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Zu G, Liu Y, Cao J, Zhao B, Zhang H, You L. BRPF1-KAT6A/KAT6B Complex: Molecular Structure, Biological Function and Human Disease. Cancers (Basel) 2022; 14:cancers14174068. [PMID: 36077605 PMCID: PMC9454415 DOI: 10.3390/cancers14174068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The bromodomain and PHD finger–containing protein1 (BRPF1) is a member of family IV of the bromodomain-containing proteins that participate in the post-translational modification of histones. It functions in the form of a tetrameric complex with a monocytic leukemia zinc finger protein (MOZ or KAT6A), MOZ-related factor (MORF or KAT6B) or HAT bound to ORC1 (HBO1 or KAT7) and two small non-catalytic proteins, the inhibitor of growth 5 (ING5) or the paralog ING4 and MYST/Esa1-associated factor 6 (MEAF6). Mounting studies have demonstrated that all the four core subunits play crucial roles in different biological processes across diverse species, such as embryonic development, forebrain development, skeletal patterning and hematopoiesis. BRPF1, KAT6A and KAT6B mutations were identified as the cause of neurodevelopmental disorders, leukemia, medulloblastoma and other types of cancer, with germline mutations associated with neurodevelopmental disorders displaying intellectual disability, and somatic variants associated with leukemia, medulloblastoma and other cancers. In this paper, we depict the molecular structures and biological functions of the BRPF1-KAT6A/KAT6B complex, summarize the variants of the complex related to neurodevelopmental disorders and cancers and discuss future research directions and therapeutic potentials.
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Affiliation(s)
- Gaoyu Zu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ying Liu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jingli Cao
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Baicheng Zhao
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Hang Zhang
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai 200040, China
- Correspondence:
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Quintela M, Sieglaff DH, Gazze AS, Zhang A, Gonzalez D, Francis L, Webb P, Conlan RS. HBO1 directs histone H4 specific acetylation, potentiating mechano-transduction pathways and membrane elasticity in ovarian cancer cells. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2019; 17:254-265. [DOI: 10.1016/j.nano.2019.01.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 12/15/2022]
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Hlupić L, Jakić-Razumović J, Bozikov J, Corić M, Belev B, Vrbanec D. Prognostic Value of Different Factors in Breast Carcinoma. TUMORI JOURNAL 2018; 90:112-9. [PMID: 15143983 DOI: 10.1177/030089160409000123] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Introduction The aggressive biological behavior of invasive and metastatic cancer is considered to be the most insidious and life-threatening aspect for breast cancer patients. It is mostly the result of changes in many molecular characteristics of tumor cells, including alterations in the mechanisms controlling cell growth and proliferation. Aim The aim of this retrospective study was to identify predictors of aggressive biological behavior and metastatic potential in breast carcinoma among a number of intrinsic bio-markers of tumor cells such as steroid receptors and oncogene and tumor suppressor gene products. Methods Routine formalin-fixed, paraffin-embedded tumor samples were used and sections were stained immunohistochemically with the DAKO Strept ABC method to determine the expression of estrogen receptors (ER), progesterone receptors (PgR), HER-2/neu, bcl-2, Ki-67, p53 and nm23 in 192 consecutive breast carcinoma patients. The results of the quantitative immunohistochemical assays were correlated with clinical and histological data such as patient age, overall survival, tumor size, axillary lymph node status, hystological type, tumor grade, Nottingham prognostic index (NPI) and therapeutic regimens. Results Univariate analysis revealed that survival was significantly longer for patients with small tumors (P = 0.007), lower tumor grade (P = 0.021), negative axillary lymph nodes (P = 0.002), presence of nm23 protein (P = 0.002), and for patients treated with adjuvant hormonal therapy (P = 0.010). In multivariate analysis the independent factors positively affecting survival were absence of axillary lymph node metastases (P = 0.002), nm23 expression (P = 0.009) and hormonal therapy (P = 0.050). Among patients with positive axillary nodes there was a significantly higher survival rate in patients with nm23 expression compared with nm23-negative patients (P <0.001). Conclusion Identification of a subset of node-positive breast cancer patients with a more favorable prognosis according to nm23 expression might be clinically useful.
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Affiliation(s)
- Ljiljana Hlupić
- Department of Pathology, Clinical Hospital Center Zagreb, Croatia.
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Lee YF, Roe T, Mangham DC, Fisher C, Grimer RJ, Judson I. Gene expression profiling identifies distinct molecular subgroups of leiomyosarcoma with clinical relevance. Br J Cancer 2016; 115:1000-1007. [PMID: 27607470 PMCID: PMC5061910 DOI: 10.1038/bjc.2016.280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/12/2016] [Accepted: 08/09/2016] [Indexed: 12/26/2022] Open
Abstract
Background: Soft tissue sarcomas are heterogeneous and a major complication in their management is that the existing classification scheme is not definitive and is still evolving. Leiomyosarcomas, a major histologic category of soft tissue sarcomas, are malignant tumours displaying smooth muscle differentiation. Although defined as a single group, they exhibit a wide range of clinical behaviour. We aimed to carry out molecular classification to identify new molecular subgroups with clinical relevance. Methods: We used gene expression profiling on 20 extra-uterine leiomyosarcomas and cross-study analyses for molecular classification of leiomyosarcomas. Clinical significance of the subgroupings was investigated. Results: We have identified two distinct molecular subgroups of leiomyosarcomas. One group was characterised by high expression of 26 genes that included many genes from the sub-classification gene cluster proposed by Nielsen et al. These sub-classification genes include genes that have importance structurally, as well as in cell signalling. Notably, we found a statistically significant association of the subgroupings with tumour grade. Further refinement led to a group of 15 genes that could recapitulate the tumour subgroupings in our data set and in a second independent sarcoma set. Remarkably, cross-study analyses suggested that these molecular subgroups could be found in four independent data sets, providing strong support for their existence. Conclusions: Our study strongly supported the existence of distinct leiomyosarcoma molecular subgroups, which have clinical association with tumour grade. Our findings will aid in advancing the classification of leiomyosarcomas and lead to more individualised and better management of the disease.
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Affiliation(s)
- Yin-Fai Lee
- Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, London SM2 5NG, UK.,Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Toby Roe
- Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, London SM2 5NG, UK
| | - D Chas Mangham
- Department of Pathology, The Royal Orthopaedic Hospital NHS Trust, Birmingham B31 2AP, UK
| | - Cyril Fisher
- Sarcoma Unit, The Royal Marsden Hospital NHS Trust, Fulham Road, London SW3 6JJ, UK
| | - Robert J Grimer
- Department of Pathology, The Royal Orthopaedic Hospital NHS Trust, Birmingham B31 2AP, UK
| | - Ian Judson
- Institute of Cancer Research, 15 Cotswold Road, Belmont, Sutton, London SM2 5NG, UK.,Sarcoma Unit, The Royal Marsden Hospital NHS Trust, Fulham Road, London SW3 6JJ, UK
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Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, French CA. The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes Dev 2015. [PMID: 26220994 PMCID: PMC4526735 DOI: 10.1101/gad.267583.115] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
NUT midline carcinoma (NMC), a subtype of squamous cell cancer, is one of the most aggressive human solid malignancies known. NMC is driven by the creation of a translocation oncoprotein, BRD4-NUT, which blocks differentiation and drives growth of NMC cells. BRD4-NUT forms distinctive nuclear foci in patient tumors, which we found correlate with ∼100 unprecedented, hyperacetylated expanses of chromatin that reach up to 2 Mb in size. These "megadomains" appear to be the result of aberrant, feed-forward loops of acetylation and binding of acetylated histones that drive transcription of underlying DNA in NMC patient cells and naïve cells induced to express BRD4-NUT. Megadomain locations are typically cell lineage-specific; however, the cMYC and TP63 regions are targeted in all NMCs tested and play functional roles in tumor growth. Megadomains appear to originate from select pre-existing enhancers that progressively broaden but are ultimately delimited by topologically associating domain (TAD) boundaries. Therefore, our findings establish a basis for understanding the powerful role played by large-scale chromatin organization in normal and aberrant lineage-specific gene transcription.
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Affiliation(s)
- Artyom A Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Erica M Walsh
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xin Wang
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Adlai R Grayson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter T Hsi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter V Kharchenko
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA; Hematology/Oncology Program, Children's Hospital, Boston, Massachusetts 02115, USA; Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
| | - Mitzi I Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Christopher A French
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Azevedo Costa M, de Souza Rodrigues T, da Costa AGF, Natowicz R, Pádua Braga A. Sequential selection of variables using short permutation procedures and multiple adjustments: An application to genomic data. Stat Methods Med Res 2015; 26:997-1020. [PMID: 25575544 DOI: 10.1177/0962280214566262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This work proposes a sequential methodology for selecting variables in classification problems in which the number of predictors is much larger than the sample size. The methodology includes a Monte Carlo permutation procedure that conditionally tests the null hypothesis of no association among the outcomes and the available predictors. In order to improve computing aspects, we propose a new parametric distribution, the Truncated and Zero Inflated Gumbel Distribution. The final application is to find compact classification models with improved performance for genomic data. Results using real data sets show that the proposed methodology selects compact models with optimized classification performances.
