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Li M, Zheng Y, Li X, Shen X, Zhang T, Weng B, Mao H, Zhao J. ATBF1 is a potential diagnostic marker of histological grade and functions via WNT5A in breast cancer. BMC Cancer 2022; 22:1280. [PMID: 36476423 PMCID: PMC9727999 DOI: 10.1186/s12885-022-10380-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Histological grade has been demonstrated to be an important factor of breast cancer outcome and is associated with cell differentiation and is currently being evaluated via H&E-stained sections. Molecular biomarkers are essential to improve the accuracy of histological grading. ATBF1, a large transcription factor, has been considered a tumor suppressor gene with frequent mutations or deletions in multiple cancers. In breast cancer, ATBF1 was reported to function in cell differentiation and mammary development. However, its role in the clinic has rarely been reported. METHODS Breast cancer tissues (BCTs) and adjacent noncancerous tissues (ANCTs) were collected to analyze the expression of ATBF1 at the mRNA and protein levels. Three anti-ATBF1 antibodies recognizing independent peptides of ATBF1 (N-terminal end, middle region and C-terminal end) were applied for IHC staining. Small interfering RNA (siRNA) was used to silence ATBF1 expression and to investigate the roles of ATBF1 in MCF7 cells. Microarrays were introduced to analyze the differentially expressed genes, enriched GO terms and KEGG terms regulated by ATBF1 and its potential downstream genes, which were further confirmed in vitro and in clinical samples. RESULTS The expression of ATBF1 was reduced in BCTs at both the mRNA and protein levels compared with that in ANCTs. ATBF1 protein was predominantly localized in the nucleus of ANCTs but in the cytoplasm of BCTs. Both the mRNA and protein levels of ATBF1 were significantly correlated with histological grade. Consistently, knockdown of ATBF1 increased stemness marker expression and reduced differentiation markers in vitro. Further analysis identified WNT5A as an essential downstream gene of ATBF1 in breast cancer cells. Treatment of WNT5A disrupted cell proliferation induced by ATBF1 silencing. In BCTs, a significant correlation was observed between the expression of WNT5A and ATBF1. CONCLUSION The results indicated that ATBF1 expression might be a useful diagnostic marker associated with histological grade and breast cancer malignancy. WNT5A and its signaling pathway are novel mechanisms by which ATBF1 contributes to breast cancer tumorigenesis.
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Affiliation(s)
- Mei Li
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China ,Ningbo Institute of Medical Sciences, Ningbo, Zhejiang China
| | - Yanan Zheng
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China
| | - Xujun Li
- grid.9227.e0000000119573309Department of Breast Surgery, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, Zhejiang China
| | - Xiaohan Shen
- Ningbo Diagnostic Pathology Center, Ningbo, Zhejiang China
| | - Tingxia Zhang
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China
| | - Bowen Weng
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China
| | - Haijiao Mao
- grid.203507.30000 0000 8950 5267Department of Orthopaedic Surgery, the Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang China
| | - Jiyuan Zhao
- grid.203507.30000 0000 8950 5267Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang 315211 China
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Tang X, Nakanishi Y, Kobayashi H, Nishimaki H, Kusumi Y, Miyagi Y, Masuda S. Mixed ductal-lobular carcinoma: an analysis of CDH1 DNA copy number variation and mutation. Breast Cancer 2021; 28:1318-1327. [PMID: 34185256 DOI: 10.1007/s12282-021-01269-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Mixed ductal-lobular carcinoma (MDL) of the breast is poorly understood. Dysfunction of E-cadherin, a cell adhesion protein encoded by the CDH1 gene located on 16q22.1, causes loss of cell adhesion and cellular polarity in lobular carcinoma (LC). This study focuses the aberrations of CDH1 in LC, ductal carcinoma (DC), and MDL to investigate the pathogenesis of MDL. METHODS The CDH1 DNA value (ratio of CDH1 copy number to the reference gene, RNase P) was calculated by digital polymerase chain reaction analysis of a total of 113 breast carcinoma cases (51 LCs, 54 DCs, and 8 MDLs). CDH1 gene mutation assay was performed for 20/51 LCs, 8/54 DCs, and 8 MDLs cases. RESULTS The CDH1 DNA values were lower in LCs (average: 0.664) than in DCs (average: 1.296) (p < 0.000). In MDL, The CDH1 DNA values were significantly lower in LC areas (average: 0.58), compared to that of DC areas (average: 1.08) (p = 0.004), and there is no significant difference between the intermingled areas (average: 1.05) and DC areas (p = 0.775). Moreover, CDH1 mutations occurred more frequently in MDLs than in pure LCs and DCs. In one MDL case, the identical CDH1 mutation was found in LC and DC areas. CONCLUSION Our study presented that MDL had more frequent CDH1 mutations. There were two possible processes for cancer cells in LC areas: one process was via DC areas with a common ancestor, and another was an independent process from DC areas.
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Affiliation(s)
- Xiaoyan Tang
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-Ku, Tokyo, 173-8610, Japan.
| | - Yoko Nakanishi
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Hiroko Kobayashi
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Haruna Nishimaki
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Yoshiaki Kusumi
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Yohei Miyagi
- Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Shinobu Masuda
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine, 30-1 Oyaguchi-Kamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
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Privitera AP, Barresi V, Condorelli DF. Aberrations of Chromosomes 1 and 16 in Breast Cancer: A Framework for Cooperation of Transcriptionally Dysregulated Genes. Cancers (Basel) 2021; 13:1585. [PMID: 33808143 PMCID: PMC8037453 DOI: 10.3390/cancers13071585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
Derivative chromosome der(1;16), isochromosome 1q, and deleted 16q-producing arm-level 1q-gain and/or 16q-loss-are recurrent cytogenetic abnormalities in breast cancer, but their exact role in determining the malignant phenotype is still largely unknown. We exploited The Cancer Genome Atlas (TCGA) data to generate and analyze groups of breast invasive carcinomas, called 1,16-chromogroups, that are characterized by a pattern of arm-level somatic copy number aberrations congruent with known cytogenetic aberrations of chromosome 1 and 16. Substantial differences were found among 1,16-chromogroups in terms of other chromosomal aberrations, aneuploidy scores, transcriptomic data, single-point mutations, histotypes, and molecular subtypes. Breast cancers with a co-occurrence of 1q-gain and 16q-loss can be distinguished in a "low aneuploidy score" group, congruent to der(1;16), and a "high aneuploidy score" group, congruent to the co-occurrence of isochromosome 1q and deleted 16q. Another three groups are formed by cancers showing separately 1q-gain or 16q-loss or no aberrations of 1q and 16q. Transcriptome comparisons among the 1,16-chromogroups, integrated with functional pathway analysis, suggested the cooperation of overexpressed 1q genes and underexpressed 16q genes in the genesis of both ductal and lobular carcinomas, thus highlighting the putative role of genes encoding gamma-secretase subunits (APH1A, PSEN2, and NCSTN) and Wnt enhanceosome components (BCL9 and PYGO2) in 1q, and the glycoprotein E-cadherin (CDH1), the E3 ubiquitin-protein ligase WWP2, the deubiquitinating enzyme CYLD, and the transcription factor CBFB in 16q. The analysis of 1,16-chromogroups is a strategy with far-reaching implications for the selection of cancer cell models and novel experimental therapies.
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Affiliation(s)
| | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Via S. Sofia 89-97, 95123 Catania, Italy;
| | - Daniele Filippo Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Via S. Sofia 89-97, 95123 Catania, Italy;
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Wilson N, Ironside A, Diana A, Oikonomidou O. Lobular Breast Cancer: A Review. Front Oncol 2021; 10:591399. [PMID: 33520704 PMCID: PMC7844138 DOI: 10.3389/fonc.2020.591399] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/30/2020] [Indexed: 12/22/2022] Open
Abstract
Invasive lobular carcinoma accounts for 5%–15% of all invasive breast cancers, with a marked increase in incidence rates over the past two decades. Distinctive biological hallmarks of invasive lobular carcinoma include the loss of cell adhesion molecule E-cadherin leading to cells with a discohesive morphology, proliferating into single-file strands and estrogen receptor positivity. These key molecular features can make diagnosis difficult, as invasive lobular carcinoma is challenging to detect both physically and with current standard imaging. Treatment of invasive lobular carcinoma strongly favors endocrine therapy due to low chemosensitivity and lower rates of pathological response as a result. This review will summarize the distinct biological and molecular features of invasive lobular carcinoma, focusing on the diagnostic challenges faced and the subsequent surgical and medical management strategies. Prospective therapeutic options will also be explored, highlighting how furthering our understanding of the unique biology of lobular breast carcinoma is essential in guiding and informing the treatment of patients in the future.
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Affiliation(s)
- Natalie Wilson
- Cancer Research UK, Edinburgh Centre, MRC Institute Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Alastair Ironside
- Edinburgh Cancer Centre, Western General Hospital, Department of Pathology, NHS Lothian, Edinburgh, United Kingdom
| | - Anna Diana
- Division of Medical Oncology, Department of Precision Medicine, School of Medicine, "Luigi Vanvitelli" University of Campania, Naples, Italy
| | - Olga Oikonomidou
- Cancer Research UK, Edinburgh Centre, MRC Institute Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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Saberi Ansar E, Eslahchii C, Rahimi M, Geranpayeh L, Ebrahimi M, Aghdam R, Kerdivel G. Significant random signatures reveals new biomarker for breast cancer. BMC Med Genomics 2019; 12:160. [PMID: 31703592 PMCID: PMC6842262 DOI: 10.1186/s12920-019-0609-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/24/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In 2012, Venet et al. proposed that at least in the case of breast cancer, most published signatures are not significantly more associated with outcome than randomly generated signatures. They suggested that nominal p-value is not a good estimator to show the significance of a signature. Therefore, one can reasonably postulate that some information might be present in such significant random signatures. METHODS In this research, first we show that, using an empirical p-value, these published signatures are more significant than their nominal p-values. In other words, the proposed empirical p-value can be considered as a complimentary criterion for nominal p-value to distinguish random signatures from significant ones. Secondly, we develop a novel computational method to extract information that are embedded within significant random signatures. In our method, a score is assigned to each gene based on the number of times it appears in significant random signatures. Then, these scores are diffused through a protein-protein interaction network and a permutation procedure is used to determine the genes with significant scores. The genes with significant scores are considered as the set of significant genes. RESULTS First, we applied our method on the breast cancer dataset NKI to achieve a set of significant genes in breast cancer considering significant random signatures. Secondly, prognostic performance of the computed set of significant genes is evaluated using DMFS and RFS datasets. We have observed that the top ranked genes from this set can successfully separate patients with poor prognosis from those with good prognosis. Finally, we investigated the expression pattern of TAT, the first gene reported in our set, in malignant breast cancer vs. adjacent normal tissue and mammospheres. CONCLUSION Applying the method, we found a set of significant genes in breast cancer, including TAT, a gene that has never been reported as an important gene in breast cancer. Our results show that the expression of TAT is repressed in tumors suggesting that this gene could act as a tumor suppressor in breast cancer and could be used as a new biomarker.
