733Gly and Val1714Gly, using a combination of insilico tools and yeast functional transcription activator assay. Our computational analysis showed that theVal1714Gly mutation was deleterious, while the other one, Asp1733Gly, predicted as neutral. Also using yeast functional transcription activator assay, we found that the Asp1733Gly mutation displayed similar ability with positive controls. In contrast, the Val1714Gly mutation completely abrogated transcriptional activity in the yeast. These results suggested that Val1714Gly and Asp1733Gly can be classified as pathogenic and benign mutations for the BRCA1, respectively.
Collapse
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
| | - Tannaz Samadi
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Keivan Majidzadeh
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| |
Collapse
|
10
|
Lodovichi S, Bellè F, Cervelli T, Lorenzoni A, Maresca L, Cozzani C, Caligo MA, Galli A. Effect of BRCA1 missense variants on gene reversion in DNA double-strand break repair mutants and cell cycle-arrested cells of Saccharomyces cerevisiae. Mutagenesis 2019; 35:189-195. [DOI: 10.1093/mutage/gez043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/31/2019] [Indexed: 12/13/2022] Open
Abstract
AbstractEvaluation of the functional impact of germline BRCA1 variants that are likely to be associated to breast and ovarian cancer could help to investigate the mechanism of BRCA1 tumorigenesis. Expression of pathogenic BRCA1 missense variants increased homologous recombination (HR) and gene reversion (GR) in yeast. We thought to exploit yeast genetics to shed light on BRCA1-induced genome instability and tumorigenesis. We determined the effect on GR of several neutral and pathogenic BRCA1 variants in the yeast strain RSY6wt and its isogenic DSB repair mutants, such as mre11∆, rad50∆ and rad51∆. In the RSY6wt, four out of five pathogenic and two out of six neutral variants significantly increased GR; rad51∆ strain, the pathogenic variants C61G and A1708E induced a weak but significant increase in GR. On the other hand, in rad50∆ mutant expressing the pathogenic variants localised at the BRCT domain, a further GR increase was seen. The neutral variant N132K and the VUS A1789T induced a weak GR increase in mre11∆ mutant. Thus, BRCA1 missense variants require specific genetic functions and presumably induced GR by different mechanisms. As DNA repair is regulated by cell cycle, we determined the effect on GR of BRCA1 variants in cell cycle-arrested RSYwt cells. GR is highly BRCA1-inducible in S-phase-arrested cells as compared to G1 or G2. Sequence analysis of genomic DNA from ILV1 revertant clones showed that BRCA1-induced ilv1-92 reversion by base substitution when GR is at least 6-fold over the control. Our study demonstrated that BRCA1 may interfere with yeast DNA repair functions that are active in S-phase causing high level of GR. In addition, we confirmed here that yeast could be a reliable model to investigate the mechanism and genetic requirements of BRCA1-induced genome instability. Finally, developing yeast-based assays to characterise BRCA1 missense variants could be useful to design more precise therapies.
Collapse
Affiliation(s)
- Samuele Lodovichi
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Francesca Bellè
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Alessandra Lorenzoni
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Luisa Maresca
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR, Pisa, Italy
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Cristina Cozzani
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR, Pisa, Italy
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology, CNR, Pisa, Italy
| |
Collapse
|
11
|
Fernandes VC, Golubeva VA, Di Pietro G, Shields C, Amankwah K, Nepomuceno TC, de Gregoriis G, Abreu RBV, Harro C, Gomes TT, Silva RF, Suarez-Kurtz G, Couch FJ, Iversen ES, Monteiro ANA, Carvalho MA. Impact of amino acid substitutions at secondary structures in the BRCT domains of the tumor suppressor BRCA1: Implications for clinical annotation. J Biol Chem 2019; 294:5980-5992. [PMID: 30765603 DOI: 10.1074/jbc.ra118.005274] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/06/2019] [Indexed: 01/07/2023] Open
Abstract
Genetic testing for BRCA1, a DNA repair protein, can identify carriers of pathogenic variants associated with a substantially increased risk for breast and ovarian cancers. However, an association with increased risk is unclear for a large fraction of BRCA1 variants present in the human population. Most of these variants of uncertain clinical significance lead to amino acid changes in the BRCA1 protein. Functional assays are valuable tools to assess the potential pathogenicity of these variants. Here, we systematically probed the effects of substitutions in the C terminus of BRCA1: the N- and C-terminal borders of its tandem BRCT domain, the BRCT-[N-C] linker region, and the α1 and α'1 helices in BRCT-[N] and -[C]. Using a validated transcriptional assay based on a fusion of the GAL4 DNA-binding domain to the BRCA1 C terminus (amino acids 1396-1863), we assessed the functional impact of 99 missense variants of BRCA1. We include the data obtained for these 99 missense variants in a joint analysis to generate the likelihood of pathogenicity for 347 missense variants in BRCA1 using VarCall, a Bayesian integrative statistical model. The results from this analysis increase our understanding of BRCA1 regions less tolerant to changes, identify functional borders of structural domains, and predict the likelihood of pathogenicity for 98% of all BRCA1 missense variants in this region recorded in the population. This knowledge will be critical for improving risk assessment and clinical treatment of carriers of BRCA1 variants.
Collapse
Affiliation(s)
- Vanessa C Fernandes
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Volha A Golubeva
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Giuliano Di Pietro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612; the Universidade Federal de Sergipe, Campus São Cristóvão, Brazil 49100-000
| | - Cara Shields
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Kwabena Amankwah
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Thales C Nepomuceno
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050; the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612
| | - Giuliana de Gregoriis
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Renata B V Abreu
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Carly Harro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612; the Department of Cell Biology, Microbiology, College of Arts and Sciences, University of South Florida Cancer Biology Ph.D. Program, Tampa, Florida 33612
| | - Thiago T Gomes
- the Instituto Federal do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Ricceli F Silva
- the Instituto Federal do Rio de Janeiro, Rio de Janeiro 20270-021, Brazil
| | - Guilherme Suarez-Kurtz
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050
| | - Fergus J Couch
- the Department of Laboratory Medicine, Mayo Clinic, Rochester, Minnesota 55905
| | - Edwin S Iversen
- the Department of Statistics, Duke University, Durham, North Carolina 27710
| | - Alvaro N A Monteiro
- the Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612.
| | - Marcelo A Carvalho
- From the Instituto Nacional de Câncer, Programa de Pesquisa Clínica, Rio de Janeiro, Brazil 20231-050.
