101
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Abstract
In this review, we discuss the repair of DNA double-strand breaks (DSBs) using a homologous DNA sequence (i.e., homologous recombination [HR]), focusing mainly on yeast and mammals. We provide a historical context for the current view of HR and describe how DSBs are processed during HR as well as interactions with other DSB repair pathways. We discuss the enzymology of the process, followed by studies on DSB repair in living cells. Whenever possible, we cite both original articles and reviews to aid the reader for further studies.
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Affiliation(s)
- Maria Jasin
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center New York, New York 10065
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102
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Fry EA, Taneja P, Maglic D, Zhu S, Sui G, Inoue K. Dmp1α inhibits HER2/neu-induced mammary tumorigenesis. PLoS One 2013; 8:e77870. [PMID: 24205004 PMCID: PMC3812138 DOI: 10.1371/journal.pone.0077870] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 08/29/2013] [Indexed: 01/09/2023] Open
Abstract
Our recent study shows a pivotal role of Dmp1 in quenching hyperproliferative signals from HER2 to the Arf-p53 pathway as a safety mechanism to prevent breast carcinogenesis. To directly demonstrate the role of Dmp1 in preventing HER2/neu-driven oncogenic transformation, we established Flag-Dmp1α transgenic mice (MDTG) under the control of the mouse mammary tumor virus (MMTV) promoter. The mice were viable but exhibited poorly developed mammary glands with markedly reduced milk production; thus more than half of parous females were unable to support the lives of new born pups. The mammary glands of the MDTG mice had very low Ki-67 expression but high levels of Arf, Ink4a, p53, and p21Cip1, markers of senescence and accelerated aging. In all strains of generated MDTG;neu mice, tumor development was significantly delayed with decreased tumor weight. Tumors from MDTG;neu mice expressed Flag-Dmp1α and Ki-67 in a mutually exclusive fashion indicating that transgenic Dmp1α prevented tumor growth in vivo. Genomic DNA analyses showed that the Dmp1α transgene was partially lost in half of the MDTG;neu tumors, and Western blot analyses showed Dmp1α protein downregulation in 80% of the cases. Our data demonstrate critical roles of Dmp1 in preventing mammary tumorigenesis and raise the possibility of treating breast cancer by restoring Dmp1α expression.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Blotting, Western
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Extracellular Matrix Proteins/physiology
- Female
- Gene Dosage
- Humans
- Immunoenzyme Techniques
- Mammary Neoplasms, Experimental/etiology
- Mammary Neoplasms, Experimental/mortality
- Mammary Neoplasms, Experimental/pathology
- Mammary Neoplasms, Experimental/prevention & control
- Mice
- Mice, Transgenic
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Receptor, ErbB-2/physiology
- Reverse Transcriptase Polymerase Chain Reaction
- Survival Rate
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Affiliation(s)
- Elizabeth A. Fry
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Pankaj Taneja
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Dejan Maglic
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- Graduate Program in Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Sinan Zhu
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- Graduate Program in Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
| | - Guangchao Sui
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- * E-mail: (GS); (KI)
| | - Kazushi Inoue
- Department of Pathology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- Department of Cancer Biology, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- Graduate Program in Molecular Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina, United States of America
- * E-mail: (GS); (KI)
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103
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Park JY, Singh TR, Nassar N, Zhang F, Freund M, Hanenberg H, Meetei AR, Andreassen PR. Breast cancer-associated missense mutants of the PALB2 WD40 domain, which directly binds RAD51C, RAD51 and BRCA2, disrupt DNA repair. Oncogene 2013; 33:4803-12. [PMID: 24141787 PMCID: PMC3994186 DOI: 10.1038/onc.2013.421] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 08/29/2013] [Accepted: 09/05/2013] [Indexed: 12/13/2022]
Abstract
Heterozygous carriers of germ-line mutations in the BRCA2/FANCD1, PALB2/FANCN and RAD51C/FANCO DNA repair genes have an increased lifetime risk of developing breast, ovarian and other cancers; bi-allelic mutations in these genes clinically manifest as Fanconi anemia (FA). Here, we demonstrate that RAD51C is part of a novel protein complex that contains PALB2 and BRCA2. Further, the PALB2 WD40 domain can directly and independently bind RAD51C and BRCA2. To understand the role of these homologous recombination (HR) proteins in DNA repair, we functionally characterize effects of missense mutants of the PALB2 WD40 domain that have been reported in breast cancer patients. In contrast to large truncations of PALB2, which display a complete loss of interaction, the L939W, T1030I and L1143P missense mutants/variants of the PALB2 WD40 domain are associated with altered patterns of direct binding to the RAD51C, RAD51 and BRCA2 HR proteins in biochemical assays. Further, the T1030I missense mutant is unstable, whereas the L939W and L1143P proteins are stable but partially disrupt the PALB2-RAD51C-BRCA2 complex in cells. Functionally, the L939W and L1143P mutants display a decreased capacity for DNA double-strand break-induced HR and an increased cellular sensitivity to ionizing radiation. As further evidence for the functional importance of the HR complex, RAD51C mutants that are associated with cancer susceptibility and FA also display decreased complex formation with PALB2. Together, our results suggest that three different cancer susceptibility and FA proteins function in a DNA repair pathway based upon the PALB2 WD40 domain binding to RAD51C and BRCA2.
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Affiliation(s)
- J-Y Park
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - T R Singh
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - N Nassar
- 1] Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA [2] Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - F Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
| | - M Freund
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University School of Medicine, Duesseldorf, Germany
| | - H Hanenberg
- 1] Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University School of Medicine, Duesseldorf, Germany [2] Unit of Pediatric Hematology/Oncology, Wells Center for Pediatric Research, Department of Pediatrics, The Riley Hospital, Indiana University School of Medicine, Indianapolis, IN, USA [3] Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - A R Meetei
- 1] Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA [2] Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - P R Andreassen
- 1] Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA [2] Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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104
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Eswaran J, Horvath A, Godbole S, Reddy SD, Mudvari P, Ohshiro K, Cyanam D, Nair S, Fuqua SAW, Polyak K, Florea LD, Kumar R. RNA sequencing of cancer reveals novel splicing alterations. Sci Rep 2013; 3:1689. [PMID: 23604310 PMCID: PMC3631769 DOI: 10.1038/srep01689] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 03/01/2013] [Indexed: 12/30/2022] Open
Abstract
Breast cancer transcriptome acquires a myriad of regulation changes, and splicing is critical for the cell to “tailor-make” specific functional transcripts. We systematically revealed splicing signatures of the three most common types of breast tumors using RNA sequencing: TNBC, non-TNBC and HER2-positive breast cancer. We discovered subtype specific differentially spliced genes and splice isoforms not previously recognized in human transcriptome. Further, we showed that exon skip and intron retention are predominant splice events in breast cancer. In addition, we found that differential expression of primary transcripts and promoter switching are significantly deregulated in breast cancer compared to normal breast. We validated the presence of novel hybrid isoforms of critical molecules like CDK4, LARP1, ADD3, and PHLPP2. Our study provides the first comprehensive portrait of transcriptional and splicing signatures specific to breast cancer sub-types, as well as previously unknown transcripts that prompt the need for complete annotation of tissue and disease specific transcriptome.
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Affiliation(s)
- Jeyanthy Eswaran
- McCormick Genomic and Proteomics Center, The George Washington University, Washington, District of Columbia 20037, USA
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105
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Monteiro LJ, Khongkow P, Kongsema M, Morris JR, Man C, Weekes D, Koo CY, Gomes AR, Pinto PH, Varghese V, Kenny LM, Coombes RC, Freire R, Medema RH, Lam EWF. The Forkhead Box M1 protein regulates BRIP1 expression and DNA damage repair in epirubicin treatment. Oncogene 2013; 32:4634-45. [PMID: 23108394 PMCID: PMC3874579 DOI: 10.1038/onc.2012.491] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/29/2012] [Accepted: 09/07/2012] [Indexed: 01/25/2023]
Abstract
FOXM1 is implicated in genotoxic drug resistance but its role and mechanism of action remain unclear. Here, we establish that γH2AX foci, indicative of DNA double-strand breaks (DSBs), accumulate in a time-dependent manner in the drug-sensitive MCF-7 cells but not in the resistant counterparts in response to epirubicin. We find that FOXM1 expression is associated with epirubicin sensitivity and DSB repair. Ectopic expression of FOXM1 can increase cell viability and abrogate DSBs sustained by MCF-7 cells following epirubicin, owing to an enhancement in repair efficiency. Conversely, alkaline comet and γH2AX foci formation assays show that Foxm1-null cells are hypersensitive to DNA damage, epirubicin and γ-irradiation. Furthermore, we find that FOXM1 is required for DNA repair by homologous recombination (HR) but not non-homologous end joining (NHEJ), using HeLa cell lines harbouring an integrated direct repeat green fluorescent protein reporter for DSB repair. We also identify BRIP1 as a direct transcription target of FOXM1 by promoter analysis and chromatin-immunoprecipitation assay. In agreement, depletion of FOXM1 expression by small interfering RNA downregulates BRIP1 expression at the protein and mRNA levels in MCF-7 and the epirubicin-resistant MCF-7 Epi(R) cells. Remarkably, the requirement for FOXM1 for DSB repair can be circumvented by reintroduction of BRIP1, suggesting that BRIP1 is an important target of FOXM1 in DSB repair. Indeed, like FOXM1, BRIP1 is needed for HR. These data suggest that FOXM1 regulates BRIP1 expression to modulate epirubicin-induced DNA damage repair and drug resistance.
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Affiliation(s)
- Lara J. Monteiro
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Pasarat Khongkow
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Mesayamas Kongsema
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Joanna R. Morris
- School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Cornelia Man
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Daniel Weekes
- Department of Medical and Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
| | - Chuay-Yeng Koo
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Ana R. Gomes
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Paola H. Pinto
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Vidhya Varghese
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Laura M. Kenny
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - R. Charles Coombes
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, La Laguna, Tenerife, Spain
| | - René H. Medema
- Division of Cell Biology, the Netherlands Cancer Institute, Amsterdam, 1066 CX, the Netherlands
| | - Eric W.-F. Lam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
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106
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Prevalence of PALB2 mutation c.509_510delGA in unselected breast cancer patients from Central and Eastern Europe. Fam Cancer 2013; 13:137-42. [DOI: 10.1007/s10689-013-9684-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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107
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Abstract
Over the last few years, evidence has been accumulated that several susceptibility genes exist that differentially impact on the lifetime risk for breast or ovarian cancer. High-to-moderate penetrance alleles have been identified in genes involved in DNA double-strand break signaling and repair, and many low-penetrance susceptibility loci have been identified through genome-wide association studies. In this review, we briefly summarize present knowledge about breast and ovarian cancer susceptibility genes and discuss their implications for risk prediction and therapy.