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Affiliation(s)
- Elnaz Saberi Ansar
- Curie Institute, INSERM U830, Translational Research Department, PSL Research University, Paris, 75005 France
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Changiz Eslahchii
- Department of Computer Sciences, Faculty of Mathematical Sciences, Shahid-Beheshti University, GC, Tehran, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Mahsa Rahimi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Lobat Geranpayeh
- Department of Surgery, Sina Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Ebrahimi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Rosa Aghdam
- Department of Computer Sciences, Faculty of Mathematical Sciences, Shahid-Beheshti University, GC, Tehran, Iran
- School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
| | - Gwenneg Kerdivel
- Institut Cochin, Department Development, Reproduction, Inserm U1016, CNRS, UMR 8104, Université Paris Descartes UMR-S1016, Paris, 75014 France
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McCart Reed AE, Lal S, Kutasovic JR, Wockner L, Robertson A, de Luca XM, Kalita-de Croft P, Dalley AJ, Coorey CP, Kuo L, Ferguson K, Niland C, Miller G, Johnson J, Reid LE, Males R, Saunus JM, Chenevix-Trench G, Coin L, Lakhani SR, Simpson PT. LobSig is a multigene predictor of outcome in invasive lobular carcinoma. NPJ Breast Cancer 2019; 5:18. [PMID: 31263747 PMCID: PMC6597578 DOI: 10.1038/s41523-019-0113-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/22/2019] [Indexed: 12/12/2022] Open
Abstract
Invasive lobular carcinoma (ILC) is the most common special type of breast cancer, and is characterized by functional loss of E-cadherin, resulting in cellular adhesion defects. ILC typically present as estrogen receptor positive, grade 2 breast cancers, with a good short-term prognosis. Several large-scale molecular profiling studies have now dissected the unique genomics of ILC. We have undertaken an integrative analysis of gene expression and DNA copy number to identify novel drivers and prognostic biomarkers, using in-house (n = 25), METABRIC (n = 125) and TCGA (n = 146) samples. Using in silico integrative analyses, a 194-gene set was derived that is highly prognostic in ILC (P = 1.20 × 10-5)-we named this metagene 'LobSig'. Assessing a 10-year follow-up period, LobSig outperformed the Nottingham Prognostic Index, PAM50 risk-of-recurrence (Prosigna), OncotypeDx, and Genomic Grade Index (MapQuantDx) in a stepwise, multivariate Cox proportional hazards model, particularly in grade 2 ILC cases (χ 2, P = 9.0 × 10-6), which are difficult to prognosticate clinically. Importantly, LobSig status predicted outcome with 94.6% accuracy amongst cases classified as 'moderate-risk' according to Nottingham Prognostic Index in the METABRIC cohort. Network analysis identified few candidate pathways, though genesets related to proliferation were identified, and a LobSig-high phenotype was associated with the TCGA proliferative subtype (χ 2, P < 8.86 × 10-4). ILC with a poor outcome as predicted by LobSig were enriched with mutations in ERBB2, ERBB3, TP53, AKT1 and ROS1. LobSig has the potential to be a clinically relevant prognostic signature and warrants further development.
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Affiliation(s)
- Amy E. McCart Reed
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Samir Lal
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
- Present Address: Pfizer Oncology Research, San Diego, CA 92121 USA
| | - Jamie R. Kutasovic
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Leesa Wockner
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006 Australia
| | - Alan Robertson
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072 Australia
| | - Xavier M. de Luca
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Priyakshi Kalita-de Croft
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Andrew J. Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Craig P. Coorey
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Luyu Kuo
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Kaltin Ferguson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Colleen Niland
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Gregory Miller
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, QLD 4029 Australia
| | - Julie Johnson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Lynne E. Reid
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Renique Males
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | - Jodi M. Saunus
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
| | | | - Lachlan Coin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD 4072 Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Herston, QLD 4029 Australia
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD 4029 Australia
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Role of columnar cell lesions in breast carcinogenesis: analysis of chromosome 16 copy number changes by multiplex ligation-dependent probe amplification. Mod Pathol 2018; 31:1816-1833. [PMID: 29976944 DOI: 10.1038/s41379-018-0099-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 11/08/2022]
Abstract
Columnar cell lesions have been proposed as precursor lesions of low-grade breast cancer. The molecular characteristic of low-grade breast neoplasia is whole-arm loss of chromosome 16q. Copy number changes of 6 genes on 16p and 20 genes on 16q were analysed by multiplex ligation-dependent probe amplification in 165 lesions of 103 patients. Twenty-three columnar cell lesions and 19 atypical ducal hyperplasia lesions arising in columnar cell lesions were included, as well as cases of usual ductal hyperplasia, blunt duct adenosis, ductal carcinoma in situ, lobular neoplasia and invasive carcinoma. Usual ductal hyperplasia and blunt duct adenosis lacked whole-arm losses of 16q. In contrast, columnar cell lesions without atypia, columnar cell lesions with atypia, atypical ductal hyperplasia, low-grade ductal carcinoma in situ and low-grade invasive carcinomas increasingly harboured whole-arm losses of 16q (17%, 27%, 47% and 57%, respectively). However, no recurrent losses in specific genes could be identified. In several patients, columnar cell lesions and atypical ductal hyperplasia harboured similar losses as related ductal carcinoma in situ or invasive carcinomas within the same breast. There were indications for 16q breakpoints near the centromere. Whole-arm gains on 16p were relatively scarce and there was no relation between whole-arm gains of 16p and progression of lesions of the low-grade breast neoplasia family. In conclusion, columnar cell lesions (with and without atypia) often harbour whole-arm losses of 16q, which underlines their role as precursors in low-grade breast carcinogenesis, in contrast with usual ductal hyperplasia and blunt duct adenosis. However, no recurrent losses in specific genes could be identified, pointing to minor events in multiple tumour suppressor genes rather than major events in a single 16q gene contributing to low-grade breast carcinogenesis.
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Li M, Zhang C, Zhong Y, Zhao J. Cellular localization of ATBF1 protein and its functional implication in breast epithelial cells. Biochem Biophys Res Commun 2017. [DOI: 10.1016/j.bbrc.2017.06.068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Wang H, Yan W, Zhang S, Gu Y, Wang Y, Wei Y, Liu H, Wang F, Wu Q, Zhang Y. Survival differences of CIMP subtypes integrated with CNA information in human breast cancer. Oncotarget 2017; 8:48807-48819. [PMID: 28415743 PMCID: PMC5564726 DOI: 10.18632/oncotarget.16178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022] Open
Abstract
CpG island methylator phenotype of breast cancer is associated with widespread aberrant methylation at specified CpG islands and distinct patient outcomes. However, the influence of copy number contributing to the prognosis of tumors with different CpG island methylator phenotypes is still unclear. We analyzed both genetic (copy number) and epigenetic alterations in 765 breast cancers from The Cancer Genome Atlas data portal and got a panel of 15 biomarkers for copy number and methylation status evaluation. The gene panel identified two groups corresponding to distinct copy number profiles. In status of mere-loss copy number, patients were faced with a greater risk if they presented a higher CpG islands methylation pattern in biomarker panels. But for samples presenting merely-gained copy number, higher methylation level of CpG islands was associated with improved viability. In all, the integration of copy number alteration and methylation information enhanced the classification power on prognosis. Moreover, we found the molecular subtypes of breast cancer presented different distributions in two CpG island methylation phenotypes. Generated by the same set of human methylation 450K data, additional copy number information could provide insights into survival prediction of cancers with less heterogeneity and might help to determine the biomarkers for diagnosis and treatment for breast cancer patients in a more personalized approach.
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Affiliation(s)
- Huihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Weili Yan
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, China
| | - Shumei Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yue Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yanjun Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hongbo Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Fang Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150001, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
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Prognostic Value of Coexisting Lobular Carcinoma In Situ With Invasive Lobular Carcinoma. Appl Immunohistochem Mol Morphol 2017; 24:738-743. [PMID: 26574630 DOI: 10.1097/pai.0000000000000254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AIMS AND OBJECTIVES Recent studies show that lobular carcinoma in situ (LCIS) and invasive lobular carcinoma (ILC) share similar genetic molecular biology. There are increasing concerns regarding the biological significance of LCIS. The aim of this study is to investigate whether the presence of coexisting LCIS in ILC affects tumor biology and behavior and to correlate it with other clinicopathologic parameters. MATERIALS AND METHODS In this study, 254 cases of ILC were included. Clinicopathologic parameters and immunohistochemical stains for estrogen receptor (ER), progesterone receptor (PR), E-cadherin, human epidermal growth factor receptor (HER2), and MIB-1 of 254 ILC cases were retrieved. The patient with ILC and coexisting LCIS were compared with pure ILC cases with respect to different clinicopathologic parameters. RESULTS Of the 254 cases, 107 cases were pure ILC and 147 cases were ILC with coexisting LCIS. Seventy-six (76/184, 41.32%) cases showed axillary lymph node metastases. Lymph node metastasis was absent in 108 cases, micrometastasis was present in 5 cases, and stage N1, N2, N3 in 51, 5, and 15 cases, respectively. Nodal involvement, locoregional and distant recurrence of ILC with LCIS were less frequent compared with ILC without LCIS with P-value of 0.034 and 0.007, respectively. The presence of coexisting LCIS in ILC predicted higher disease-free survival (DFS) compared with pure ILC (P=0.034, log-rank test). When divided into different strata, ER-positive ILC cases with associated LCIS cases showed better DFS than ER-positive pure ILC cases (P=0.021, log-rank test). Similarly, ILC cases with LCIS in patient less than 50 years showed better DFS than the patient less than 50 years with pure ILC (P=0.045, log-rank test). CONCLUSIONS In conclusion, ILC coexisting with lobular carcinoma in situ (ILC+LCIS) is characterized by less nodal involvement, lower locoregional, and distant recurrence and better DFS than pure ILC. When divided into different strata, ER-positive and less than 50-year groups with ILC+LCIS show even significant better DFS than pure ILC. These findings suggest that there is biological significance of coexisting LCIS in ILC and that this may have more effect on tumor aggressiveness in certain strata of ILC.