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Affiliation(s)
- Marcelo Azevedo Costa
- 1 Department of Industrial Engineering, Universidade Federal de Minas Gerais, Belo Horizonte,Brazil
| | | | | | - René Natowicz
- 4 Computer Sciences Department, University of Paris-ESIEE/Paris, Paris, France
| | - Antônio Pádua Braga
- 5 Graduate Program in Electrical Engineering, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Spivey TL, De Giorgi V, Zhao Y, Bedognetti D, Pos Z, Liu Q, Tomei S, Ascierto ML, Uccellini L, Reinboth J, Chouchane L, Stroncek DF, Wang E, Marincola FM. The stable traits of melanoma genetics: an alternate approach to target discovery. BMC Genomics 2012; 13:156. [PMID: 22537248 PMCID: PMC3362771 DOI: 10.1186/1471-2164-13-156] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 04/26/2012] [Indexed: 12/18/2022] Open
Abstract
Background The weight that gene copy number plays in transcription remains controversial; although in specific cases gene expression correlates with copy number, the relationship cannot be inferred at the global level. We hypothesized that genes steadily expressed by 15 melanoma cell lines (CMs) and their parental tissues (TMs) should be critical for oncogenesis and their expression most frequently influenced by their respective copy number. Results Functional interpretation of 3,030 transcripts concordantly expressed (Pearson's correlation coefficient p-value < 0.05) by CMs and TMs confirmed an enrichment of functions crucial to oncogenesis. Among them, 968 were expressed according to the transcriptional efficiency predicted by copy number analysis (Pearson's correlation coefficient p-value < 0.05). We named these genes, "genomic delegates" as they represent at the transcriptional level the genetic footprint of individual cancers. We then tested whether the genes could categorize 112 melanoma metastases. Two divergent phenotypes were observed: one with prevalent expression of cancer testis antigens, enhanced cyclin activity, WNT signaling, and a Th17 immune phenotype (Class A). This phenotype expressed, therefore, transcripts previously associated to more aggressive cancer. The second class (B) prevalently expressed genes associated with melanoma signaling including MITF, melanoma differentiation antigens, and displayed a Th1 immune phenotype associated with better prognosis and likelihood to respond to immunotherapy. An intermediate third class (C) was further identified. The three phenotypes were confirmed by unsupervised principal component analysis. Conclusions This study suggests that clinically relevant phenotypes of melanoma can be retraced to stable oncogenic properties of cancer cells linked to their genetic back bone, and offers a roadmap for uncovering novel targets for tailored anti-cancer therapy.
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Affiliation(s)
- Tara L Spivey
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD 20892, USA
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Mediator subunits MED1 and MED24 cooperatively contribute to pubertal mammary gland development and growth of breast carcinoma cells. Mol Cell Biol 2012; 32:1483-95. [PMID: 22331469 DOI: 10.1128/mcb.05245-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Mediator subunit MED1 is essential for mammary gland development and lactation, whose contribution through direct interaction with estrogen receptors (ERs) is restricted to involvement in pubertal mammary gland development and luminal cell differentiation. Here, we provide evidence that the MED24-containing submodule of Mediator functionally communicates specifically with MED1 in pubertal mammary gland development. Mammary glands from MED1/MED24 double heterozygous knockout mice showed profound retardation in ductal branching during puberty, while single haploinsufficient glands developed normally. DNA synthesis of both luminal and basal cells were impaired in double mutant mice, and the expression of ER-targeted genes encoding E2F1 and cyclin D1, which promote progression through the G(1)/S phase of the cell cycle, was attenuated. Luciferase reporter assays employing double mutant mouse embryonic fibroblasts showed selective impairment in ER functions. Various breast carcinoma cell lines expressed abundant amounts of MED1, MED24, and MED30, and attenuated expression of MED1 and MED24 in breast carcinoma cells led to attenuated DNA synthesis and growth. These results indicate functional communications between the MED1 subunit and the MED24-containing submodule that mediate estrogen receptor functions and growth of both normal mammary epithelial cells and breast carcinoma cells.
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Geng H, Iqbal J, Chan WC, Ali HH. Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma. BMC Med Genomics 2011; 4:32. [PMID: 21486456 PMCID: PMC3086850 DOI: 10.1186/1755-8794-4-32] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 04/12/2011] [Indexed: 01/27/2023] Open
Abstract
Background Comparative Genomic Hybridization (CGH) is a molecular approach for detecting DNA Copy Number Alterations (CNAs) in tumor, which are among the key causes of tumorigenesis. However in the post-genomic era, most studies in cancer biology have been focusing on Gene Expression Profiling (GEP) but not CGH, and as a result, an enormous amount of GEP data had been accumulated in public databases for a wide variety of tumor types. We exploited this resource of GEP data to define possible recurrent CNAs in tumor. In addition, the CNAs identified by GEP would be more functionally relevant CNAs in the disease pathogenesis since the functional effects of CNAs can be reflected by altered gene expression. Methods We proposed a novel computational approach, coined virtual CGH (vCGH), which employs hidden Markov models (HMMs) to predict DNA CNAs from their corresponding GEP data. vCGH was first trained on the paired GEP and CGH data generated from a sufficient number of tumor samples, and then applied to the GEP data of a new tumor sample to predict its CNAs. Results Using cross-validation on 190 Diffuse Large B-Cell Lymphomas (DLBCL), vCGH achieved 80% sensitivity, 90% specificity and 90% accuracy for CNA prediction. The majority of the recurrent regions defined by vCGH are concordant with the experimental CGH, including gains of 1q, 2p16-p14, 3q27-q29, 6p25-p21, 7, 11q, 12 and 18q21, and losses of 6q, 8p23-p21, 9p24-p21 and 17p13 in DLBCL. In addition, vCGH predicted some recurrent functional abnormalities which were not observed in CGH, including gains of 1p, 2q and 6q and losses of 1q, 6p and 8q. Among those novel loci, 1q, 6q and 8q were significantly associated with the clinical outcomes in the DLBCL patients (p < 0.05). Conclusions We developed a novel computational approach, vCGH, to predict genome-wide genetic abnormalities from GEP data in lymphomas. vCGH can be generally applied to other types of tumors and may significantly enhance the detection of functionally important genetic abnormalities in cancer research.
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Affiliation(s)
- Huimin Geng
- Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182, USA
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Wang WZ, Liu HO, Wu YH, Hong Y, Yang JW, Liu YH, Wu WB, Zhou L, Sun LL, Xu JJ, Yun XJ, Gu JX. Estrogen receptor α (ERα) mediates 17β-estradiol (E2)-activated expression of HBO1. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2010; 29:140. [PMID: 21040551 PMCID: PMC2989947 DOI: 10.1186/1756-9966-29-140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 11/01/2010] [Indexed: 12/21/2022]
Abstract
BACKGROUND HBO1 (histone acetyltransferase binding to ORC1) is a histone acetyltransferase (HAT) which could exert oncogenic function in breast cancer. However, the biological role and underlying mechanism of HBO1 in breast cancer remains largely unknown. In the current study, we aimed to investigate the role of HBO1 in breast cancer and uncover the underlying molecular mechanism. METHODS Immunohistochemistry was applied to detect HBO1 protein expression in breast cancer specimens (n=112). The expression of protein level was scored by integral optical density (IOD) for further statistical analyses using SPSS. Real-time PCR was used to simultaneously measure mRNA levels of HBO1. The HBO1 protein expression in breast cancer cells was confirmed by western blot. RESULTS HBO1 was highly expressed in breast cancer tissues and significantly correlated with estrogen receptor α (ERα) (p<0.001) and progestational hormone (PR) (p=0.002). HBO1 protein level also correlated positively with histology grade in ERα positive tumors (p=0.016) rather than ERα negative tumors. 17β-estradiol (E2) could upregulate HBO1 gene expression which was significantly inhibited by ICI 182,780 or ERα RNAi. E2-increased HBO1 protein expression was significantly suppressed by treatment with inhibitor of MEK1/2 (U0126) in T47 D and MCF-7 cells. CONCLUSIONS HBO1 was an important downstream molecule of ERα, and ERK1/2 signaling pathway may involved in the expression of HBO1 increased by E2.
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Affiliation(s)
- Wen-zhong Wang
- Department of Biochemistry and Molecular Biology, Shanghai Medical College of Fudan University, Shanghai, 200032, China
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Kim YR, Oh KJ, Park RY, Xuan NT, Kang TW, Kwon DD, Choi C, Kim MS, Nam KI, Ahn KY, Jung C. HOXB13 promotes androgen independent growth of LNCaP prostate cancer cells by the activation of E2F signaling. Mol Cancer 2010; 9:124. [PMID: 20504375 PMCID: PMC2890607 DOI: 10.1186/1476-4598-9-124] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 05/27/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Androgen signaling plays a critical role in the development of prostate cancer and its progression. However, androgen-independent prostate cancer cells emerge after hormone ablation therapy, resulting in significant clinical problems. We have previously demonstrated that the HOXB13 homeodomain protein functions as a prostate cancer cell growth suppressor by inhibiting androgen-mediated signals. However, the role of the HOXB13 in androgen-independent growth of prostate cancer cells remains unexplained. RESULTS In this report, we first demonstrated that HOXB13 was highly overexpressed in hormone-refractory tumors compared to tumors without prostate-specific antigen after initial treatment. Functionally, in an androgen-free environment minimal induction of HOXB13 in LNCaP prostate cancer cells, to the level of the normal prostate, markedly promoted cell proliferation while suppression inhibited cell proliferation. The HOXB13-mediated cell growth promotion in the absence of androgen, appears to be mainly accomplished through the activation of RB-E2F signaling by inhibiting the expression of the p21waf tumor suppressor. Indeed, forced expression of HOXB13 dramatically decreased expression of p21waf; this inhibition largely affected HOXB13-mediated promotion of E2F signaling. CONCLUSIONS Taken together, the results of this study demonstrated the presence of a novel pathway that helps understand androgen-independent survival of prostate cancer cells. These findings suggest that upregulation of HOXB13 is associated with an additive growth advantage of prostate cancer cells in the absence of or low androgen concentrations, by the regulation of p21-mediated E2F signaling.
