1
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Dai Y, Zhang X, Ou Y, Zou L, Zhang D, Yang Q, Qin Y, Du X, Li W, Yuan Z, Xiao Z, Wen Q. Anoikis resistance--protagonists of breast cancer cells survive and metastasize after ECM detachment. Cell Commun Signal 2023; 21:190. [PMID: 37537585 PMCID: PMC10399053 DOI: 10.1186/s12964-023-01183-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/04/2023] [Indexed: 08/05/2023] Open
Abstract
Breast cancer exhibits the highest global incidence among all tumor types. Regardless of the type of breast cancer, metastasis is a crucial cause of poor prognosis. Anoikis, a form of apoptosis initiated by cell detachment from the native environment, is an outside-in process commencing with the disruption of cytosolic connectors such as integrin-ECM and cadherin-cell. This disruption subsequently leads to intracellular cytoskeletal and signaling pathway alterations, ultimately activating caspases and initiating programmed cell death. Development of an anoikis-resistant phenotype is a critical initial step in tumor metastasis. Breast cancer employs a series of stromal alterations to suppress anoikis in cancer cells. Comprehensive investigation of anoikis resistance mechanisms can inform strategies for preventing and regressing metastatic breast cancer. The present review first outlines the physiological mechanisms of anoikis, elucidating the alterations in signaling pathways, cytoskeleton, and protein targets that transpire from the outside in upon adhesion loss in normal breast cells. The specific anoikis resistance mechanisms induced by pathological changes in various spatial structures during breast cancer development are also discussed. Additionally, the genetic loci of targets altered in the development of anoikis resistance in breast cancer, are summarized. Finally, the micro-RNAs and targeted drugs reported in the literature concerning anoikis are compiled, with keratocin being the most functionally comprehensive. Video Abstract.
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Affiliation(s)
- Yalan Dai
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Department of Oncology, Garze Tibetan Autonomous Prefecture People's Hospital, Kangding, China
| | - Xinyi Zhang
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shenzhen, China
| | - Yingjun Ou
- Clinical Medicine School, Southwest Medicial Univercity, Luzhou, China
- Orthopaedics, Garze Tibetan Autonomous Prefecture People's Hospital, Kangding, China
| | - Linglin Zou
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Duoli Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Qingfan Yang
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yi Qin
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiuju Du
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Wei Li
- Southwest Medical University, Luzhou, China
| | | | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
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2
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Taverniti V, Krynska H, Venuti A, Straub ML, Sirand C, Lohmann E, Romero-Medina MC, Moro S, Robitaille A, Negroni L, Martinez-Zapien D, Masson M, Tommasino M, Zanier K. The E2F4/p130 Repressor Complex Cooperates with Oncogenic ΔNp73α To Inhibit Gene Expression in Human Papillomavirus 38 E6/E7-Transformed Keratinocytes and in Cancer Cells. mSphere 2023; 8:e0005623. [PMID: 36883841 PMCID: PMC10117100 DOI: 10.1128/msphere.00056-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
Tumor suppressor p53 and its related proteins, p63 and p73, can be synthesized as multiple isoforms lacking part of the N- or C-terminal regions. Specifically, high expression of the ΔNp73α isoform is notoriously associated with various human malignancies characterized by poor prognosis. This isoform is also accumulated by oncogenic viruses, such as Epstein-Barr virus (EBV), as well as genus beta human papillomaviruses (HPV) that appear to be involved in carcinogenesis. To gain additional insight into ΔNp73α mechanisms, we have performed proteomics analyses using human keratinocytes transformed by the E6 and E7 proteins of the beta-HPV type 38 virus as an experimental model (38HK). We find that ΔNp73α associates with the E2F4/p130 repressor complex through a direct interaction with E2F4. This interaction is favored by the N-terminal truncation of p73 characteristic of ΔNp73 isoforms. Moreover, it is independent of the C-terminal splicing status, suggesting that it could represent a general feature of ΔNp73 isoforms (α, β, γ, δ, ε, ζ, θ, η, and η1). We show that the ΔNp73α-E2F4/p130 complex inhibits the expression of specific genes, including genes encoding for negative regulators of proliferation, both in 38HK and in HPV-negative cancer-derived cell lines. Such genes are not inhibited by E2F4/p130 in primary keratinocytes lacking ΔNp73α, indicating that the interaction with ΔNp73α rewires the E2F4 transcriptional program. In conclusion, we have identified and characterized a novel transcriptional regulatory complex with potential implications in oncogenesis. IMPORTANCE The TP53 gene is mutated in about 50% of human cancers. In contrast, the TP63 and TP73 genes are rarely mutated but rather expressed as ΔNp63 and ΔNp73 isoforms in a wide range of malignancies, where they act as p53 antagonists. Accumulation of ΔNp63 and ΔNp73, which is associated with chemoresistance, can result from infection by oncogenic viruses such as EBV or HPV. Our study focuses on the highly carcinogenic ΔNp73α isoform and uses a viral model of cellular transformation. We unveil a physical interaction between ΔNp73α and the E2F4/p130 complex involved in cell cycle control, which rewires the E2F4/p130 transcriptional program. Our work shows that ΔNp73 isoforms can establish interactions with proteins that do not bind to the TAp73α tumor suppressor. This situation is analogous to the gain-of-function interactions of p53 mutants supporting cellular proliferation.