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108
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Bogdanova N, Helbig S, Dörk T. Hereditary breast cancer: ever more pieces to the polygenic puzzle. Hered Cancer Clin Pract 2013; 11:12. [PMID: 24025454 PMCID: PMC3851033 DOI: 10.1186/1897-4287-11-12] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 09/02/2013] [Indexed: 12/21/2022] Open
Abstract
Several susceptibility genes differentially impact on the lifetime risk for breast cancer. Technological advances over the past years have enabled the detection of genetic risk factors through high-throughput screening of large breast cancer case-control series. High- to intermediate penetrance alleles have now been identified in more than 20 genes involved in DNA damage signalling and repair, and more than 70 low-penetrance loci have been discovered through recent genome-wide association studies. In addition to classical germ-line mutation and single-nucleotide polymorphism, copy number variation and somatic mosaicism have been proposed as potential predisposing mechanisms. Many of the identified loci also appear to influence breast tumour characteristics such as estrogen receptor status. In this review, we briefly summarize present knowledge about breast cancer susceptibility genes and discuss their implications for risk prediction and clinical practice.
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Affiliation(s)
- Natalia Bogdanova
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
- Clinics of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Sonja Helbig
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Thilo Dörk
- Clinics of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
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109
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Nalepa G, Enzor R, Sun Z, Marchal C, Park SJ, Yang Y, Tedeschi L, Kelich S, Hanenberg H, Clapp DW. Fanconi anemia signaling network regulates the spindle assembly checkpoint. J Clin Invest 2013; 123:3839-47. [PMID: 23934222 DOI: 10.1172/jci67364] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 05/30/2013] [Indexed: 12/21/2022] Open
Abstract
Fanconi anemia (FA) is a heterogenous genetic disease with a high risk of cancer. The FA proteins are essential for interphase DNA damage repair; however, it is incompletely understood why FA-deficient cells also develop gross aneuploidy, leading to cancer. Here, we systematically evaluated the role of the FA proteins in chromosome segregation through functional RNAi screens and analysis of primary cells from patients with FA. We found that FA signaling is essential for the spindle assembly checkpoint and is therefore required for high-fidelity chromosome segregation and prevention of aneuploidy. Furthermore, we discovered that FA proteins differentially localize to key structures of the mitotic apparatus in a cell cycle-dependent manner. The essential role of the FA pathway in mitosis offers a mechanistic explanation for the aneuploidy and malignant transformation known to occur after disruption of FA signaling. Collectively, our findings provide insight into the genetically unstable cancers resulting from inactivation of the FA/BRCA pathway.
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Affiliation(s)
- Grzegorz Nalepa
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana 46202, USA.
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110
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Peng M, Bakker JL, Dicioccio RA, Gille JJP, Zhao H, Odunsi K, Sucheston L, Jaafar L, Mivechi NF, Waisfisz Q, Ko L. Inactivating Mutations in GT198 in Familial and Early-Onset Breast and Ovarian Cancers. Genes Cancer 2013; 4:15-25. [PMID: 23946868 DOI: 10.1177/1947601913486344] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 03/16/2013] [Indexed: 01/03/2023] Open
Abstract
The human GT198 gene (gene symbol PSMC3IP) is located at chromosome 17q21, 470 kb proximal to BRCA1, a locus previously linked to breast and ovarian cancer predisposition. Its protein product (also known as TBPIP and Hop2) has been shown to regulate steroid hormone receptor-mediated gene activation and to stimulate homologous recombination in DNA repair. Here, we screened germline mutations in GT198 in familial and early-onset breast and ovarian cancer patients. We have identified 8 germline variants in a total of 212 index patients including reoccurring nonsense mutation c.310C>T (p.Q104X) and 5' UTR mutation c.-37A>T, each found in 2 unrelated families. Most identified index patients from cancer families had early onsets with a median age of 35 years. c.310C>T was absent in a total of 564 control individuals analyzed. GT198 gene amplification with an imbalanced mutant copy gain was identified in the blood DNA of one of the patients carrying c.310C>T. When tested, this truncating mutation abolished DNA damage-induced Rad51 foci formation. In addition, we have identified 15 somatic mutations in 2 tumors from 1 patient carrying germline mutation c.-37A>T. The presence of a somatic mutation on the wild-type allele showed that GT198 was biallelically mutated in the tumor. The somatic mutations identified near a splicing junction site caused defective alternative splicing and truncated the open reading frame. Therefore, distinct mutations may cause a similar consequence by truncating the full-length protein and inducing a loss of the wild type. Our study provides the first evidence of the presence of inactivating mutations in GT198 in familial and early-onset breast and ovarian cancer patients. Mutations in GT198, a gene regulating DNA repair, potentially contribute to an increased risk in familial breast and ovarian cancers.
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Affiliation(s)
- Min Peng
- Cancer Center, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA
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111
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Lynch H, Wen H, Kim YC, Snyder C, Kinarsky Y, Chen PX, Xiao F, Goldgar D, Cowan KH, Wang SM. Can unknown predisposition in familial breast cancer be family-specific? Breast J 2013; 19:520-8. [PMID: 23800003 DOI: 10.1111/tbj.12145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genetic predisposition plays a key role in the development of familial breast cancer. In spite of strong familial clustering of the disease and extensive efforts made during the past decade; however, progress has been slow in identifying genetic predisposition for the majority of familial breast cancer families. The question arises therefore as to whether current approaches are adequate in identifying the unknown genetic predisposition. We analyzed eight members of a BRCA1-, BRCA2-, p53-, and PTEN-negative breast cancer family, of which five had breast cancer, one is an obligate gene carrier, and two were unaffected. We sequenced the entire coding region of the genome for each member using exome sequencing to identify nonsynonymous variants. We identified 55 nonsynonymous germline variants affecting 49 genes in multiple members of the family, of which 22 are predicted to have damaging effects. We validated 20 of the 22 selected variants in the family by Sanger sequencing. Two variants in KAT6B, an acetal transferase gene, were identified in six family members of which five were affected with breast cancer and one is the unaffected obligate carrier. We further examined the presence of the identified variants in a cohort of 40 additional breast cancer cases from 22 familial breast cancer families, but none of the 22 variants was detected in these cases. Sequencing the entire coding exons in KAT6B detects no variants in these cases. Our results show that genetic predisposition for familial breast cancer can be rich in an affected family, but the predisposition can be family-specific. As such, it will be difficult to detect them by applying population-based approach. Our study supports the concept that focusing on each affected family will be required to determine the genetic predisposition for many familial breast cancer families whose genetic dispositions remain unknown.
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Affiliation(s)
- Henry Lynch
- Hereditary Cancer Center, Department of Preventive Medicine, Creighton University, Omaha, Nebraska
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112
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Abstract
Background SLX4 encodes a DNA repair protein that regulates three structure-specific endonucleases and is necessary for resistance to DNA crosslinking agents, topoisomerase I and poly (ADP-ribose) polymerase (PARP) inhibitors. Recent studies have reported mutations in SLX4 in a new subtype of Fanconi anemia (FA), FA-P. Monoallelic defects in several FA genes are known to confer susceptibility to breast and ovarian cancers. Methods and Results To determine if SLX4 is involved in breast cancer susceptibility, we sequenced the entire SLX4 coding region in 738 (270 Jewish and 468 non-Jewish) breast cancer patients with 2 or more family members affected by breast cancer and no known BRCA1 or BRCA2 mutations. We found a novel nonsense (c.2469G>A, p.W823*) mutation in one patient. In addition, we also found 51 missense variants [13 novel, 23 rare (MAF<0.1%), and 15 common (MAF>1%)], of which 22 (5 novel and 17 rare) were predicted to be damaging by Polyphen2 (score = 0.65–1). We performed functional complementation studies using p.W823* and 5 SLX4 variants (4 novel and 1 rare) cDNAs in a human SLX4-null fibroblast cell line, RA3331. While wild type SLX4 and all the other variants fully rescued the sensitivity to mitomycin C (MMC), campthothecin (CPT), and PARP inhibitor (Olaparib) the p.W823* SLX4 mutant failed to do so. Conclusion Loss-of-function mutations in SLX4 may contribute to the development of breast cancer in very rare cases.
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113
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Jobim MR, Jobim M, Salim PH, Portela P, Jobim LF, Leistner-Segal S, Bittelbrunn AC, Menke CH, Biazús JV, Roesler R, Schwartsmann G. Analysis of KIR gene frequencies and HLA class I genotypes in breast cancer and control group. Hum Immunol 2013; 74:1130-3. [PMID: 23792055 DOI: 10.1016/j.humimm.2013.06.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/17/2013] [Accepted: 06/07/2013] [Indexed: 12/26/2022]
Abstract
Breast cancer is the main cause of cancer-related death among women, with a 0.5% increase in incidence per year. Natural killer cells (NK) are part of the innate immune system recognizing class I HLA molecules on target cells through their membrane receptors, called killer cell immunoglobulin-like receptors (KIR). The aim of our study was to evaluate the association between the KIR genes and HLA alleles in patients with breast cancer and healthy controls. Two hundred thirty patients with breast cancer and 272 healthy controls were typed for HLA class I and KIR genes by PCR-SSO. When both groups were compared, the presence of inhibitory KIR2DL2 receptors was significantly higher in breast cancer patients than in healthy controls. No significant differences were found for HLA-C2 and HLA-Bw4. However, a higher frequency of HLA-C1 in breast cancer patients was observed. These findings suggest a potential role for the KIR gene system in breast cancer. Further studies to confirm this observation are warranted.
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Affiliation(s)
- Maria Regina Jobim
- Department of Immunology, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
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114
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Abstract
Deleterious mutations in the RAD51C gene, which encodes a DNA double-strand break repair protein, have been reported to confer high-penetrance susceptibility to both breast and ovarian cancer. To confirm this we conducted a mutation screen of the RAD51C gene in 192 probands from high-risk breast and/or ovarian cancer families that do not carry BRCA1 or BRCA2 mutations. The nine exons of the RAD51C gene containing protein coding sequence were screened for mutations in genomic DNA from family probands by high-resolution melting analysis and direct DNA sequencing. Four missense variants, p.Ser364Gly, p.Ala126Thr, p.Val169Ala, and p.Thr287Ala were detected in six patients. The p.Ser364Gly variant is a novel variant predicted to have little influence on RAD51C activity. The p.Ala126Thr and p.Val169Ala variants have been reported to have no association with risk of breast cancer in a case-control study. However, p.Thr287Ala disrupts the DNA repair activity of RAD51C, suggesting some influence on risk. Consistent with published results from similar follow-up studies, we suggest that RAD51C mutations are rare events among high-risk breast cancer and breast/ovarian cancer families. Large population-based studies will be needed to reliably assess the prevalence and penetrance of inactivating mutations in the RAD51C susceptibility gene.