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Christgen M, Steinemann D, Kühnle E, Länger F, Gluz O, Harbeck N, Kreipe H. Lobular breast cancer: Clinical, molecular and morphological characteristics. Pathol Res Pract 2016; 212:583-97. [DOI: 10.1016/j.prp.2016.05.002] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/11/2016] [Accepted: 05/04/2016] [Indexed: 01/20/2023]
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Zhao D, Ma G, Zhang X, He Y, Li M, Han X, Fu L, Dong XY, Nagy T, Zhao Q, Fu L, Dong JT. Zinc Finger Homeodomain Factor Zfhx3 Is Essential for Mammary Lactogenic Differentiation by Maintaining Prolactin Signaling Activity. J Biol Chem 2016; 291:12809-12820. [PMID: 27129249 DOI: 10.1074/jbc.m116.719377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 12/13/2022] Open
Abstract
The zinc finger homeobox 3 (ZFHX3, also named ATBF1 for AT motif binding factor 1) is a transcription factor that suppresses prostatic carcinogenesis and induces neuronal differentiation. It also interacts with estrogen receptor α to inhibit cell proliferation and regulate pubertal mammary gland development in mice. In the present study, we examined whether and how Zfhx3 regulates lactogenic differentiation in mouse mammary glands. At different stages of mammary gland development, Zfhx3 protein was expressed at varying levels, with the highest level at lactation. In the HC11 mouse mammary epithelial cell line, an in vitro model of lactogenesis, knockdown of Zfhx3 attenuated prolactin-induced β-casein expression and morphological changes, indicators of lactogenic differentiation. In mouse mammary tissue, knock-out of Zfhx3 interrupted lactogenesis, resulting in underdeveloped glands with much smaller and fewer alveoli, reduced β-casein expression, accumulation of large cytoplasmic lipid droplets in luminal cells after parturition, and failure in lactation. Mechanistically, Zfhx3 maintained the expression of Prlr (prolactin receptor) and Prlr-Jak2-Stat5 signaling activity, whereas knockdown and knock-out of Zfhx3 in HC11 cells and mammary tissues, respectively, decreased Prlr expression, Stat5 phosphorylation, and the expression of Prlr-Jak2-Stat5 target genes. These findings indicate that Zfhx3 plays an essential role in proper lactogenic development in mammary glands, at least in part by maintaining Prlr expression and Prlr-Jak2-Stat5 signaling activity.
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Affiliation(s)
- Dan Zhao
- From the Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Gui Ma
- From the Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiaolin Zhang
- From the Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yuan He
- From the Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mei Li
- the Ningbo Institute of Medical Sciences, Ningbo 315020, China
| | - Xueying Han
- From the Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Liya Fu
- From the Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xue-Yuan Dong
- the Department of Hematology and Medical Oncology, School of Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322
| | - Tamas Nagy
- the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, and
| | - Qiang Zhao
- From the Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Li Fu
- the Cancer Hospital of Tianjin Medical University, Tianjin 300060, China
| | - Jin-Tang Dong
- From the Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China,; the Department of Hematology and Medical Oncology, School of Medicine, Winship Cancer Institute, Emory University, Atlanta, Georgia 30322,.
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Benavente CA, Dyer MA. Genetics and epigenetics of human retinoblastoma. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2015; 10:547-62. [PMID: 25621664 DOI: 10.1146/annurev-pathol-012414-040259] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Retinoblastoma is a pediatric tumor of the developing retina from which the genetic basis for cancer development was first described. Inactivation of both copies of the RB1 gene is the predominant initiating genetic lesion in retinoblastoma and is rate limiting for tumorigenesis. Recent whole-genome sequencing of retinoblastoma uncovered a tumor that had no coding-region mutations or focal chromosomal lesions other than in the RB1 gene, shifting the paradigm in the field. The retinoblastoma genome can be very stable; therefore, epigenetic deregulation of tumor-promoting pathways is required for tumorigenesis. This review highlights the genetic and epigenetic changes in retinoblastoma that have been reported, with special emphasis on recent whole-genome sequencing and epigenetic analyses that have identified novel candidate genes as potential therapeutic targets.
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Affiliation(s)
- Claudia A Benavente
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105;
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McCart Reed AE, Kutasovic JR, Lakhani SR, Simpson PT. Invasive lobular carcinoma of the breast: morphology, biomarkers and 'omics. Breast Cancer Res 2015; 17:12. [PMID: 25849106 PMCID: PMC4310190 DOI: 10.1186/s13058-015-0519-x] [Citation(s) in RCA: 204] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Invasive lobular carcinoma of the breast is the most common 'special' morphological subtype of breast cancer, comprising up to 15% of all cases. Tumours are generally of a good prognostic phenotype, being low histological grade and low mitotic index, hormone receptor positive and HER2, p53 and basal marker negative, and with a generally good response to endocrine therapy. Despite this, clinicians face countless challenges in the diagnosis and long-term management of patients, as they encounter a tumour that can be difficult to detect through screening, elicits a very invasive nature, a propensity for widespread metastatic colonisation and, consequently, in some studies a worse long-term poor outcome compared with invasive carcinoma of no special type. Here we review the morphological and molecular features that underpin the disparate biological and clinical characteristics of this fascinating tumour type.
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15
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Rye IH, Lundin P, Månér S, Fjelldal R, Naume B, Wigler M, Hicks J, Børresen-Dale AL, Zetterberg A, Russnes HG. Quantitative multigene FISH on breast carcinomas identifies der(1;16)(q10;p10) as an early event in luminal A tumors. Genes Chromosomes Cancer 2014; 54:235-48. [PMID: 25546585 PMCID: PMC4369137 DOI: 10.1002/gcc.22237] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/09/2014] [Accepted: 12/10/2014] [Indexed: 11/10/2022] Open
Abstract
In situ detection of genomic alterations in cancer provides information at the single cell level, making it possible to investigate genomic changes in cells in a tissue context. Such topological information is important when studying intratumor heterogeneity as well as alterations related to different steps in tumor progression. We developed a quantitative multigene fluorescence in situ hybridization (QM FISH) method to detect multiple genomic regions in single cells in complex tissues. As a “proof of principle” we applied the method to breast cancer samples to identify partners in whole arm (WA) translocations. WA gain of chromosome arm 1q and loss of chromosome arm 16q are among the most frequent genomic events in breast cancer. By designing five specific FISH probes based on breakpoint information from comparative genomic hybridization array (aCGH) profiles, we visualized chromosomal translocations in clinical samples at the single cell level. By analyzing aCGH data from 295 patients with breast carcinoma with known molecular subtype, we found concurrent WA gain of 1q and loss of 16q to be more frequent in luminal A tumors compared to other molecular subtypes. QM FISH applied to a subset of samples (n = 26) identified a derivative chromosome der(1;16)(q10;p10), a result of a centromere-close translocation between chromosome arms 1q and 16p. In addition, we observed that the distribution of cells with the translocation varied from sample to sample, some had a homogenous cell population while others displayed intratumor heterogeneity with cell-to-cell variation. Finally, for one tumor with both preinvasive and invasive components, the fraction of cells with translocation was lower and more heterogeneous in the preinvasive tumor cells compared to the cells in the invasive component. © 2014 The Authors Genes, Chromosomes & Cancer Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Inga H Rye
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0424, Oslo, 0310, Norway; The K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Bond CE, Nancarrow DJ, Wockner LF, Wallace L, Montgomery GW, Leggett BA, Whitehall VLJ. Microsatellite stable colorectal cancers stratified by the BRAF V600E mutation show distinct patterns of chromosomal instability. PLoS One 2014; 9:e91739. [PMID: 24651849 PMCID: PMC3961279 DOI: 10.1371/journal.pone.0091739] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/13/2014] [Indexed: 02/07/2023] Open
Abstract
The BRAF (V600E) mutation in colorectal cancers that are microsatellite stable (MSS) confers a poor patient prognosis, whereas BRAF mutant microsatellite-unstable (MSI) colorectal cancers have an excellent prognosis. BRAF wild type cancers are typically MSS and display chromosomal instability (CIN). CIN has not been extensively studied on a genome-wide basis in relation to BRAF mutational status in colorectal cancer. BRAF mutant/MSS (BRAFmut/MSS) cancers (n = 33) and BRAF mutant/MSI (BRAFmut/MSI) cancers (n = 30) were compared for presence of copy number aberrations (CNAs) indicative of CIN, with BRAF wild type/MSS (BRAFwt/MSS) cancers (n = 18) using Illumina CytoSNP-12 arrays. BRAFmut/MSS and BRAFwt/MSS cancers showed comparable numbers of CNAs/cancer at 32.8 and 29.8 respectively. However, there were differences in patterns of CNA length between MSS cohorts, with BRAFmut/MSS cancers having significantly greater proportions of focal CNAs compared to BRAFwt/MSS cancers (p<0.0001); whereas whole chromosomal arm CNAs were more common in BRAFwt/MSS cancers (p<0.0001). This related to a reduced average CNA length in BRAFmut/MSS compared to BRAFwt/MSS cancers (20.7 Mb vs 33.4 Mb;p<0.0001); and a smaller average percent of CIN affected genomes in BRAFmut/MSS compared to BRAFwt/MSS cancers (23.9% vs 34.9% respectively). BRAFmut/MSI cancers were confirmed to have low CNA rates (5.4/cancer) and minimal CIN-affected genomes (average of 4.5%) compared to MSS cohorts (p<0.0001). BRAFmut/MSS cancers had more frequent deletion CNAs compared to BRAFwt/MSS cancers on 6p and 17q at loci not typically correlated with colorectal cancer, and greater amplification CNAs on 8q and 18q compared to BRAFwt/MSS cancers. These results indicate that comparable rates of CIN occur between MSS subgroups, however significant differences in their patterns of instability exist, with BRAFmut/MSS cancers showing a ‘focal pattern’ and BRAFwt/MSS cancers having a ‘whole arm pattern’ of CIN. This and the genomic loci more frequently affected in BRAFmut/MSS cancers provides further evidence of the biological distinctions of this important cancer subgroup.