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Affiliation(s)
- Valerio Taverniti
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Hanna Krynska
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France
| | - Assunta Venuti
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Marie-Laure Straub
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France
| | - Cécilia Sirand
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Eugenie Lohmann
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | | | - Stefano Moro
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France
| | - Alexis Robitaille
- International Agency for Research on Cancer (IARC), World Health Organization, Lyon, France
| | - Luc Negroni
- Proteomics platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC)/INSERM U964/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Denise Martinez-Zapien
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France
| | - Murielle Masson
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France
| | | | - Katia Zanier
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR 7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, Illkirch, France
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3
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High Expression of E2F4 Is an Adverse Prognostic Factor and Related to Immune Infiltration in Oral Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4731364. [PMID: 36567912 PMCID: PMC9780755 DOI: 10.1155/2022/4731364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/01/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
Background We aimed to evaluate the prognostic value of E2F4 expression in oral squamous cell carcinoma (OSCC) and clarify its influence on immune cell infiltration and biological functions. Methods The Cancer Genome Atlas (TCGA) database, the STRING database, and related online tools as well as single-sample gene set enrichment analysis (ssGSEA) were used for the analyses in our study. Results The E2F4 expression was elevated in OSCC tumor tissue compared with paracancerous tissues. The high expression of E2F4 was closely related to the poorer overall survival, disease-free survival, and progression-free interval of OSCC. In addition, pathway enrichment analyses revealed that the top 49 genes most closely related to E2F4 were strongly associated with the cell cycle. E2F4-related proteins were closely related to the following KEGG pathways: cell cycle, cellular senescence, PI3K-Akt signaling pathway, Wnt signaling pathway, and notch signaling pathway. It was also demonstrated that the E2F4 expression was negatively correlated with immune purity and strongly related to immune cell infiltration in OSCC. Conclusions E2F4 can be used as a novel biomarker for the diagnosis and prognosis of OSCC.
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4
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Chen Y, He R, Han Z, Wu Y, Wang Q, Zhu X, Huang Z, Ye J, Tang Y, Huang H, Chen J, Shan H, Xiao F. Cooperation of ATF4 and CTCF promotes adipogenesis through transcriptional regulation. Cell Biol Toxicol 2021; 38:741-763. [PMID: 33950334 DOI: 10.1007/s10565-021-09608-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 04/23/2021] [Indexed: 12/12/2022]
Abstract
Adipogenesis is a multi-step process orchestrated by activation of numerous TFs, whose cooperation and regulatory network remain elusive. Activating transcription factor 4 (ATF4) is critical for adipogenesis, yet its regulatory network is unclarified. Here, we mapped genome-wide ATF4 binding landscape and its regulatory network by Chip-seq and RNA-seq and found ATF4 directly modulated transcription of genes enriching in fat cell differentiation. Motifs of TFs especially CTCF were found from ATF4 binding sites, suggesting a direct role of ATF4 in regulating adipogenesis associated with CTCF and other TFs. Deletion of CTCF attenuated adipogenesis while overexpression enhanced adipocyte differentiation, indicating CTCF is indispensable for adipogenesis. Intriguingly, combined analysis of Chip-seq data of these two TFs showed that ATF4 co-localized with CTCF in the promoters of key adipogenic genes including Cebpd and PPARg and co-regulated their transactivation. Moreover, ATF4 directly regulated CTCF expression and interacted with CTCF in differentiated 3T3-L1 cells. In vivo, downregulation of ATF4 suppressed the expression of CTCF, Cebpd, and PPARg, leading to reduced adipose tissue expansion in refeeding mice. Consistently, mRNA expression of ATF4 and CTCF was positively correlated with each other in human subcutaneous adipose tissue and inversely associated with BMI, indicating a possible involvement of these two TFs in adipose development. Taken together, our data propose for the first time that ATF4 and CTCF work cooperatively to control adipogenesis and adipose development via orchestrating transcription of adipogenic genes. Our findings reveal novel therapeutic targets in obesity treatment.
