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Felicio PS, Bidinotto LT, Melendez ME, Grasel RS, Campacci N, Galvão HCR, Scapulatempo-Neto C, Dufloth RM, Evangelista AF, Palmero EI. Genetic alterations detected by comparative genomic hybridization in BRCAX breast and ovarian cancers of Brazilian population. Oncotarget 2018; 9:27525-27534. [PMID: 29938003 PMCID: PMC6007956 DOI: 10.18632/oncotarget.25537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 05/14/2018] [Indexed: 12/19/2022] Open
Abstract
Background About 5–10% of breast/ovarian cancers are hereditary. However, for a large proportion of cases (around 50%), the genetic cause remains unknown. These cases are grouped in a separated BRCAX category. The aim of this study was to identify genomic alterations in BRCA1/BRCA2 wild-type tumor samples from women with family history strongly suggestive of hereditary breast/ovarian cancer. Results A cohort of 31 Brazilian women was included in the study. Using the GISTIC algorithm, we identified 20 regions with genomic gains and 31 with losses. The most frequent altered regions were 1q21.2, 6p22.1 and 8p23.3 in breast tumors and Xq26 and Xp22.32-22.31 among the ovarian cancer cases. An interesting association identified was the loss of 22q13.31-13.32 and the presence of ovarian cancer cases. Among the genes present in the frequently altered regions, we found FGFR1, NSMCE2, CTTN, CRLF2, ERBB2, STARD3, MIR3201 and several genes of RAET and ULBP family. Conclusions In conclusion, our results suggest that alterations on chromosomes 1, 6, 8 and X are common on BRCAX tumors and that the loss on 22q can be associated with the presence of ovarian cancer. Methods DNA copy number alterations were analyzed by 60K array comparative genomic hybridization in breast and ovarian FFPE tumors.
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Affiliation(s)
- Paula Silva Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Lucas Tadeu Bidinotto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Barretos School of Health Sciences-FACISB, Barretos, SP, Brazil
| | | | | | - Natalia Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | | | | | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Barretos School of Health Sciences-FACISB, Barretos, SP, Brazil
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Downs B, Xiao F, Kim YC, Chen PX, Huang D, Fleissner EA, Cowan K, Wang SM. Single-base LOH can be used as Specific Marker to Classify BRCAx Familial Breast Cancer into More Homogenous Subtypes. Breast J 2017; 23:479-481. [PMID: 28117528 DOI: 10.1111/tbj.12777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Bradley Downs
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Fengxia Xiao
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Yeong C Kim
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
| | - Pei Xian Chen
- Department of Medicine, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Dali Huang
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Elizabeth A Fleissner
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Kenneth Cowan
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - San Ming Wang
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska
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3
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DNA copy number profiling reveals extensive genomic loss in hereditary BRCA1 and BRCA2 ovarian carcinomas. Br J Cancer 2013; 108:1732-42. [PMID: 23558894 PMCID: PMC3668473 DOI: 10.1038/bjc.2013.141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: Few studies have attempted to characterise genomic changes occurring in hereditary epithelial ovarian carcinomas (EOCs) and inconsistent results have been obtained. Given the relevance of DNA copy number alterations in ovarian oncogenesis and growing clinical implications of the BRCA-gene status, we aimed to characterise the genomic profiles of hereditary and sporadic ovarian tumours. Methods: High-resolution array Comparative Genomic Hybridisation profiling of 53 familial (21 BRCA1, 6 BRCA2 and 26 non-BRCA1/2) and 15 sporadic tumours in combination with supervised and unsupervised analysis was used to define common and/or specific copy number features. Results: Unsupervised hierarchical clustering did not stratify tumours according to their familial or sporadic condition or to their BRCA1/2 mutation status. Common recurrent changes, spanning genes potentially fundamental for ovarian carcinogenesis, regardless of BRCA mutations, and several candidate subtype-specific events were defined. Despite similarities, greater contribution of losses was revealed to be a hallmark of BRCA1 and BRCA2 tumours. Conclusion: Somatic alterations occurring in the development of familial EOCs do not differ substantially from the ones occurring in sporadic carcinomas. However, some specific features like extensive genomic loss observed in BRCA1/2 tumours may be of clinical relevance helping to identify BRCA-related patients likely to respond to PARP inhibitors.