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Affiliation(s)
- Catherine E. Bond
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
| | - Derek J. Nancarrow
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leesa F. Wockner
- Cancer and Population Studies Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Leanne Wallace
- Molecular Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W. Montgomery
- Molecular Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Barbara A. Leggett
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Medicine, University of Queensland, Brisbane, Queensland, Australia
- Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Vicki L. J. Whitehall
- Conjoint Gastroenterology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- Pathology Queensland, Brisbane, Queensland, Australia
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Analysis of copy number changes on chromosome 16q in male breast cancer by multiplex ligation-dependent probe amplification. Mod Pathol 2013; 26:1461-7. [PMID: 23743929 DOI: 10.1038/modpathol.2013.94] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/26/2013] [Accepted: 04/28/2013] [Indexed: 11/08/2022]
Abstract
Gene copy number changes have an important role in carcinogenesis and could serve as potential biomarkers for prognosis and targets for therapy. Copy number changes mapping to chromosome 16 have been reported to be the most frequent alteration observed in female breast cancer and a loss on 16q has been shown to be associated with low grade and better prognosis. In the present study, we aimed to characterize copy number changes on 16q in a group of 135 male breast cancers using a novel multiplex ligation-dependent probe amplification kit. One hundred and twelve out of 135 (83%) male breast cancer showed copy number changes of at least one gene on chromosome 16, with frequent loss of 16q (71/135; 53%), either partial (66/135; 49%) or whole arm loss (5/135; 4%). Losses on 16q were thereby less often seen in male breast cancer than previously described in female breast cancer. Loss on 16q was significantly correlated with favorable clinicopathological features such as negative lymph node status, small tumor size, and low grade. Copy number gain of almost all genes on the short arm was also significantly correlated with lymph node negative status. A combination of 16q loss and 16p gain correlated even stronger with negative lymph node status (n=112; P=0.012), which was also underlined by unsupervised clustering. In conclusion, copy number loss on 16q is less frequent in male breast cancer than in female breast cancer, providing further evidence that male breast cancer and female breast cancer are genetically different. Gain on 16p and loss of 16q identify a group of male breast cancer with low propensity to develop lymph node metastases.
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Abstract
The development of breast malignancy has been recognised to progress through a number of morphological precursor lesions. More recently, specific molecular alterations have been recognised in these precursor lesions. These changes appear to determine a specific malignant phenotype, which in turn, may realign the current opinion on the classification of breast cancer along molecular characteristics. This review will highlight the morphological features of these precursor lesions and their relationship to the complex molecular processes involved in their development.
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Dual-color fluorescence in situ hybridization reveals an association of chromosome 8q22 but not 8p21 imbalance with high grade invasive breast carcinoma. PLoS One 2013; 8:e70790. [PMID: 23936250 PMCID: PMC3723675 DOI: 10.1371/journal.pone.0070790] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/24/2013] [Indexed: 12/14/2022] Open
Abstract
We previously reported molecular karyotype analysis of invasive breast tumour core needle biopsies by comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH) (Walker et al, Genes Chromosomes Cancer, 2008 May;47(5):405-17). That study identified frequently recurring gains and losses involving chromosome bands 8q22 and 8p21, respectively. Moreover, these data highlighted an association between 8q22 gain and typically aggressive grade 3 tumors. Here we validate and extend our previous investigations through FISH analysis of tumor touch imprints prepared from excised breast tumor specimens. Compared to post-surgical tumor excisions, core needle biopsies are known to be histologically less precise when predicting tumor grade. Therefore investigating these chromosomal aberrations in tumor samples that offer more reliable pathological assessment is likely to give a better overall indication of association. A series of 60 breast tumors were screened for genomic copy number changes at 8q22 and 8p21 by dual-color FISH. Results confirm previous findings that 8p loss (39%) and 8q gain (74%) occur frequently in invasive breast cancer. Both absolute quantification of 8q22 gain across the sample cohort, and a separate relative assessment by 8q22:8p21 copy number ratio, showed that the incidence of 8q22 gain significantly increased with grade (p = 0.004, absolute and p = 0.02, relative). In contrast, no association was found between 8p21 loss and tumor grade. These findings support the notion that 8q22 is a region of interest for invasive breast cancer pathogenesis, potentially harboring one or more genes that, when amplified, precipitate the molecular events that define high tumor grade.
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20
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Thériault BL, Dimaras H, Gallie BL, Corson TW. The genomic landscape of retinoblastoma: a review. Clin Exp Ophthalmol 2013; 42:33-52. [PMID: 24433356 DOI: 10.1111/ceo.12132] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/07/2013] [Indexed: 12/13/2022]
Abstract
Retinoblastoma is a paediatric ocular tumour that continues to reveal much about the genetic basis of cancer development. Study of genomic aberrations in retinoblastoma tumours has exposed important mechanisms of cancer development and identified oncogenes and tumour suppressors that offer potential points of therapeutic intervention. The recent development of next-generation genomic technologies has allowed further refinement of the genomic landscape of retinoblastoma at high resolution. In a relatively short period of time, a wealth of genetic and epigenetic data has emerged on a small number of tumour samples. These data highlight the inherent molecular complexity of this cancer despite the fact that most retinoblastomas are initiated by the inactivation of a single tumour suppressor gene. This review outlines the current understanding of the genomic, genetic and epigenetic changes in retinoblastoma, highlighting recent genome-wide analyses that have identified exciting candidate genes worthy of further validation as potential prognostic and therapeutic targets.
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Affiliation(s)
- Brigitte L Thériault
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
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21
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Li M, Fu X, Ma G, Sun X, Dong X, Nagy T, Xing C, Li J, Dong JT. Atbf1 regulates pubertal mammary gland development likely by inhibiting the pro-proliferative function of estrogen-ER signaling. PLoS One 2012; 7:e51283. [PMID: 23251482 PMCID: PMC3520988 DOI: 10.1371/journal.pone.0051283] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022] Open
Abstract
ATBF1 is a candidate tumor suppressor that interacts with estrogen receptor (ER) to inhibit the function of estrogen-ER signaling in gene regulation and cell proliferation control in human breast cancer cells. We therefore tested whether Atbf1 and its interaction with ER modulate the development of pubertal mammary gland, where estrogen is the predominant steroid hormone. In an in vitro model of cell differentiation, i.e., MCF10A cells cultured in Matrigel, ATBF1 expression was significantly increased, and knockdown of ATBF1 inhibited acinus formation. During mouse mammary gland development, Atbf1 was expressed at varying levels at different stages, with higher levels during puberty, lower during pregnancy, and the highest during lactation. Knockout of Atbf1 at the onset of puberty enhanced ductal elongation and bifurcation and promoted cell proliferation in both ducts and terminal end buds of pubertal mammary glands. Enhanced cell proliferation primarily occurred in ER-positive cells and was accompanied by increased expression of ER target genes. Furthermore, inactivation of Atbf1 reduced the expression of basal cell markers (CK5, CK14 and CD44) but not luminal cell markers. These findings indicate that Atbf1 plays a role in the development of pubertal mammary gland likely by modulating the function of estrogen-ER signaling in luminal cells and by modulating gene expression in basal cells.
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Affiliation(s)
- Mei Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Xiaoying Fu
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Gui Ma
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaodong Sun
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Xueyuan Dong
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail: (XD) (XD); (JTD) (JD)
| | - Tamas Nagy
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Changsheng Xing
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jie Li
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jin-Tang Dong
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin, China
- Department of Hematology and Medical Oncology, Emory Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia, United States of America
- * E-mail: (XD) (XD); (JTD) (JD)
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Bonnet F, Guedj M, Jones N, Sfar S, Brouste V, Elarouci N, Banneau G, Orsetti B, Primois C, de Lara CT, Debled M, de Mascarel I, Theillet C, Sévenet N, de Reynies A, MacGrogan G, Longy M. An array CGH based genomic instability index (G2I) is predictive of clinical outcome in breast cancer and reveals a subset of tumors without lymph node involvement but with poor prognosis. BMC Med Genomics 2012. [PMID: 23186559 PMCID: PMC3558323 DOI: 10.1186/1755-8794-5-54] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background Despite entering complete remission after primary treatment, a substantial proportion of patients with early stage breast cancer will develop metastases. Prediction of such an outcome remains challenging despite the clinical use of several prognostic parameters. Several reports indicate that genomic instability, as reflected in specific chromosomal aneuploidies and variations in DNA content, influences clinical outcome but no precise definition of this parameter has yet been clearly established. Methods To explore the prognostic value of genomic alterations present in primary tumors, we performed a comparative genomic hybridization study on BAC arrays with a panel of breast carcinomas from 45 patients with metastatic relapse and 95 others, matched for age and axillary node involvement, without any recurrence after at least 11 years of follow-up. Array-CGH data was used to establish a two-parameter index representative of the global level of aneusomy by chromosomal arm, and of the number of breakpoints throughout the genome. Results Application of appropriate thresholds allowed us to distinguish three classes of tumors highly associated with metastatic relapse. This index used with the same thresholds on a published set of tumors confirms its prognostic significance with a hazard ratio of 3.24 [95CI: 1.76-5.96] p = 6.7x10-5 for the bad prognostic group with respect to the intermediate group. The high prognostic value of this genomic index is related to its ability to individualize a specific group of breast cancers, mainly luminal type and axillary node negative, showing very high genetic instability and poor outcome. Indirect transcriptomic validation was obtained on independent data sets. Conclusion Accurate evaluation of genetic instability in breast cancers by a genomic instability index (G2I) helps individualizing specific tumors with previously unexpected very poor prognosis.