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Affiliation(s)
- Yingchun Chen
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China.,Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 53002, People's Republic of China
| | - Rongquan He
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China
| | - Zhiqiang Han
- Department of Plastic and Aesthetic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 530021, People's Republic of China
| | - Yanyan Wu
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China
| | - Qiuyan Wang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 53002, People's Republic of China
| | - Xiujuan Zhu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 53002, People's Republic of China
| | - Zhiguang Huang
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, 53002, People's Republic of China
| | - Juan Ye
- Department of Infectious Diseases, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China
| | - Yao Tang
- Department of Infectious Diseases, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China
| | - Hongbin Huang
- Department of Infectious Diseases, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China
| | - Jianxu Chen
- Department of Infectious Diseases, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China
| | - Hong Shan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China.
| | - Fei Xiao
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China. .,Department of Infectious Diseases, the Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, 519000, People's Republic of China.
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5
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Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis. Sci Rep 2020; 10:17199. [PMID: 33057153 PMCID: PMC7566486 DOI: 10.1038/s41598-020-74276-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
AbstractAnalysis of large gene expression datasets from biopsies of cancer patients can identify co-expression signatures representing particular biomolecular events in cancer. Some of these signatures involve genomically co-localized genes resulting from the presence of copy number alterations (CNAs), for which analysis of the expression of the underlying genes provides valuable information about their combined role as oncogenes or tumor suppressor genes. Here we focus on the discovery and interpretation of such signatures that are present in multiple cancer types due to driver amplifications and deletions in particular regions of the genome after doing a comprehensive analysis combining both gene expression and CNA data from The Cancer Genome Atlas.
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6
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Marshall AD, Bailey CG, Champ K, Vellozzi M, O'Young P, Metierre C, Feng Y, Thoeng A, Richards AM, Schmitz U, Biro M, Jayasinghe R, Ding L, Anderson L, Mardis ER, Rasko JEJ. CTCF genetic alterations in endometrial carcinoma are pro-tumorigenic. Oncogene 2017; 36:4100-4110. [PMID: 28319062 PMCID: PMC5519450 DOI: 10.1038/onc.2017.25] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/21/2016] [Accepted: 01/05/2017] [Indexed: 12/14/2022]
Abstract
CTCF is a haploinsufficient tumour suppressor gene with diverse normal functions in genome structure and gene regulation. However the mechanism by which CTCF haploinsufficiency contributes to cancer development is not well understood. CTCF is frequently mutated in endometrial cancer. Here we show that most CTCF mutations effectively result in CTCF haploinsufficiency through nonsense-mediated decay of mutant transcripts, or loss-of-function missense mutation. Conversely, we identified a recurrent CTCF mutation K365T, which alters a DNA binding residue, and acts as a gain-of-function mutation enhancing cell survival. CTCF genetic deletion occurs predominantly in poor prognosis serous subtype tumours, and this genetic deletion is associated with poor overall survival. In addition, we have shown that CTCF haploinsufficiency also occurs in poor prognosis endometrial clear cell carcinomas and has some association with endometrial cancer relapse and metastasis. Using shRNA targeting CTCF to recapitulate CTCF haploinsufficiency, we have identified a novel role for CTCF in the regulation of cellular polarity of endometrial glandular epithelium. Overall, we have identified two novel pro-tumorigenic roles (promoting cell survival and altering cell polarity) for genetic alterations of CTCF in endometrial cancer.