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Hilbers FS, Meijers CM, Laros JFJ, van Galen M, Hoogerbrugge N, Vasen HFA, Nederlof PM, Wijnen JT, van Asperen CJ, Devilee P. Exome sequencing of germline DNA from non-BRCA1/2 familial breast cancer cases selected on the basis of aCGH tumor profiling. PLoS One 2013; 8:e55734. [PMID: 23383274 PMCID: PMC3561352 DOI: 10.1371/journal.pone.0055734] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/30/2012] [Indexed: 12/17/2022] Open
Abstract
The bulk of familial breast cancer risk (∼70%) cannot be explained by mutations in the known predisposition genes, primarily BRCA1 and BRCA2. Underlying genetic heterogeneity in these cases is the probable explanation for the failure of all attempts to identify further high-risk alleles. While exome sequencing of non-BRCA1/2 breast cancer cases is a promising strategy to detect new high-risk genes, rational approaches to the rigorous pre-selection of cases are needed to reduce heterogeneity. We selected six families in which the tumours of multiple cases showed a specific genomic profile on array comparative genomic hybridization (aCGH). Linkage analysis in these families revealed a region on chromosome 4 with a LOD score of 2.49 under homogeneity. We then analysed the germline DNA of two patients from each family using exome sequencing. Initially focusing on the linkage region, no potentially pathogenic variants could be identified in more than one family. Variants outside the linkage region were then analysed, and we detected multiple possibly pathogenic variants in genes that encode DNA integrity maintenance proteins. However, further analysis led to the rejection of all variants due to poor co-segregation or a relatively high allele frequency in a control population. We concluded that using CGH results to focus on a sub-set of families for sequencing analysis did not enable us to identify a common genetic change responsible for the aggregation of breast cancer in these families. Our data also support the emerging view that non-BRCA1/2 hereditary breast cancer families have a very heterogeneous genetic basis.
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Affiliation(s)
- Florentine S Hilbers
- Department of Human Genetics, Leiden University Medical Centre, Leiden, The Netherlands.
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5
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Genomic analysis: Toward a new approach in breast cancer management. Crit Rev Oncol Hematol 2012; 81:207-23. [DOI: 10.1016/j.critrevonc.2011.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/02/2011] [Accepted: 03/16/2011] [Indexed: 12/11/2022] Open
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6
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Kais Z, Barsky SH, Mathsyaraja H, Zha A, Ransburgh DJR, He G, Pilarski RT, Shapiro CL, Huang K, Parvin JD. KIAA0101 interacts with BRCA1 and regulates centrosome number. Mol Cancer Res 2011; 9:1091-9. [PMID: 21673012 DOI: 10.1158/1541-7786.mcr-10-0503] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To find genes and proteins that collaborate with BRCA1 or BRCA2 in the pathogenesis of breast cancer, we used an informatics approach and found a candidate BRCA interactor, KIAA0101, to function like BRCA1 in exerting a powerful control over centrosome number. The effect of KIAA0101 on centrosomes is likely direct, as its depletion does not affect the cell cycle, KIAA0101 localizes to regions coincident with the centrosomes, and KIAA0101 binds to BRCA1. We analyzed whether KIAA0101 protein is overexpressed in breast cancer tumor samples in tissue microarrays, and we found that overexpression of KIAA0101 correlated with positive Ki67 staining, a biomarker associated with increased disease severity. Furthermore, overexpression of the KIAA0101 gene in breast tumors was found to be associated with significantly decreased survival time. This study identifies KIAA0101 as a protein important for breast tumorigenesis, and as this factor has been reported as a UV repair factor, it may link the UV damage response to centrosome control.
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Affiliation(s)
- Zeina Kais
- Molecular, Cellular, and Development Program, Ohio State University, Columbus, OH, USA
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Tommasi S, Mangia A, Iannelli G, Chiarappa P, Rossi E, Ottini L, Mottolese M, Zoli W, Zuffardi O, Paradiso A. Gene copy number variation in male breast cancer by aCGH. Cell Oncol (Dordr) 2011; 34:467-73. [PMID: 21547577 DOI: 10.1007/s13402-011-0041-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2010] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Male breast cancer (MBC) is a rare disease and little is known about its etiopathogenesis. Array comparative genomic hybridization (aCGH) provides a method to quantitatively measure the changes of DNA copy number and to map them directly onto the complete linear genome sequences. The aim of this study was to investigate DNA imbalances by aCGH and compare them with a female breast cancer dataset. METHODS We used Agilent Human Genome CGH Microarray Kit 44B and 44 K to compare genomic alterations in 25 male breast cancer tissues studied at NCC of Bari and 16 female breast cancer deposited with the Gene Expression Omnibus (GSE 12659). Data analysis was performed with Nexus Copy Number 5.0 software. RESULTS All the 25 male and 16 female breast cancer samples displayed some chromosomal instability (110,93 alterations per patient in female, 69 in male). However, male samples presented a lower frequency of genetic alterations both in terms of loss and gains. CONCLUSION aCGH is an effective tool for analysis of cytogenetic aberrations in MBC, which involves different biological processes than female. Male most significant altered regions contained genes involved in cell communication, cell division and immunological response, while female cell-cell junction maintenance, regulation of transcription and neuron development.