| |
Collapse
|
12
|
Langerud J, Jarhelle E, Van Ghelue M, Ariansen SL, Iversen N. Trans-activation-based risk assessment of BRCA1 BRCT variants with unknown clinical significance. Hum Genomics 2018; 12:51. [PMID: 30458859 PMCID: PMC6247502 DOI: 10.1186/s40246-018-0183-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 11/08/2018] [Indexed: 11/30/2022] Open
Abstract
Background Deleterious variants in the tumour suppressor BRCA1 are known to cause hereditary breast and ovarian cancer syndrome (HBOC). Missense variants in BRCA1 pose a challenge in clinical care, as their effect on protein functionality often remains unknown. Many of the pathogenic missense variants found in BRCA1 are located in the BRCA1 C-terminal (BRCT) domains, domains that are known to be vital for key functions such as homologous recombination repair, protein-protein interactions and trans-activation (TA). We investigated the TA activity of 12 BRCA1 variants of unknown clinical significance (VUSs) located in the BRCT domains to aid in the classification of these variants. Results Twelve BRCA1 VUSs were investigated using a modified version of the dual luciferase TA activity assay (TA assay) that yielded increased sensitivity and sample throughput. Variants were classified according to American College of Medical Genetics and Genomics (ACMG) criteria using TA assay results and available data. In combining our TA-assay results and available data, in accordance with the ACMG guidelines for variant classification, we proposed the following variant classifications: c.5100A>G, c.5326C>T, c.5348T>C and c.5477A>T as likely benign (class 2) variants. c.5075A>C, c.5116G>A and c.5513T>G were likely pathogenic (class 4), whereas c.5096G>A likely represents a likely pathogenic variant with moderate penetrance. Variants c.5123C>T, c.5125G>A, c.5131A>C and c.5504G>A remained classified as VUSs (class 3). Conclusions The modified TA assay provides efficient risk assessment of rare missense variants found in the BRCA1 BRCT-domains. We also report that increased post-transfection incubation time yielded a significant increase in TA assay sensitivity. Electronic supplementary material The online version of this article (10.1186/s40246-018-0183-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jonas Langerud
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway
| | | | - Nina Iversen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
13
|
Petitalot A, Dardillac E, Jacquet E, Nhiri N, Guirouilh-Barbat J, Julien P, Bouazzaoui I, Bonte D, Feunteun J, Schnell JA, Lafitte P, Aude JC, Noguès C, Rouleau E, Lidereau R, Lopez BS, Zinn-Justin S, Caputo SM. Combining Homologous Recombination and Phosphopeptide-binding Data to Predict the Impact of BRCA1 BRCT Variants on Cancer Risk. Mol Cancer Res 2018; 17:54-69. [PMID: 30257991 DOI: 10.1158/1541-7786.mcr-17-0357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 02/07/2018] [Accepted: 09/11/2018] [Indexed: 11/16/2022]
Abstract
BRCA1 mutations have been identified that increase the risk of developing hereditary breast and ovarian cancers. Genetic screening is now offered to patients with a family history of cancer, to adapt their treatment and the management of their relatives. However, a large number of BRCA1 variants of uncertain significance (VUS) are detected. To better understand the significance of these variants, a high-throughput structural and functional analysis was performed on a large set of BRCA1 VUS. Information on both cellular localization and homology-directed DNA repair (HR) capacity was obtained for 78 BRCT missense variants in the UMD-BRCA1 database and measurement of the structural stability and phosphopeptide-binding capacities was performed for 42 mutated BRCT domains. This extensive and systematic analysis revealed that most characterized causal variants affect BRCT-domain solubility in bacteria and all impair BRCA1 HR activity in cells. Furthermore, binding to a set of 5 different phosphopeptides was tested: all causal variants showed phosphopeptide-binding defects and no neutral variant showed such defects. A classification is presented on the basis of mutated BRCT domain solubility, phosphopeptide-binding properties, and VUS HR capacity. These data suggest that HR-defective variants, which present, in addition, BRCT domains either insoluble in bacteria or defective for phosphopeptide binding, lead to an increased cancer risk. Furthermore, the data suggest that variants with a WT HR activity and whose BRCT domains bind with a WT affinity to the 5 phosphopeptides are neutral. The case of variants with WT HR activity and defective phosphopeptide binding should be further characterized, as this last functional defect might be sufficient per se to lead to tumorigenesis. IMPLICATIONS: The analysis of the current study on BRCA1 structural and functional defects on cancer risk and classification presented may improve clinical interpretation and therapeutic selection.
Collapse
Affiliation(s)
- Ambre Petitalot
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France.,Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Elodie Dardillac
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Naima Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Josée Guirouilh-Barbat
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Patrick Julien
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Isslam Bouazzaoui
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dorine Bonte
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France
| | - Jean Feunteun
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France
| | - Jeff A Schnell
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Lafitte
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Jean-Christophe Aude
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Catherine Noguès
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Etienne Rouleau
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Rosette Lidereau
- Service de Génétique, Département de Biologie des Tumeurs, Institut Curie, Paris, France
| | - Bernard S Lopez
- Institut Gustave Roussy, CNRS UMR 8200, Université Paris-Saclay, Villejuif, France.,Team labeled "Ligue 2014," Villejuif, France
| | - Sophie Zinn-Justin
- Institut de Biologie Intégrative de la Cellule, CEA, CNRS, Université Paris Sud, UMR 9198, Université Paris-Saclay, Gif-sur-Yvette, France.
| | | | | |
Collapse
|
14
|
Maresca L, Lodovichi S, Lorenzoni A, Cervelli T, Monaco R, Spugnesi L, Tancredi M, Falaschi E, Zavaglia K, Landucci E, Roncella M, Congregati C, Gadducci A, Naccarato AG, Caligo MA, Galli A. Functional Interaction Between BRCA1 and DNA Repair in Yeast May Uncover a Role of RAD50, RAD51, MRE11A, and MSH6 Somatic Variants in Cancer Development. Front Genet 2018; 9:397. [PMID: 30283497 PMCID: PMC6156519 DOI: 10.3389/fgene.2018.00397] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/31/2018] [Indexed: 01/07/2023] Open
Abstract
In this study, we determined if BRCA1 partners involved in DNA double-strand break (DSB) and mismatch repair (MMR) may contribute to breast and ovarian cancer development. Taking advantage the functional conservation of DNA repair pathways between yeast and human, we expressed several BRCA1 missense variants in DNA repair yeast mutants to identify functional interaction between BRCA1 and DNA repair in BRCA1-induced genome instability. The pathogenic p.C61G, pA1708E, p.M775R, and p.I1766S, and the neutral pS1512I BRCA1 variants increased intra-chromosomal recombination in the DNA-repair proficient strain RSY6. In the mre11, rad50, rad51, and msh6 deletion strains, the BRCA1 variants p.C61G, pA1708E, p.M775R, p.I1766S, and pS1215I did not increase intra-chromosomal recombination suggesting that a functional DNA repair pathway is necessary for BRCA1 variants to determine genome instability. The pathogenic p.C61G and p.I1766S and the neutral p.N132K, p.Y179C, and p.N550H variants induced a significant increase of reversion in the msh2Δ strain; the neutral p.Y179C and the pathogenic p.I1766S variant induced gene reversion also, in the msh6Δ strain. These results imply a functional interaction between MMR and BRCA1 in modulating genome instability. We also performed a somatic mutational screening of MSH6, RAD50, MRE11A, and RAD51 genes in tumor samples from 34 patients and identified eight pathogenic or predicted pathogenic rare missense variants: four in MSH6, one in RAD50, one in MRE11A, and two in RAD51. Although we found no correlation between BRCA1 status and these somatic DNA repair variants, this study suggests that somatic missense variants in DNA repair genes may contribute to breast and ovarian tumor development.
Collapse
Affiliation(s)
- Luisa Maresca
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Samuele Lodovichi
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy.,PhD Program in Clinical and Translational Sciences, University of Pisa, Pisa, Italy
| | - Alessandra Lorenzoni
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
| | - Tiziana Cervelli
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
| | - Rossella Monaco
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Laura Spugnesi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Mariella Tancredi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Elisabetta Falaschi
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Katia Zavaglia
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | | | | | - Caterina Congregati
- Department of Clinical and Experimental Medicine, Division of Internal Medicine, University Hospital of Pisa, Pisa, Italy
| | - Angiolo Gadducci
- Department of Clinical and Experimental Medicine, Division of Gynecology and Obstetrics, University Hospital of Pisa, Pisa, Italy
| | - Antonio Giuseppe Naccarato
- Department of Translational Research and New Technologies in Medicine and Surgery, University Hospital of Pisa, Pisa, Italy
| | - Maria Adelaide Caligo
- Molecular Genetics Unit, Department of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics, Institute of Clinical Physiology, CNR Pisa, Pisa, Italy
| |
Collapse
|
15
|
Jarhelle E, Riise Stensland HMF, Mæhle L, Van Ghelue M. Characterization of BRCA1 and BRCA2 variants found in a Norwegian breast or ovarian cancer cohort. Fam Cancer 2017; 16:1-16. [PMID: 27495310 DOI: 10.1007/s10689-016-9916-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Germline mutations in BRCA1 and BRCA2 cause hereditary breast and ovarian cancer. Molecular screening of these two genes in patients with a family history of breast or ovarian cancer has revealed pathogenic variants as well as genetic variants of unknown significance (VUS). These VUS may cause a challenge in the genetic counseling process regarding clinical management of the patient and the family. We investigated 32 variants previously detected in 33 samples from patients with a family history of breast or ovarian cancer. cDNA was analyzed for alternative transcripts and selected missense variants located in the BRCT domains of BRCA1 were assessed for their trans-activation ability. Although an extensive cDNA analysis was done, only three of the 32 variants appeared to affect the splice-process (BRCA1 c.213-5T>A, BRCA1 c.5434C>G and BRCA2 c.68-7T>A). In addition, two variants located in the BRCT domains of BRCA1 (c.5075A>C p.Asp1692Ala and c.5513T>G p.Val1838Gly) were shown to abolish the BRCT domain trans-activation ability, whereas BRCA1 c.5125G>A p.Gly1709Arg exhibited equal trans-activation capability as the WT domain. These functional studies may offer further insights into the pathogenicity of certain identified variants; however, this assay is only applicable for a subset of missense variants.