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Affiliation(s)
- Young-Rang Kim
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea
| | - Kyung-Jin Oh
- Department of Urology, Chonnam National University Medical School, Gwangju, Korea
| | - Ra-Young Park
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea
| | - Nguyen Thi Xuan
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea
| | - Taek-Won Kang
- Department of Urology, Chonnam National University Medical School, Gwangju, Korea
- Research Institute of Medical Sciences, Chonnam National University, Gwangju, Korea
| | - Dong-Deuk Kwon
- Department of Urology, Chonnam National University Medical School, Gwangju, Korea
- Research Institute of Medical Sciences, Chonnam National University, Gwangju, Korea
| | - Chan Choi
- Department of Pathology, Chonnam National University Medical School, Gwangju, Korea
- Research Institute of Medical Sciences, Chonnam National University, Gwangju, Korea
| | - Min Soo Kim
- Department of Statistics, Chonnam National University, Gwangju, Korea
| | - Kwang Il Nam
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea
- Research Institute of Medical Sciences, Chonnam National University, Gwangju, Korea
| | - Kyu Youn Ahn
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea
- Research Institute of Medical Sciences, Chonnam National University, Gwangju, Korea
| | - Chaeyong Jung
- Department of Anatomy, Chonnam National University Medical School, Gwangju, Korea
- Research Institute of Medical Sciences, Chonnam National University, Gwangju, Korea
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Missiaglia E, Selfe J, Hamdi M, Williamson D, Schaaf G, Fang C, Koster J, Summersgill B, Messahel B, Versteeg R, Pritchard-Jones K, Kool M, Shipley J. Genomic imbalances in rhabdomyosarcoma cell lines affect expression of genes frequently altered in primary tumors: an approach to identify candidate genes involved in tumor development. Genes Chromosomes Cancer 2009; 48:455-67. [PMID: 19235922 DOI: 10.1002/gcc.20655] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Rhabdomyosarcomas (RMS) are the most common pediatric soft tissue sarcomas. They resemble developing skeletal muscle and are histologically divided into two main subtypes; alveolar and embryonal RMS. Characteristic genomic aberrations, including the PAX3- and PAX7-FOXO1 fusion genes in alveolar cases, have led to increased understanding of their molecular biology. Here, we determined the effect of genomic copy number on gene expression levels through array comparative genomic hybridization (CGH) analysis of 13 RMS cell lines, confirmed by multiplex ligation-dependent probe amplification copy number analyses, combined with their corresponding expression profiles. Genes altered at the transcriptional level by genomic imbalances were identified and the effect on expression was proportional to the level of genomic imbalance. Extrapolating to a public expression profiling dataset for 132 primary RMS identified features common to the cell lines and primary samples and associations with subtypes and fusion gene status. Genes identified such as CDK4 and MYCN are known to be amplified, overexpressed, and involved in RMS tumorigenesis. Of the many genes identified, those with likely functional relevance included CENPF, DTL, MYC, EYA2, and FGFR1. Copy number and expression of FGFR1 was validated in additional primary material and found amplified in 6 out of 196 cases and overexpressed relative to skeletal muscle and myoblasts, with significantly higher expression levels in the embryonal compared with alveolar subtypes. This illustrates the ability to identify genes of potential significance in tumor development through combining genomic and transcriptomic profiles from representative cell lines with publicly available expression profiling data from primary tumors.
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Affiliation(s)
- Edoardo Missiaglia
- Molecular Cytogenetics Team, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
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Iizuka M, Takahashi Y, Mizzen CA, Cook RG, Fujita M, Allis CD, Frierson HF, Fukusato T, Smith MM. Histone acetyltransferase Hbo1: catalytic activity, cellular abundance, and links to primary cancers. Gene 2009; 436:108-14. [PMID: 19393168 DOI: 10.1016/j.gene.2009.01.020] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Revised: 01/09/2009] [Accepted: 01/24/2009] [Indexed: 12/27/2022]
Abstract
In addition to the well-characterized proteins that comprise the pre-replicative complex, recent studies suggest that chromatin structure plays an important role in DNA replication initiation. One of these chromatin factors is the histone acetyltransferase (HAT) Hbo1 which is unique among HAT enzymes in that it serves as a positive regulator of DNA replication. However, several of the basic properties of Hbo1 have not been previously examined, including its intrinsic catalytic activity, its molecular abundance in cells, and its pattern of expression in primary cancer cells. Here we show that recombinant Hbo1 can acetylate nucleosomal histone H4 in vitro, with a preference for lysines 5 and 12. Using semi-quantitative western blot analysis, we find that Hbo1 is approximately equimolar with the number of active replication origins in normal human fibroblasts but is an order of magnitude more abundant in both MCF7 and Saos-2 established cancer cell lines. Immunohistochemistry for Hbo1 in 11 primary human tumor types revealed strong Hbo1 protein expression in carcinomas of the testis, ovary, breast, stomach/esophagus, and bladder.
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Affiliation(s)
- Masayoshi Iizuka
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908-0734, USA
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Cavalli LR, Man YG, Schwartz AM, Rone JD, Zhang Y, Urban CA, Lima RS, Haddad BR, Berg PE. Amplification of the BP1 homeobox gene in breast cancer. ACTA ACUST UNITED AC 2008; 187:19-24. [PMID: 18992636 DOI: 10.1016/j.cancergencyto.2008.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 07/18/2008] [Accepted: 07/23/2008] [Indexed: 10/21/2022]
Abstract
The homeobox gene BP1 is expressed in over 80% of breast cancers and is associated with tumor progression and invasion. However, the mechanism of BP1 activation in these tumors remains unknown. Therefore our aim in this study is to assess the amplification status of the BP1 gene in breast cancer and to determine whether BP1 protein expression is caused by gene amplification in these tumors. BP1 amplification and expression were assessed in 36 samples. Twenty primary breast tumors (PBT) and 14 sentinel lymph node (SLN) metastases were analyzed using fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), respectively. Because of the close proximity of BP1 and HER2/NEU genes on 17q, correlation between their amplification/expression was also investigated. Increased BP1 copy number was observed in 33% of the cases, with a frequency of 36% and 29% in the PBT and SLN metastasis, respectively. BP1 protein was expressed in 91% of the samples: in all of the PBT with increased BP1 copy number and 65% of PBT with normal copy number. HER2/NEU amplification was detected in 22% of the cases. Concordance between BP1 and HER2/NEU copy numbers was found in 68% of the PBT and 90% of the SLN metastasis. In conclusion, we demonstrated that the BP1 homeobox gene is amplified in breast cancer, both in PBT and SLN metastasis, with a significant correlation with HER2/NEU amplification. Considering that BP1 expression was observed in cases with both increased and normal BP1 copy number, we conclude that other mechanisms in addition to gene amplification play a role in BP1 protein expression.
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Affiliation(s)
- Luciane R Cavalli
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3800 Reservoir Rd, Room S165A - LL Lombardi Building, Washington, DC 20007, USA.
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15
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Nikolsky Y, Sviridov E, Yao J, Dosymbekov D, Ustyansky V, Kaznacheev V, Dezso Z, Mulvey L, Macconaill LE, Winckler W, Serebryiskaya T, Nikolskaya T, Polyak K. Genome-Wide Functional Synergy between Amplified and Mutated Genes in Human Breast Cancer. Cancer Res 2008; 68:9532-40. [DOI: 10.1158/0008-5472.can-08-3082] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Hurtado A, Holmes KA, Geistlinger TR, Hutcheson IR, Nicholson RI, Brown M, Jiang J, Howat WJ, Ali S, Carroll JS. Regulation of ERBB2 by oestrogen receptor-PAX2 determines response to tamoxifen. Nature 2008; 456:663-6. [PMID: 19005469 DOI: 10.1038/nature07483] [Citation(s) in RCA: 225] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 10/02/2008] [Indexed: 02/08/2023]
Abstract
Crosstalk between the oestrogen receptor (ER) and ERBB2/HER-2 pathways has long been implicated in breast cancer aetiology and drug response, yet no direct connection at a transcriptional level has been shown. Here we show that oestrogen-ER and tamoxifen-ER complexes directly repress ERBB2 transcription by means of a cis-regulatory element within the ERBB2 gene in human cell lines. We implicate the paired box 2 gene product (PAX2), in a previously unrecognized role, as a crucial mediator of ER repression of ERBB2 by the anti-cancer drug tamoxifen. We show that PAX2 and the ER co-activator AIB-1/SRC-3 compete for binding and regulation of ERBB2 transcription, the outcome of which determines tamoxifen response in breast cancer cells. The repression of ERBB2 by ER-PAX2 links these two breast cancer subtypes and suggests that aggressive ERBB2-positive tumours can originate from ER-positive luminal tumours by circumventing this repressive mechanism. These data provide mechanistic insight into the molecular basis of endocrine resistance in breast cancer.
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Affiliation(s)
- Antoni Hurtado
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
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17
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Shepherd CJ, Rizzo S, Ledaki I, Davies M, Brewer D, Attard G, de Bono J, Hudson DL. Expression profiling of CD133+ and CD133- epithelial cells from human prostate. Prostate 2008; 68:1007-24. [PMID: 18398820 DOI: 10.1002/pros.20765] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Recent evidence suggests that prostate stem cells in benign and tumor tissue express the cell surface marker CD133, but these cells have not been well characterized. The aim of our study was to gene expression profile CD133-expressing cells. METHODS We analyzed CD133-positive (CD133+) and -negative (CD133-) sub-populations of high-integrin expressing epithelial cells isolated from benign human prostate tissue and hormone-refractory prostate cancer (HRPC). RESULTS CD133+ cells freshly isolated from benign prostate tissue exhibited an expression profile characteristic of a putative stem/progenitor cell population, with transcripts involved in biological processes ranging from development and ion homeostasis to cell communication. The profile of CD133- cells was consistent with that of a transit amplifying population, suggesting up-regulated proliferation and metabolism. Comparison of benign populations to those from HRPC showed some similarities between CD133+ profiles but also revealed significant differences that provide a tumor-specific pattern, which included evidence of increased metabolic activity and active proliferation. Subsequently, we demonstrated protein expression of a number of candidate genes in these cell populations and in benign tissue. In a novel observation we also found expression of some of these markers in prostate tumors, including the oligodendrocyte lineage transcription factor OLIG1. CONCLUSIONS This study provides a unique genome-wide molecular signature of CD133+ and CD133- human prostate epithelial cells. This will provide a valuable resource for prostate stem cell biology research and the identification of novel therapeutic targets for the treatment of prostate cancer.