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115
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Involvement of IGF-1R regulation by miR-515-5p modifies breast cancer risk among BRCA1 carriers. Breast Cancer Res Treat 2013; 138:753-60. [DOI: 10.1007/s10549-013-2502-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 03/23/2013] [Indexed: 12/21/2022]
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116
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De Brakeleer S, De Grève J, Lissens W, Teugels E. Systematic detection of pathogenic alu element insertions in NGS-based diagnostic screens: the BRCA1/BRCA2 example. Hum Mutat 2013; 34:785-91. [PMID: 23420552 DOI: 10.1002/humu.22297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 02/06/2013] [Indexed: 12/24/2022]
Abstract
Pathogenic Alu element insertions are rarely reported, whereas their occurrence is expected to be much higher. Alu containing alleles are usually out-competed during the PCR process and consequently undetectable with the classical screening methods. However, with the introduction of the next generation sequencing (NGS) technology in the diagnostic field, new opportunities are emerging. NGS data for a particular genomic region can be seen as the summation of all the individual sequences (reads) obtained for that region and no longer as the mean of this sum as it is the case for traditional Sanger sequencing. Because each single read covering that region is expected to be generated from a different template molecule, the presence of one single mutant read must theoretically be sufficient to identify the mutation. However, generation and identification of mutant reads bearing Alu insertions remains challenging and several wet/dry bench parameters need to be optimized. Hereby we present the proof of principle of a NGS-based mutation screening procedure allowing the detection of inherited Alu insertions within any predefined sequence by investigating 2 cases: c.1739_1740insAlu in BRCA1 and c.156_157insAlu in BRCA2.
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Affiliation(s)
- Sylvia De Brakeleer
- Laboratory of Molecular and Medical Oncology, Vrije Universiteit Brussel, Belgium
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Hu M, Han D, Sun S, Yan Y, Zhang J, Zhou Y. Bleomycin-induced mutagen sensitivity, passive smoking, and risk of breast cancer in Chinese women: a case-control study. Cancer Causes Control 2013; 24:629-36. [PMID: 23371556 DOI: 10.1007/s10552-012-0137-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 12/17/2012] [Indexed: 10/27/2022]
Abstract
BACKGROUND It is well recognized that genetic variation as well as environmental factors modulates breast cancer risk. Deficiencies in DNA repair capacity are thought to associate with breast cancer risk. The main aim of this study was to use the mutagen sensitivity assay as an indirect measure of DNA repair capacity to assess breast cancer risk and the relationship between passive smoking and breast cancer risk among women in China. METHODS We carried out a case-control study, involving 196 Chinese patients with breast cancer and 211 controls without the disease and with no history of cancer. We investigated the association between mutagen sensitivity and breast cancer risk using bleomycin as the mutagen. Mutagen sensitivity was measured by quantifying the chromatid breaks induced by mutagens in short-term cultures of peripheral blood lymphocytes. Nonparametric tests and the Fisher's exact test were used to determine the statistical significance of the crude case-control comparisons, followed by logistic regression to adjust for important covariates. RESULTS The mean number of bleomycin-induced breaks per cell was 0.81 for cases compared with 0.73 for the controls (p = 0.016). A greater number of bleomycin-induced chromosomal breaks per cell was associated with an increased risk of breast cancer (adjusted odds ratio of 1.82, p trend <0.01). The association between bleomycin sensitivity and breast cancer risk was greater for women who were exposed to tobacco smoke (passive smokers). The combination of bleomycin sensitivity and exposure to tobacco smoke increased risk further; women passive smokers with high sensitivity to bleomycin had a 2.77-fold increased risk of breast cancer. CONCLUSIONS Our data indicate that increased bleomycin-induced mutagen sensitivity is significantly associated with an increased risk of breast cancer among Chinese women. Exposure to passive smoke is also associated with increased breast cancer risk, and the correlation is even greater for women with both longer passive exposure to tobacco smoke and high sensitivity to bleomycin.
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Affiliation(s)
- Mingbai Hu
- Department of Oncology, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Tumor Biological Behaviors and Hubei Cancer Clinical Study Center, Wuhan, China.
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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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119
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Ruark E, Snape K, Humburg P, Loveday C, Bajrami I, Brough R, Rodrigues DN, Renwick A, Seal S, Ramsay E, Duarte SDV, Rivas MA, Warren-Perry M, Zachariou A, Campion-Flora A, Hanks S, Murray A, Pour NA, Douglas J, Gregory L, Rimmer A, Walker NM, Yang TP, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Brice G, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Eccles D, Evans DG, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Shanley S, Walker L, Gore M, Houlston R, Brown MA, Caufield MJ, Deloukas P, McCarthy MI, Todd JA, Turnbull C, Reis-Filho JS, Ashworth A, Antoniou AC, Lord CJ, Donnelly P, Rahman N. Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature 2013; 493:406-10. [PMID: 23242139 PMCID: PMC3759028 DOI: 10.1038/nature11725] [Citation(s) in RCA: 191] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 10/26/2012] [Indexed: 02/06/2023]
Abstract
Improved sequencing technologies offer unprecedented opportunities for investigating the role of rare genetic variation in common disease. However, there are considerable challenges with respect to study design, data analysis and replication. Using pooled next-generation sequencing of 507 genes implicated in the repair of DNA in 1,150 samples, an analytical strategy focused on protein-truncating variants (PTVs) and a large-scale sequencing case-control replication experiment in 13,642 individuals, here we show that rare PTVs in the p53-inducible protein phosphatase PPM1D are associated with predisposition to breast cancer and ovarian cancer. PPM1D PTV mutations were present in 25 out of 7,781 cases versus 1 out of 5,861 controls (P = 1.12 × 10(-5)), including 18 mutations in 6,912 individuals with breast cancer (P = 2.42 × 10(-4)) and 12 mutations in 1,121 individuals with ovarian cancer (P = 3.10 × 10(-9)). Notably, all of the identified PPM1D PTVs were mosaic in lymphocyte DNA and clustered within a 370-base-pair region in the final exon of the gene, carboxy-terminal to the phosphatase catalytic domain. Functional studies demonstrate that the mutations result in enhanced suppression of p53 in response to ionizing radiation exposure, suggesting that the mutant alleles encode hyperactive PPM1D isoforms. Thus, although the mutations cause premature protein truncation, they do not result in the simple loss-of-function effect typically associated with this class of variant, but instead probably have a gain-of-function effect. Our results have implications for the detection and management of breast and ovarian cancer risk. More generally, these data provide new insights into the role of rare and of mosaic genetic variants in common conditions, and the use of sequencing in their identification.
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Affiliation(s)
- Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Katie Snape
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Peter Humburg
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Chey Loveday
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Ilirjana Bajrami
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Daniel Nava Rodrigues
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Emma Ramsay
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | | | - Manuel A. Rivas
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7LD, UK
| | - Margaret Warren-Perry
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Anna Zachariou
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Adriana Campion-Flora
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Sandra Hanks
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Anne Murray
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Naser Ansari Pour
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Jenny Douglas
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Lorna Gregory
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Andrew Rimmer
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Neil M. Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Tsun-Po Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Julian W. Adlard
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Julian Barwell
- Leicestershire Genetics Centre, University Hospitals of Leicester NHS Trust, LE1 5WW, UK
| | - Jonathan Berg
- Human genetics, Division of Medical Sciences, University of Dundee, DD1 9SY, UK
| | - Angela F. Brady
- NW Thames Regional Genetics Service, Kennedy Galton Centre, London, HA1 3UJ, UK
| | - Carole Brewer
- Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter, EX1 2ED, UK
| | - Glen Brice
- SW Thames Regional Genetics Service, St George’s Hospital, London, SW17 0RE, UK
| | - Cyril Chapman
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham, B15 2TG, UK
| | - Jackie Cook
- Sheffield Regional Genetics Service, Sheffield Children’s NHS Foundation Trust, S10 2TH, UK
| | - Rosemarie Davidson
- West of Scotland Regional Genetics Service, Laboratory Medicine, Southern General Hospital, Glasgow, G51 4TF, UK
| | - Alan Donaldson
- South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust, BS2 8EG, UK
| | - Fiona Douglas
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 3BZ, UK
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, SO16 5YA, UK
| | - D. Gareth Evans
- Genetic Medicine, Manchester Academic Health Science Centre, St. Mary’s Hospital, Manchester M13 9WL, UK
| | - Lynn Greenhalgh
- Merseyside and Cheshire Clinical Genetics Service, Liverpool Women’s NHS Foundation Trust, Liverpool, L8 7SS, UK
| | - Alex Henderson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 3BZ, UK
| | - Louise Izatt
- SE Thames Regional Genetics Service, Guy’s and St Thomas NHS Foundation Trust, London, SE1 9RT, UK
| | - Ajith Kumar
- NE Thames Regional Genetics Service, Great Ormond St Hospital, London, WC1N 3JH, UK
| | - Fiona Lalloo
- University Dept of Medical Genetics & Regional Genetics Service, St Mary’s Hospital, Manchester, M13 9WL, UK
| | - Zosia Miedzybrodzka
- University of Aberdeen and North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary, AB25 2ZA, UK
| | - Patrick J. Morrison
- Northern Ireland Regional Genetics Service, Belfast HSC Trust, Department of Medical Genetics, Queen’s University Belfast, BT9 7AB, UK
| | - Joan Paterson
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, CB2 0QQ, UK
| | - Mary Porteous
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Mark T. Rogers
- All Wales Medical Genetics Service, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Susan Shanley
- Dept of Cancer Genetics, Royal Marsden NHS Foundation Trust, Sutton, SM2 5PT, UK
| | - Lisa Walker
- Oxford Regional Genetics Service, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK
| | - Martin Gore
- Dept of Gynaecologic Oncology, Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Richard Houlston
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Matthew A. Brown
- University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Woolloongabba, Brisbane, 4102, Australia
| | - Mark J. Caufield
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Panagiotis Deloukas
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Mark I. McCarthy
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Medicine, University of Oxford, Churchill Hospital, Oxford, OX3 7LI, UK
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LI, UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | | | | | - Clare Turnbull
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
- Dept of Cancer Genetics, Royal Marsden NHS Foundation Trust, Sutton, SM2 5PT, UK
| | - Jorge S. Reis-Filho
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Christopher J. Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Peter Donnelly
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3TG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK
- Dept of Cancer Genetics, Royal Marsden NHS Foundation Trust, Sutton, SM2 5PT, UK
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Abstract
Biomarkers are characteristics objectively measured and evaluated as indicators of: normal biologic processes, pathogenic processes, or pharmacologic response(s) to a therapeutic intervention. In environmental research and risk assessment, biomarkers are frequently referred to as indicators of human or environmental hazards. Discovering and implementing new biomarkers for toxicity caused by exposure to a chemical either from a therapeutic intervention or accidentally through the environment continues to be pursued through the use of animal models to predict potential human effects, from human studies (clinical or epidemiologic) or biobanked human samples, or the combination of all such approaches. The key to discovering or inferring biomarkers through computational means involves the identification or prediction of the molecular target(s) of the chemical(s) and the association of these targets with perturbed biological pathways. Two examples are given in this chapter: (1) inferring potential human biomarkers from animal toxicogenomics data, and (2) the identification of protein targets through computational means and associating these in one example with potential drug interactions and in another case with increasing the risk of developing certain human diseases.