Collapse
Affiliation(s)
- Elisabeth Jarhelle
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway
| | - Hilde Monica Frostad Riise Stensland
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway.,Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway
| | - Lovise Mæhle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Marijke Van Ghelue
- Department of Medical Genetics, Division of Child and Adolescent Health, University Hospital of North Norway, Tromsø, Norway. .,Department of Clinical Medicine, University of Tromsø, Tromsø, Norway. .,Northern Norway Family Cancer Center, University Hospital of North Norway, Tromsø, Norway.
| |
Collapse
|
16
|
Data sharing as a national quality improvement program: reporting on BRCA1 and BRCA2 variant-interpretation comparisons through the Canadian Open Genetics Repository (COGR). Genet Med 2017; 20:294-302. [PMID: 28726806 DOI: 10.1038/gim.2017.80] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/17/2017] [Indexed: 12/23/2022] Open
Abstract
PurposeThe purpose of this study was to develop a national program for Canadian diagnostic laboratories to compare DNA-variant interpretations and resolve discordant-variant classifications using the BRCA1 and BRCA2 genes as a case study.MethodsBRCA1 and BRCA2 variant data were uploaded and shared through the Canadian Open Genetics Repository (COGR; http://www.opengenetics.ca). A total of 5,554 variant observations were submitted; classification differences were identified and comparison reports were sent to participating laboratories. Each site had the opportunity to reclassify variants. The data were analyzed before and after the comparison report process to track concordant- or discordant-variant classifications by three different models.ResultsVariant-discordance rates varied by classification model: 38.9% of variants were discordant when using a five-tier model, 26.7% with a three-tier model, and 5.0% with a two-tier model. After the comparison report process, the proportion of discordant variants dropped to 30.7% with the five-tier model, to 14.2% with the three-tier model, and to 0.9% using the two-tier model.ConclusionWe present a Canadian interinstitutional quality improvement program for DNA-variant interpretations. Sharing of variant knowledge by clinical diagnostic laboratories will allow clinicians and patients to make more informed decisions and lead to better patient outcomes.
Collapse
|
17
|
Pesaran T, Karam R, Huether R, Li S, Farber-Katz S, Chamberlin A, Chong H, LaDuca H, Elliott A. Beyond DNA: An Integrated and Functional Approach for Classifying Germline Variants in Breast Cancer Genes. Int J Breast Cancer 2016; 2016:2469523. [PMID: 27822389 PMCID: PMC5086358 DOI: 10.1155/2016/2469523] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 09/04/2016] [Accepted: 09/19/2016] [Indexed: 11/17/2022] Open
Abstract
Genetic testing for hereditary breast cancer is an integral part of individualized care in the new era of precision medicine. The accuracy of an assay is reliant on not only the technology and bioinformatics analysis utilized but also the experience and infrastructure required to correctly classify genetic variants as disease-causing. Interpreting the clinical significance of germline variants identified by hereditary cancer testing is complex and has a significant impact on the management of patients who are at increased cancer risk. In this review we give an overview of our clinical laboratory's integrated approach to variant assessment. We discuss some of the nuances that should be considered in the assessment of genomic variants. In addition, we highlight lines of evidence such as functional assays and structural analysis that can be useful in the assessment of rare and complex variants.
Collapse
Affiliation(s)
- T. Pesaran
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - R. Karam
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - R. Huether
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - S. Li
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - S. Farber-Katz
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - A. Chamberlin
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - H. Chong
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - H. LaDuca
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| | - A. Elliott
- Ambry Genetics Corp., 15 Argonaut, Aliso Viejo, CA 92656, USA
| |
Collapse
|
18
|
Kamaraj B, Purohit R. Mutational Analysis on Membrane Associated Transporter Protein (MATP) and Their Structural Consequences in Oculocutaeous Albinism Type 4 (OCA4)-A Molecular Dynamics Approach. J Cell Biochem 2016; 117:2608-19. [PMID: 27019209 DOI: 10.1002/jcb.25555] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/24/2016] [Indexed: 12/11/2022]
Abstract
Oculocutaneous albinism type IV (OCA4) is an autosomal recessive inherited disorder which is characterized by reduced biosynthesis of melanin pigmentation in skin, hair, and eyes and caused by the genetic mutations in the membrane-associated transporter protein (MATP) encoded by SLC45A2 gene. The MATP protein consists of 530 amino acids which contains 12 putative transmembrane domains and plays an important role in pigmentation and probably functions as a membrane transporter in melanosomes. We scrutinized the most OCA4 disease-associated mutation and their structural consequences on SLC45A2 gene. To understand the atomic arrangement in 3D space, the native and mutant structures were modeled. Further the structural behavior of native and mutant MATP protein was investigated by molecular dynamics simulation (MDS) approach in explicit lipid and water background. We found Y317C as the most deleterious and disease-associated SNP on SLC45A2 gene. In MDS, mutations in MATP protein showed loss of stability and became more flexible, which alter its structural conformation and function. This phenomenon has indicated a significant role in inducing OCA4. Our study explored the understanding of molecular mechanism of MATP protein upon mutation at atomic level and further helps in the field of pharmacogenomics to develop a personalized medicine for OCA4 disorder. J. Cell. Biochem. 117: 2608-2619, 2016. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Balu Kamaraj
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk-Antwerp, Belgium
| | - Rituraj Purohit
- Department of Biotechnology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India.
| |
Collapse
|
19
|
Functional assays provide a robust tool for the clinical annotation of genetic variants of uncertain significance. NPJ Genom Med 2016; 1. [PMID: 28781887 PMCID: PMC5539989 DOI: 10.1038/npjgenmed.2016.1] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Variants of Uncertain Significance (VUS) are genetic variants whose association with a disease phenotype has not been established. They are a common finding in sequencing-based genetic tests and pose a significant clinical challenge. The objective of this study was to assess the use of functional data to classify variants according to pathogenicity. We conduct functional analysis of a large set of BRCA1 VUS combining a validated functional assay with VarCall, a Bayesian hierarchical model to estimate the likelihood of pathogenicity given the functional data. The results from the functional assays were incorporated into a joint analysis of 214 BRCA1 VUS to predict their likelihood of pathogenicity (breast cancer). We show that applying the VarCall model (1.0 sensitivity; lower bound of 95% confidence interval (CI)=0.75 and 1.0 specificity; lower bound of 95% CI=0.83) to the current set of BRCA1 variants, use of the functional data would significantly reduce the number of VUS associated with the C-terminal region of the BRCA1 protein by ~87%. We extend this work developing yeast-based functional assays for two other genes coding for BRCT domain containing proteins, MCPH1 and MDC1. Analysis of missense variants in MCPH1 and MDC1 shows that structural inference based on the BRCA1 data set can aid in prioritising variants for further analysis. Taken together our results indicate that systematic functional assays can provide a robust tool to aid in clinical annotation of VUS. We propose that well-validated functional assays could be used for clinical annotation even in the absence of additional sources of evidence.
Collapse
|
20
|
Phenotype Prediction of Pathogenic Nonsynonymous Single Nucleotide Polymorphisms in WFS1. Sci Rep 2015; 5:14731. [PMID: 26435059 PMCID: PMC4592972 DOI: 10.1038/srep14731] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 08/25/2015] [Indexed: 01/20/2023] Open
Abstract
Wolfram syndrome (WS) is a rare, progressive, neurodegenerative disorder that has an autosomal recessive pattern of inheritance. The gene for WS, wolfram syndrome 1 gene (WFS1), is located on human chromosome 4p16.1 and encodes a transmembrane protein. To date, approximately 230 mutations in WFS1 have been confirmed, in which nonsynonymous single nucleotide polymorphisms (nsSNPs) are the most common forms of genetic variation. Nonetheless, there is poor knowledge on the relationship between SNP genotype and phenotype in other nsSNPs of the WFS1 gene. Here, we analysed 395 nsSNPs associated with the WFS1 gene using different computational methods and identified 20 nsSNPs to be potentially pathogenic. Furthermore, to identify the amino acid distributions and significances of pathogenic nsSNPs in the protein of WFS1, its transmembrane domain was constructed by the TMHMM server, which suggested that mutations outside of the TMhelix could have more effects on protein function. The predicted pathogenic mutations for the nsSNPs of the WFS1 gene provide an excellent guide for screening pathogenic mutations.