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Affiliation(s)
- Françoise Bonnet
- Inserm U 916 Institut Bergonié, Université de Bordeaux, Bordeaux, France
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Schymik B, Buerger H, Krämer A, Voss U, van der Groep P, Meinerz W, van Diest PJ, Korsching E. Is there 'progression through grade' in ductal invasive breast cancer? Breast Cancer Res Treat 2012; 135:693-703. [PMID: 22886478 DOI: 10.1007/s10549-012-2195-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/01/2012] [Indexed: 10/28/2022]
Abstract
Recent molecular data pointed towards the possibility of a stepwise dedifferentiation in a subgroup of invasive breast cancer (BC) cases. It was hypothesized that oestrogen receptor positive (ER+) grade 3 (G3) ductal invasive BCs are the end stage of a dedifferentiation process of luminal BC. A progression of luminal A towards luminal B BCs associated with a 'progression through grade' and an increased cell proliferation seemed the obvious explanation. In order to verify this hypothesis on a morphological and immunohistochemical level, we investigated 865 invasive BC cases. All cases were reviewed for the presence of intratumoural heterogeneity in grade of the invasive cancer and the presence of associated ductal carcinoma in situ (DCIS). With the use of tissue microarrays, the molecular subtype was determined and correlated with clinico-pathological features. In addition, all cases were stained for p21, p27, Ki-67, Cyclin D1, bcl-2, p53, and p16 and the results subjected to a biomathematical dependency analysis. The frequency of ER-positivity decreased with tumour size. The frequency of luminal A BC decreased as well, whereas the number of luminal B BCs remained constant. A gradual increase of the frequency of basal-like, HER2-driven and non-expressor BCs with tumour size was seen. In only 1 out of 865 BC cases, both a G1 and a G3 invasive cancer component was seen within the same BC. In two cases, a ductal invasive G1 carcinoma was associated with a poorly-differentiated DCIS. The frequency of columnar cell lesions was evenly distributed over ER+ and ER- ductal invasive G3 carcinomas. The biomathematical analysis gave striking hints against an obligate progression of BC trough grade. In conclusion, our results show that a morphological recognizable striking 'progression through grade' at least in its extreme form from G1 towards G3 is a very rare event in the natural course of invasive BC, including luminal BC.
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Affiliation(s)
- Barbara Schymik
- Clinics of Gynecology, St. Vincenz Hospital, Paderborn, Germany
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de Oliveira MMC, de Oliveira SFV, Lima RS, de Andrade Urban C, Cavalli LR, de Souza Fonseca Ribeiro EM, Cavalli IJ. Differential loss of heterozygosity profile on chromosome 3p in ductal and lobular breast carcinomas. Hum Pathol 2012; 43:1661-7. [PMID: 22503535 DOI: 10.1016/j.humpath.2011.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 12/15/2011] [Accepted: 12/16/2011] [Indexed: 01/18/2023]
Abstract
The 2 main histologic types of infiltrating breast cancer, invasive lobular and invasive ductal carcinoma, are morphologically and clinically distinct. Studies revealed that different patterns of gene expression and loss of heterozygosity can also distinguish these 2 subtypes. A whole-genome study using single nucleotide polymorphism array found a significantly higher frequency of loss of heterozygosity on 3p in invasive ductal carcinoma when compared with invasive lobular carcinoma. In this study, we performed a loss of heterozygosity analysis of the 3p chromosome region in ductal and lobular breast tumors. Seven microsatellite markers were evaluated in a series of 136 sporadic breast cancer cases (118 invasive ductal carcinoma and 18 invasive lobular carcinoma) and correlated with clinical-histopathologic parameters from the patients. A significantly higher frequency of loss of heterozygosity was observed in invasive ductal carcinoma (65.3%) when compared with invasive lobular carcinoma (38.9%). When the markers were analyzed separately, loss of heterozygosity at 3 of them, D3S1307 in 3p26.3, D3S1286 in 3p24.3, and D3S1300 in 3p14.2, were significantly more frequent in ductal than in lobular tumors. D3S1307 marker showed the highest frequency of loss of heterozygosity in invasive ductal carcinoma (46.2%), and associations between loss of this marker and loss of estrogen and progesterone receptors were found in these samples. Our results confirm the observations that invasive ductal carcinoma has a higher frequency of loss of heterozygosity events across the 3p region than invasive lobular carcinoma and show that specific losses on 3p26.3, 3p24.3, and 3p14.2 regions are more frequent in ductal than in lobular tumors. We discuss our data in relation to the known tumor suppressor genes that are mapped at the 3p loci investigated and their present relevant roles in breast cancer.
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Duprez R, Wilkerson PM, Lacroix-Triki M, Lambros MB, MacKay A, A’Hern R, Gauthier A, Pawar V, Colombo PE, Daley F, Natrajan R, Ward E, MacGrogan G, Arbion F, Michenet P, Weigelt B, Vincent-Salomon A, Reis-Filho JS. Immunophenotypic and genomic characterization of papillary carcinomas of the breast. J Pathol 2012; 226:427-441. [PMID: 22025283 PMCID: PMC4962905 DOI: 10.1002/path.3032] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/21/2011] [Accepted: 10/12/2011] [Indexed: 12/20/2022]
Abstract
Papillary carcinomas are a special histological type of breast cancer and have a relatively good outcome. We characterized the genomic and phenotypic characteristics of papillary carcinomas to determine whether they would constitute an entity distinct from grade- and oestrogen receptor (ER)-matched invasive ductal carcinomas of no special type (IDC-NSTs). The phenotype of 63 papillary carcinomas of the breast and grade- and ER-matched IDC-NSTs was determined by immunohistochemistry. DNA of sufficient quality was extracted from 49 microdissected papillary carcinomas and 49 microdissected grade- and ER-matched IDC-NSTs. These samples were subjected to high-resolution microarray-based comparative genomic hybridization (aCGH) and Sequenom MassARRAY sequencing analysis of 19 known oncogenes. Papillary carcinomas were predominantly of low histological grade, expressed immunohistochemical markers consistent with a luminal phenotype, and a lower rate of lymph node metastasis and p53 expression than grade- and ER-matched IDC-NSTs. Papillary carcinomas displayed less genomic aberrations than grade- and ER-matched IDC-NSTs; however, the patterns of gene copy number aberrations found in papillary carcinomas were similar to those of ER- and grade-matched IDC-NSTs, including 16q losses. Furthermore, PIK3CA mutations were found in 43% and 29% of papillary carcinomas and grade- and ER-matched IDC-NSTs, respectively. The genomic profiles of encapsulated, solid and invasive papillary carcinomas, the three morphological subtypes, were remarkably similar. Our results demonstrate that papillary carcinomas are a homogeneous special histological type of breast cancer. The similarities in the genomic profiles of papillary carcinomas and grade- and ER-matched IDC-NSTs suggest that papillary carcinomas may be best positioned as part of the spectrum of ER-positive breast cancers, rather than as a distinct entity. Furthermore, the good prognosis of papillary carcinomas may stem from the low rates of lymph node metastasis and p53 expression, low number of gene copy number aberrations and high prevalence of PIK3CA mutations.
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Affiliation(s)
- Raphaëlle Duprez
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Paul M Wilkerson
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Magali Lacroix-Triki
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- Institut Claudius Regaud, 31052 Toulouse, France
| | - Maryou B Lambros
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Alan MacKay
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Roger A’Hern
- CRUK Clinical Trials Unit, The Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Arnaud Gauthier
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
- Institut Curie, 75005 Paris, France
| | - Vidya Pawar
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Pierre-Emanuel Colombo
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Frances Daley
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachael Natrajan
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Eric Ward
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | | | - Flavie Arbion
- Centre Hospitalier Universitaire, 37044 Tours, France
| | | | - Britta Weigelt
- Signal Transduction Laboratory, Cancer Research UK London Research Institute, London WC2A 3LY, UK
| | | | - Jorge S Reis-Filho
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
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The human cadherin 11 is a pro-apoptotic tumor suppressor modulating cell stemness through Wnt/β-catenin signaling and silenced in common carcinomas. Oncogene 2011; 31:3901-12. [PMID: 22139084 PMCID: PMC3426851 DOI: 10.1038/onc.2011.541] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic alterations of 16q21-q22, the locus of a 6-cadherin cluster, are frequently involved in multiple tumors, suggesting the presence of critical tumor suppressor genes (TSGs). Using 1 Mb array comparative genomic hybridization (aCGH), we refined a small hemizygous deletion (∼1 Mb) at 16q21-22.1, which contains a single gene Cadherin-11 (CDH11, OB-cadherin). CDH11 was broadly expressed in human normal adult and fetal tissues, while its silencing and promoter CpG methylation were frequently detected in tumor cell lines, but not in immortalized normal epithelial cells. Aberrant methylation was also frequently detected in multiple primary tumors. CDH11 silencing could be reversed by pharmacologic or genetic demethylation, indicating an epigenetic mechanism. Ectopic expression of CDH11 strongly suppressed tumorigenecity and induced tumor cell apoptosis. Moreover, CDH11 was found to inhibit Wnt/β-catenin and AKT/Rho A signaling, as well as actin stress fiber formation, thus further inhibiting tumor cell migration and invasion. CDH11 also inhibited epithelial-to-mesenchymal transition and downregulated stem cell markers. Thus, our work identifies CDH11 as a functional tumor suppressor and an important antagonist of Wnt/β-catenin and AKT/Rho A signaling, with frequent epigenetic inactivation in common carcinomas.
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Abstract
Breast cancer is a heterogeneous disease. The traditional classification uses morphology to divide tumours into distinct categories with differing prognosis and behavior. Despite providing high quality data cheaply, it has limitations and hence there has been a hope that the new molecular methods may help to refine the classification systems. Much has been learned in the last few years however, the molecular taxonomy is still in evolution and likely to change over the coming years. Whether the molecular classification is as useful for special subtypes of breast cancers as it has been for ductal carcinoma, no special type, remains to be determined.
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Coco S, Valdora F, Bonassi S, Scaruffi P, Stigliani S, Oberthuer A, Berthold F, Andolfo I, Servidei T, Riccardi R, Basso E, Iolascon A, Tonini GP. Chromosome 9q and 16q loss identified by genome-wide pooled-analysis are associated with tumor aggressiveness in patients with classic medulloblastoma. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2011; 15:273-80. [PMID: 21348762 DOI: 10.1089/omi.2010.0103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Medulloblastoma (MB) is one of the most aggressive pediatric brain tumor. We report genome-wide pooled-analysis of classic MB variant of patients over 3 years of age at diagnosis. We combined array comparative genomic hybridization (aCGH) results from experimental analysis (31 cases) with two public databases (55 cases) in a final evaluation of 86 MBs. The most common chromosome structural aberrations were gains of 17q (45.3%), 1q (22.1%), and losses of 8p (15.1%), 10q (19.8%), 17p (37.2%), and 16q (16.3%). Isochromome (17q) was observed in 29.1% MBs. A significant association between poor patients survival and losses of 9q (p < 0.0023), 10q (p < 0.012), and 16q (p < 0.036) was observed. Univariate analysis showed association of 9q loss (p < 0.008) and 16q loss (p = 0.05) with adverse overall survival (OS). Chromosome 6 monosomy was a protective event although statistically borderline (p = 0.066). After adjusting for confounding factors, a poor OS was found for patients whose tumor has 9q loss [hazard ratio (HR) = 3.97; p < 0.006) or 16q loss (HR = 2.41; p = 0.038). Our results highlight the importance of genomic studies in different MB histological variants and indicate a genotype-phenotype correlation.