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Gudmundsdottir ET, Barkardottir RB, Arason A, Gunnarsson H, Amundadottir LT, Agnarsson BA, Johannsson OT, Reynisdottir I. The risk allele of SNP rs3803662 and the mRNA level of its closest genes TOX3 and LOC643714 predict adverse outcome for breast cancer patients. BMC Cancer 2012; 12:621. [PMID: 23270421 PMCID: PMC3553017 DOI: 10.1186/1471-2407-12-621] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 12/21/2012] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The minor allele of SNP rs3803662 has been shown to correlate with increased breast cancer risk and with lower expression of TOX3. The SNP is closely located to TOX3 residing within an uncharacterised gene LOC643714. The aim of the study was to examine the association of the risk allele with expression of TOX3 and LOC643714, and of mRNA levels and genotype with clinical and pathological characteristics. METHODS The SNP was genotyped in DNA isolated from blood and normal tissue from 160 breast cancer patients and mRNA levels were measured by microarrays and quantitative real-time (qRT)-PCR in breast tumours. Association with clinical and pathological characteristics was analysed by parametric tests. RESULTS An association of the risk allele of rs3803662 with lower TOX3 expression was confirmed in oestrogen receptor (ER) positive tumours. It was more often observed in lobular tumours (p = 0.04), and carriers of the risk allele who had been diagnosed with luminal A tumours had shorter overall survival (OS) than carriers of the non-risk allele (p = 0.01). Positive correlation between the mRNA levels of TOX3 and LOC643714 was observed (r = 0.44 and p < 0.001). Association analysis with tumour pathology showed that low TOX3 and LOC643714 expression correlated with high Ki67 levels (p = 0.026 and p = 0.002) and the basal subtype (p < 0.001 and p < 0.001), whereas high expression correlated with ER (p = 0.004 and p < 0.001) and progesterone receptor (PgR) (p = 0.005 and p < 0.001) expression. Furthermore, high TOX3 and LOC643714 correlated with positive lymph nodes (p < 0.001 and p = 0.01). Patients with ER positive tumours and high levels of TOX3 mRNA had shorter overall- and distant metastasis free-survival (p = 0.017 and p = 0.021), an effect mostly attributable to patients with luminal B tumours. CONCLUSIONS The results suggest that the effect of the risk allele of rs3803662 is strongest in luminal A tumours and that the expression levels of TOX3 and/or LOC643714 affect the progression of breast cancer. The effect may vary depending on the subtype and developmental stage of the tumour.
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Affiliation(s)
- Eydis Th Gudmundsdottir
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
- BMC, Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
| | - Adalgeir Arason
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
- BMC, Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
| | - Haukur Gunnarsson
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
- Present address: Actavis, Hafnarfjordur, Iceland
| | - Laufey Th Amundadottir
- Department of Health and Human Services, Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bjarni A Agnarsson
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
- BMC, Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
| | - Oskar Th Johannsson
- BMC, Faculty of Medicine, University of Iceland, Vatnsmyrarvegi 16, 101, Reykjavik, Iceland
- Department of Oncology, 20A, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
| | - Inga Reynisdottir
- Department of Pathology, Landspitali-University Hospital, Hringbraut, 101, Reykjavik, Iceland
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Prokofyeva D, Bogdanova N, Dubrowinskaja N, Bermisheva M, Takhirova Z, Antonenkova N, Turmanov N, Datsyuk I, Gantsev S, Christiansen H, Park-Simon TW, Hillemanns P, Khusnutdinova E, Dörk T. Nonsense mutation p.Q548X in BLM, the gene mutated in Bloom's syndrome, is associated with breast cancer in Slavic populations. Breast Cancer Res Treat 2012; 137:533-9. [PMID: 23225144 DOI: 10.1007/s10549-012-2357-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 11/22/2012] [Indexed: 11/24/2022]
Abstract
Bloom's syndrome is a rare autosomal recessive chromosomal instability disorder with a high incidence of various types of neoplasia, including breast cancer. Whether monoallelic BLM mutations predispose to breast cancer has been a long-standing question. A nonsense mutation, p.Q548X, has recently been associated with an increased risk for breast cancer in a Russian case-control study. In the present work, we have investigated the prevalence of this Slavic BLM founder mutation in a total of 3,188 breast cancer cases and 2,458 controls from Bashkortostan, Belarus, Ukraine, and Kazakhstan. The p.Q548X allele was most frequent in Russian patients (0.8 %) but was also prevalent in Byelorussian and Ukrainian patients (0.5 and 0.6 %, respectively), whereas it was absent in Altaic or other non-European subpopulations. In a combined analysis of our four case-control series, the p.Q548X mutation was significantly associated with breast cancer (Mantel-Haenszel OR 5.1, 95 % CI 1.2; 21.9, p = 0.03). A meta-analysis with the previous study from the St. Petersburg area corroborates the association (OR 5.7, 95 % CI 2.0; 15.9, p = 3.7 × 10(-4)). A meta-analysis for all published truncating mutations further supports the association of BLM with breast cancer, with an estimated two- to five-fold increase in risk (OR 3.3, 95 %CI 1.9; 5.6, p = 1.9 × 10(-5)). Altogether, these data indicate that BLM is not only a gene for Bloom's syndrome but also might represent a breast cancer susceptibility gene.
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Affiliation(s)
- Darya Prokofyeva
- Institute of Biochemistry and Genetics, Ufa Science Center, Ufa, Russia
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Han JY, Wang H, Xie YT, Li Y, Zheng LY, Ruan Y, Song AP, Tian XX, Fang WG. Association of germline variation in CCNE1 and CDK2 with breast cancer risk, progression and survival among Chinese Han women. PLoS One 2012; 7:e49296. [PMID: 23185313 PMCID: PMC3504019 DOI: 10.1371/journal.pone.0049296] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Accepted: 10/04/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Somatic alterations of cyclin-dependent kinase 2 (CDK2)-cyclin E complex have been shown to contribute to breast cancer (BC) development and progression. This study aimed to explore the effects of single nucleotide polymorphisms (SNPs) in CDK2 and CCNE1 (a gene encoding G1/S specific cyclin E1 protein, formerly called cyclin E) on BC risk, progression and survival in a Chinese Han population. METHODOLOGY/PRINCIPAL FINDINGS We herein genotyped 6 haplotype-tagging SNPs (htSNPs) of CCNE1 and 2 htSNPs of CDK2 in 1207 BC cases and 1207 age-matched controls among Chinese Han women, and then reconstructed haplotype blocks according to our genotyping data and linkage disequilibrium status of these htSNPs. For CCNE1, the minor allele homozygotes of three htSNPs were associated with BC risk (rs3218035: adjusted odds ratio [aOR] = 3.35, 95% confidence interval [CI] = 1.69-6.67; rs3218038: aOR = 1.81, 95% CI = 1.22-2.70; rs3218042: aOR = 2.64, 95% CI = 1.31-5.34), and these three loci showed a dose-dependent manner in increasing BC risk (P(trend) = 0.0001). Moreover, the 5-SNP haplotype CCGTC, which carried none of minor alleles of the 3 at-risk SNPs, was associated with a favorable event-free survival (hazard ratio [HR] = 0.53, 95% CI = 0.32-0.90). Stratified analysis suggested that the minor-allele homozygote carriers of rs3218038 had a worse event-free survival among patients with aggressive tumours (in tumour size>2 cm group: HR = 2.06, 95% CI = 1.06-3.99; in positive lymph node metastasis group: HR = 2.41, 95% CI = 1.15-5.03; in stage II-IV group: HR = 2.03, 95% CI = 1.09-3.79). For CDK2, no significant association was found. CONCLUSIONS/SIGNIFICANCE This study indicates that genetic variants in CCNE1 may contribute to BC risk and survival in Chinese Han population. They may become molecular markers for individual evaluation of BC susceptibility and prognosis. Nevertheless, further validation studies are needed.
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Affiliation(s)
- Ji-Yuan Han
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Hui Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Yun-Tao Xie
- Breast Center, Peking University School of Oncology, Beijing Cancer Hospital & Institute, Beijing, People' Republic of China
| | - Yan Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Li-Yuan Zheng
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Yuan Ruan
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Ai-Ping Song
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Xin-Xia Tian
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
| | - Wei-Gang Fang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People' Republic of China
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124
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Plourde KV, Labrie Y, Desjardins S, Belleau P, Ouellette G, Durocher F. Analysis of ZNF350/ZBRK1 promoter variants and breast cancer susceptibility in non-BRCA1/2 French Canadian breast cancer families. J Hum Genet 2012; 58:59-66. [PMID: 23151675 DOI: 10.1038/jhg.2012.127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
ZNF350/ZBRK1 is a transcription factor, which associates with BRCA1 to co-repress GADD45A to regulate DNA damage repair, and the expression of ZNF350 is altered in different human carcinomas. In a previous study, we identified ZNF350 genomic variants potentially involved in breast cancer susceptibility in high-risk non-BRCA1/2 breast cancer individuals, which pointed toward a potential association for variants in the 5'-UTR and promoter regions. Therefore, direct sequencing was undertaken and identified 12 promoter variants, whereas haplotype analyses put in evidence four common haplotypes with a frequency>2%. However, based on their frequency observed in breast cancer and unrelated healthy individuals, these are not statistically associated with breast cancer risk. Luciferase promoter assays in two breast cancer cell lines identified two haplotypes (H11 and H12) stimulating significantly the expression of ZNF350 transcript compared with the common haplotype H8. The high expression of the H11 allele was associated with the variant c.-874A. Using MatInspector and Transcription Element Search softwares, in silico analyses predicted that the variant c.-874A created a binding site for the factors c-Myc and myogenin. This study represents the first characterization step of the ZNF350 promoter. Additional studies in larger cohorts and other populations will be needed to further evaluate whether common and/or rare ZNF350 promoter variants and haplotypes could be associated with a modest risk of breast cancer.
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Affiliation(s)
- Karine V Plourde
- Cancer Genomics Laboratory, Oncology and Molecular Endocrinology Research Centre, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, QC, Canada
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125
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HER2 Ile655Val and PTEN IVS4 polymorphisms in patients with breast cancer. Mol Biol Rep 2012; 40:1813-8. [DOI: 10.1007/s11033-012-2235-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/10/2012] [Indexed: 10/27/2022]
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126
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Bradbury AR, Patrick-Miller L, Egleston BL, Schwartz LA, Sands CB, Shorter R, Moore CW, Tuchman L, Rauch P, Malhotra S, Rowan B, Van Decker S, Schmidheiser H, Bealin L, Sicilia P, Daly MB. Knowledge and perceptions of familial and genetic risks for breast cancer risk in adolescent girls. Breast Cancer Res Treat 2012; 136:749-57. [PMID: 23065030 DOI: 10.1007/s10549-012-2254-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 09/11/2012] [Indexed: 01/03/2023]
Abstract
Evidence suggests early events might modify adult breast cancer risk and many adolescents learn of familial and genetic risks for breast cancer. Little is known about how adolescent girls understand and respond to breast cancer risk. Semi-structured interviews with 11-19 year-old girls at high-risk and population-risk for breast cancer evaluated knowledge and perceptions of breast cancer risk and risk modification. Framework analysis and descriptive statistics were utilized to analyze open-ended responses. Risk group and age differences were evaluated by Fisher's exact and McNemar's tests. Fifty-four girls (86 % of invited), 35 high-risk (65 %), and 19 population-risk (35 %) completed interviews. The most frequently reported risk for breast cancer was family history/hereditary predisposition (66 %). Only 17 % of girls were aware of BRCA1/2 genes. The majority (76 %) of high-risk girls perceive themselves to be at increased risk for breast cancer, compared to 22 % of population-risk girls (p = 0.001). Half of girls reported that women can get breast cancer before 20-years-old. The majority believe there are things women (70 %) and girls (67 %) can do to prevent breast cancer. Mother was the most frequently reported source of information for breast cancer among both high-risk (97 %) and population-risk (89 %) girls. In this study, many high-risk girls perceive themselves to be at increased risk for breast cancer, and many girls believe that breast cancer can occur in teens. Yet, most girls believe there are things women and girls can do to prevent breast cancer. Research evaluating the impact of awareness and perceptions of breast cancer risk on psychosocial, health, and risk behaviors is needed to develop strategies to optimize responses to cancer risk.