Collapse
|
21
|
Maresca L, Spugnesi L, Lodovichi S, Cozzani C, Naccarato AG, Tancredi M, Collavoli A, Falaschi E, Rossetti E, Aretini P, Cervelli T, Galli A, Caligo MA. MSH2 role in BRCA1-driven tumorigenesis: A preliminary study in yeast and in human tumors from BRCA1-VUS carriers. Eur J Med Genet 2015; 58:531-9. [PMID: 26381082 DOI: 10.1016/j.ejmg.2015.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 09/02/2015] [Accepted: 09/11/2015] [Indexed: 01/18/2023]
Abstract
BRCA1 interacts with several proteins implicated in homologous and non homologous recombination and in mismatch repair. The aim of this study is to determine if MSH2, a well known partner of BRCA1 involved in DNA repair, may contribute to breast and ovarian cancer development and progression. To better understand the functional interaction between BRCA1 and MSH2, we studied the effect of the deletion of MSH2 gene on BRCA1-induced genome instability in yeast. Preliminary results in yeast indicated that MSH2 and BRCA1 may interact to modulate homologous recombination (HR). We also carried out a genetic and epigenetic profiling of MSH2 gene by mutational analysis and promoter methylation evaluation in 9 breast and 2 ovarian tumors from carriers of BRCA1 unknown significance variants (VUS). 2/2 ovarian and 2/9 breast tumors carried MSH2 somatic mutations possible pathogenics (4/11, 36%): a missense mutation in exon 3 (p.G162R), a duplication of exon 1 and a deletion of exon 2. In addition, two germline synonymous variants in exon 11 were identified. None of the tumors showed promoter methylation. In conclusion, a surprisingly high frequency of MSH2 gene mutations has been found in tumor tissues from BRCA1 VUS carrier patients. This result supports the indication deriving from the yeast model that BRCA1 driven tumorigenesis may be modulated by MSH2.
Collapse
Affiliation(s)
- Luisa Maresca
- Section of Genetic Oncology, University of Pisa, Pisa, Italy
| | - Laura Spugnesi
- Section of Genetic Oncology, University of Pisa, Pisa, Italy
| | | | | | | | | | - Anita Collavoli
- Section of Genetic Oncology, University of Pisa, Pisa, Italy
| | | | | | | | | | - Alvaro Galli
- Institute of Clinical Physiology, CNR, Pisa, Italy.
| | | |
Collapse
|
22
|
Jhuraney A, Velkova A, Johnson RC, Kessing B, Carvalho RS, Whiley P, Spurdle AB, Vreeswijk MPG, Caputo SM, Millot GA, Vega A, Coquelle N, Galli A, Eccles D, Blok MJ, Pal T, van der Luijt RB, Santamariña Pena M, Neuhausen SL, Donenberg T, Machackova E, Thomas S, Vallée M, Couch FJ, Tavtigian SV, Glover JNM, Carvalho MA, Brody LC, Sharan SK, Monteiro AN. BRCA1 Circos: a visualisation resource for functional analysis of missense variants. J Med Genet 2015; 52:224-30. [PMID: 25643705 PMCID: PMC4392196 DOI: 10.1136/jmedgenet-2014-102766] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/29/2014] [Accepted: 12/05/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND Inactivating germline mutations in the tumour suppressor gene BRCA1 are associated with a significantly increased risk of developing breast and ovarian cancer. A large number (>1500) of unique BRCA1 variants have been identified in the population and can be classified as pathogenic, non-pathogenic or as variants of unknown significance (VUS). Many VUS are rare missense variants leading to single amino acid changes. Their impact on protein function cannot be directly inferred from sequence information, precluding assessment of their pathogenicity. Thus, functional assays are critical to assess the impact of these VUS on protein activity. BRCA1 is a multifunctional protein and different assays have been used to assess the impact of variants on different biochemical activities and biological processes. METHODS AND RESULTS To facilitate VUS analysis, we have developed a visualisation resource that compiles and displays functional data on all documented BRCA1 missense variants. BRCA1 Circos is a web-based visualisation tool based on the freely available Circos software package. The BRCA1 Circos web tool (http://research.nhgri.nih.gov/bic/circos/) aggregates data from all published BRCA1 missense variants for functional studies, harmonises their results and presents various functionalities to search and interpret individual-level functional information for each BRCA1 missense variant. CONCLUSIONS This research visualisation tool will serve as a quick one-stop publically available reference for all the BRCA1 missense variants that have been functionally assessed. It will facilitate meta-analysis of functional data and improve assessment of pathogenicity of VUS.
Collapse
Affiliation(s)
- Ankita Jhuraney
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- University of South Florida Cancer Biology PhD Program, Tampa, Florida, USA
| | - Aneliya Velkova
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Randall C Johnson
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Bailey Kessing
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Fredrick, Maryland, USA
| | - Renato S Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Phillip Whiley
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Population Health Division, QIMR, BNE, Brisbane, Queensland, Australia
| | - Maaike P G Vreeswijk
- Department of Human Genetics, Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sandrine M Caputo
- Service de Génétique, Institut Curie, Hôpital René Huguenin, Paris, France
| | - Gael A Millot
- Institut Curie, Université Pierre et Marie Curie, Paris, France
| | - Ana Vega
- Fundación Pública Galega de Medicina Xenómica, Santiago, Spain
| | - Nicolas Coquelle
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Alvaro Galli
- Instituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | | | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Tuya Pal
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Rob B van der Luijt
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | | | - Eva Machackova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Simon Thomas
- Salisbury District Hospital, Salisbury, Wiltshire, UK
| | - Maxime Vallée
- International Agency for Research on Cancer, Lyon, France
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, and Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Alberta, Canada
| | - Marcelo A Carvalho
- Instituto Federal de Educação, Ciência e Tecnologia, Rio de Janeiro, RJ, Brazil
- Instituto Nacional de Câncer, Divisão de Farmacologia, Rio de Janeiro, Brazil
| | - Lawrence C Brody
- Genome Technology Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Shyam K Sharan
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Alvaro N Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | |
Collapse
|
23
|
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.
Collapse
|
24
|
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.
Collapse
|
25
|
Loke J, Pearlman A, Upadhyay K, Tesfa L, Shao Y, Ostrer H. Functional variant analyses (FVAs) predict pathogenicity in the BRCA1 DNA double-strand break repair pathway. Hum Mol Genet 2015; 24:3030-7. [DOI: 10.1093/hmg/ddv048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/02/2015] [Indexed: 01/19/2023] Open
|
26
|
ENGIN HBILLUR, HOFREE MATAN, CARTER HANNAH. Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2015; 20:84-95. [PMID: 25592571 PMCID: PMC4299875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Here we present a method for extracting candidate cancer pathways from tumor 'omics data while explicitly accounting for diverse consequences of mutations for protein interactions. Disease-causing mutations are frequently observed at either core or interface residues mediating protein interactions. Mutations at core residues frequently destabilize protein structure while mutations at interface residues can specifically affect the binding energies of protein-protein interactions. As a result, mutations in a protein may result in distinct interaction profiles and thus have different phenotypic consequences. We describe a protein structure-guided pipeline for extracting interacting protein sets specific to a particular mutation. Of 59 cancer genes with 3D co-complexed structures in the Protein Data Bank, 43 showed evidence of mutations with different functional consequences. Literature survey reciprocated functional predictions specific to distinct mutations on APC, ATRX, BRCA1, CBL and HRAS. Our analysis suggests that accounting for mutation-specific perturbations to cancer pathways will be essential for personalized cancer therapy.