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Affiliation(s)
- Simona Coco
- Translational Oncopathology, National Cancer Research Institute (IST), Genoa, Italy
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Shiu KK, Natrajan R, Geyer FC, Ashworth A, Reis-Filho JS. DNA amplifications in breast cancer: genotypic-phenotypic correlations. Future Oncol 2010; 6:967-84. [PMID: 20528234 DOI: 10.2217/fon.10.56] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA copy number changes in cancer cells, in particular, amplifications, occur frequently, have prognostic impact and are associated with subtypes of breast cancer. Some amplicons contain well-characterized oncogenes, including 11q13 (CCND1) and 17q12 (HER2). HER2 amplification and overexpression defines the HER2+ subgroup of breast cancer patients and is both a prognostic marker for poor outcome and a predictive marker for response to anti-HER2 targeted therapies. Therefore, there is considerable interest in documenting the locations of other recurring amplifications in breast cancers as they may also provide a rich source of new biomarkers and novel therapeutic targets for these subgroups. This article focuses on the genomic profiling of breast cancer, with an emphasis on the characteristics of the amplifications found in subtypes of breast cancer, including luminal (ER+)/HER2(-)), HER2+ and basal-like (ER(-)/HER2(-)), and discusses their known or potential roles in cancer biology and their clinical implications.
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Affiliation(s)
- Kai-Keen Shiu
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, 237 Fulham Road, London SW36JB, UK
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Gravier E, Pierron G, Vincent-Salomon A, Gruel N, Raynal V, Savignoni A, De Rycke Y, Pierga JY, Lucchesi C, Reyal F, Fourquet A, Roman-Roman S, Radvanyi F, Sastre-Garau X, Asselain B, Delattre O. A prognostic DNA signature for T1T2 node-negative breast cancer patients. Genes Chromosomes Cancer 2010; 49:1125-34. [DOI: 10.1002/gcc.20820] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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Desouki MM, Liao S, Huang H, Conroy J, Nowak NJ, Shepherd L, Gaile DP, Geradts J. Identification of metastasis-associated breast cancer genes using a high-resolution whole genome profiling approach. J Cancer Res Clin Oncol 2010; 137:795-809. [PMID: 20680643 DOI: 10.1007/s00432-010-0937-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 07/05/2010] [Indexed: 01/23/2023]
Abstract
PURPOSE We employed a whole genome tumor profiling approach in an attempt to identify DNA copy number alterations (CNAs) and new candidate genes that are correlated with the metastatic potential of a primary breast carcinoma and with progression at the metastatic site. METHODS Fifty-four small (≤ 2 cm), high grade, ER-positive, formalin-fixed invasive ductal carcinomas were suitable for whole genome profiling analysis. Twenty-four of them did not form metastases within 5-10 years (unmatched primaries, UP). Thirty tumors had at least one synchronous axillary lymph node metastasis (matched primaries, MP; matched lymph node metastases, ML). Genomic DNA was hybridized to high density (19k) BAC arrays. Statistical analysis revealed differential distributions of CNAs between UP and MP and between MP and ML, respectively. We selected 27 candidate genes for validation experiments using quantitative (Q-)PCR of genomic DNA. For tetraspanin TSPAN1, we studied mRNA expression levels in a separate cohort of primary breast carcinomas and in breast cell lines. RESULTS Matched primary (MP) tumors had a threefold higher rate of DNA copy number losses compared to UP tumors. In the UP-MP comparison, 186 BACs were differentially amplified or deleted. Most of them were localized to chromosomes 7p, 16q and 18q. In the MP-ML comparison, 131 BACs showed differential CNAs. Most of them were localized to chromosomes 1q and 20. By Q-PCR, seven candidate genes could be confirmed to show differential distributions of CNAs. TSPAN1 was amplified in UP and deleted in MP tumors. The gene was markedly downregulated in ER-negative and high-grade breast cancers. CONCLUSIONS Metastasizing tumors had a higher rate of deletions, suggesting possible inactivation of metastasis suppressor genes. We provide preliminary evidence that TSPAN1 may be another important breast cancer suppressor gene belonging to the tetraspanin superfamily.
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Affiliation(s)
- Mohamed M Desouki
- Department of Pathology, Medical University of South Carolina, Charleston, SC 29425, USA
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Jönsson G, Staaf J, Vallon-Christersson J, Ringnér M, Holm K, Hegardt C, Gunnarsson H, Fagerholm R, Strand C, Agnarsson BA, Kilpivaara O, Luts L, Heikkilä P, Aittomäki K, Blomqvist C, Loman N, Malmström P, Olsson H, Th Johannsson O, Arason A, Nevanlinna H, Barkardottir RB, Borg Å. Genomic subtypes of breast cancer identified by array-comparative genomic hybridization display distinct molecular and clinical characteristics. Breast Cancer Res 2010; 12:R42. [PMID: 20576095 PMCID: PMC2917037 DOI: 10.1186/bcr2596] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 05/18/2010] [Accepted: 06/24/2010] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Breast cancer is a profoundly heterogeneous disease with respect to biologic and clinical behavior. Gene-expression profiling has been used to dissect this complexity and to stratify tumors into intrinsic gene-expression subtypes, associated with distinct biology, patient outcome, and genomic alterations. Additionally, breast tumors occurring in individuals with germline BRCA1 or BRCA2 mutations typically fall into distinct subtypes. METHODS We applied global DNA copy number and gene-expression profiling in 359 breast tumors. All tumors were classified according to intrinsic gene-expression subtypes and included cases from genetically predisposed women. The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was used to identify significant DNA copy-number aberrations and genomic subgroups of breast cancer. RESULTS We identified 31 genomic regions that were highly amplified in > 1% of the 359 breast tumors. Several amplicons were found to co-occur, the 8p12 and 11q13.3 regions being the most frequent combination besides amplicons on the same chromosomal arm. Unsupervised hierarchical clustering with 133 significant GISTIC regions revealed six genomic subtypes, termed 17q12, basal-complex, luminal-simple, luminal-complex, amplifier, and mixed subtypes. Four of them had striking similarity to intrinsic gene-expression subtypes and showed associations to conventional tumor biomarkers and clinical outcome. However, luminal A-classified tumors were distributed in two main genomic subtypes, luminal-simple and luminal-complex, the former group having a better prognosis, whereas the latter group included also luminal B and the majority of BRCA2-mutated tumors. The basal-complex subtype displayed extensive genomic homogeneity and harbored the majority of BRCA1-mutated tumors. The 17q12 subtype comprised mostly HER2-amplified and HER2-enriched subtype tumors and had the worst prognosis. The amplifier and mixed subtypes contained tumors from all gene-expression subtypes, the former being enriched for 8p12-amplified cases, whereas the mixed subtype included many tumors with predominantly DNA copy-number losses and poor prognosis. CONCLUSIONS Global DNA copy-number analysis integrated with gene-expression data can be used to dissect the complexity of breast cancer. This revealed six genomic subtypes with different clinical behavior and a striking concordance to the intrinsic subtypes. These genomic subtypes may prove useful for understanding the mechanisms of tumor development and for prognostic and treatment prediction purposes.
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Affiliation(s)
- Göran Jönsson
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, BMC C13, SE 22184, Lund, Sweden
| | - Johan Staaf
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, BMC C13, SE 22184, Lund, Sweden
| | - Johan Vallon-Christersson
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, BMC C13, SE 22184, Lund, Sweden
| | - Markus Ringnér
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, BMC C13, SE 22184, Lund, Sweden
| | - Karolina Holm
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
| | - Cecilia Hegardt
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, BMC B10, SE 22184, Lund, Sweden
| | - Haukur Gunnarsson
- Department of Pathology, Landspitali-University Hospital, 101 Reykjavik, Iceland
| | - Rainer Fagerholm
- Departments of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Carina Strand
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
| | - Bjarni A Agnarsson
- Department of Pathology, Landspitali-University Hospital, 101 Reykjavik, Iceland
| | - Outi Kilpivaara
- Departments of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Lena Luts
- Department of Pathology, Clinical Sciences, Lund University and Skåne University Hospital, SE 22185 Lund, Sweden
| | - Päivi Heikkilä
- Department of Pathology, Helsinki University Central Hospital, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Niklas Loman
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
| | - Per Malmström
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
| | - Håkan Olsson
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
| | - Oskar Th Johannsson
- Department of Oncology, Landspitali-University Hospital, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Adalgeir Arason
- Department of Pathology, Landspitali-University Hospital, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Heli Nevanlinna
- Departments of Obstetrics and Gynaecology, Helsinki University Central Hospital, Helsinki, Finland
| | - Rosa B Barkardottir
- Department of Pathology, Landspitali-University Hospital, 101 Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Åke Borg
- Department of Oncology, Clinical Sciences, Lund University and Skåne University Hospital, Barngatan 2B, SE 22185 Lund, Sweden
- CREATE Health Strategic Center for Translational Cancer Research, Lund University, BMC C13, SE 22184, Lund, Sweden
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, BMC B10, SE 22184, Lund, Sweden
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Lopez-Garcia MA, Geyer FC, Lacroix-Triki M, Marchió C, Reis-Filho JS. Breast cancer precursors revisited: molecular features and progression pathways. Histopathology 2010; 57:171-92. [PMID: 20500230 DOI: 10.1111/j.1365-2559.2010.03568.x] [Citation(s) in RCA: 215] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Increasingly more coherent data on the molecular characteristics of benign breast lesions and breast cancer precursors have led to the delineation of new multistep pathways of breast cancer progression through genotypic-phenotypic correlations. It has become apparent that oestrogen receptor (ER)-positive and -negative breast lesions are fundamentally distinct diseases. Within the ER-positive group, histological grade is strongly associated with the number and complexity of genetic abnormalities in breast cancer cells. Genomic analyses of high-grade ER-positive breast cancers have revealed that a substantial proportion of these tumours harbour the characteristic genetic aberrations found in low-grade ER-positive disease, suggesting that at least a subgroup of high-grade ER-positive breast cancers may originate from low-grade lesions. The ER-negative group is more complex and heterogeneous, comprising distinct molecular entities, including basal-like, HER2 and molecular apocrine lesions. Importantly, the type and pattern of genetic aberrations found in ER-negative cancers differ from those of ER-positive disease. Here, we review the available molecular data on breast cancer risk indicator and precursor lesions, the putative mechanisms of progression from in situ to invasive disease, and propose a revised model of breast cancer evolution based on the molecular characteristics of distinct subtypes of in situ and invasive breast cancers.