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Affiliation(s)
- Angela R Bradbury
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, 3 West Perelman Center 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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127
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Baykara M, Ozturk SC, Buyukberber S, Helvaci K, Ozdemir N, Alkis N, Berk V, Koca D, Coskun U, Oksuzoglu B, Uncu D, Arpaci E, Ustaalioglu BO, Demirci U, Kucukoner M, Dogu GG, Alici S, Akman T, Ozkan M, Aslan UY, Durnali AG, Benekli M. Clinicopathological Features in Bilateral Breast Cancer. Asian Pac J Cancer Prev 2012; 13:4571-5. [DOI: 10.7314/apjcp.2012.13.9.4571] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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128
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Snape K, Ruark E, Tarpey P, Renwick A, Turnbull C, Seal S, Murray A, Hanks S, Douglas J, Stratton MR, Rahman N. Predisposition gene identification in common cancers by exome sequencing: insights from familial breast cancer. Breast Cancer Res Treat 2012; 134:429-33. [PMID: 22527104 PMCID: PMC3781770 DOI: 10.1007/s10549-012-2057-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 04/01/2012] [Indexed: 10/28/2022]
Abstract
The genetic component of breast cancer predisposition remains largely unexplained. Candidate gene case-control resequencing has identified predisposition genes characterised by rare, protein truncating mutations that confer moderate risks of disease. In theory, exome sequencing should yield additional genes of this class. Here, we explore the feasibility and design considerations of this approach. We performed exome sequencing in 50 individuals with familial breast cancer, applying frequency and protein function filters to identify variants most likely to be pathogenic. We identified 867,378 variants that passed the call quality filters of which 1,296 variants passed the frequency and protein truncation filters. The median number of validated, rare, protein truncating variants was 10 in individuals with, and without, mutations in known genes. The functional candidacy of mutated genes was similar in both groups. Without prior knowledge, the known genes would not have been recognisable as breast cancer predisposition genes. Everyone carries multiple rare mutations that are plausibly related to disease. Exome sequencing in common conditions will therefore require intelligent sample and variant prioritisation strategies in large case-control studies to deliver robust genetic evidence of disease association.
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Affiliation(s)
- Katie Snape
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
| | - Elise Ruark
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
| | - Patrick Tarpey
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Anthony Renwick
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
| | - Sheila Seal
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
| | - Anne Murray
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
| | - Sandra Hanks
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
| | - Jenny Douglas
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
| | | | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research and Royal Marsden Hospital Foundation Trust, Sutton, Surrey UK
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129
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Xiang C, Gao H, Meng L, Qin Z, Ma R, Liu Y, Jiang Y, Dang C, Jin L, He F, Wang H. Functional variable number of tandem repeats variation in the promoter of proto-oncogene PTTG1IP is associated with risk of estrogen receptor-positive breast cancer. Cancer Sci 2012; 103:1121-8. [PMID: 22404099 DOI: 10.1111/j.1349-7006.2012.02266.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 02/23/2012] [Accepted: 03/04/2012] [Indexed: 01/09/2023] Open
Abstract
Genetic polymorphisms in the signalling pathway of estrogen receptor (ER) could modify the risk of breast cancer. A variable number of tandem repeats (VNTR) polymorphism in the promoter of PTTG1IP, pituitary tumor transforming gene binding factor targeted by estrogen receptor α (ERα) in endocrine neoplasia, has been shown to be functional, but its relevance to cancer etiology was unknown. We investigated its association with breast cancer risk by genotyping in 658 patients and 866 controls and further analysed its differential interaction with ERα. We found nine types of alleles ranging from 2 to 9 and 11 repeats that form 29 distinct genotypes and 11 different biallelic repeat numbers. Subjects who carry the six-repeats allele (odds ratio [OR], 1.45; 95% confidence interval [CI], 1.17-1.79), long alleles (≥6 repeats) (OR, 1.55; 95% CI, 1.17-2.05) or a high dose of biallelic repeats (OR, 1.38; 95% CI, 1.07-1.77) were at significantly increased risk of cancer. In stratification analysis, these associations consistently manifested in ER-positive breast cancer: in ER positive, PR-positive subtype, genotypes with the six-repeats allele (OR, 1.42; 95% CI, 1.06-1.90), long alleles (OR, 1.77; 95% CI, 1.17-2.67) or a high dose of biallelic repeats (OR, 1.67; 95% CI, 1.19-2.33) were associated with cancer risk; in ER positive, HER2-negative subtype, they were susceptible factors with the ORs being 1.46 (95% CI, 1.06-2.02), 2.06 (95% CI, 1.28-3.32) and 1.85 (95% CI, 1.26-2.71), respectively. Furthermore, functional analysis revealed that an increase in the number of tandem repeats enhances the binding affinity of ERα. The present study provides the first epidemiological evidence that functional regulatory variants of PTTG1IP were associated with the risk of ER-positive breast cancer, further supporting its relevance as one proto-oncogene in breast cancer.
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Affiliation(s)
- Chan Xiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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130
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Rare mutations in XRCC2 increase the risk of breast cancer. Am J Hum Genet 2012; 90:734-9. [PMID: 22464251 DOI: 10.1016/j.ajhg.2012.02.027] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 01/16/2012] [Accepted: 02/29/2012] [Indexed: 01/18/2023] Open
Abstract
An exome-sequencing study of families with multiple breast-cancer-affected individuals identified two families with XRCC2 mutations, one with a protein-truncating mutation and one with a probably deleterious missense mutation. We performed a population-based case-control mutation-screening study that identified six probably pathogenic coding variants in 1,308 cases with early-onset breast cancer and no variants in 1,120 controls (the severity grading was p < 0.02). We also performed additional mutation screening in 689 multiple-case families. We identified ten breast-cancer-affected families with protein-truncating or probably deleterious rare missense variants in XRCC2. Our identification of XRCC2 as a breast cancer susceptibility gene thus increases the proportion of breast cancers that are associated with homologous recombination-DNA-repair dysfunction and Fanconi anemia and could therefore benefit from specific targeted treatments such as PARP (poly ADP ribose polymerase) inhibitors. This study demonstrates the power of massively parallel sequencing for discovering susceptibility genes for common, complex diseases.
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131
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Catucci I, Colombo M, Verderio P, Bernard L, Ficarazzi F, Mariette F, Barile M, Peissel B, Cattaneo E, Manoukian S, Radice P, Peterlongo P. Sequencing analysis of SLX4/FANCP gene in Italian familial breast cancer cases. PLoS One 2012; 7:e31038. [PMID: 22383991 PMCID: PMC3285620 DOI: 10.1371/journal.pone.0031038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 12/30/2011] [Indexed: 12/31/2022] Open
Abstract
Breast cancer can be caused by germline mutations in several genes that are responsible for different hereditary cancer syndromes. Some of the genes causing the Fanconi anemia (FA) syndrome, such as BRCA2, BRIP1, PALB2, and RAD51C, are associated with high or moderate risk of developing breast cancer. Very recently, SLX4 has been established as a new FA gene raising the question of its implication in breast cancer risk. This study aimed at answering this question sequencing the entire coding region of SLX4 in 526 familial breast cancer cases from Italy. We found 81 different germline variants and none of these were clearly pathogenic. The statistical power of our sample size allows concluding that in Italy the frequency of carriers of truncating mutations of SLX4 may not exceed 0.6%. Our results indicate that testing for SLX4 germline mutations is unlikely to be relevant for the identification of individuals at risk of breast cancer, at least in the Italian population.
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Affiliation(s)
- Irene Catucci
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mara Colombo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Verderio
- Unit of Medical Statistics and Biometry, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia, Milan, Italy
| | | | | | - Monica Barile
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, Milan, Italy
| | - Bernard Peissel
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elisa Cattaneo
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Medical Genetics, Department of Medicine, Surgery and Dentistry, Università degli Studi di Milano, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Radice
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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132
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Turnbull C, Seal S, Renwick A, Warren-Perry M, Hughes D, Elliott A, Pernet D, Peock S, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Brice G, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Shanley S, Walker L, Ahmed M, Eccles D, Evans DG, Donnelly P, Easton DF, Stratton MR, Rahman N. Gene-gene interactions in breast cancer susceptibility. Hum Mol Genet 2012; 21:958-62. [PMID: 22072393 PMCID: PMC4125627 DOI: 10.1093/hmg/ddr525] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 10/26/2011] [Accepted: 11/07/2011] [Indexed: 11/13/2022] Open
Abstract
There have been few definitive examples of gene-gene interactions in humans. Through mutational analyses in 7325 individuals, we report four interactions (defined as departures from a multiplicative model) between mutations in the breast cancer susceptibility genes ATM and CHEK2 with BRCA1 and BRCA2 (case-only interaction between ATM and BRCA1/BRCA2 combined, P = 5.9 × 10(-4); ATM and BRCA1, P= 0.01; ATM and BRCA2, P= 0.02; CHEK2 and BRCA1/BRCA2 combined, P = 2.1 × 10(-4); CHEK2 and BRCA1, P= 0.01; CHEK2 and BRCA2, P= 0.01). The interactions are such that the resultant risk of breast cancer is lower than the multiplicative product of the constituent risks, and plausibly reflect the functional relationships of the encoded proteins in DNA repair. These findings have important implications for models of disease predisposition and clinical translation.