Collapse
Affiliation(s)
- H. BILLUR ENGIN
- School of Medicine, University of California San Diego, 9500 Gilman Dr. San Diego, CA 92093, USA
| | - MATAN HOFREE
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Dr. San Diego, CA 92093, USA
| | | |
Collapse
|
27
|
Gierman HJ, Fortney K, Roach JC, Coles NS, Li H, Glusman G, Markov GJ, Smith JD, Hood L, Coles LS, Kim SK. Whole-genome sequencing of the world's oldest people. PLoS One 2014; 9:e112430. [PMID: 25390934 PMCID: PMC4229186 DOI: 10.1371/journal.pone.0112430] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/29/2014] [Indexed: 11/18/2022] Open
Abstract
Supercentenarians (110 years or older) are the world's oldest people. Seventy four are alive worldwide, with twenty two in the United States. We performed whole-genome sequencing on 17 supercentenarians to explore the genetic basis underlying extreme human longevity. We found no significant evidence of enrichment for a single rare protein-altering variant or for a gene harboring different rare protein altering variants in supercentenarian compared to control genomes. We followed up on the gene most enriched for rare protein-altering variants in our cohort of supercentenarians, TSHZ3, by sequencing it in a second cohort of 99 long-lived individuals but did not find a significant enrichment. The genome of one supercentenarian had a pathogenic mutation in DSC2, known to predispose to arrhythmogenic right ventricular cardiomyopathy, which is recommended to be reported to this individual as an incidental finding according to a recent position statement by the American College of Medical Genetics and Genomics. Even with this pathogenic mutation, the proband lived to over 110 years. The entire list of rare protein-altering variants and DNA sequence of all 17 supercentenarian genomes is available as a resource to assist the discovery of the genetic basis of extreme longevity in future studies.
Collapse
Affiliation(s)
- Hinco J. Gierman
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
| | - Kristen Fortney
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
| | - Jared C. Roach
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Natalie S. Coles
- Gerontology Research Group, Los Angeles, CA, United States of America
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Hong Li
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Gustavo Glusman
- Institute for Systems Biology, Seattle, WA, United States of America
| | - Glenn J. Markov
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
| | - Justin D. Smith
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, United States of America
| | - L. Stephen Coles
- Gerontology Research Group, Los Angeles, CA, United States of America
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States of America
| | - Stuart K. Kim
- Depts. of Developmental Biology and Genetics, Stanford University, Stanford, CA, United States of America
- * E-mail:
| |
Collapse
|
28
|
Computational Analysis Reveals the Association of Threonine 118 Methionine Mutation in PMP22 Resulting in CMT-1A. Adv Bioinformatics 2014; 2014:502618. [PMID: 25400662 PMCID: PMC4220619 DOI: 10.1155/2014/502618] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/26/2014] [Accepted: 09/26/2014] [Indexed: 12/31/2022] Open
Abstract
The T118M mutation in PMP22 gene is associated with Charcot Marie Tooth, type 1A (CMT1A). CMT1A is a form of Charcot-Marie-Tooth disease, the most common inherited disorder of the peripheral nervous system. Mutations in CMT related disorder are seen to increase the stability of the protein resulting in the diseased state. We performed SNP analysis for all the nsSNPs of PMP22 protein and carried out molecular dynamics simulation for T118M mutation to compare the stability difference between the wild type protein structure and the mutant protein structure. The mutation T118M resulted in the overall increase in the stability of the mutant protein. The superimposed structure shows marked structural variation between the wild type and the mutant protein structures.
Collapse
|
29
|
Kumar CV, Swetha RG, Ramaiah S, Anbarasu A. Tryptophan to Glycine mutation in the position 116 leads to protein aggregation and decreases the stability of the LITAF protein. J Biomol Struct Dyn 2014; 33:1695-709. [DOI: 10.1080/07391102.2014.968211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
30
|
Song H, Cicek MS, Dicks E, Harrington P, Ramus SJ, Cunningham JM, Fridley BL, Tyrer JP, Alsop J, Jimenez-Linan M, Gayther SA, Goode EL, Pharoah PDP. The contribution of deleterious germline mutations in BRCA1, BRCA2 and the mismatch repair genes to ovarian cancer in the population. Hum Mol Genet 2014; 23:4703-9. [PMID: 24728189 PMCID: PMC4119409 DOI: 10.1093/hmg/ddu172] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 04/02/2014] [Accepted: 04/08/2014] [Indexed: 12/20/2022] Open
Abstract
The aim of this study was to estimate the contribution of deleterious mutations in BRCA1, BRCA2, MLH1, MSH2, MSH6 and PMS2 to invasive epithelial ovarian cancer (EOC) in the population. The coding sequence and splice site boundaries of all six genes were amplified in germline DNA from 2240 invasive EOC cases and 1535 controls. Barcoded fragment libraries were sequenced using the Illumina GAII or HiSeq and sequence data for each subject de-multiplexed prior to interpretation. GATK and Annovar were used for variant detection and annotation. After quality control 2222 cases (99.2%) and 1528 controls (99.5%) were included in the final analysis. We identified 193 EOC cases (8.7%) carrying a deleterious mutation in at least one gene compared with 10 controls (0.65%). Mutations were most frequent in BRCA1 and BRCA2, with 84 EOC cases (3.8%) carrying a BRCA1 mutation and 94 EOC cases (4.2%) carrying a BRCA2 mutation. The combined BRCA1 and BRCA2 mutation prevalence was 11% in high-grade serous disease. Seventeen EOC cases carried a mutation in a mismatch repair gene, including 10 MSH6 mutation carriers (0.45%) and 4 MSH2 mutation carriers (0.18%). At least 1 in 10 women with high-grade serous EOC has a BRCA1 or BRCA2 mutation. The development of next generation sequencing technologies enables rapid mutation screening for multiple susceptibility genes at once, suggesting that routine clinical testing of all incidence cases should be considered.
Collapse
Affiliation(s)
- Honglin Song
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK,
| | - Mine S Cicek
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ed Dicks
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Patricia Harrington
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Susan J Ramus
- Department of Preventive Medicine, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, University of Southern California, CA, USA
| | | | - Brooke L Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas, USA and
| | - Jonathan P Tyrer
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jennifer Alsop
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | | | - Simon A Gayther
- Department of Preventive Medicine, Keck School of Medicine, USC/Norris Comprehensive Cancer Center, University of Southern California, CA, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Paul D P Pharoah
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| |
Collapse
|
31
|
Computational screening of disease associated mutations on NPC1 gene and its structural consequence in Niemann-Pick type-C1. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11515-014-1314-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
32
|
Evidence of colorectal cancer-associated mutation in MCAK: a computational report. Cell Biochem Biophys 2014; 67:837-51. [PMID: 23564489 DOI: 10.1007/s12013-013-9572-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Computational prediction of disease-associated non-synonymous polymorphism (nsSNP) has provided a significant platform to filter out the pathological mutations from large pool of SNP datasets at a very low cost input. Several methodologies and complementary protocols have been previously implemented and has provided significant prediction results. Although the previously implicated prediction methods were capable of investigating the most likely deleterious nsSNPs, but due to the lack of genotype-phenotype association analysis, the prediction results lacked in accuracy level. In this work we implemented the computational compilation of protein conformational changes as well as the probable disease-associated phenotypic outcomes. Our result suggested E403K mutation in mitotic centromere-associated kinesin protein as highly damaging and showed strong concordance to the previously observed colorectal cancer mutations aggregation tendency and energy value changes. Moreover, the molecular dynamics simulation results showed major loss in conformation and stability of mutant N-terminal kinesin-like domain structure. The result obtained in this study will provide future prospect of computational approaches in determining the SNPs that may affect the native conformation of protein structure and lead to cancer-associated disorders.