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Affiliation(s)
- Maria A Lopez-Garcia
- Molecular Pathology Team, The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, 237 Fulham Road, London, UK
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Guerrero AA, Martínez-A C, van Wely KH. Merotelic attachments and non-homologous end joining are the basis of chromosomal instability. Cell Div 2010; 5:13. [PMID: 20478024 PMCID: PMC2878296 DOI: 10.1186/1747-1028-5-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Accepted: 05/17/2010] [Indexed: 11/10/2022] Open
Abstract
Although the large majority of solid tumors show a combination of mitotic spindle defects and chromosomal instability, little is known about the mechanisms that govern the initial steps in tumorigenesis. The recent report of spindle-induced DNA damage provides evidence for a single mechanism responsible for the most prominent genetic defects in chromosomal instability. Spindle-induced DNA damage is brought about by uncorrected merotelic attachments, which cause kinetochore distortion, chromosome breakage at the centromere, and possible activation of DNA damage repair pathways. Although merotelic attachments are common early in mitosis, some escape detection by the kinetochore pathway. As a consequence, a proportion of merotelic attachments gives rise to chromosome breakage in normal cells and in carcinomas. An intrinsic chromosome segregation defect might thus form the basis of tumor initiation. We propose a hypothesis in which merotelic attachments and chromosome breakage establish a feedback loop that results in relaxation of the spindle checkpoint and suppression of anti-proliferative pathways, thereby promoting carcinogenesis.
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Affiliation(s)
- Astrid Alonso Guerrero
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Darwin 3, UAM Campus Cantoblanco, 28049 Madrid, Spain.
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Fu L, Dong SS, Xie YW, Tai LS, Chen L, Kong KL, Man K, Xie D, Li Y, Cheng Y, Tao Q, Guan XY. Down-regulation of tyrosine aminotransferase at a frequently deleted region 16q22 contributes to the pathogenesis of hepatocellular carcinoma. Hepatology 2010; 51:1624-34. [PMID: 20209601 DOI: 10.1002/hep.23540] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
UNLABELLED Loss of 16q is one of the most frequent alterations in many malignancies including hepatocellular carcinomas (HCC), suggesting the existence of a tumor suppressor gene (TSG) within the frequently deleted region. In this report we describe the identification and characterization of one candidate TSG, tyrosine aminotransferase gene (TAT), at 16q22.1. Loss of one TAT allele was detected in 27/50 (54%) of primary HCCs by quantitative real-time polymerase chain reaction. In addition, homo-deletion of TAT alleles was detected in two cases. Down-regulation of TAT was detected in 28/50 (56%) of HCCs, which was significantly associated with the loss of TAT allele and hypermethylation of TAT 5' CpG island (CGI) region (P < 0.001). Functional studies found that TAT has a strong tumor suppressive ability. Introduction of the TAT gene into HCC cell lines could effectively inhibit colony formation in soft agar, foci formation, and tumor formation in nude mice. Further study found that the tumor suppressive mechanism of TAT was associated with its proapoptotic role in a mitochondrial-dependent manner by promoting cytochrome-c release and activating caspase-9 and PARP. CONCLUSION Taken together, our findings suggest that TAT plays an important suppressive role in the development and progression of HCC.
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Affiliation(s)
- Li Fu
- State Key Laboratory of Oncology in Southern China, Cancer Center, Sun Yat-sen University, Guangzhou, China
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Abstract
Breast cancer is a heterogeneous disease and pathologists have evolved a system of classification that reflects this heterogeneity as well as provide prognostic and predictive information to manage patients. Professor Azzopardi's contribution to understanding and classifying breast disease is significant and reflected by the many articles in this issue. Nonetheless, there are limitations to the morphologic classification and new molecular methods promise to refine the biological understanding as well as provide better biomarkers for prognostication and targets for the development of novel therapeutics. The degree to which the new methods add value to the morphology remains to be seen, but there is hope that a symbiosis between morphology and molecular techniques will advance traditional histopathology and improve the care of patients with breast cancer.
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Affiliation(s)
- Peter T Simpson
- University of Queensland Centre for Clinical Research, The Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
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Downing TE, Oktay MH, Fazzari MJ, Montagna C. Prognostic and predictive value of 16p12.1 and 16q22.1 copy number changes in human breast cancer. ACTA ACUST UNITED AC 2010; 198:52-61. [PMID: 20303015 DOI: 10.1016/j.cancergencyto.2009.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 12/03/2009] [Accepted: 12/08/2009] [Indexed: 11/25/2022]
Abstract
The present study investigated DNA copy number changes mapping to the p and q arms of chromosome 16 in breast cancer with the goal to determine their potential in identifying breast cancer patients with poor prognosis. We identified the minimal overlapping regions on chromosome 16 that are commonly deleted and amplified in breast tumors. Fluorescence in situ hybridization was used to screen a custom-made breast carcinoma tissue microarray representing all tumor grades, in order to detect DNA copy number changes mapping to 16p12.1 and 16q22.1. We generated 16q/16p ratios for each patient and examined the correlation between DNA copy number alterations and the patients' clinical and pathological parameters. We observed lower q/p ratios in grade I invasive carcinomas, compared with grade III carcinomas, which consistently showed high q/p ratios (P < 0.0091 and 0.0075). In addition, age adjusted for grade analysis revealed that tumors from younger patients (<45 yr) had significantly higher q/p ratios, suggesting that in younger individuals those tumors might be more aggressive (P < 0.0001). The finding that higher q/p ratios occur in younger patients offers a tool to identify high-risk individuals most likely to proceed to high grade.
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Affiliation(s)
- Tricia E Downing
- Jacobi Medical Center, Department of Internal Medicine, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
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Genetic Alterations in Normal and Malignant Breast Tissue. Breast Cancer 2010. [DOI: 10.1007/978-1-84996-314-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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Wagner PL, Kitabayashi N, Chen YT, Shin SJ. Clonal relationship between closely approximated low-grade ductal and lobular lesions in the breast: a molecular study of 10 cases. Am J Clin Pathol 2009; 132:871-6. [PMID: 19926578 DOI: 10.1309/ajcp7ak1vwfnmcsw] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The relationship between ductal and lobular breast carcinoma is highlighted in cases in which these morphologically divergent carcinomas coexist in proximity within a single patient. We hypothesized that such cases may result from the proliferation of a precursor lesion into a tumor containing areas of divergent morphologic features. In this study, we analyzed loss of heterozygosity (LOH) in 10 cases of coexistent ductal carcinoma in situ (DCIS), lobular carcinoma in situ (LCIS), and invasive carcinoma. DNA from the separate components of each lesion was subjected to LOH analysis using 13 markers on 7 chromosomes. In 7 cases, the DCIS and LCIS shared loss of a common allele, suggesting a clonal relationship. The invasive component shared loss of the same allele in 5 tumors. This finding indicates that coexistent lobular and ductal carcinomas exhibit shared genetic abnormalities, contradicting the conventional concept that these lesions represent separate, exclusive pathways of breast neoplasia. Instead, these traditionally segregated classes of breast cancer may, in fact, share common precursor lesions.
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41
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Ellsworth RE, Hooke JA, Shriver CD, Ellsworth DL. Genomic heterogeneity of breast tumor pathogenesis. Clin Med Oncol 2009; 3:77-85. [PMID: 20689613 PMCID: PMC2872596 DOI: 10.4137/cmo.s2946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pathological grade is a useful prognostic factor for stratifying breast cancer patients into favorable (low-grade, well-differentiated tumors) and less favorable (high-grade, poorly-differentiated tumors) outcome groups. Under the current system of tumor grading, however, a large proportion of tumors are characterized as intermediate-grade, making determination of optimal treatments difficult. In an effort to increase objectivity in the pathological assessment of tumor grade, differences in chromosomal alterations and gene expression patterns have been characterized in low-grade, intermediate-grade, and high-grade disease. In this review, we outline molecular data supporting a linear model of progression from low-grade to high-grade carcinomas, as well as contradicting genetic data suggesting that low-grade and high-grade tumors develop independently. While debate regarding specific pathways of development continues, molecular data suggest that intermediate-grade tumors do not comprise an independent disease subtype, but represent clinical and molecular hybrids between low-grade and high-grade tumors. Finally, we discuss the clinical implications associated with different pathways of development, including a new clinical test to assign grade and guide treatment options.
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Affiliation(s)
- Rachel E Ellsworth
- Clinical Breast Care Project, Henry M. Jackson Foundation for the Advancement of Military Medicine, 620 Seventh Street, Windber, PA, 15963, USA
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42
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Tsuda H. Gene and chromosomal alterations in sporadic breast cancer: correlation with histopathological features and implications for genesis and progression. Breast Cancer 2009; 16:186-201. [PMID: 19472036 DOI: 10.1007/s12282-009-0124-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2009] [Accepted: 03/29/2009] [Indexed: 12/31/2022]
Abstract
A number of gene and chromosome alterations have been identified in sporadic breast carcinomas, and their clinical implications have been investigated. Changes in proto-oncogenes and tumor-suppressor genes, e.g., HER2, p53, and E-cadherin, and various numerical and structural chromosome alterations are strongly correlated with histological type and grade in breast carcinomas. The amount of information on these alterations has been dramatically increased by the introduction of high-throughput molecular cytogenetic approaches. In the near future, breast cancers will be classified into specific groups according to their profile of gene and chromosome alterations, allowing more effective personalized therapies targeting the associated molecular pathways.