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18
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Lee YS, Tsai CN, Tsai CL, Chang SD, Hsueh DW, Liu CT, Ma CC, Lin SH, Wang TH, Wang HS. Comparison of Whole Genome Amplification Methods for Further Quantitative Analysis with Microarray-based Comparative Genomic Hybridization. Taiwan J Obstet Gynecol 2008; 47:32-41. [DOI: 10.1016/s1028-4559(08)60052-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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19
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Abstract
Hbo1 is a histone acetyltransferase (HAT) that is required for global histone H4 acetylation, steroid-dependent transcription, and chromatin loading of MCM2-7 during DNA replication licensing. It is the catalytic subunit of protein complexes that include ING and JADE proteins, growth regulatory factors and candidate tumor suppressors. These complexes are thought to act via tumor suppressor p53, but the molecular mechanisms and links between stress signaling and chromatin, are currently unknown. Here, we show that p53 physically interacts with Hbo1 and negatively regulates its HAT activity in vitro and in cells. Two physiological stresses that stabilize p53, hyperosmotic shock and DNA replication fork arrest, also inhibit Hbo1 HAT activity in a p53-dependent manner. Hyperosmotic stress during G(1) phase specifically inhibits the loading of the MCM2-7 complex, providing an example of the chromatin output of this pathway. These results reveal a direct regulatory connection between p53-responsive stress signaling and Hbo1-dependent chromatin pathways.
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20
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Abstract
Histone modifications such as acetylation, methylation and phosphorylation have been implicated in fundamental cellular processes such as epigenetic regulation of gene expression, organization of chromatin structure, chromosome segregation, DNA replication and DNA repair. Males absent on the first (MOF) is responsible for acetylating histone H4 at lysine 16 (H4K16) and is a key component of the MSL complex required for dosage compensation in Drosophila. The human ortholog of MOF (hMOF) has the same substrate specificity and recent purification of the human and Drosophila MOF complexes showed that these complexes were also highly conserved through evolution. Several studies have shown that loss of hMOF in mammalian cells leads to a number of different phenotypes; a G2/M cell cycle arrest, nuclear morphological defects, spontaneous chromosomal aberrations, reduced transcription of certain genes and an impaired DNA repair response upon ionizing irradiation. Moreover, hMOF is involved in ATM activation in response to DNA damage and acetylation of p53 by hMOF influences the cell's decision to undergo apoptosis instead of a cell cycle arrest. These data, highlighting hMOF as an important component of many cellular processes, as well as links between hMOF and cancer will be discussed.
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Affiliation(s)
- S Rea
- Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
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21
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Goddard NC, McIntyre A, Summersgill B, Gilbert D, Kitazawa S, Shipley J. KIT and RAS signalling pathways in testicular germ cell tumours: new data and a review of the literature. ACTA ACUST UNITED AC 2007; 30:337-48; discussion 349. [PMID: 17573850 DOI: 10.1111/j.1365-2605.2007.00769.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Testicular germ cell tumours (TGCTs) are the leading cause of cancer deaths in young male Caucasians. Identifying changes in DNA copy number can pinpoint genes involved in tumour development. We defined the smallest overlapping regions of imbalance in TGCTs using array comparative genomic hybridization analysis. Novel regions, or regions which refined those previously reported, were identified. The expression profile of genes from 12p, which is invariably gained in TGCTs, and amplicons defined at 12p11.2-12.1 and 4q12, suggest KRAS and KIT involvement in TGCT and seminoma development, respectively. Amplification of these genes was not found in intratubular germ cell neoplasia adjacent to invasive disease showing these changes, suggesting their involvement in tumour progression. Activating mutations of RAS genes (KRAS or NRAS) and overexpression of KRAS were mutually exclusive events. These, correlations between the expression levels of KIT, KRAS and GRB7 (which encodes an adapter molecule known to interact with the KIT tyrosine kinase receptor) and other reported evidence reviewed here, are consistent with a role for activation of KIT and RAS signalling in TGCT development. In order to assess a role for KIT in seminomas, we modulated the level of KIT expression in TCam-2, a seminoma cell line. The likely seminomatous origin of this cell line was supported by demonstrating KIT and OCT3/4 overexpression and gain of 12p material. Reducing the expression of KIT in TCam-2 through RNA inhibition resulted in decreased cell viability. Further understanding of KIT and RAS signalling in TGCTs may lead to novel therapeutic approaches for these tumours.
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Affiliation(s)
- N C Goddard
- Molecular Cytogenetics, Section of Molecular Carcinogenesis, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
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22
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Maloney A, Clarke PA, Naaby-Hansen S, Stein R, Koopman JO, Akpan A, Yang A, Zvelebil M, Cramer R, Stimson L, Aherne W, Banerji U, Judson I, Sharp S, Powers M, deBilly E, Salmons J, Walton M, Burlingame A, Waterfield M, Workman P. Gene and Protein Expression Profiling of Human Ovarian Cancer Cells Treated with the Heat Shock Protein 90 Inhibitor 17-Allylamino-17-Demethoxygeldanamycin. Cancer Res 2007; 67:3239-53. [PMID: 17409432 DOI: 10.1158/0008-5472.can-06-2968] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The promising antitumor activity of 17-allylamino-17-demethoxygeldanamycin (17AAG) results from inhibition of the molecular chaperone heat shock protein 90 (HSP90) and subsequent degradation of multiple oncogenic client proteins. Gene expression microarray and proteomic analysis were used to profile molecular changes in the A2780 human ovarian cancer cell line treated with 17AAG. Comparison of results with an inactive analogue and an alternative HSP90 inhibitor radicicol indicated that increased expression of HSP72, HSC70, HSP27, HSP47, and HSP90beta at the mRNA level were on-target effects of 17AAG. HSP27 protein levels were increased in tumor biopsies following treatment of patients with 17AAG. A group of MYC-regulated mRNAs was decreased by 17AAG. Of particular interest and novelty were changes in expression of chromatin-associated proteins. Expression of the heterochromatin protein 1 was increased, and expression of the histone acetyltransferase 1 and the histone arginine methyltransferase PRMT5 was decreased by 17AAG. PRMT5 was shown to be a novel HSP90-binding partner and potential client protein. Cellular protein acetylation was reduced by 17AAG, which was shown to have an antagonistic interaction on cell proliferation with the histone deacetylase inhibitor trichostatin A. This mRNA and protein expression analysis has provided new insights into the complex molecular pharmacology of 17AAG and suggested new genes and proteins that may be involved in response to the drug or be potential biomarkers of drug action.
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Affiliation(s)
- Alison Maloney
- Haddow Laboratories, Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Surrey, United Kingdom
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Pärssinen J, Kuukasjärvi T, Karhu R, Kallioniemi A. High-level amplification at 17q23 leads to coordinated overexpression of multiple adjacent genes in breast cancer. Br J Cancer 2007; 96:1258-64. [PMID: 17353917 PMCID: PMC2360139 DOI: 10.1038/sj.bjc.6603692] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Increased copy numbers of 17q23 chromosomal region have been shown to occur in different tumour types and to be associated with tumour progression and with poor prognosis. Several genes have earlier been proposed as potential oncogenes at this region largely on the grounds of cell lines studies. In this study, we performed a systematic gene expression survey on 26 primary breast tumours with known 17q23 amplification status by quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The 17q23 amplicon is restricted to an approximately 5 MB region in breast cancer and contains 29 known genes. Our survey revealed a statistically significant (P<0.01) difference between the high level and no amplification groups in a set of eleven genes whereas no difference between the moderate and the non-amplified tumour groups were observed. Interestingly, these 11 genes were located adjacent to one another within a 1.56 Mb core region in which all except one of the genes were overexpressed. These data suggest that only high-level amplification at the 17q23 amplicon core leads to elevated gene expression in breast cancer. Moreover, our results highlight the fact that 17q23 amplicon carries multiple candidate genes and that this may be a more common event in gene amplification than previously thought.
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Affiliation(s)
- J Pärssinen
- Laboratory of Cancer Genetics, Institute of Medical Technology, Tampere University Hospital and University of Tampere, University of Tampere, Tampere, FIN-33014, Finland
| | - T Kuukasjärvi
- Department of Pathology, Tampere University Hospital, Tampere, FIN-33520, Finland
| | - R Karhu
- Laboratory of Cancer Genetics, Institute of Medical Technology, Tampere University Hospital and University of Tampere, University of Tampere, Tampere, FIN-33014, Finland
| | - A Kallioniemi
- Laboratory of Cancer Genetics, Institute of Medical Technology, Tampere University Hospital and University of Tampere, University of Tampere, Tampere, FIN-33014, Finland
- E-mail:
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24
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Mano MS, Rosa DD, De Azambuja E, Ismael GFV, Durbecq V. The 17q12-q21 amplicon: Her2 and topoisomerase-IIalpha and their importance to the biology of solid tumours. Cancer Treat Rev 2006; 33:64-77. [PMID: 17113234 DOI: 10.1016/j.ctrv.2006.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 10/01/2006] [Accepted: 10/04/2006] [Indexed: 02/08/2023]
Abstract
Her2 and topoisomerase-IIalpha (T2A) gene amplification are separate events, although the latter is more frequently seen in Her2 amplified (34-90%) than in Her2 non-amplified (5-10%) tumours. There is a better correlation between Her2 amplification and protein overexpression in breast cancer (BC) than in other tumour types. This marker is also considered a powerful prognostic factor in BC, with similar data emerging in other solid tumours such as bladder, ovarian, endometrial, gastro-oesophageal and non-small cell lung cancer. Her2 amplification and/or overexpression are highly predictive of response to HER2-targeted compounds such as trastuzumab and lapatinib but have been inconsistent predictors of response to cytotoxic chemotherapy. There is also evidence that these tumours are relatively resistant to anti-oestrogen therapy (tamoxifen) but not to oestrogen deprivation (e.g. with aromatase inhibitors). T2A aberrations are uncommon events in solid tumours, with an overall prevalence of approximately 10%. T2A amplification has shown inconsistent correlation with T2A protein expression in preclinical and clinical studies, mainly because non-genetic events such as proliferation rate can also affect protein expression. Expression of T2A protein has not been shown to reliably predict response to T2A inhibitors, despite the fact that this enzyme is the direct target for these compounds. In BC, T2A amplification appears to be a good predictor of response to anthracyclines, but these data are still in the process of validation. The significance of T2A deletions is currently under investigation, but contrary to what was previously thought, it may also predict benefit from treatment with T2A inhibitors. The prognostic significance of T2A aberrations is currently unknown.