Collapse
|
33
|
Carvalho RS, Abreu RBV, Velkova A, Marsillac S, Rodarte RS, Suarez-Kurtz G, Iversen ES, Monteiro ANA, Carvalho MA. Probing structure-function relationships in missense variants in the carboxy-terminal region of BRCA1. PLoS One 2014; 9:e97766. [PMID: 24845084 PMCID: PMC4028255 DOI: 10.1371/journal.pone.0097766] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/23/2014] [Indexed: 11/25/2022] Open
Abstract
Germline inactivating variants in BRCA1 lead to a significantly increased risk of breast and ovarian cancers in carriers. While the functional effect of many variants can be inferred from the DNA sequence, determining the effect of missense variants present a significant challenge. A series of biochemical and cell biological assays have been successfully used to explore the impact of these variants on the function of BRCA1, which contribute to assessing their likelihood of pathogenicity. It has been determined that variants that co-localize with structural or functional motifs are more likely to disrupt the stability and function of BRCA1. Here we assess the functional impact of 37 variants chosen to probe the functional impact of variants in phosphorylation sites and in the BRCT domains. In addition, we perform a meta-analysis of 170 unique variants tested by the transcription activation assays in the carboxy-terminal domain of BRCA1 using a recently developed computation model to provide assessment for functional impact and their likelihood of pathogenicity.
Collapse
Affiliation(s)
- Renato S Carvalho
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America; Programa de Farmacologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Renata B V Abreu
- Programa de Farmacologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - Aneliya Velkova
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Sylvia Marsillac
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | | | | | - Edwin S Iversen
- Department of Statistical Science, Duke University, Durham, North Carolina, United States of America
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Marcelo A Carvalho
- Programa de Farmacologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil; Instituto Federal de Educação, Ciência e Tecnologia do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
34
|
Kamaraj B, Rajendran V, Sethumadhavan R, Kumar CV, Purohit R. Mutational analysis of FUS gene and its structural and functional role in amyotrophic lateral sclerosis 6. J Biomol Struct Dyn 2014; 33:834-44. [DOI: 10.1080/07391102.2014.915762] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Balu Kamaraj
- School of Bio Sciences and Technology (SBST), Bioinformatics Division, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu, India
| | - Vidya Rajendran
- School of Bio Sciences and Technology (SBST), Bioinformatics Division, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu, India
| | - Rao Sethumadhavan
- School of Bio Sciences and Technology (SBST), Bioinformatics Division, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu, India
| | - Chundi Vinay Kumar
- School of Bio Sciences and Technology (SBST), Bioinformatics Division, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu, India
| | - Rituraj Purohit
- School of Bio Sciences and Technology (SBST), Bioinformatics Division, Vellore Institute of Technology University, Vellore 632014, Tamil Nadu, India
| |
Collapse
|
35
|
Comprehensive BRCA1 and BRCA2 mutational profile in Lithuania. Cancer Genet 2014; 207:195-205. [DOI: 10.1016/j.cancergen.2014.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 04/30/2014] [Accepted: 05/01/2014] [Indexed: 01/11/2023]
|
36
|
Christou CM, Hadjisavvas A, Kyratzi M, Flouri C, Neophytou I, Anastasiadou V, Loizidou MA, Kyriacou K. The BRCA1 variant p.Ser36Tyr abrogates BRCA1 protein function and potentially confers a moderate risk of breast cancer. PLoS One 2014; 9:e93400. [PMID: 24695549 PMCID: PMC3973689 DOI: 10.1371/journal.pone.0093400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 03/04/2014] [Indexed: 11/30/2022] Open
Abstract
The identification of variants of unknown clinical significance (VUS) in the BRCA1 gene complicates genetic counselling and causes additional anxiety to carriers. In silico approaches currently used for VUS pathogenicity assessment are predictive and often produce conflicting data. Furthermore, functional assays are either domain or function specific, thus they do not examine the entire spectrum of BRCA1 functions and interpretation of individual assay results can be misleading. PolyPhen algorithm predicted that the BRCA1 p.Ser36Tyr VUS identified in the Cypriot population was damaging, whereas Align-GVGD predicted that it was possibly of no significance. In addition the BRCA1 p.Ser36Tyr variant was found to be associated with increased risk (OR = 3.47, 95% CI 1.13-10.67, P = 0.02) in a single case-control series of 1174 cases and 1109 controls. We describe a cellular system for examining the function of exogenous full-length BRCA1 and for classifying VUS. We achieved strong protein expression of full-length BRCA1 in transiently transfected HEK293T cells. The p.Ser36Tyr VUS exhibited low protein expression similar to the known pathogenic variant p.Cys61Gly. Co-precipitation analysis further demonstrated that it has a reduced ability to interact with BARD1. Further, co-precipitation analysis of nuclear and cytosolic extracts as well as immunofluorescence studies showed that a high proportion of the p.Ser36Tyr variant is withheld in the cytoplasm contrary to wild type protein. In addition the ability of p.Ser36Tyr to co-localize with conjugated ubiquitin foci in the nuclei of S-phase synchronized cells following genotoxic stress with hydroxyurea is impaired at more pronounced levels than that of the p.Cys61Gly pathogenic variant. The p.Ser36Tyr variant demonstrates abrogated function, and based on epidemiological, genetic, and clinical data we conclude that the p.Ser36Tyr variant is probably associated with a moderate breast cancer risk.
Collapse
Affiliation(s)
- Charita M. Christou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Maria Kyratzi
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
- The University of Cyprus, Department of Biological Sciences, Nicosia, Cyprus
| | - Christina Flouri
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Ioanna Neophytou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Violetta Anastasiadou
- The Cyprus Institute of Neurology and Genetics, Department of Clinical Genetics, Nicosia, Cyprus
| | - Maria A. Loizidou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- The Cyprus Institute of Neurology and Genetics, Department of Electron Microscopy/Molecular Pathology, Nicosia, Cyprus
- * E-mail:
| |
Collapse
|
37
|
Vinay Kumar C, Kumar KM, Swetha R, Ramaiah S, Anbarasu A. Protein aggregation due to nsSNP resulting in P56S VABP protein is associated with amyotrophic lateral sclerosis. J Theor Biol 2014; 354:72-80. [PMID: 24681403 DOI: 10.1016/j.jtbi.2014.03.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 12/13/2022]
Abstract
Mutations in the gene encoding vesicle-associated membrane protein (VAPB) cause amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder. The VAPB gene is mapped to chromosome number 20 and can be found at cytogenetic location 20q13.33 of the chromosome. VAPB is seen to play a significant role in the unfolded protein response (UPR), which is a process that suppresses the accumulation of unfolded proteins in the endoplasmic reticulum. Earlier studies have reported two points; which we have analyzed in our study. Firstly, the mutation P56S in the VAPB is seen to increase the stability of the protein and secondly, the mutation P56S in VAPB is seen to interrupt the functioning of the gene and loses its ability to be involved in the activation of the IRE1/XBP1 pathway which leads to ALS. With correlation on the previous research studies on the stability of this protein, we carried out Molecular dynamics (MD) simulation. We analyzed the SNP results of 17 nsSNPs obtained from dbSNP using SIFT, polyphen, I-Mutant, SNP&GO, PhDSNP and Mutpred to predict the role of nsSNPs in VAPB. MD simulation is carried out and plots for RMSD, RMSF, Rg, SASA, H-bond and PCA are obtained to check and prove the stability of the wild type and the mutant protein structure. The protein is checked for its aggregation and the results obtained show changes in the protein structure that might result in the loss of function.
Collapse
Affiliation(s)
- Chundi Vinay Kumar
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - K M Kumar
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Rayapadi Swetha
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India
| | - Anand Anbarasu
- School of Biosciences and Technology, VIT University, Vellore 632014, Tamil Nadu, India.
| |
Collapse
|
38
|
Functional analysis of BRCA1 missense variants of uncertain significance in Japanese breast cancer families. J Hum Genet 2013; 58:618-21. [PMID: 23842040 DOI: 10.1038/jhg.2013.71] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 05/27/2013] [Accepted: 06/01/2013] [Indexed: 11/08/2022]
Abstract
Germline mutations in the tumor suppressor genes BRCA1 and BRCA2 are responsible for a large proportion of familial breast cancer cases, and therefore, BRCA1 and BRCA2 genetic testing has become increasingly common in clinical practice. However, variants of uncertain significance (VUS) have been detected in 16.3% of Japanese patients suspected of having hereditary breast and ovarian cancers. The clinical importance of VUS is unknown, and their incidence has led to issues in risk counseling, assessment and treatment of cancer patients. In the present study, we performed functional analyses of two VUS in BRCA1, A1752G and Y1853C that were detected in two independent breast cancer patients who were suspected of having hereditary breast cancer. Segregation analysis revealed that Y1853C, but not A1752G, was cosegregated in affected family members. Conservation, transcription and structure analyses also supported the pathogenic potential of Y1853C. Detailed segregation and in silico and in vitro analyses will enhance our understanding of VUS and improve the management of cancer patients and their families.