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Affiliation(s)
- A D Marshall
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - C G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - K Champ
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - M Vellozzi
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - P O'Young
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - C Metierre
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Y Feng
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - A Thoeng
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - A M Richards
- Gynaecological Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - U Schmitz
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - M Biro
- Cell Motility and Mechanobiology, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - R Jayasinghe
- Cancer Genomics, McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.,Division of Oncology, Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - L Ding
- Cancer Genomics, McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.,Division of Oncology, Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - L Anderson
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - E R Mardis
- Cancer Genomics, McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.,Division of Oncology, Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - J E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, Camperdown, New South Wales, Australia.,Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Sydney, New South Wales, Australia
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7
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Abstract
The E2F family of transcription factors is a key determinant of cell proliferation in response to extra- and intra-cellular signals. Within this family, E2F4 is a transcriptional repressor whose activity is critical to engage and maintain cell cycle arrest in G0/G1 in conjunction with members of the retinoblastoma (RB) family. However, recent observations challenge this paradigm and indicate that E2F4 has a multitude of functions in cells besides this cell cycle regulatory role, including in embryonic and adult stem cells, during regenerative processes, and in cancer. Some of these new functions are independent of the RB family and involve direct activation of target genes. Here we review the canonical functions of E2F4 and discuss recent evidence expanding the role of this transcription factor, with a focus on cell fate decisions in tissue homeostasis and regeneration.
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Affiliation(s)
- Jenny Hsu
- a Departments of Pediatrics and Genetics , Stanford University , Stanford , CA , USA
| | - Julien Sage
- a Departments of Pediatrics and Genetics , Stanford University , Stanford , CA , USA
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8
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Abstract
Mutations of the retinoblastoma tumour suppressor gene (RB1) or components regulating the RB pathway have been identified in almost every human malignancy. The E2F transcription factors function in cell cycle control and are intimately regulated by RB. Studies of model organisms have revealed conserved functions for E2Fs during development, suggesting that the cancer-related proliferative roles of E2F family members represent a recent evolutionary adaptation. However, given that some human tumours have concurrent RB1 inactivation and E2F amplification and overexpression, we propose that there are alternative tumour-promoting activities for the E2F family, which are independent of cell cycle regulation.
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Affiliation(s)
- Hui-Zi Chen
- Human Cancer Genetics Program, Department of Molecular Virology, Immunology and Medical Genetics and Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210, USA
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9
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Riener MO, Nikolopoulos E, Herr A, Wild PJ, Hausmann M, Wiech T, Orlowska-Volk M, Lassmann S, Walch A, Werner M. Microarray comparative genomic hybridization analysis of tubular breast carcinoma shows recurrent loss of the CDH13 locus on 16q. Hum Pathol 2008; 39:1621-9. [PMID: 18656243 DOI: 10.1016/j.humpath.2008.02.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 02/15/2008] [Accepted: 02/28/2008] [Indexed: 11/18/2022]
Abstract
Tubular breast carcinoma is a highly differentiated carcinoma with an excellent prognosis. Distinct genetic alterations in tubular breast carcinoma cells have been described, especially broad genetic losses on the q-arm of chromosome 16. These are more common in lobular breast carcinoma and low-grade ductal carcinoma in situ than in ductal breast carcinoma and high-grade ductal carcinoma in situ. To further delineate the molecular changes involved in tubular breast carcinoma more precisely, we examined 23 formalin-fixed and paraffin wax-embedded tissue samples (21 of tubular breast carcinoma and 2 of nonneoplastic breast epithelium) by microarray-based comparative genomic hybridization focusing on 287 genomic target clones of oncogenes and tumor suppressor genes. The results obtained from all nonneoplastic tissue samples of breast epithelium indicate no DNA copy number changes. In the tubular breast carcinoma samples, the highest frequencies for DNA sequence copy number losses were detected for CDH13 (in 86% of the samples) and MSH2, KCNK12 (in 52% of the samples). The highest frequencies of DNA sequence copy number gains were detected for HRAS and D13S319XYZ (each in 62% of the samples). Using principal component analysis, 3 subgroups of tubular breast carcinomas showing relative genetic changes were identified. For validation, the most frequent DNA copy number loss for CDH13 (18/21) was confirmed using fluorescence in situ hybridization in 4 of 5 tubular breast carcinomas analyzed. The newly identified genes with considerable copy number changes may include so far unknown candidate genes for the development and progression of tubular breast carcinoma, such as CDH13. The study provides the starting point for further delineating their detailed influence on the pathogenesis of tubular breast carcinoma.