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Affiliation(s)
- Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Anthony Renwick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Margaret Warren-Perry
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Deborah Hughes
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Anna Elliott
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - David Pernet
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Susan Peock
- Department of Public Health and Primary Care, Cancer Research UK, Genetic Epidemiology Unit, University of Cambridge, Cambridge CB1 8RN, UK
| | - Julian W. Adlard
- Yorkshire Regional Genetics Service, Chapel Allerton Hospital, Leeds LS7 4SA, UK
| | - Julian Barwell
- Leicestershire Genetics Centre, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Jonathan Berg
- Human Genetics, Division of Medical Sciences, University of Dundee, Dundee DD1 9SY, UK
| | - Angela F. Brady
- NW Thames Regional Genetics Service, Kennedy-Galton Centre, London HA1 3UJ, UK
| | - Carole Brewer
- Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter EX1 2ED, UK
| | - Glen Brice
- SW Thames Regional Genetics Service, St George's Hospital, London SW17 9RE, UK
| | - Cyril Chapman
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham B15 2TG, UK
| | - Jackie Cook
- Sheffield Regional Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield S10 2TH, UK
| | - Rosemarie Davidson
- West of Scotland Regional Genetics Service, Ferguson Smith Centre for Clinical Genetics, Glasgow G3 8SJ, UK
| | - Alan Donaldson
- South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust, Bristol BS2 8EG, UK
| | - Fiona Douglas
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne NE1 3BZ, UK
| | - Lynn Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Alder Hey Children's NHS Foundation Trust, Liverpool L12 2AP, UK
| | - Alex Henderson
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne NE1 3BZ, UK
| | - Louise Izatt
- SE Thames Regional Genetics Service, Guy's and St Thomas NHS Foundation Trust, London SE1 9RT, UK
| | - Ajith Kumar
- NE Thames Regional Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Fiona Lalloo
- University Department of Medical Genetics and Regional Genetics Service, St Mary's Hospital, Manchester, M13 9WL, UK
| | - Zosia Miedzybrodzka
- University of Aberdeen & North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary, Aberdeen, AB25 2ZA, UK
| | - Patrick J Morrison
- Department of Medical Genetics, Northern Ireland Regional Genetics Service, Belfast HSC Trust, Queen's University Belfast, Belfast BT9 7AB, UK
| | - Joan Paterson
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Mary Porteous
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Mark T. Rogers
- All Wales Medical Genetics Service, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Susan Shanley
- Royal Marsden NHS Foundation Trust, Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lisa Walker
- Oxford Regional Genetics Service, Oxford Radcliffe Hospitals NHS Trust, Oxford OX3 7LJ, UK
| | | | - Munaza Ahmed
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton SO16 6YD, UK
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust, Southampton SO16 6YD, UK
| | - D. Gareth Evans
- University Department of Medical Genetics and Regional Genetics Service, St Mary's Hospital, Manchester, M13 9WL, UK
| | - Peter Donnelly
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
- Department of Statistics, University of Oxford, Oxford OX1 3TG, UK and
| | - Douglas F. Easton
- Department of Public Health and Primary Care, Cancer Research UK, Genetic Epidemiology Unit, University of Cambridge, Cambridge CB1 8RN, UK
| | - Michael R. Stratton
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Cancer Genome Project, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
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Balmaña J, Díez O, Rubio IT, Cardoso F. BRCA in breast cancer: ESMO Clinical Practice Guidelines. Ann Oncol 2011; 22 Suppl 6:vi31-4. [PMID: 21908500 DOI: 10.1093/annonc/mdr373] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- J Balmaña
- Medical Oncology Department, Breast Cancer Center, University Hospital Vall d'Hebron, Barcelona, Spain
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134
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Ossovskaya V, Koo IC, Kaldjian EP, Alvares C, Sherman BM. Upregulation of Poly (ADP-Ribose) Polymerase-1 (PARP1) in Triple-Negative Breast Cancer and Other Primary Human Tumor Types. Genes Cancer 2011; 1:812-21. [PMID: 21779467 DOI: 10.1177/1947601910383418] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 08/10/2010] [Accepted: 08/10/2010] [Indexed: 01/31/2023] Open
Abstract
Poly (ADP-ribose) polymerase-1 (PARP1) is a key facilitator of DNA repair and is implicated in pathways of tumorigenesis. PARP inhibitors have gained recent attention as rationally designed therapeutics for the treatment of several malignancies, particularly those associated with dysfunctional DNA repair pathways, including triple-negative breast cancer (TNBC). We investigated the PARP1 gene expression profile in surgical samples from more than 8,000 primary malignant and normal human tissues. PARP1 expression was found to be significantly increased in several malignant tissues, including those isolated from patients with breast, uterine, lung, ovarian, and skin cancers, and non-Hodgkin's lymphoma. Within breast infiltrating ductal carcinoma (IDC) samples tested, mean PARP1 expression was significantly higher relative to normal breast tissue, with over 30% of IDC samples demonstrating upregulation of PARP1, compared with 2.9% of normal tissues. Because of known DNA repair defects, including BRCA1 dysfunction, associated with TNBC, exploration of PARP1 expression in breast cancers related to expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) led to the observation that negative expression of any of the 3 receptors was associated with upregulation of PARP1 expression, compared with receptor-positive tissues. To validate these observations, an independent set of breast adenocarcinomas was evaluated and demonstrated >2-fold upregulation of PARP1 in approximately 70% of primary breast adenocarcinomas, including TNBC, compared with syngeneic nonmalignant breast tissues. Immunohistochemistry (IHC) showed that upregulation of the PARP1 gene was consistent with increased protein expression in TNBC. These analyses suggest a potential biological role for PARP1 in several distinct malignancies, including TNBC. Further investigation of PARP1 as a biomarker for the therapeutic activity of PARP inhibitor-based therapy is warranted.
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135
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Harlid S, Ivarsson MIL, Butt S, Grzybowska E, Eyfjörd JE, Lenner P, Försti A, Hemminki K, Manjer J, Dillner J, Carlson J. Combined effect of low-penetrant SNPs on breast cancer risk. Br J Cancer 2011; 106:389-96. [PMID: 22045194 PMCID: PMC3261688 DOI: 10.1038/bjc.2011.461] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Although many low-penetrant genetic risk factors for breast cancer have been discovered, knowledge about the effect of multiple risk alleles is limited, especially in women <50 years. We therefore investigated the association between multiple risk alleles and breast cancer risk as well as individual effects according to age-approximated pre- and post-menopausal status. METHODS Ten previously described breast cancer-associated single-nucleotide polymorphisms (SNPs) were analysed in a joint European biobank-based study comprising 3584 breast cancer cases and 5063 cancer-free controls. Genotyping was performed using MALDI-TOF mass spectrometry, and odds ratios were estimated using logistic regression. RESULTS Significant associations with breast cancer were confirmed for 7 of the 10 SNPs. Analysis of the joint effect of the original 10 as well as the statistically significant 7 SNPs (rs2981582, rs3803662, rs889312, rs13387042, rs13281615, rs3817198 and rs981782) found a highly significant trend for increasing breast cancer risk with increasing number of risk alleles (P-trend 5.6 × 10(-20) and 1.5 × 10(-25), respectively). Odds ratio for breast cancer of 1.84 (95% confidence interval (CI): 1.59-2.14; 10 SNPs) and 2.12 (95% CI: 1.80-2.50; 7 SNPs) was seen for the maximum vs the minimum number of risk alleles. Additionally, one of the examined SNPs (rs981782 in HCN1) had a protective effect that was significantly stronger in premenopausal women (P-value: 7.9 × 10(-4)). CONCLUSION The strongly increasing risk seen when combining many low-penetrant risk alleles supports the polygenic inheritance model of breast cancer.
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Affiliation(s)
- S Harlid
- Departments of Medical Microbiology and Clinical Chemistry, Lund University, SUS entrance 78, Malmö S-205 02, Sweden.
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Focken T, Steinemann D, Skawran B, Hofmann W, Ahrens P, Arnold N, Kroll P, Kreipe H, Schlegelberger B, Gadzicki D. Human BRCA1-associated breast cancer: no increase in numerical chromosomal instability compared to sporadic tumors. Cytogenet Genome Res 2011; 135:84-92. [PMID: 22024613 DOI: 10.1159/000332005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2011] [Indexed: 12/28/2022] Open
Abstract
BRCA1 is a major gatekeeper of genomic stability. Acting in multiple central processes like double-strand break repair, centrosome replication, and checkpoint control, BRCA1 participates in maintaining genomic integrity and protects the cell against genomic instability. Chromosomal instability (CIN) as part of genomic instability is an inherent characteristic of most solid tumors and is also involved in breast cancer development. In this study, we determined the extent of CIN in 32 breast cancer tumors of women with a BRCA1 germline mutation compared to 62 unselected breast cancers. We applied fluorescence in situ hybridization (FISH) with centromere-specific probes for the chromosomes 1, 7, 8, 10, 17, and X and locus-specific probes for 3q27 (BCL6), 5p15.2 (D5S23), 5q31 (EGR1), 10q23.3 (PTEN), and 14q32 (IGH@) on formalin-fixed paraffin-embedded tissue microarray sections. Our hypothesis of an increased level of CIN in BRCA1-associated breast cancer could not be confirmed by this approach. Surprisingly, we detected no significant difference in the extent of CIN in BRCA1-mutated versus sporadic tumors. The only exception was the CIN value for chromosome 1. Here, the extent of CIN was slightly higher in the group of sporadic tumors.
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Affiliation(s)
- T Focken
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
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137
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Sokolenko AP, Iyevleva AG, Preobrazhenskaya EV, Mitiushkina NV, Abysheva SN, Suspitsin EN, Kuligina ES, Gorodnova TV, Pfeifer W, Togo AV, Turkevich EA, Ivantsov AO, Voskresenskiy DV, Dolmatov GD, Bit-Sava EM, Matsko DE, Semiglazov VF, Fichtner I, Larionov AA, Kuznetsov SG, Antoniou AC, Imyanitov EN. High prevalence and breast cancer predisposing role of the BLM c.1642 C>T (Q548X) mutation in Russia. Int J Cancer 2011; 130:2867-73. [PMID: 21815139 DOI: 10.1002/ijc.26342] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 07/21/2011] [Indexed: 11/11/2022]
Abstract
The BLM gene belongs to the RecQ helicase family and has been implicated in the maintenance of genomic stability. Its homozygous germline inactivation causes Bloom syndrome, a severe genetic disorder characterized by growth retardation, impaired fertility and highly elevated cancer risk. We hypothesized that BLM is a candidate gene for breast cancer (BC) predisposition. Sequencing of its entire coding region in 95 genetically enriched Russian BC patients identified two heterozygous carriers of the c.1642 C>T (Q548X) mutation. The extended study revealed this allele in 17/1,498 (1.1%) BC cases vs. 2/1,093 (0.2%) healthy women (p = 0.004). There was a suggestion that BLM mutations were more common in patients reporting first-degree family history of BC (6/251 (2.4%) vs. 11/1,247 (0.9%), p = 0.05), early-onset cases (12/762 (1.6%) vs. 5/736 (0.7%), p = 0.14) and women with bilateral appearance of the disease (2/122 (1.6%) vs. 15/1376 (1.1%), p = 0.64). None of the BLM-associated BC exhibited somatic loss of heterozygosity at the BLM gene locus. This study demonstrates that BLM Q548X allele is recurrent in Slavic subjects and may be associated with BC risk.