Collapse
|
39
|
Kamaraj B, Purohit R. Computational Screening of Disease-Associated Mutations in OCA2 Gene. Cell Biochem Biophys 2013; 68:97-109. [DOI: 10.1007/s12013-013-9697-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
40
|
In silico screening and molecular dynamics simulation of disease-associated nsSNP in TYRP1 gene and its structural consequences in OCA3. BIOMED RESEARCH INTERNATIONAL 2013; 2013:697051. [PMID: 23862152 PMCID: PMC3703794 DOI: 10.1155/2013/697051] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 05/23/2013] [Accepted: 05/23/2013] [Indexed: 11/17/2022]
Abstract
Oculocutaneous albinism type III (OCA3), caused by mutations of TYRP1 gene, is an autosomal recessive disorder characterized by reduced biosynthesis of melanin pigment in the hair, skin, and eyes. The TYRP1 gene encodes a protein called tyrosinase-related protein-1 (Tyrp1). Tyrp1 is involved in maintaining the stability of tyrosinase protein and modulating its catalytic activity in eumelanin synthesis. Tyrp1 is also involved in maintenance of melanosome structure and affects melanocyte proliferation and cell death. In this work we implemented computational analysis to filter the most probable mutation that might be associated with OCA3. We found R326H and R356Q as most deleterious and disease associated by using PolyPhen 2.0, SIFT, PANTHER, I-mutant 3.0, PhD-SNP, SNP&GO, Pmut, and Mutpred tools. To understand the atomic arrangement in 3D space, the native and mutant (R326H and R356Q) structures were modelled. Finally the structural analyses of native and mutant Tyrp1 proteins were investigated using molecular dynamics simulation (MDS) approach. MDS results showed more flexibility in native Tyrp1 structure. Due to mutation in Tyrp1 protein, it became more rigid and might disturb the structural conformation and catalytic function of the structure and might also play a significant role in inducing OCA3. The results obtained from this study would facilitate wet-lab researches to develop a potent drug therapies against OCA3.
Collapse
|
41
|
Berzina D, Nakazawa-Miklasevica M, Zestkova J, Aksenoka K, Irmejs A, Gardovskis A, Kalniete D, Gardovskis J, Miklasevics E. BRCA1/2 mutation screening in high-risk breast/ovarian cancer families and sporadic cancer patient surveilling for hidden high-risk families. BMC MEDICAL GENETICS 2013; 14:61. [PMID: 23767878 PMCID: PMC3686592 DOI: 10.1186/1471-2350-14-61] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 06/11/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND The estimated ratio of hereditary breast/ovarian cancer (HBOC) based on family history is 1.5% in Latvia. This is significantly lower than the European average of 5-10%. Molecular markers like mutations and SNPs can help distinguish HBOC patients in the sporadic breast and ovarian cancer group. METHODS 50 patients diagnosed with HBOC in the Latvian Cancer Registry from January 2005 to December 2008 were screened for BRCA1 founder mutation-negatives and subjected to targeted resequencing of BRCA1 and BRCA2 genes. The newly found mutations were screened for in the breast and ovarian cancer group of 1075 patients by Real Time-PCR/HRM analysis and RFLP. RESULTS Four BRCA2 mutations including three novel BRCA2 frameshift mutations and one previously known BRCA2 frameshift mutation and one BRCA1 splicing mutation were identified. Two of the BRCA2 mutations were found in a group of consecutive breast cancer patients with a frequency of 0.51% and 0.38%. CONCLUSIONS Molecular screening of sequential cancer patients is an important tool to identify HBOC families.
Collapse
Affiliation(s)
- Dace Berzina
- Institute of Oncology, Riga Stradins University, Dzirciema Street 16, LV1007 Riga, Latvia
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Tram E, Savas S, Ozcelik H. Missense variants of uncertain significance (VUS) altering the phosphorylation patterns of BRCA1 and BRCA2. PLoS One 2013; 8:e62468. [PMID: 23704879 PMCID: PMC3660339 DOI: 10.1371/journal.pone.0062468] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2012] [Accepted: 03/21/2013] [Indexed: 12/20/2022] Open
Abstract
Mutations in BRCA1 and BRCA2 are responsible for a large proportion of breast-ovarian cancer families. Protein-truncating mutations have been effectively used in the clinical management of familial breast cancer due to their deleterious impact on protein function. However, the majority of missense variants identified throughout the genes continue to pose an obstacle for predictive informative testing due to low frequency and lack of information on how they affect BRCA1/2 function. Phosphorylation of BRCA1 and BRCA2 play an important role in their function as regulators of DNA repair, transcription and cell cycle in response to DNA damage but whether missense variants of uncertain significance (VUS) are able to disrupt this important process is not known. Here we employed a novel approach using NetworKIN which predicts in vivo kinase-substrate relationship, and evolutionary conservation algorithms SIFT, PolyPhen and Align-GVGD. We evaluated whether 191 BRCA1 and 43 BRCA2 VUS from the Breast Cancer Information Core (BIC) database can functionally alter the consensus phosphorylation motifs and abolish kinase recognition and binding to sites known to be phosphorylated in vivo. Our results show that 13.09% (25/191) BRCA1 and 13.95% (6/43) BRCA2 VUS altered the phosphorylation of BRCA1 and BRCA2. We highlight six BRCA1 (K309T, S632N, S1143F, Q1144H, Q1281P, S1542C) and three BRCA2 (S196I, T207A, P3292L) VUS as potentially clinically significant. These occurred rarely (n<2 in BIC), mutated evolutionarily conserved residues and abolished kinase binding to motifs established in the literature involved in DNA repair, cell cycle regulation, transcription or response to DNA damage. Additionally in vivo phosphorylation sites identified via through-put methods are also affected by VUS and are attractive targets for studying their biological and functional significance. We propose that rare VUS affecting phosphorylation may be a novel and important mechanism for which BRCA1 and BRCA2 functions are disrupted in breast cancer.
Collapse
Affiliation(s)
- Eric Tram
- Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Sevtap Savas
- Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Hilmi Ozcelik
- Fred A. Litwin Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
43
|
Lindor NM, Goldgar DE, Tavtigian SV, Plon SE, Couch FJ. BRCA1/2 sequence variants of uncertain significance: a primer for providers to assist in discussions and in medical management. Oncologist 2013; 18:518-24. [PMID: 23615697 DOI: 10.1634/theoncologist.2012-0452] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION DNA variants of uncertain significance (VUS) are common outcomes of clinical genetic testing for susceptibility to cancer. A statistically rigorous model that provides a pathogenicity score for each variant has been developed to aid in the clinical management of patients undergoing genetic testing. METHODS The information in this article is derived from multiple publications on VUS in BRCA genes, distilled for communicating with clinicians who may encounter VUS in their practice. RESULTS The posterior probability scores for BRCA1 or BRCA2 VUS, calculated from a multifactorial likelihood model, are explained, and links for looking up specific VUS are provided. The International Agency on Cancer Research (IARC) of the World Health Organization has proposed a simple five-tier system for clinical management that is not widely known to clinicians. Classes 1 and 2 in this system are managed as neutral variants, classes 4 and 5 are managed as pathogenic variants, and class 3 variants still have insufficient evidence to move to either end of this scale and, thus, cannot be used in medical management. CONCLUSIONS Development of models that integrate multiple independent lines of evidence has allowed classification of a growing number of VUS in the BRCA1 and BRCA2 genes. The pathogenicity score that is generated by this model maps to the IARC system for clinical management, which will assist clinicians in the medical management of those patients who obtain a VUS result upon testing.