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Affiliation(s)
- Marc-Oliver Riener
- Institute of Pathology, University Hospital Freiburg, Freiburg i. Br., Germany
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10
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Shaposhnikov SA, Akopov SB, Chernov IP, Thomsen PD, Joergensen C, Collins AR, Frengen E, Nikolaev LG. A map of nuclear matrix attachment regions within the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1. Genomics 2007; 89:354-61. [PMID: 17188460 DOI: 10.1016/j.ygeno.2006.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 10/23/2006] [Accepted: 11/01/2006] [Indexed: 10/23/2022]
Abstract
There is abundant evidence that the DNA in eukaryotic cells is organized into loop domains that represent basic structural and functional units of chromatin packaging. To explore the DNA domain organization of the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1, we have identified a significant portion of the scaffold/matrix attachment regions (S/MARs) within this region. Forty independent putative S/MAR elements were assigned within the 16q22.1 locus. More than 90% of these S/MARs are AT rich, with GC contents as low as 27% in 2 cases. Thirty-nine (98%) of the S/MARs are located within genes and 36 (90%) in gene introns, of which 15 are in first introns of different genes. The clear tendency of S/MARs from this region to be located within the introns suggests their regulatory role. The S/MAR resource constructed may contribute to an understanding of how the genes in the region are regulated and of how the structural architecture and functional organization of the DNA are related.
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Affiliation(s)
- Sergey A Shaposhnikov
- Department of Nutrition, Faculty of Medicine, University of Oslo, PB 1046 Blindern, 0316 Oslo, Norway
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11
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Abstract
Recent advances in studying long-range chromatin interactions have shifted focus from the transcriptional regulation by nearby regulatory elements to recognition of the role of higher-order chromatin organization within the nucleus. These advances have also suggested that CCCTC-binding factor (CTCF), a known chromatin insulator protein, may play a central role in mediating long-range chromatin interactions, directing DNA segments into transcription factories and/or facilitating interactions with other DNA regions. Several models that describe possible mechanisms for multiple functions of CTCF in establishment and maintenance of epigenetic programs are now emerging. Epigenetics plays an important role in normal development and disease including cancer. CTCF involvement in multiple aspects of epigenetic regulation, including regulation of genomic imprinting and X-chromosome inactivation, has been well established. More recently, CTCF was found to play a role in regulation of noncoding transcription and establishing local chromatin structure at the repetitive elements in mammalian genomes, suggesting a new epigenetic basis for several repeat-associated genetic disorders. Emerging evidence also points to the role of CTCF deregulation in the epigenetic imbalance in cancer. These studies provide some of the important missing links in our understanding of epigenetic control of both development and cancer.
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Affiliation(s)
- Galina N Filippova
- Human Biology Division, Fred Hutchinson Cancer Research Center Seattle, Washington 98109, USA
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12
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Sun X, Zhou Y, Otto KB, Wang M, Chen C, Zhou W, Subramanian K, Vertino PM, Dong JT. Infrequent mutation of ATBF1 in human breast cancer. J Cancer Res Clin Oncol 2006; 133:103-5. [PMID: 16932943 DOI: 10.1007/s00432-006-0148-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2006] [Revised: 07/20/2006] [Accepted: 07/28/2006] [Indexed: 10/24/2022]
Abstract
Deletion at chromosome 16q is frequent in prostate and breast cancers, suggesting the existence of one or more tumor suppressor genes in 16q. Recently, the transcription factor ATBF1 at 16q22 was identified as a strong candidate tumor suppressor gene in prostate cancer, and loss of ATBF1 expression was associated with poorer prognosis in breast cancer. In the present study, we examined mutation, expression, and promoter methylation of ATBF1 in 32 breast cancer cell lines. Only 2 of the 32 cancer cell lines had mutations, although 18 nucleotide polymorphisms were detected. In addition, 24 of 32 (75%) cancer cell lines had reduced ATBF1 mRNA levels, yet promoter methylation was not involved in gene silencing. These findings suggest that ATBF1 plays a role in breast cancer through transcriptional downregulation rather than mutations.