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Affiliation(s)
- Stefania Tommasi
- Clinical Experimental Oncology Laboratory, National Cancer Centre of Bari, viale Orazio Flacco 65, 70124 Bari, Italy
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Tommasi S, Iannelli G, Menolascina F, Fedele V, Bevilacqua V, Paradiso A. Determining and Interpreting New Predictive Rules for Breast Cancer Familial Inheritance. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:125-31. [DOI: 10.1089/omi.2010.0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | | | - Filippo Menolascina
- National Cancer Centre of Bari, Italy
- Electrotechnic and Electronic Department, Polytechnic—Bari, Italy
| | - Vita Fedele
- National Cancer Centre of Bari, Italy
- Lawrence Berkeley National Laboratory, Berkeley, California
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Sabatier R, Adélaïde J, Finetti P, Ferrari A, Huiart L, Sobol H, Chaffanet M, Birnbaum D, Bertucci F. BARD1 homozygous deletion, a possible alternative to BRCA1 mutation in basal breast cancer. Genes Chromosomes Cancer 2011; 49:1143-51. [PMID: 20842729 DOI: 10.1002/gcc.20822] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hereditary breast cancers (BCs) are incompletely explained by BRCA genes abnormalities, as ∼70% of them are not associated with known genetic alterations. Array-based comparative genomic hybridization (aCGH) of tumors provides an opportunity for identifying new BC susceptibility genes. By analyzing our database of high-resolution aCGH profiles of 330 BCs, we identified a case with homozygous deletion of the entire BARD1 gene. The BARD1-deleted case displayed a familial history of BC and other clinico-pathological features of BRCAness, and a 17% probability of BRCA1/2 mutation. Analysis of constitutional DNA showed a BARD1 germline heterozygous deletion without BRCA1/2 mutation. Gene expression analysis using DNA microarrays classified the tumor as basal-like, with very low BARD1 and ID4 expression, but high expression of BRCA1, RAD51, PARP1, CHEK1, and FANCA. The tumor displayed a BRCA1-mutated expression profile. This is the first report of a non-BRCA1/2-mutated BC with somatic homozygous and germ-line heterozygous deletion of the entire BARD1 gene. This observation suggests that BARD1 might be a BC susceptibility gene that follows the Knudson rule. Identification of BARD1 deletion could have clinical applications including screening for hereditary forms. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Renaud Sabatier
- Department of Molecular Oncology, Centre de Recherche en Cancérologie de Marseille, INSERM/UMR891, Marseille, France
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Popławski AB, Jankowski M, Erickson SW, Díaz de Ståhl T, Partridge EC, Crasto C, Guo J, Gibson J, Menzel U, Bruder CE, Kaczmarczyk A, Benetkiewicz M, Andersson R, Sandgren J, Zegarska B, Bała D, Srutek E, Allison DB, Piotrowski A, Zegarski W, Dumanski JP. Frequent genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression. Eur J Hum Genet 2010; 18:560-8. [PMID: 20051991 DOI: 10.1038/ejhg.2009.230] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Breast cancer is a major cause of morbidity and mortality in women and its metastatic spread is the principal reason behind the fatal outcome. Metastasis-related research of breast cancer is however underdeveloped when compared with the abundant literature on primary tumors. We applied an unexplored approach comparing at high resolution the genomic profiles of primary tumors and synchronous axillary lymph node metastases from 13 patients with breast cancer. Overall, primary tumors displayed 20% higher number of aberrations than metastases. In all but two patients, we detected in total 157 statistically significant differences between primary lesions and matched metastases. We further observed differences that can be linked to metastatic disease and there was also an overlapping pattern of changes between different patients. Many of the differences described here have been previously linked to poor patient survival, suggesting that this is a viable approach toward finding biomarkers for disease progression and definition of new targets useful for development of anticancer drugs. Frequent genetic differences between primary tumors and metastases in breast cancer also question, at least to some extent, the role of primary tumors as a surrogate subject of study for the systemic disease.
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Affiliation(s)
- Andrzej B Popławski
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
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