Collapse
Affiliation(s)
- Noralane M Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, Arizona 85259, USA.
| | | | | | | | | |
Collapse
|
44
|
Quiles F, Fernández-Rodríguez J, Mosca R, Feliubadaló L, Tornero E, Brunet J, Blanco I, Capellá G, Pujana MÀ, Aloy P, Monteiro A, Lázaro C. Functional and structural analysis of C-terminal BRCA1 missense variants. PLoS One 2013; 8:e61302. [PMID: 23613828 PMCID: PMC3629201 DOI: 10.1371/journal.pone.0061302] [Citation(s) in RCA: 16] [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: 01/29/2013] [Accepted: 03/07/2013] [Indexed: 11/18/2022] Open
Abstract
Germline inactivating mutations in BRCA1 and BRCA2 genes are responsible for Hereditary Breast and Ovarian Cancer Syndrome (HBOCS). Genetic testing of these genes is available, although approximately 15% of tests identify variants of uncertain significance (VUS). Classification of these variants into pathogenic or non-pathogenic type is an important challenge in genetic diagnosis and counseling. The aim of the present study is to functionally assess a set of 7 missense VUS (Q1409L, S1473P, E1586G, R1589H, Y1703S, W1718L and G1770V) located in the C-terminal region of BRCA1 by combining in silico prediction tools and structural analysis with a transcription activation (TA) assay. The in silico prediction programs gave discrepant results making its interpretation difficult. Structural analysis of the three variants located in the BRCT domains (Y1703S, W1718L and G1770V) reveals significant alterations of BRCT structure. The TA assay shows that variants Y1703S, W1718L and G1770V dramatically compromise the transcriptional activity of BRCA1, while variants Q1409L, S1473P, E1586G and R1589H behave like wild-type BRCA1. In conclusion, our results suggest that variants Y1703S, W1718L and G1770V can be classified as likely pathogenic BRCA1 mutations.
Collapse
Affiliation(s)
- Francisco Quiles
- Hereditary Cancer Program, Catalan Institute of Oncology-(Bellvitge Institute for Biomedical Research; Girona Institute for Biomedical Research; Germans Trial i Pujol Research Institute) (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Juana Fernández-Rodríguez
- Hereditary Cancer Program, Catalan Institute of Oncology-(Bellvitge Institute for Biomedical Research; Girona Institute for Biomedical Research; Germans Trial i Pujol Research Institute) (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Roberto Mosca
- Institute for Research in Biomedicine (IRB) Barcelona, Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
| | - Lídia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology-(Bellvitge Institute for Biomedical Research; Girona Institute for Biomedical Research; Germans Trial i Pujol Research Institute) (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Eva Tornero
- Hereditary Cancer Program, Catalan Institute of Oncology-(Bellvitge Institute for Biomedical Research; Girona Institute for Biomedical Research; Germans Trial i Pujol Research Institute) (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology-(Bellvitge Institute for Biomedical Research; Girona Institute for Biomedical Research; Germans Trial i Pujol Research Institute) (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ignacio Blanco
- Hereditary Cancer Program, Catalan Institute of Oncology-(Bellvitge Institute for Biomedical Research; Girona Institute for Biomedical Research; Germans Trial i Pujol Research Institute) (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-(Bellvitge Institute for Biomedical Research; Girona Institute for Biomedical Research; Germans Trial i Pujol Research Institute) (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Miquel Àngel Pujana
- Breast Cancer Unit, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB) Barcelona, Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Alvaro Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, United States of America
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology-(Bellvitge Institute for Biomedical Research; Girona Institute for Biomedical Research; Germans Trial i Pujol Research Institute) (ICO-IDIBELL, ICO-IdIBGi, ICO-IGTP), L'Hospitalet de Llobregat, Barcelona, Spain
- * E-mail:
| |
Collapse
|
45
|
Roadmap to determine the point mutations involved in cardiomyopathy disorder: A Bayesian approach. Gene 2013; 519:34-40. [DOI: 10.1016/j.gene.2013.01.056] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/31/2012] [Accepted: 01/27/2013] [Indexed: 11/18/2022]
|
46
|
Hinrichsen I, Brieger A, Trojan J, Zeuzem S, Nilbert M, Plotz G. Expression defect size among unclassified MLH1 variants determines pathogenicity in Lynch syndrome diagnosis. Clin Cancer Res 2013; 19:2432-41. [PMID: 23403630 DOI: 10.1158/1078-0432.ccr-12-3299] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Lynch syndrome is caused by a germline mutation in a mismatch repair gene, most commonly the MLH1 gene. However, one third of the identified alterations are missense variants with unclear clinical significance. The functionality of these variants can be tested in the laboratory, but the results cannot be used for clinical diagnosis. We therefore aimed to establish a laboratory test that can be applied clinically. EXPERIMENTAL DESIGN We assessed the expression, stability, and mismatch repair activity of 38 MLH1 missense variants and determined the pathogenicity status of recurrent variants using clinical data. RESULTS Four recurrent variants were classified as neutral (K618A, H718Y, E578G, V716M) and three as pathogenic (A681T, L622H, P654L). All seven variants were proficient in mismatch repair but showed defects in expression. Quantitative PCR, pulse-chase, and thermal stability experiments confirmed decreases in protein stability, which were stronger in the pathogenic variants. The minimal cellular MLH1 concentration for mismatch repair was determined, which corroborated that strongly destabilized variants can cause repair deficiency. Loss of MLH1 tumor immunostaining is consistently reported in carriers of the pathogenic variants, showing the impact of this protein instability on these tumors. CONCLUSIONS Expression defects are frequent among MLH1 missense variants, but only severe defects cause Lynch syndrome. The data obtained here enabled us to establish a threshold for distinguishing tolerable (clinically neutral) from pathogenic expression defects. This threshold allows the translation of laboratory results for uncertain MLH1 variants into pathogenicity statements for diagnosis, thereby improving the targeting of cancer prevention measures in affected families.
Collapse
Affiliation(s)
- Inga Hinrichsen
- Medizinische Klinik 1, Biomedical Research Laboratory, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | | | | | | | | | | |
Collapse
|
47
|
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.
Collapse
Affiliation(s)
- Abdelilah Laraqui
- Laboratoire de Recherche et de Biosécurité P3, Hôpital Militaire d'Instruction Mohammed V, Rabat, Maroc
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Towler WI, Zhang J, Ransburgh DJR, Toland AE, Ishioka C, Chiba N, Parvin JD. Analysis of BRCA1 variants in double-strand break repair by homologous recombination and single-strand annealing. Hum Mutat 2012; 34:439-45. [PMID: 23161852 DOI: 10.1002/humu.22251] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/24/2012] [Indexed: 01/13/2023]
Abstract
Missense substitutions of uncertain clinical significance in the BRCA1 gene are a vexing problem in genetic counseling for women who have a family history of breast cancer. In this study, we evaluated the functions of 29 missense substitutions of BRCA1 in two DNA repair pathways. Repair of double-strand breaks by homology-directed recombination (HDR) had been previously analyzed for 16 of these BRCA1 variants, and 13 more variants were analyzed in this study. All 29 variants were also analyzed for function in double-strand break repair by the single-strand annealing (SSA) pathway. We found that among the pathogenic mutations in BRCA1, all were defective for DNA repair by either pathway. The HDR assay was accurate because all pathogenic mutants were defective for HDR, and all nonpathogenic variants were fully functional for HDR. Repair by SSA accurately identified pathogenic mutants, but several nonpathogenic variants were scored as defective or partially defective. These results indicated that specific amino acid residues of the BRCA1 protein have different effects in the two related DNA repair pathways, and these results validate the HDR assay as highly correlative with BRCA1-associated breast cancer.
Collapse
Affiliation(s)
- William I Towler
- Department of Biomedical Informatics and the Ohio State University Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | | | | | | | | | | | | |
Collapse
|
49
|
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.
Collapse
Affiliation(s)
- Gaël A Millot
- Institut Curie, CNRS, UMR 3244 Université Pierre et Marie Curie, Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Computational investigation of pathogenic nsSNPs in CEP63 protein. Gene 2012; 503:75-82. [DOI: 10.1016/j.gene.2012.04.032] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 04/01/2012] [Accepted: 04/11/2012] [Indexed: 12/11/2022]
|