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Affiliation(s)
- Xiaodong Sun
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, USA
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13
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Rakha EA, Green AR, Powe DG, Roylance R, Ellis IO. Chromosome 16 tumor-suppressor genes in breast cancer. Genes Chromosomes Cancer 2006; 45:527-35. [PMID: 16518845 DOI: 10.1002/gcc.20318] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Loss of heterozygosity on the long arm of chromosome 16 is one of the most frequent genetic events in breast cancer, suggesting the presence of one or more classic tumor-suppressor genes (TSGs). It has been shown that E-cadherin is the TSG on 16q in lobular tumors. In a search for the target genes in more frequently occurring low-grade nonlobular tumors, the smallest region of overlap (SRO) in this area of the genome has been exhaustively searched for. However, the results have demonstrated remarkable complexity, and so a clear consensus on identification of the SRO boundaries has not been reached. Several genes in the vicinity of these SROs have been scrutinized as putative TSGs in breast cancer, but so far, none has fulfilled the criteria for target genes. This review discusses the complexity of the 16q region and the different approaches that have been, are being, and will be used to detect the target genes in this area.
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Affiliation(s)
- Emad A Rakha
- Department of Histopathology, the Breast Unit, Nottingham City Hospital NHS Trust and University of Nottingham, Nottingham, United Kingdom
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Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006; 6:96. [PMID: 16620391 PMCID: PMC1459181 DOI: 10.1186/1471-2407-6-96] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 04/18/2006] [Indexed: 01/24/2023] Open
Abstract
Background Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes. Methods We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability. Results We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability. Conclusion Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.
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Affiliation(s)
- Jane Fridlyand
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, San Francisco, CA 94143, USA
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
| | - Antoine M Snijders
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Bauke Ylstra
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Micro Array Core Facility, VUMC University Medical Center, 1081BT Amsterdam, The Netherlands
| | - Hua Li
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Adam Olshen
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York 20021, USA
| | - Richard Segraves
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Shanaz Dairkee
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Geraldine Brush Cancer Research Institute, California Pacific Medical Center, San Francisco, California 94115, USA
| | - Taku Tokuyasu
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Britt Marie Ljung
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Ajay N Jain
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Jane McLennan
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
| | - John Ziegler
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
| | - Koei Chin
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Sandy Devries
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Heidi Feiler
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Division of Life Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joe W Gray
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Division of Life Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederic Waldman
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Daniel Pinkel
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
| | - Donna G Albertson
- University of California San Francisco Comprehensive Cancer Center, San Francisco, CA 94143, USA
- Cancer Research Institute, University of California San Francisco, San Francisco, CA 94143-0808, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94143-0808, USA
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Hata N, Yoshimoto K, Yokoyama N, Mizoguchi M, Shono T, Guan Y, Tahira T, Kukita Y, Higasa K, Nagata S, Iwaki T, Sasaki T, Hayashi K. Allelic Losses of Chromosome 10 in Glioma Tissues Detected by Quantitative Single-Strand Conformation Polymorphism Analysis. Clin Chem 2006; 52:370-8. [PMID: 16397012 DOI: 10.1373/clinchem.2005.060954] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Abstract
Background: Detection of loss of heterozygosity (LOH) in clinical tissue samples is frequently difficult because samples are usually contaminated with noncancerous cells or because tumor cells in single tissues have genetic heterogeneity, and the precision of available techniques is insufficient for reliable analysis in such materials. We hypothesized that single-strand conformation polymorphism (SSCP) analysis can precisely quantify the gene dosage in mixed samples and is suitable for detection of LOH in clinical tissue samples.
Methods: We assessed the accuracy of a fluorescent SSCP method for the quantification of single-nucleotide polymorphism (SNP) alleles, using DNAs that were composed of cancerous DNA mixed with noncancerous DNA at various ratios. We applied this method to precisely characterize LOH in glioma tissue samples, using 96 SNPs that were evenly distributed throughout chromosome 10.