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Affiliation(s)
- Max S Mano
- Medical Oncology Unit, Jules Bordet Institut, Bd de Waterloo, 125, 1000 Brussels, Belgium.
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25
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Dolled-Filhart M, Rydén L, Cregger M, Jirström K, Harigopal M, Camp RL, Rimm DL. Classification of Breast Cancer Using Genetic Algorithms and Tissue Microarrays. Clin Cancer Res 2006; 12:6459-68. [PMID: 17085660 DOI: 10.1158/1078-0432.ccr-06-1383] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE A multitude of breast cancer mRNA profiling studies has stratified breast cancer and defined gene sets that correlate with outcome. However, the number of genes used to predict patient outcome or define tumor subtypes by RNA expression studies is variable, nonoverlapping, and generally requires specialized technologies that are beyond those used in the routine pathology laboratory. It would be ideal if the familiarity and streamlined nature of immunohistochemistry could be combined with the rigorously quantitative and highly specific properties of nucleic acid-based analysis to predict patient outcome. EXPERIMENTAL DESIGN We have used AQUA-based objective quantitative analysis of tissue microarrays toward the goal of discovery of a minimal number of markers with maximal prognostic or predictive value that can be applied to the conventional formalin-fixed, paraffin-embedded tissue section. RESULTS The minimal discovered multiplexed set of tissue biomarkers was GATA3, NAT1, and estrogen receptor. Genetic algorithms were then applied after division of our cohort into a training set of 223 breast cancer patients to discover a prospectively applicable solution that can define a subset of patients with 5-year survival of 96%. This algorithm was then validated on an internal validation set (n=223, 5-year survival=95.8%) and further validated on an independent cohort from Sweden, which showed 5-year survival of 92.7% (n=149). CONCLUSIONS With further validation, this test has both the familiarity and specificity for widespread use in management of breast cancer. More generally, this work illustrates the potential for multiplexed biomarker discovery on the tissue microarray platform.
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Affiliation(s)
- Marisa Dolled-Filhart
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520-8023, USA
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26
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Hockley SL, Arlt VM, Brewer D, Giddings I, Phillips DH. Time- and concentration-dependent changes in gene expression induced by benzo(a)pyrene in two human cell lines, MCF-7 and HepG2. BMC Genomics 2006; 7:260. [PMID: 17042939 PMCID: PMC1621085 DOI: 10.1186/1471-2164-7-260] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Accepted: 10/16/2006] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The multi-step process of carcinogenesis can be more fully understood by characterizing gene expression changes induced in cells by carcinogens. In this study, expression microarrays were used to monitor the activity of 18,224 cDNA clones in MCF-7 and HepG2 cells exposed to the carcinogen benzo(a)pyrene (BaP) or its non-carcinogenic isomer benzo(e)pyrene (BeP). Time and concentration gene expression effects of BaP exposure have been assessed and linked to other measures of cellular stress to aid in the identification of novel genes/pathways involved in the cellular response to genotoxic carcinogens. RESULTS BaP (0.25-5.0 muM; 6-48 h exposure) modulated 202 clones in MCF-7 cells and 127 in HepG2 cells, including 27 that were altered in both. In contrast, BeP did not induce consistent gene expression changes at the same concentrations. Significant time- and concentration-dependent responses to BaP were seen in both cell lines. Expression changes observed in both cell lines included genes involved in xenobiotic metabolism (e.g., CYP1B1, NQO1, MGST1, AKR1C1, AKR1C3,CPM), cell cycle regulation (e.g., CDKN1A), apoptosis/anti-apoptosis (e.g., BAX, IER3), chromatin assembly (e.g., histone genes), and oxidative stress response (e.g., TXNRD1). RTqPCR was used to validate microarray data. Phenotypic anchoring of the expression data to DNA adduct levels detected by 32P-postlabelling, cell cycle data and p53 protein expression identified a number of genes that are linked to these biological outcomes, thereby strengthening the identification of target genes. The overall response to BaP consisted of up-regulation of tumour suppressor genes and down-regulation of oncogenes promoting cell cycle arrest and apoptosis. Anti-apoptotic signalling that may increase cell survival and promote tumourigenesis was also evident. CONCLUSION This study has further characterised the gene expression response of human cells after genotoxic insult, induced after exposure to concentrations of BaP that result in minimal cytotoxicity. We have demonstrated that investigating the time and concentration effect of a carcinogen on gene expression related to other biological end-points gives greater insight into cellular responses to such compounds and strengthens the identification of target genes.
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Affiliation(s)
- Sarah L Hockley
- Section of Molecular Carcinogenesis, Institute of Cancer Research, Brookes Lawley Building, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Volker M Arlt
- Section of Molecular Carcinogenesis, Institute of Cancer Research, Brookes Lawley Building, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Daniel Brewer
- Section of Molecular Carcinogenesis, Institute of Cancer Research, Brookes Lawley Building, Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Cancer Research UK DNA Microarray Facility, Institute of Cancer Research, Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Ian Giddings
- Section of Molecular Carcinogenesis, Institute of Cancer Research, Brookes Lawley Building, Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Cancer Research UK DNA Microarray Facility, Institute of Cancer Research, Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - David H Phillips
- Section of Molecular Carcinogenesis, Institute of Cancer Research, Brookes Lawley Building, Cotswold Road, Sutton, Surrey SM2 5NG, UK
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Contzler R, Regamey A, Favre B, Roger T, Hohl D, Huber M. Histone acetyltransferase HBO1 inhibits NF-kappaB activity by coactivator sequestration. Biochem Biophys Res Commun 2006; 350:208-13. [PMID: 16997280 DOI: 10.1016/j.bbrc.2006.09.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Accepted: 09/08/2006] [Indexed: 11/16/2022]
Abstract
The MYST acetyltransferase HBO1 is implicated in the regulation of DNA replication and activities of transcription factors such as the androgen receptor. Since the androgen receptor and NF-kappaB transcription factors crossmodulate their transcriptional activity, we investigated whether HBO1 regulates NF-kappaB signaling. Here, we report that in 293T cells HBO1 reduced dose-dependently NF-kappaB activity stimulated by TNFalpha, or by overexpressing p65/RelA, RelB, or cRel. Mutational analysis showed that the N-terminal serine-rich region of HBO1 but not the acetyltransferase function was required for inhibition. Electrophoretic mobility-shift assays demonstrated that HBO1 was neither perturbing the formation of p65/RelA DNA complexes nor binding itself to the kappaB consensus sequence or to p65/RelA, suggesting that HBO1 reduced NF-kappaB activity by squelching a cofactor. These data establish a novel function for HBO1 showing that it reduced NF-kappaB activity by sequestrating an essential coactivator from the NF-kappaB transcriptional complex.
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Affiliation(s)
- Romuald Contzler
- Laboratory of Cutaneous Biology, CHUV, Service of Dermatology, Hospital Beaumont 04-421, Lausanne 1011, Switzerland
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28
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Olsson AY, Feber A, Edwards S, Te Poele R, Giddings I, Merson S, Cooper CS. Role of E2F3 expression in modulating cellular proliferation rate in human bladder and prostate cancer cells. Oncogene 2006; 26:1028-37. [PMID: 16909110 DOI: 10.1038/sj.onc.1209854] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amplification and overexpression of the E2F3 gene at 6p22 in human bladder cancer is associated with increased tumour stage, grade and proliferation index, and in prostate cancer E2F3 overexpression is linked to tumour aggressiveness. We first used small interfering RNA technology to confirm the potential importance of E2F3 overexpression in bladder cancer development. Knockdown of E2F3 expression in bladder cells containing the 6p22 amplicon strongly reduced the extent of bromodeoxyuridine (BrdU) incorporation and the rate of cellular proliferation. In contrast, knockdown of CDKAL1/FLJ20342, another proposed oncogene, from this amplicon had no effect. Expression cDNA microarray analysis on bladder cancer cells following E2F3 knockdown was then used to identify genes regulated by E2F3, leading to the identification of known E2F3 targets such as Cyclin A and CDC2 and novel targets including pituitary tumour transforming gene 1, Polo-like kinase 1 (PLK1) and Caveolin-2. For both bladder and prostate cancer, we have proposed that E2F3 protein overexpression may cooperate with removal of the E2F inhibitor retinoblastoma tumor suppressor protein (pRB) to drive cellular proliferation. In support of this model, we found that ectopic expression of E2F3a enhanced the BrdU incorporation, a marker of cellular proliferation rate, of prostate cancer DU145 cells, which lack pRB, but had no effect on the proliferation rate of PC3 prostate cancer cells that express wild-type pRB. BrdU incorporation in PC3 cells could, however, be increased by overexpressing E2F3a in cells depleted of pRB. When taken together, these observations indicate that E2F3 levels have a critical role in modifying cellular proliferation rate in human bladder and prostate cancer.
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Affiliation(s)
- A Y Olsson
- Section of Molecular Carcinogenesis, Institute of Cancer Research, Male Urological Cancer Research Centre, Sutton, Surrey, UK.