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Affiliation(s)
- Hitoshi Tsuda
- Pathology Section, Clinical Laboratory Division, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
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43
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Natrajan R, Lambros MB, Rodríguez-Pinilla SM, Moreno-Bueno G, Tan DSP, Marchió C, Vatcheva R, Rayter S, Mahler-Araujo B, Fulford LG, Hungermann D, Mackay A, Grigoriadis A, Fenwick K, Tamber N, Hardisson D, Tutt A, Palacios J, Lord CJ, Buerger H, Ashworth A, Reis-Filho JS. Tiling path genomic profiling of grade 3 invasive ductal breast cancers. Clin Cancer Res 2009; 15:2711-22. [PMID: 19318498 DOI: 10.1158/1078-0432.ccr-08-1878] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
PURPOSE To characterize the molecular genetic profiles of grade 3 invasive ductal carcinomas of no special type using high-resolution microarray-based comparative genomic hybridization (aCGH) and to identify recurrent amplicons harboring putative therapeutic targets associated with luminal, HER-2, and basal-like tumor phenotypes. EXPERIMENTAL DESIGN Ninety-five grade 3 invasive ductal carcinomas of no special type were classified into luminal, HER-2, and basal-like subgroups using a previously validated immunohistochemical panel. Tumor samples were microdissected and subjected to aCGH using a tiling path 32K BAC array platform. Selected regions of recurrent amplification were validated by means of in situ hybridization. Expression of genes pertaining to selected amplicons was investigated using quantitative real-time PCR and gene silencing was done using previously validated short hairpin RNA constructs. RESULTS We show that basal-like and HER-2 tumors are characterized by "sawtooth" and "firestorm" genetic patterns, respectively, whereas luminal cancers were more heterogeneous. Apart from confirming known amplifications associated with basal-like (1q21, 10p, and 12p), luminal (8p12, 11q13, and 11q14), and HER-2 (17q12) cancers, we identified previously unreported recurrent amplifications associated with each molecular subgroup: 19q12 in basal-like, 1q32.1 in luminal, and 14q12 in HER-2 cancers. PPM1D gene amplification (17q23.2) was found in 20% and 8% of HER-2 and luminal cancers, respectively. Silencing of PPM1D by short hairpin RNA resulted in selective loss of viability in tumor cell lines harboring the 17q23.2 amplification. CONCLUSIONS Our results show the power of aCGH analysis in unraveling the genetic profiles of specific subgroups of cancer and for the identification of novel therapeutic targets.
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Affiliation(s)
- Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
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Natrajan R, Lambros MBK, Geyer FC, Marchio C, Tan DSP, Vatcheva R, Shiu KK, Hungermann D, Rodriguez-Pinilla SM, Palacios J, Ashworth A, Buerger H, Reis-Filho JS. Loss of 16q in high grade breast cancer is associated with estrogen receptor status: Evidence for progression in tumors with a luminal phenotype? Genes Chromosomes Cancer 2009; 48:351-65. [PMID: 19156836 DOI: 10.1002/gcc.20646] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Loss of the long arm of chromosome 16 (16q) is observed in the vast majority of low grade/grade I (GI) invasive ductal carcinomas of no special type (IDC-NSTs), whereas this event is uncommonly seen in high grade/grade III (GIII) IDC-NSTs. Together with data on the pathology and genetics of breast cancer recurrences, this has led to the proposal that GI and GIII breast cancers evolve through distinct genetic pathways and that progression from GI to GIII is an unlikely biological phenomenon. We compared the genomic profiles of GIII-IDC-NSTs with 16q whole arm loss (16qWL) according to estrogen receptor (ER) status. 16qWL was found in 36.5% of cases and was significantly associated with ER expression and luminal phenotype. ER+ GIII-IDC-NSTs with 16qWL displayed significantly higher levels of genomic instability than ER+ IDC-NSTs without 16qWL. Furthermore, ER+ and ER- IDC-NSTs stratified according to the presence of 16qWL harbored distinct patterns of genetic aberrations. Interestingly, ER+/16qWL tumors displayed genetic features usually found in tumors with homologous DNA repair defects and significantly more frequently harbored heterozygous loss of BRCA2 than the remaining ER+ cancers. Our results demonstrate that approximately one third of GIII tumors harbor 16qWL, confirming that progression from low to high grade breast cancer is not found in the majority of breast cancers. 16qWL was significantly more prevalent in ER+/luminal GIII-IDC-NSTs. Given that GI breast cancers harbor a luminal phenotype, our results suggest that if progression from GI to GIII breast cancer does happen, it may preferentially occur in breast cancers of luminal phenotype.
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Affiliation(s)
- Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, UK
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45
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Loo LWM, Ton C, Wang YW, Grove DI, Bouzek H, Vartanian N, Lin MG, Yuan X, Lawton TL, Daling JR, Malone KE, Li CI, Hsu L, Porter PL. Differential patterns of allelic loss in estrogen receptor-positive infiltrating lobular and ductal breast cancer. Genes Chromosomes Cancer 2008; 47:1049-66. [PMID: 18720524 DOI: 10.1002/gcc.20610] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The two main histological types of infiltrating breast cancer, lobular (ILC) and the more common ductal (IDC) carcinoma are morphologically and clinically distinct. To assess the molecular alterations associated with these breast cancer subtypes, we conducted a whole-genome study of 166 archival estrogen receptor (ER)-positive tumors (89 IDC and 77 ILC) using the Affymetrix GeneChip(R) Mapping 10K Array to identify sites of loss of heterozygosity (LOH) that either distinguished, or were shared by, the two phenotypes. We found single nucleotide polymorphisms (SNPs) of high-frequency LOH (>50%) common to both ILC and IDC tumors predominately in 11q, 16q, and 17p. Overall, IDC had a slightly higher frequency of LOH events across the genome than ILC (fractional allelic loss = 0.186 and 0.156). By comparing the average frequency of LOH by chromosomal arm, we found IDC tumors with significantly (P < 0.05) higher frequency of LOH on 3p, 5q, 8p, 9p, 20p, and 20q than ILC tumors. We identified additional chromosomal arms differentiating the subtypes when tumors were stratified by tumor size, mitotic rate, or DNA content. Of 5,754 informative SNPs (>25% informativity), we identified 78 and 466 individual SNPs with a higher frequency of LOH (P < 0.05) in ILC and IDC tumors, respectively. Hierarchical clustering of these 544 SNPs grouped tumors into four major groups based on their patterns of LOH and retention of heterozygosity. LOH in chromosomal arms 8p and 5q was common in higher grade IDC tumors, whereas ILC and low-grade IDC grouped together by virtue of LOH in 16q.
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Affiliation(s)
- L W M Loo
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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46
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Nordgard SH, Johansen FE, Alnaes GIG, Bucher E, Syvänen AC, Naume B, Børresen-Dale AL, Kristensen VN. Genome-wide analysis identifies 16q deletion associated with survival, molecular subtypes, mRNA expression, and germline haplotypes in breast cancer patients. Genes Chromosomes Cancer 2008; 47:680-96. [PMID: 18398821 DOI: 10.1002/gcc.20569] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Breast carcinomas are characterized by DNA copy number alterations (CNAs) with biological and clinical significance. This explorative study integrated CNA, expression, and germline genotype data of 112 early-stage breast cancer patients. Recurrent CNAs differed substantially between tumor subtypes classified according to expression pattern. Deletion of 16q was overrepresented in Luminal A, and a predictor of good prognosis, both overall and for the nonluminal A subgroups. The deleted region most significantly associated with survival mapped to 16q22.2, harboring the genes TXNL4B and DXH38, whose expression was strongly correlated with the deletion. The area most frequently deleted resided on 16q23.1, 3.5 MB downstream of the area most significantly associated with survival, and included the tumor suppressor gene ADAMTS18 and the cell recognition gene CNTNAP4. Whole-genome association analysis identified germline single nucleotide polymorphisms (SNPs) and their corresponding haplotypes, residing on several different chromosomes, to be associated with deletion of 16q. The genes where these SNPs reside encode proteins involved in the extracellular matrix (CHST3 and SPOCK2), in regulation of the cell cycle (JMY, PTPRN2, and Cwf19L2) and chromosome stability (KPNB1).
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Affiliation(s)
- Silje H Nordgard
- Department of Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
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47
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Ellsworth RE, Vertrees A, Love B, Hooke JA, Ellsworth DL, Shriver CD. Chromosomal Alterations Associated with the Transition from In Situ to Invasive Breast Cancer. Ann Surg Oncol 2008; 15:2519-25. [DOI: 10.1245/s10434-008-0051-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 05/29/2008] [Accepted: 05/29/2008] [Indexed: 12/12/2022]
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48
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Melchor L, Benítez J. An integrative hypothesis about the origin and development of sporadic and familial breast cancer subtypes. Carcinogenesis 2008; 29:1475-82. [PMID: 18596026 DOI: 10.1093/carcin/bgn157] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Do breast cancer tumours have a common cell origin? Do different breast cancer molecular phenotypes arise from distinct cell types? The studies we have performed during the last few years in familial breast tumours (BRCA1, BRCA2 and non-BRCA1/2) widen questions about the development of sporadic breast cancer to hereditary breast cancer. Array-comparative genomic hybridisation (CGH) studies show universal genomic aberrations in both familial and sporadic breast cancer subtypes that may be selected in the breast tumour development. The inactivation of BRCA1 seems to play a critical role in oestrogen receptor (ER)-negative cancer stem cells (CSCs), driving the tumour development mostly towards a basal-like or, in some cases, to a luminal B phenotype, but other carcinogenetic events are proposed to explain the remaining tumour subtypes. The existence of common genomic alterations in basal-like, ERBB2 and luminal B breast tumours may suggest a common cell origin or clonal selection of these tumour subtypes, arising from an ER-negative CSC or from a progenitor cell (PC). Finally, specific genomic aberrations in ER-positive tumours could provide cellular proliferation advantages when the cells are exposed to oestrogen. We propose a combination of the CSC hypothesis (for the carcinogenesis processes) and the clonal selection model (in terms of tumour development). We uphold that the basal-like-, ERBB2- and luminal B-sporadic and familial tumour subtypes have an ER-negative breast stem/PC origin, whereas luminal A tumours arise from an ER-positive PC, supporting a hierarchical breast carcinogenesis model, whereas crucial genomic imbalances are clonally selected during the tumour development.
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Affiliation(s)
- Lorenzo Melchor
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Centre (CNIO), Madrid E-28029, Spain.
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49
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Simpson PT, Reis-Filho JS, Lambros MBK, Jones C, Steele D, Mackay A, Iravani M, Fenwick K, Dexter T, Jones A, Reid L, Da Silva L, Shin SJ, Hardisson D, Ashworth A, Schmitt FC, Palacios J, Lakhani SR. Molecular profiling pleomorphic lobular carcinomas of the breast: evidence for a common molecular genetic pathway with classic lobular carcinomas. J Pathol 2008; 215:231-44. [DOI: 10.1002/path.2358] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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50
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Walker LC, Harris GC, Wells JE, Robinson BA, Morris CM. Association of chromosome band 8q22 copy number gain with high grade invasive breast carcinomas by assessment of core needle biopsies. Genes Chromosomes Cancer 2008; 47:405-17. [DOI: 10.1002/gcc.20545] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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