Results: LOH could be detected even in the cancerous DNA heavily contaminated (up to 80%) with noncancerous DNA. Using this method, we obtained LOH profiles of 56 gliomas with resolution at the SNP level (i.e., 1.5-Mbp interval). Anaplastic astrocytomas exhibited both 10p and 10q LOH, whereas diffuse astrocytomas frequently (63% of the cases) exhibited loss of 10p alone. We also found a possible new LOH region (around 10p13) in gliomas.
Conclusions: The present method is effective for precise mapping of LOH region in surgically obtained tumor tissues and could be applicable to the genetic diagnosis of cancers other than gliomas.
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Affiliation(s)
- Nobuhiro Hata
- Department of Neurosurgery, Graduate School of Medical Sciences, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Vanden Bempt I, Vanhentenrijk V, Drijkoningen M, De Wolf-Peeters C. Comparative expressed sequence hybridization reveals differential gene expression in morphological breast cancer subtypes. J Pathol 2006; 208:486-94. [PMID: 16402338 DOI: 10.1002/path.1911] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this study, comparative expressed sequence hybridization (CESH) has been used to compare gene expression patterns in three morphologically different breast cancer subtypes: classic-type invasive lobular carcinoma (ILC), poorly differentiated ERBB2-negative invasive ductal carcinoma-not otherwise specified (IDC-NOS), and poorly differentiated ERBB2-positive IDC-NOS. CESH allows global detection of chromosomal regions with differential gene expression in a way similar to that of comparative genomic hybridization (CGH). Eight cases of each breast cancer subtype were included in the study. For each subtype, two pools of four cases each were constructed. CESH was used to compare both pools within the same morphological subtype, followed by a comparison of pools belonging to different subtypes. This revealed three chromosomal regions that were differentially expressed in ductal and lobular carcinomas, including relative overexpression at 8q13-q23 and 16q22, and relative underexpression at 8p21-p22. In addition, an expression signature characterized by relative overexpression at 3q24-q26.3, 14q23-31, 17q12, and 20q12-13 was identified for ERBB2-positive IDC-NOS. In summary, CESH analysis highlights chromosomal regions of differential gene expression that are associated with morphologically defined breast cancer subtypes and suggests that regions on chromosome 8 are of interest in the discrimination between ductal and lobular carcinomas. In addition, using CESH, it was possible to identify an ERBB2 expression signature, comprising four chromosomal regions with potential significance in the aggressive behaviour of ERBB2-positive IDC-NOS.
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MESH Headings
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/pathology
- Chromosomes, Human, Pair 8
- Diagnosis, Differential
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genes, erbB-2
- Humans
- In Situ Hybridization/methods
- Oligonucleotide Array Sequence Analysis
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Affiliation(s)
- Isabelle Vanden Bempt
- Department of Pathology, University Hospital of KU Leuven, Minderbroedersstraat 12, 3000 Leuven, Belgium.
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Patsalis PC, Kousoulidou L, Sismani C, Männik K, Kurg A. MAPH: from gels to microarrays. Eur J Med Genet 2005; 48:241-9. [PMID: 16179220 DOI: 10.1016/j.ejmg.2005.04.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Revised: 03/18/2005] [Accepted: 04/07/2005] [Indexed: 12/15/2022]
Abstract
The development of accurate and sensitive methodologies to detect small chromosomal imbalances (<3 Mb) is extremely important in clinical diagnostics and research in human genetics. The technique of array-comparative genomic hybridization (CGH) using BAC and PAC clones is very sensitive methodology and is rapidly becoming the method of choice for high-resolution screening of genomic copy-number changes. An alternative methodology to CGH is the multiplex amplifiable probe hybridization (MAPH) methodology, a DNA based method that allows the accurate and reliable determination of changes in copy number in "known" or "unknown locations" in the human genome. MAPH uses probes of 100-500 bp in size, that can be specifically designed for any gene or locus in the genome and cover any gene exons, the subtelomeric or subcentromeric regions, any chromosomal segment, a whole chromosome or the total human genome. MAPH can provide extremely high resolution and enable the sensitive detection of loss or gain of genomic DNA sequences as small as 150 bp. Very recently we succeeded in the advancement of MAPH from gel and capillary analyses to microarrays. The array-MAPH methodology offers an alternative methodology to array-CGH and provides a new sensitive microarray-based method including several advantages for the detection of copy number changes in the human genome.
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Affiliation(s)
- Philippos C Patsalis
- Department of Cytogenetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
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