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29
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Mourtada-Maarabouni M, Keen J, Clark J, Cooper CS, Williams GT. Candidate tumor suppressor LUCA-15/RBM5/H37 modulates expression of apoptosis and cell cycle genes. Exp Cell Res 2006; 312:1745-52. [PMID: 16546166 DOI: 10.1016/j.yexcr.2006.02.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 02/06/2006] [Accepted: 02/08/2006] [Indexed: 11/16/2022]
Abstract
RBM5 (RNA-binding motif protein 5/LUCA-15/H37) is encoded at the lung cancer tumor suppressor locus 3p21.3 and itself has several important characteristics of a tumor suppressor, including both potentiation of apoptosis and inhibition of the cell cycle. Here, we report the effects of both upregulation and downregulation of LUCA-15/RBM5 on gene expression monitored using cDNA microarrays. Many of the genes modulated by LUCA-15/RBM5 are involved in the control of apoptosis, the cell cycle, or both. These effects were confirmed for the most significant genes using real-time RT-PCR and/or Western blotting. In particular, LUCA-15/RBM5 increased the expression of Stat5b and BMP5 and decreased the expression of AIB1 (Amplified In Breast Cancer 1), proto-oncogene Pim-1, caspase antagonist BIRC3 (cIAP-2, MIHC), and CDK2 (cyclin-dependent kinase 2). These effects on multiple genes controlling both apoptosis and proliferation are in line with the functional effects of LUCA-15/RBM5 and indicate that it plays a central role in regulating cell fate consistent with its tumor suppressor activity.
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Sikela JM, Maclaren EJ, Kim Y, Karimpour-Fard A, Cai WW, Pollack J, Hitzemann R, Belknap J, McWeeney S, Kerns RT, Downing C, Johnson TE, Grant KJ, Tabakoff B, Hoffman P, Wu CC, Miles MF. DNA microarray and proteomic strategies for understanding alcohol action. Alcohol Clin Exp Res 2006; 30:700-8. [PMID: 16573589 PMCID: PMC2709534 DOI: 10.1111/j.1530-0277.2006.00081.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This article summarizes the proceedings of a symposium presented at the 2005 annual meeting of the Research Society on Alcoholism in Santa Barbara, California. The organizer was James M. Sikela, and he and Michael F. Miles were chairs. The presentations were (1) Genomewide Surveys of Gene Copy Number Variation in Human and Mouse: Implications for the Genetics of Alcohol Action, by James M. Sikela; (2) Regional Differences in the Regulation of Brain Gene Expression: Relevance to the Detection of Genes Associated with Alcohol-Related Traits, by Robert Hitzemann; (3) Identification of Ethanol Quantitative Trait Loci Candidate Genes by Expression Profiling in Inbred Long Sleep/Inbred Short Sleep Congenic Mice, by Robnet T. Kerns; and (4) Quantitative Proteomic Analysis of AC7-Modified Mice, by Kathleen J. Grant.
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Affiliation(s)
- James M Sikela
- University of Colorado at Denver and Health Sciences Center, Aurora, Colorado, USA
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Park K, Han S, Gwak GH, Kim HJ, Kim J, Kim KM. Topoisomerase II-alpha gene deletion is not frequent as its amplification in breast cancer. Breast Cancer Res Treat 2006; 98:337-42. [PMID: 16502015 DOI: 10.1007/s10549-006-9170-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Accepted: 01/09/2006] [Indexed: 11/28/2022]
Abstract
Topoisomerase II-alpha (TOP2A) has been investigated as a potential predictor for the response to doxorubicin-based chemotherapy which is a representative TOP2A inhibitor and one of the most effective chemotherapeutics for the breast cancer treatment. We performed the assay for the TOP2A gene amplification and deletion on a tissue microarray (TMA) of 284 breast tumor samples from the patients treated by doxorubicin-based adjuvant chemotherapy. TOP2A gene was deleted in six patients (2.1%), whereas TOP2A gene was amplified in 20 (7.1%) of 284 tumors. Twenty-four of 26 TOP2A amplifications and deletions were associated with HER2 co-amplification. TOP2A amplification or deletion was not associated with poor clinical outcome. Nine (34.6%) of 26 patients with TOP2A amplification or deletion had recurrent disease. Thirty percent of the patients with TOP2A amplification had systemic recurrence whereas 50% of the patients with TOP2A deletion had systemic recurrence. On multivariate analysis, histologic grade and tumor size were the significant predictors for the disease-free survival and histologic grade was an only significant predictor for the overall survival. Our study indicates that response to the doxorubicin-based chemotherapy might be stratified by TOP2A amplification and deletion. However, relative low frequency of TOP2A genetic changes seems to hamper its clinical utility.
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Affiliation(s)
- Kyeongmee Park
- Department of Pathology, Inje University Sanggye Paik Hospital, 761-1, Sanggye-dong, Nowon-gu, 139-707, Seoul, South Korea
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Shadeo A, Lam WL. Comprehensive copy number profiles of breast cancer cell model genomes. Breast Cancer Res 2006; 8:R9. [PMID: 16417655 PMCID: PMC1413994 DOI: 10.1186/bcr1370] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Revised: 10/11/2005] [Accepted: 11/18/2005] [Indexed: 01/05/2023] Open
Abstract
Introduction Breast cancer is the most commonly diagnosed cancer in women worldwide and consequently has been extensively investigated in terms of histopathology, immunochemistry and familial history. Advances in genome-wide approaches have contributed to molecular classification with respect to genomic changes and their subsequent effects on gene expression. Cell lines have provided a renewable resource that is readily used as model systems for breast cancer cell biology. A thorough characterization of their genomes to identify regions of segmental DNA loss (potential tumor-suppressor-containing loci) and gain (potential oncogenic loci) would greatly facilitate the interpretation of biological data derived from such cells. In this study we characterized the genomes of seven of the most commonly used breast cancer model cell lines at unprecedented resolution using a newly developed whole-genome tiling path genomic DNA array. Methods Breast cancer model cell lines MCF-7, BT-474, MDA-MB-231, T47D, SK-BR-3, UACC-893 and ZR-75-30 were investigated for genomic alterations with the submegabase-resolution tiling array (SMRT) array comparative genomic hybridization (CGH) platform. SMRT array CGH provides tiling coverage of the human genome permitting break-point detection at about 80 kilobases resolution. Two novel discrete alterations identified by array CGH were verified by fluorescence in situ hybridization. Results Whole-genome tiling path array CGH analysis identified novel high-level alterations and fine-mapped previously reported regions yielding candidate genes. In brief, 75 high-level gains and 48 losses were observed and their respective boundaries were documented. Complex alterations involving multiple levels of change were observed on chromosome arms 1p, 8q, 9p, 11q, 15q, 17q and 20q. Furthermore, alignment of whole-genome profiles enabled simultaneous assessment of copy number status of multiple components of the same biological pathway. Investigation of about 60 loci containing genes associated with the epidermal growth factor family (epidermal growth factor receptor, HER2, HER3 and HER4) revealed that all seven cell lines harbor copy number changes to multiple genes in these pathways. Conclusion The intrinsic genetic differences between these cell lines will influence their biologic and pharmacologic response as an experimental model. Knowledge of segmental changes in these genomes deduced from our study will facilitate the interpretation of biological data derived from such cells.
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Affiliation(s)
- Ashleen Shadeo
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, V5Z 1L3, Canada
| | - Wan L Lam
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, V5Z 1L3, Canada
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Raaphorst FM. Deregulated expression of Polycomb-group oncogenes in human malignant lymphomas and epithelial tumors. Hum Mol Genet 2005; 14 Spec No 1:R93-R100. [PMID: 15809278 DOI: 10.1093/hmg/ddi111] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genes belonging to the Polycomb-group (PcG) are epigenetic gene silencers with a vital role in the maintenance of cell identity. They contribute to regulation of various processes in both embryos and adults, including the cell cycle and lymphopoiesis. A growing body of work has linked human PcG genes to various hematological and epithelial cancers, identifying novel mechanisms of malignant transformation and paving the way to development of new cancer treatments and identification of novel diagnostic markers. This review addresses the current insights in the role of PcG genes in development of human malignancies.
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Affiliation(s)
- Frank M Raaphorst
- Department of Pathology, VU Medical Center, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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Bernardini M, Lee CH, Beheshti B, Prasad M, Albert M, Marrano P, Begley H, Shaw P, Covens A, Murphy J, Rosen B, Minkin S, Squire JA, Macgregor PF. High-resolution mapping of genomic imbalance and identification of gene expression profiles associated with differential chemotherapy response in serous epithelial ovarian cancer. Neoplasia 2005; 7:603-13. [PMID: 16036111 PMCID: PMC1501280 DOI: 10.1593/neo.04760] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Revised: 03/21/2005] [Accepted: 03/21/2005] [Indexed: 12/27/2022]
Abstract
Array comparative genomic hybridization (aCGH) and microarray expression profiling were used to subclassify DNA and RNA alterations associated with differential response to chemotherapy in ovarian cancer. Two to 4 Mb interval arrays were used to map genomic imbalances in 26 sporadic serous ovarian tumors. Cytobands 1p36, 1q42-44, 6p22.1-p21.2, 7q32.1-q34 9q33.3-q34.3, 11p15.2, 13q12.2-q13.1, 13q21.31, 17q11.2, 17q24.2-q25.3, 18q12.2, and 21q21.2-q21.3 were found to be statistically associated with chemotherapy response, and novel regions of loss at 15q11.2-q15.1 and 17q21.32-q21.33 were identified. Gene expression profiles were obtained from a subset of these tumors and identified a group of genes whose differential expression was significantly associated with drug resistance. Within this group, five genes (GAPD, HMGB2, HSC70, GRP58, and HMGB1), previously shown to form a nuclear complex associated with resistance to DNA conformation-altering chemotherapeutic drugs in in vitro systems, may represent a novel class of genes associated with in vivo drug response in ovarian cancer patients. Although RNA expression change indicated only weak DNA copy number dependence, these data illustrate the value of molecular profiling at both the RNA and DNA levels to identify small genomic regions and gene subsets that could be associated with differential chemotherapy response in ovarian cancer.