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Affiliation(s)
- Anna P Sokolenko
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
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138
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Zheng Y, Zhang J, Niu Q, Huo D, Olopade OI. Novel germline PALB2 truncating mutations in African American breast cancer patients. Cancer 2011; 118:1362-70. [PMID: 21932393 DOI: 10.1002/cncr.26388] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 06/02/2011] [Accepted: 06/03/2011] [Indexed: 12/16/2022]
Abstract
BACKGROUND It has been demonstrated that the partner and localizer of breast cancer 2 (PALB2) acts as a bridging molecule between the breast cancer 1 (BRCA1) and BRCA2 proteins and is responsible for facilitating BRCA2-mediated DNA repair. Truncating mutations in the PALB2 gene reportedly are enriched in patients with Fanconi anemia and breast cancer in various populations. METHODS The authors evaluated the contribution of PALB2 germline mutations in 279 African American women with breast cancer, including 29 patients with a strong family history, 29 patients with a moderate family history, 75 patients with a weak family history, and 146 patients with nonfamilial or sporadic breast cancer. RESULTS After direct sequencing of all the coding exons, exon/intron boundaries, and 5' and 3' untranslated regions of PALB2, 3 novel, monoallelic, truncating mutations (1.08%; 3 in 279 patients) were identified (c.758dupT [exon 4], c.1479delC [exon 4], and c.3048delT [exon 10]) together with 50 sequence variants, 27 of which were novel. None of the truncating mutations were identified in a group of 262 controls from the same population. CONCLUSIONS PALB2 mutations were present in both familial and nonfamilial breast cancers among African Americans. Rare PALB2 mutations accounted for a small but substantial proportion of patients with breast cancer.
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Affiliation(s)
- Yonglan Zheng
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, Illinois 60637, USA
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139
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Loveday C, Turnbull C, Ramsay E, Hughes D, Ruark E, Frankum JR, Bowden G, Kalmyrzaev B, Warren-Perry M, Snape K, Adlard JW, Barwell J, Berg J, Brady AF, Brewer C, Brice G, Chapman C, Cook J, Davidson R, Donaldson A, Douglas F, Greenhalgh L, Henderson A, Izatt L, Kumar A, Lalloo F, Miedzybrodzka Z, Morrison PJ, Paterson J, Porteous M, Rogers MT, Shanley S, Walker L, Eccles D, Evans DG, Renwick A, Seal S, Lord CJ, Ashworth A, Reis-Filho JS, Antoniou AC, Rahman N. Germline mutations in RAD51D confer susceptibility to ovarian cancer. Nat Genet 2011; 43:879-882. [PMID: 21822267 PMCID: PMC4845885 DOI: 10.1038/ng.893] [Citation(s) in RCA: 375] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 07/01/2011] [Indexed: 01/13/2023]
Abstract
Recently, RAD51C mutations were identified in families with breast and ovarian cancer. This observation prompted us to investigate the role of RAD51D in cancer susceptibility. We identified eight inactivating RAD51D mutations in unrelated individuals from 911 breast-ovarian cancer families compared with one inactivating mutation identified in 1,060 controls (P = 0.01). The association found here was principally with ovarian cancer, with three mutations identified in the 59 pedigrees with three or more individuals with ovarian cancer (P = 0.0005). The relative risk of ovarian cancer for RAD51D mutation carriers was estimated to be 6.30 (95% CI 2.86-13.85, P = 4.8 × 10(-6)). By contrast, we estimated the relative risk of breast cancer to be 1.32 (95% CI 0.59-2.96, P = 0.50). These data indicate that RAD51D mutation testing may have clinical utility in individuals with ovarian cancer and their families. Moreover, we show that cells deficient in RAD51D are sensitive to treatment with a PARP inhibitor, suggesting a possible therapeutic approach for cancers arising in RAD51D mutation carriers.
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Affiliation(s)
- Chey Loveday
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Clare Turnbull
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Emma Ramsay
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Deborah Hughes
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Elise Ruark
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Jessica R Frankum
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London
| | - Georgina Bowden
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Bolot Kalmyrzaev
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | | | - Katie Snape
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Julian W Adlard
- Yorkshire Regional Centre for Cancer Treatment, Cookridge Hospital, Leeds
| | - Julian Barwell
- Leicestershire Genetics Centre, University Hospitals of Leicester NHS Trust
| | - Jonathan Berg
- Human genetics, Division of Medical Sciences, University of Dundee
| | - Angela F Brady
- NW Thames Regional Genetics Service, Kennedy Galton Centre, London
| | - Carole Brewer
- Peninsula Regional Genetics Service, Royal Devon & Exeter Hospital, Exeter
| | - Glen Brice
- SW Thames Regional Genetics Service, St George's Hospital, London
| | - Cyril Chapman
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham
| | - Jackie Cook
- Sheffield Regional Genetics Service, Sheffield Children's NHS Foundation Trust
| | - Rosemarie Davidson
- West of Scotland Regional Genetics Service, FergusonSmith Centre for Clinical Genetics, Glasgow
| | - Alan Donaldson
- South Western Regional Genetics Service, University Hospitals of Bristol NHS Foundation Trust
| | - Fiona Douglas
- Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust
| | - Lynn Greenhalgh
- Cheshire and Merseyside Clinical Genetics Service, Alder Hey Children's NHS Foundation Trust, Liverpool
| | - Alex Henderson
- Northern Genetics Service (Cumbria), Newcastle upon Tyne Hospitals NHS Trust
| | - Louise Izatt
- SE Thames Regional Genetics Service, Guy's and St Thomas NHS Foundation Trust
| | - Ajith Kumar
- NE Thames Regional Genetics Service, Great Ormond St Hospital, London
| | - Fiona Lalloo
- University Dept of Medical Genetics & Regional Genetics Service, St Mary's Hospital, Manchester
| | - Zosia Miedzybrodzka
- University of Aberdeen and North of Scotland Clinical Genetics Service, Aberdeen Royal Infirmary
| | - Patrick J Morrison
- Northern Ireland Regional Genetics Service, Belfast HSC Trust, & Department of Medical Genetics, Queen's University Belfast
| | - Joan Paterson
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust
| | - Mary Porteous
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh
| | - Mark T Rogers
- All Wales Medical Genetics Service, University Hospital of Wales, Cardiff
| | - Susan Shanley
- Royal Marsden NHS Foundation Trust, Royal Marsden NHS Foundation Trust
| | - Lisa Walker
- Oxford Regional Genetics Service, Oxford Radcliffe Hospitals NHS Trust
| | - Diana Eccles
- Faculty of Medicine, University of Southampton, Southampton University Hospitals NHS Trust
| | - D Gareth Evans
- University Dept of Medical Genetics & Regional Genetics Service, St Mary's Hospital, Manchester
| | - Anthony Renwick
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Sheila Seal
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
| | - Christopher J Lord
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London
| | - Alan Ashworth
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London
| | - Jorge S Reis-Filho
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London
| | - Antonis C Antoniou
- Center for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge
| | - Nazneen Rahman
- Section of Cancer Genetics, The Institute of Cancer Research, Sutton
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140
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Germline mutational analysis of the C19orf62 gene in African-American women with breast cancer. Breast Cancer Res Treat 2011; 127:871-7. [DOI: 10.1007/s10549-011-1445-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 03/09/2011] [Indexed: 10/18/2022]
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141
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Sriram KB, Relan V, Clarke BE, Duhig EE, Yang IA, Bowman RV, Lee YCG, Fong KM. Diagnostic molecular biomarkers for malignant pleural effusions. Future Oncol 2011; 7:737-52. [DOI: 10.2217/fon.11.45] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Malignant pleural effusions (MPEs) are a common and important cause of cancer-related mortality and morbidity. Prompt diagnosis using minimally invasive tests is important because the median survival after diagnosis is only 4–9 months. Pleural fluid cytology is pivotal to current MPE diagnostic algorithms but has limited sensitivity (30–60%). Consequently, many patients need to undergo invasive diagnostic tests such as thoracoscopic pleural biopsy. Recent genomic, transcriptomic, methylation and proteomic studies on cells within pleural effusions have identified novel molecular diagnostic biomarkers that demonstrate potential in complementing cytology in the diagnosis of MPEs. Several challenges will need to be addressed prior to the incorporation of these molecular tests into routine clinical diagnosis, including validation of molecular diagnostic markers in well-designed prospective, comparative and cost–effectiveness studies. Ultimately, minimally invasive diagnostic tests that can be performed quickly will enable clinicians to provide the most effective therapies for patients with MPEs in a timely fashion.
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Affiliation(s)
| | - Vandana Relan
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Queensland, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Queensland, Australia
| | - Belinda E Clarke
- Department of Anatomical Pathology, The Prince Charles Hospital, Queensland, Australia
| | - Edwina E Duhig
- Department of Anatomical Pathology, The Prince Charles Hospital, Queensland, Australia
| | - Ian A Yang
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Queensland, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Queensland, Australia
| | - Rayleen V Bowman
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Queensland, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Queensland, Australia
| | - YC Gary Lee
- School of Medicine & Pharmacology & CAARR, University of Western Australia, Perth, Australia
- Respiratory Department, Sir Charles Gairdner Hospital, Perth, Australia
- Pleural Disease Unit, Lung Institute of Western Australia, Perth, Australia
| | - Kwun M Fong
- University of Queensland Thoracic Research Centre, School of Medicine, The University of Queensland, Queensland, Australia
- Department of Thoracic Medicine, The Prince Charles Hospital, Queensland, Australia
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142
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Gadzicki D, Evans DG, Harris H, Julian-Reynier C, Nippert I, Schmidtke J, Tibben A, van Asperen CJ, Schlegelberger B. Genetic testing for familial/hereditary breast cancer-comparison of guidelines and recommendations from the UK, France, the Netherlands and Germany. J Community Genet 2011; 2:53-69. [PMID: 22109790 PMCID: PMC3186026 DOI: 10.1007/s12687-011-0042-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 02/09/2011] [Indexed: 12/19/2022] Open
Abstract
In this review, the national guidelines and recommendations for genetic testing for familial/hereditary breast cancer from the UK, France, the Netherlands and Germany were evaluated as to the inclusion criteria for genetic testing. In all four countries, access to genetic testing relies basically on the family history of breast and ovarian cancer. Similarities are obvious for most selection criteria. All four guidelines recommend embedding genetic testing within a framework of genetic counselling, and all agree to perform genetic testing first in an affected person. However, there are differences regarding the thresholds based on certain familial constellations, detailed description of selection criteria, the degree of relatedness between affected individuals and the counsellee, the age of diagnosis, the individual history of early onset breast cancer, bilateral breast cancer, the tumour morphology or the access to intensified surveillance. These differences and open questions not covered by the guidelines, e.g. on how to deal with phenocopies, unclassified variants, genetic variants in newly identified breast cancer susceptibility genes or with family constellations not fitting the criteria, are discussed. New evidence is usually slowly integrated into the guidelines. An exchange process towards the harmonization of the guidelines will ensure high quality health care across Europe.