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Affiliation(s)
- Marcus Bernardini
- Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada
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Yao J, Ren X, Ireland JJ, Coussens PM, Smith TPL, Smith GW. Generation of a bovine oocyte cDNA library and microarray: resources for identification of genes important for follicular development and early embryogenesis. Physiol Genomics 2005; 19:84-92. [PMID: 15375196 DOI: 10.1152/physiolgenomics.00123.2004] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The oocyte is a key regulator of ovarian folliculogenesis and early embryonic development. However, the composition of the oocyte transcriptome and identities and functions of key oocyte-specific genes involved in the above processes are relatively unknown. Using a PCR-based cDNA amplification method (SMART technology), we constructed a bovine oocyte cDNA library. Analysis of 230 expressed sequence tags (ESTs) from this library identified 102 unique sequences. Although some correspond to housekeeping genes (e.g., ribosomal protein L15) and some represent genes previously known to be expressed in oocytes and other tissues, most encode for genes whose expression in mammalian oocytes has not been reported previously (e.g., cocaine- and amphetamine-regulated transcript) or genes of unknown function. Sixteen did not show significant sequence similarity to any entries in the GenBank database and were classified as novel. Using over 2,000 unsequenced, randomly selected cDNA clones from the library, we constructed an oocyte microarray and performed experiments to identify genes preferentially expressed in fetal ovary (an enriched source of oocytes) relative to somatic tissues. Eleven clones were identified by microarray analysis with consistently higher expression in fetal ovaries (collected from animals at days 210-260 of gestation) compared with spleen and liver. DNA sequence analysis of these clones revealed that two correspond to JY-1, a novel bovine oocyte-specific gene. The remaining nine clones represent five identified genes and one additional completely novel gene. Increased abundance of mRNA in fetal ovary for five of the six genes identified was confirmed by real-time PCR. Results demonstrate the potential utility of these unique resources for identification of oocyte-expressed genes potentially important for reproductive function.
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Affiliation(s)
- Jianbo Yao
- Division of Animal and Veterinary Sciences, West Virginia University, Morgantown, West Virginia 26506-6108, USA.
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McIntyre A, Summersgill B, Jafer O, Rodriguez S, Zafarana G, Oosterhuis JW, Gillis AJ, Looijenga L, Cooper C, Huddart R, Clark J, Shipley J. Defining minimum genomic regions of imbalance involved in testicular germ cell tumors of adolescents and adults through genome wide microarray analysis of cDNA clones. Oncogene 2005; 23:9142-7. [PMID: 15489896 DOI: 10.1038/sj.onc.1208115] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Identifying changes in DNA copy number can pinpoint genes that may be involved in tumor development. Here we have defined the smallest overlapping regions of imbalance (SORI) in testicular germ cell tumors other than the 12p region, which has been previously investigated. Definition of the regions was achieved through comparative genomic hybridization (CGH) analysis of a 4559 cDNA clone microarray. A total of 14 SORI were identified, which involved at least five of the 11 samples analysed. Many of these refined regions were previously reported using chromosomal or allelic imbalance studies. The SORI included gain of material from the regions 4q12, 17q21.3, 22q11.23 and Xq22, and loss from 5q33, 11q12.1, 16q22.3 and 22q11. Comparison with parallel chromosomal CGH data supported involvement of most regions. The various SORI span between one and 20 genes and highlight potential oncogenes/tumor suppressor genes to be investigated further.
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Affiliation(s)
- Alan McIntyre
- Molecular Cytogenetics, Section of Molecular Carcinogenesis, Institute of Cancer Research, Sutton, Surrey, UK
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Edwards S, Campbell C, Flohr P, Shipley J, Giddings I, te-Poele R, Dodson A, Foster C, Clark J, Jhavar S, Kovacs G, Cooper CS. Expression analysis onto microarrays of randomly selected cDNA clones highlights HOXB13 as a marker of human prostate cancer. Br J Cancer 2005; 92:376-81. [PMID: 15583692 PMCID: PMC2361840 DOI: 10.1038/sj.bjc.6602261] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In a strategy aimed at identifying novel markers of human prostate cancer, we performed expression analysis using microarrays of clones randomly selected from a cDNA library prepared from the LNCaP prostate cancer cell line. Comparisons of expression profiles in primary human prostate cancer, adjacent normal prostate tissue, and a selection of other (nonprostate) normal human tissues, led to the identification of a set of clones that were judged as the best candidate markers of normal and/or malignant prostate tissue. DNA sequencing of the selected clones revealed that they included 10 genes that had previously been established as prostate markers: NKX3.1, KLK2, KLK3 (PSA), FOLH1 (PSMA), STEAP2, PSGR, PRAC, RDH11, Prostein and FASN. Following analysis of the expression patterns of all selected and sequenced genes through interrogation of SAGE databases, a further three genes from our clone set, HOXB13, SPON2 and NCAM2, emerged as additional candidate markers of human prostate cancer. Quantitative RT-PCR demonstrated the specificity of expression of HOXB13 in prostate tissue and revealed its ubiquitous expression in a series of 37 primary prostate cancers and 20 normal prostates. These results demonstrate the utility of this expression-microarray approach in hunting for new markers of individual human cancer types.
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Affiliation(s)
- S Edwards
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - C Campbell
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TR, UK
| | - P Flohr
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - J Shipley
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - I Giddings
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - R te-Poele
- CRUK Centre for Cancer Therapeutics, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - A Dodson
- Department of Pathology & Molecular Genetics, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C Foster
- Department of Pathology & Molecular Genetics, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - J Clark
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - S Jhavar
- Section of Cancer Genetics, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - G Kovacs
- Laboratory of Molecular Oncology, University Surgical Hospital, Im Neuenheimer Feld 365, Heidelberg 69120, Germany
| | - C S Cooper
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK. E-mail:
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Callagy G, Pharoah P, Chin SF, Sangan T, Daigo Y, Jackson L, Caldas C. Identification and validation of prognostic markers in breast cancer with the complementary use of array-CGH and tissue microarrays. J Pathol 2005; 205:388-96. [PMID: 15682439 DOI: 10.1002/path.1694] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Gene amplification, an important mechanism of oncogene activation in breast cancer, can have both prognostic and therapeutic implications. In this work, an attempt is made to identify amplified genes that can be used to improve prognostication in breast cancer. A series of 52 node-negative tumours was screened for genomic gains at 57 loci by array-CGH. A subset of these genes was identified that could divide the series into two divergent outcome groups of either long-term survivors or early disease-related deaths (p = 0.01) using a combination of k-means clustering and statistical analysis. The prognostic significance of amplification of four of the genes (EMS1, TOP2A, CCNE1, and ERBB2) was then evaluated, using fluorescent in situ hybridization on a tissue microarray, in a second larger 'validation' series of 232 tumours with a median follow-up of 4.8 years. Adverse disease-related outcome was associated with amplification of TOP2A (p = 0.004); ERBB2 (p = 0.002); and with the combined amplification of TOP2A, ERBB2, and EMS1 (p = 0.01). EMS1 amplification was more common (26% of cases) than previously reported but, in isolation, had no prognostic significance. Amplification of CCNE1, seen in only 6% of cases, had no prognostic role. These results indicate that the complementary use of array-CGH and tissue microarrays has the potential to help in the identification and validation of molecular markers that can be used to classify breast cancers into different prognostic groups.
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Affiliation(s)
- Grace Callagy
- Cancer Genomics Program, Department of Oncology, University of Cambridge, Cambridge, UK
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Scaruffi P, Parodi S, Mazzocco K, Defferrari R, Fontana V, Bonassi S, Tonini GP. Detection of MYCN amplification and chromosome 1p36 loss in neuroblastoma by cDNA microarray comparative genomic hybridization. ACTA ACUST UNITED AC 2004; 8:93-100. [PMID: 15527323 DOI: 10.1007/bf03260051] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND In the last decade, microarray technology has been extensively used to evaluate gene expression profiles and genome imbalances. We have developed a microarray-based comparative genomic hybridization (CGH) approach to identify MYCN gene amplification and 1p36 chromosome loss, two markers of tumor aggressiveness in neuroblastoma. AIM The aim was to use microarray CGH technology to detect the two major prognostic markers for neuroblastoma, MYCN amplification and 1p36 chromosome deletion, in neuroblastoma patients and, therefore, confirm the usefulness of this approach in this cancer. METHODS DNA was purified from 16 tumors containing at least 90% malignant neuroblasts and collected at the onset of disease. Pooled fluorescent-labeled reference and neuroblastoma tumor genomic DNA was hybridized to epoxide-coated glass slides on laboratory-made complementary DNA microarray. The microarray contained cDNA mapped at the 1p36.33-36.1 chromosomal region and MYCN gene. cDNA from the 2q33-q34 and 12p13 chromosomes was used as a control and Arabidopsis thaliana DNA was spotted to control unspecific hybridization. Fluorescence in situ hybridization analysis was also performed to validate results from the microarray CGH. RESULTS Both MYCN amplification and 1p36 chromosome deletion were detected by microarray CGH. The sensitivity and specificity for 1p36 loss detection were 66.7% and 90.0%, respectively. The method had a sensitivity of 66.7% and specificity of 90.9% to detect MYCN amplification. DISCUSSION Our results demonstrated that the microarray CGH can be efficiently applied to study DNA gain and loss of specific chromosome regions.