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Affiliation(s)
- Dorothea Gadzicki
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany,
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143
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Reed SH. Nucleotide excision repair in chromatin: damage removal at the drop of a HAT. DNA Repair (Amst) 2011; 10:734-42. [PMID: 21600858 DOI: 10.1016/j.dnarep.2011.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In an earlier review of our understanding of the mechanism of nucleotide excision repair (NER) we examined the process with respect to how it occurs in chromatin [1]. We described how much of our mechanistic understanding of NER was derived from biochemical studies that analysed the repair reaction in DNA substrates not representative of that which exists in the living cell. We pointed out that our efforts to understand how NER operates in chromatin had been hampered in part because of the well-known inhibition of NER that occurs when DNA is assembled into nucleosomes and used as the substrate to examine the repair reaction in vitro. Despite this technical bottleneck, we summarized the biochemical, genetic and cell-based studies which have provided insights into the molecular mechanism of NER in the cellular context. More recently, we revisited the topic of how UV induced DNA damage is repaired in chromatin. In this review we examined the commonly held view that depicts a struggle in which the DNA repair machinery battles to overcome the inhibitory effect of chromatin during the repair process. We suggested that in this interpretation of events, the DNA repair mechanisms might be described as 'tilting at windmills': fighting an imaginary foe [2]. We surmised that this scenario was overly simplistic, and we described an emerging picture in which the DNA repair process and chromatin remodeling were mechanistically linked and were in fact functioning cooperatively to organize the efficient removal of DNA damage from the genome. Here we discuss the latest findings, which contribute to the idea that DNA damage induced changes to chromatin represent an important way in which the DNA repair process is initiated and organized throughout the genome to promote the efficient removal of damage in response to UV radiation.
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Affiliation(s)
- Simon H Reed
- Department of Medical Genetics, Haematology and Pathology, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.
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144
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Meindl A, Ditsch N, Kast K, Rhiem K, Schmutzler RK. Hereditary breast and ovarian cancer: new genes, new treatments, new concepts. DEUTSCHES ARZTEBLATT INTERNATIONAL 2011; 108:323-30. [PMID: 21637635 DOI: 10.3238/arztebl.2011.0323] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Accepted: 03/14/2011] [Indexed: 12/12/2022]
Abstract
BACKGROUND Every year, 60,000 women in Germany are found to have breast cancer, and 9000 to have ovarian cancer. Familial clustering of carcinoma is seen in about 20% of cases. METHODS We selectively review relevant articles published up to December 2010 that were retrieved by a search in PubMed, and we also discuss findings from the experience of the German Consortium for Hereditary Breast and Ovarian Cancer. RESULTS High risk is conferred by the highly penetrant BRCA1 and BRCA2 genes as well as by other genes such as RAD51C. Genes for breast cancer that were originally designated as moderately penetrant display higher penetrance than previously thought in families with a hereditary predisposition. The role these genes play in DNA repair is thought to explain why tumors associated with them are sensitive to platin derivatives and PARP inhibitors. In carriers of BRCA1 and BRCA2, prophylactic bilateral mastectomy and adnexectomy significantly lowers the incidence of breast and ovarian cancer. Moreover, prophylactic adnexectomy also lowers the breast-and-ovarian-cancer-specific mortality, as well as the overall mortality. If a woman bearing a mutation develops cancer in one breast, her risk of developing cancer in the other breast depends on the particular gene that is mutated and on her age at the onset of disease. CONCLUSION About half of all monogenically determined carcinomas of the breast and ovary are due to a mutation in one or the other of the highly penetrant BRCA genes (BRCA1 and BRCA2). Women carrying a mutated gene have an 80% to 90% chance of developing breast cancer and a 20% to 50% chance of developing ovarian cancer. Other predisposing genes for breast and ovarian cancer have been identified. Clinicians should develop and implement evidence-based treatments on the basis of these new findings.
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Affiliation(s)
- Alfons Meindl
- Klinikum rechts der Isar, aBteilung Gyn. Tumorgenetik, München.
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145
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Cuzick J, DeCensi A, Arun B, Brown PH, Castiglione M, Dunn B, Forbes JF, Glaus A, Howell A, von Minckwitz G, Vogel V, Zwierzina H. Preventive therapy for breast cancer: a consensus statement. Lancet Oncol 2011; 12:496-503. [DOI: 10.1016/s1470-2045(11)70030-4] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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146
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Calvert H, Azzariti A. The clinical development of inhibitors of poly(ADP-ribose) polymerase. Ann Oncol 2011; 22 Suppl 1:i53-9. [PMID: 21285153 DOI: 10.1093/annonc/mdq667] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A number of inhibitors of DNA repair have been evaluated or are undergoing development as potential cancer treatments. Inhibitors of poly(ADP-ribose) polymerase (PARP) are of particular interest in treating hereditary breast cancers occurring in patients who are carriers of BRCA1 or BRCA2 mutations. In vitro PARP inhibitors are highly cytotoxic to cell lines carrying BRCA mutations while only minimally toxic to cell lines without these mutations. This is thought to be due to a phenomenon known as synthetic lethality where the accumulation of single-strand breaks consequent on PARP inhibition are converted to double-strand breaks on cell division. Cancer cells in BRCA carriers are uniquely unable to repair the consequent double-strand breaks that result during cell division. PARP inhibitors were initially developed as possible chemo-potentiating agents but have now been evaluated clinically in BRCA-related tumors, showing remarkable single-agent activity. The potential future development and use is reviewed.
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Affiliation(s)
- H Calvert
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
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147
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BRIP1, PALB2, and RAD51C mutation analysis reveals their relative importance as genetic susceptibility factors for breast cancer. Breast Cancer Res Treat 2011; 127:853-9. [PMID: 21409391 DOI: 10.1007/s10549-011-1443-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 03/05/2011] [Indexed: 12/12/2022]
Abstract
Mutations in the recognized breast cancer susceptibility genes BRCA1, BRCA2, TP53, ATM, and CHEK2 account for approximately 20% of hereditary breast cancer. This raises the possibility that mutations in other biologically relevant genes may be involved in genetic predisposition to breast cancer. In this study, BRIP1, PALB2, and RAD51C were sequenced for mutations as a result of previously being associated with breast cancer risk due to their role in the double-strand break repair pathway and their close association with BRCA1 and BRCA2. Two truncating mutations in PALB2 (Q66X and W1038X), one of which is has not been reported before, were detected in an independent Australian cohort of 70 individuals with breast or ovarian cancer, and have strong family histories of breast or breast/ovarian cancer. In addition, six missense variants predicted to be causative were detected, one in BRIP1 and five in PALB2. No causative variants were identified in RAD51C. This study supports recent observations that although rare, PALB2 mutations are present in a small but substantial proportion of inherited breast cancer cases, and indicates that RAD51C at a population level does not account for a substantial number of familial breast cancer cases.
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148
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Harlid S, Ivarsson MIL, Butt S, Hussain S, Grzybowska E, Eyfjörd JE, Lenner P, Försti A, Hemminki K, Manjer J, Dillner J, Carlson J. A candidate CpG SNP approach identifies a breast cancer associated ESR1-SNP. Int J Cancer 2011; 129:1689-98. [PMID: 21105050 DOI: 10.1002/ijc.25786] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 10/25/2010] [Indexed: 11/10/2022]
Abstract
Altered DNA methylation is often seen in malignant cells, potentially contributing to carcinogenesis by suppressing gene expression. We hypothesized that heritable methylation potential might be a risk factor for breast cancer and evaluated possible association with breast cancer for single nucleotide polymorphisms (SNPs) either involving CpG sequences in extended 5'-regulatory regions of candidate genes (ESR1, ESR2, PGR, and SHBG) or CpG and missense coding SNPs in genes involved in methylation (MBD1, MECP2, DNMT1, MGMT, MTHFR, MTR, MTRR, MTHFD1, MTHFD2, BHMT, DCTD, and SLC19A1). Genome-wide searches for genetic risk factors for breast cancers have in general not investigated these SNPs, because of low minor allele frequency or weak haplotype associations. Genotyping was performed using Mass spectrometry-Maldi-Tof in a screening panel of 538 cases and 1,067 controls. Potential association to breast cancer was identified for 15 SNPs and one of these SNPs (rs7766585 in ESR1) was found to associate strongly with breast cancer, OR 1.30 (95% CI 1.17-1.45; p-value 2.1 × 10(-6)), when tested in a verification panel consisting of 3,211 unique breast cancer cases and 4,223 unique controls from five European biobank cohorts. In conclusion, a candidate gene search strategy focusing on methylation-related SNPs did identify a SNP that associated with breast cancer at high significance.
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Affiliation(s)
- Sophia Harlid
- Department of Medical Microbiology, Lund University, Malmö, Sweden
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149
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Abstract
Cohesin is a conserved multisubunit protein complex with diverse cellular roles, making key contributions to the coordination of chromosome segregation, the DNA damage response and chromatin regulation by epigenetic mechanisms. Much has been learned in recent years about the roles of cohesin in a physiological context, whereas its potential and emerging role in tumour initiation and/or progression has received relatively little attention. In this Opinion article we examine how cohesin deregulation could contribute to cancer development on the basis of its physiological roles.
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Affiliation(s)
- Huiling Xu
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria 8006, Australia
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150
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Didraga MA, van Beers EH, Joosse SA, Brandwijk KIM, Oldenburg RA, Wessels LFA, Hogervorst FBL, Ligtenberg MJ, Hoogerbrugge N, Verhoef S, Devilee P, Nederlof PM. A non-BRCA1/2 hereditary breast cancer sub-group defined by aCGH profiling of genetically related patients. Breast Cancer Res Treat 2011; 130:425-36. [PMID: 21286804 DOI: 10.1007/s10549-011-1357-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 01/17/2011] [Indexed: 02/04/2023]
Abstract
Germline mutations in BRCA1 and BRCA2 explain approximately 25% of all familial breast cancers. Despite intense efforts to find additional high-risk breast cancer genes (BRCAx) using linkage analysis, none have been reported thus far. Here we explore the hypothesis that BRCAx breast tumors from genetically related patients share a somatic genetic etiology that might be revealed by array comparative genomic hybridization (aCGH) profiling. As BRCA1 and BRCA2 tumors can be identified on the basis of specific genomic profiles, the same may be true for a subset of BRCAx families. Analyses used aCGH to compare 58 non-BRCA1/2 familial breast tumors (designated BRCAx) to sporadic (non-familiar) controls, BRCA1 and BRCA2 tumors. The selection criteria for BRCAx families included at least three cases of breast cancer diagnosed before the age of 60 in the family, and the absence of ovarian or male breast cancer. Hierarchical cluster analysis was performed to determine sub-groups within the BRCAx tumor class and family heterogeneity. Analysis of aCGH profiles of BRCAx tumors indicated that they constitute a heterogeneous class, but are distinct from both sporadic and BRCA1/2 tumors. The BRCAx class could be divided into sub-groups. One subgroup was characterized by a gain of chromosome 22. Tumors from family members were classified within the same sub-group in agreement with the hypothesis that tumors from the same family would harbor a similar genetic background. This approach provides a method to target a sub-group of BRCAx families for further linkage analysis studies.
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Affiliation(s)
- M A Didraga
- Department of Experimental Therapy, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
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