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Affiliation(s)
- Paola Scaruffi
- Laboratory of Neuroblastoma, National Cancer Research Institute (IST), Genoa, Italy
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Renshaw J, Orr RM, Walton MI, te Poele R, Williams RD, Wancewicz EV, Monia BP, Workman P, Pritchard-Jones K. Disruption of WT1 gene expression and exon 5 splicing following cytotoxic drug treatment: Antisense down-regulation of exon 5 alters target gene expression and inhibits cell survival. Mol Cancer Ther 2004. [DOI: 10.1158/1535-7163.1467.3.11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Deregulated expression of the Wilms' tumor gene (WT1) has been implicated in the maintenance of a malignant phenotype in leukemias and a wide range of solid tumors through interference with normal signaling in differentiation and apoptotic pathways. Expression of high levels of WT1 is associated with poor prognosis in leukemias and breast cancer. Using real-time (Taqman) reverse transcription-PCR and RNase protection assay, we have shown up-regulation of WT1 expression following cytotoxic treatment of cells exhibiting drug resistance, a phenomenon not seen in sensitive cells. WT1 is subject to alternative splicing involving exon 5 and three amino acids (KTS) at the end of exon 9, producing four major isoforms. Exon 5 splicing was disrupted in all cell lines studied following a cytotoxic insult probably due to increased exon 5 skipping. Disruption of exon 5 splicing may be a proapoptotic signal because specific targeting of WT1 exon 5–containing transcripts using a nuclease-resistant antisense oligonucleotide (ASO) killed HL60 leukemia cells, which were resistant to an ASO targeting all four alternatively spliced transcripts simultaneously. K562 cells were sensitive to both target-specific ASOs. Gene expression profiling following treatment with WT1 exon 5–targeted antisense showed up-regulation of the known WT1 target gene, thrombospondin 1, in HL60 cells, which correlated with cell death. In addition, novel potential WT1 target genes were identified in each cell line. These studies highlight a new layer of complexity in the regulation and function of the WT1 gene product and suggest that antisense directed to WT1 exon 5 might have therapeutic potential.
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Affiliation(s)
| | - Rosanne M. Orr
- 2Cancer Research UK Centre of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey, United Kingdom and
| | - Michael I. Walton
- 2Cancer Research UK Centre of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey, United Kingdom and
| | - Robert te Poele
- 2Cancer Research UK Centre of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey, United Kingdom and
| | | | | | | | - Paul Workman
- 2Cancer Research UK Centre of Cancer Therapeutics, Institute of Cancer Research, Sutton, Surrey, United Kingdom and
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Lee YF, John M, Falconer A, Edwards S, Clark J, Flohr P, Roe T, Wang R, Shipley J, Grimer RJ, Mangham DC, Thomas JM, Fisher C, Judson I, Cooper CS. A Gene Expression Signature Associated with Metastatic Outcome in Human Leiomyosarcomas. Cancer Res 2004; 64:7201-4. [PMID: 15492233 DOI: 10.1158/0008-5472.can-04-1673] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Metastasis is a major factor associated with poor prognosis in cancer, but little is known of its molecular mechanisms. Although the clinical behavior of soft tissue sarcomas is highly variable, few reliable determinants of outcome have been identified. New markers that predict clinical outcome, in particular the ability of primary tumors to develop metastatic tumors, are urgently needed. Here, we have chosen leiomyosarcoma as a model for examining the relationship between gene expression profile and the development of metastasis in soft tissue sarcomas. Using cDNA microarray, we have identified a gene expression signature associated with metastasis in sarcoma that allowed prediction of the future development of metastases of primary tumors (Kaplan-Meier analysis P = 0.001). Our finding may aid the tailoring of therapy for individual sarcoma patients, where the aggressiveness of treatment is affected by the predicted outcome of disease.
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Affiliation(s)
- Yin-Fai Lee
- The Male Urological Cancer Research Centre, Institute of Cancer Research, Surrey, United Kingdom.
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Chen YJ, Lin SC, Kao T, Chang CS, Hong PS, Shieh TM, Chang KW. Genome-wide profiling of oral squamous cell carcinoma. J Pathol 2004; 204:326-32. [PMID: 15372456 DOI: 10.1002/path.1640] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is a common malignancy, the incidence of which is particularly high in some Asian countries due to the geographically linked areca quid (AQ) chewing habit. In this study, array-based comparative genomic hybridization was used to screen microdissected OSCCs for genome-wide alterations. The highest frequencies of gene gain were detected for TP63, Serpine1, FGF4/FGF3, c-Myc and DMD. The highest frequencies of deletion were detected for Caspase8 and MTAP. Gained genes, classified by hierarchical clustering, were mainly on 17q21-tel; 20q; 11q13; 3q27-29 and the X chromosome. Among these, gains of EGFR at 7p, FGF4/FGF3, CCND1 and EMS1 at 11q13, and AIB1 at 20q were significantly associated with lymph node metastasis. The genomic profiles of FHIT and EXT1 in AQ-associated and non-AQ-associated OSCCs exhibited the most prominent differences. RT-PCR confirmed the significant increase of TP63 and Serpine1 mRNA expression in OSCC relative to non-malignant matched tissue. A significant increase in Serpine1 immunoreactivity was observed from non-malignant matched tissue to OSCC. However, there was no correlation between the frequent genomic loss of Caspase 8 and a significant decrease in Caspase8 expression. These data demonstrate that genomic profiling can be useful in analysing pathogenetic events involved in the genesis or progression of OSCC.
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Affiliation(s)
- Yann-Jang Chen
- Department of Life Science, National Yang-Ming University, Taipei, Taiwan
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Orsetti B, Nugoli M, Cervera N, Lasorsa L, Chuchana P, Ursule L, Nguyen C, Redon R, du Manoir S, Rodriguez C, Theillet C. Genomic and Expression Profiling of Chromosome 17 in Breast Cancer Reveals Complex Patterns of Alterations and Novel Candidate Genes. Cancer Res 2004; 64:6453-60. [PMID: 15374954 DOI: 10.1158/0008-5472.can-04-0756] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chromosome 17 is severely rearranged in breast cancer. Whereas the short arm undergoes frequent losses, the long arm harbors complex combinations of gains and losses. In this work we present a comprehensive study of quantitative anomalies at chromosome 17 by genomic array-comparative genomic hybridization and of associated RNA expression changes by cDNA arrays. We built a genomic array covering the entire chromosome at an average density of 1 clone per 0.5 Mb, and patterns of gains and losses were characterized in 30 breast cancer cell lines and 22 primary tumors. Genomic profiles indicated severe rearrangements. Compiling data from all samples, we subdivided chromosome 17 into 13 consensus segments: 4 regions showing mainly losses, 6 regions showing mainly gains, and 3 regions showing either gains or losses. Within these segments, smallest regions of overlap were defined (17 for gains and 16 for losses). Expression profiles were analyzed by means of cDNA arrays comprising 358 known genes at 17q. Comparison of expression changes with quantitative anomalies revealed that about half of the genes were consistently affected by copy number changes. We identified 85 genes overexpressed when gained (39 of which mapped within the smallest regions of overlap), 67 genes underexpressed when lost (32 of which mapped to minimal intervals of losses), and, interestingly, 32 genes showing reduced expression when gained. Candidate genes identified in this study belong to very diverse functional groups, and a number of them are novel candidates.
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Affiliation(s)
- Béatrice Orsetti
- Génotypes et Phénotypes Tumoraux, EMI229 INSERM/Université Montpellier I, Montpellier, France
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Lee CH, Macgregor PF. Using microarrays to predict resistance to chemotherapy in cancer patients. Pharmacogenomics 2004; 5:611-25. [PMID: 15335284 DOI: 10.1517/14622416.5.6.611] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Chemotherapy resistance remains a major obstacle to successful treatment and better outcome in cancer patients. The advent of whole genome experimental strategies, such as DNA microarrays, has transformed the way researchers approach cancer research. There is considerable hope that microarray technology will lead to the identification of new targets for therapeutic intervention, a better understanding of the disease process, and, ultimately, to higher survival rates and more personalized medicine. The question at hand is what is the best approach to apply these new technologies to the study of anticancer drug resistance, and how can the results obtained in the laboratory be quickly moved to a clinical setting? This review offers an overview of the microarray technology, including its recently associated strategies, such as array comparative genomic hybridization and promoter arrays. It also highlights some recent examples of microarray studies, which represent a first step toward a better understanding of drug resistance in cancer and, ultimately, personalized medicine.
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Affiliation(s)
- Chung-Hae Lee
- Microarray Centre, Clinical Genomics Centre, University Health Network, Canadian Breast Cancer Research Alliance, 790 Bay Street, Ste. 1000, Toronto, ON, M5G 1NB, Canada
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Abstract
The normal development and maintenance of the prostate is dependent on androgen acting through the androgen receptor (AR). AR remains important in the development and progression of prostate cancer. AR expression is maintained throughout prostate cancer progression, and the majority of androgen-independent or hormone refractory prostate cancers express AR. Mutation of AR, especially mutations that result in a relaxation of AR ligand specificity, may contribute to the progression of prostate cancer and the failure of endocrine therapy by allowing AR transcriptional activation in response to antiandrogens or other endogenous hormones. Similarly, alterations in the relative expression of AR coregulators have been found to occur with prostate cancer progression and may contribute to differences in AR ligand specificity or transcriptional activity. Prostate cancer progression is also associated with increased growth factor production and an altered response to growth factors by prostate cancer cells. The kinase signal transduction cascades initiated by mitogenic growth factors modulate the transcriptional activity of AR and the interaction between AR and AR coactivators. The inhibition of AR activity through mechanisms in addition to androgen ablation, such as modulation of signal transduction pathways, may delay prostate cancer progression.
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Affiliation(s)
- Cynthia A Heinlein
- George Whipple Laboratory for Cancer Research, Department of Pathology, University of Rochester, Rochester, NY 14642, USA
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Feber A, Clark J, Goodwin G, Dodson AR, Smith PH, Fletcher A, Edwards S, Flohr P, Falconer A, Roe T, Kovacs G, Dennis N, Fisher C, Wooster R, Huddart R, Foster CS, Cooper CS. Amplification and overexpression of E2F3 in human bladder cancer. Oncogene 2004; 23:1627-30. [PMID: 14716298 DOI: 10.1038/sj.onc.1207274] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We demonstrate that, in human bladder cancer, amplification of the E2F3 gene, located at 6p22, is associated with overexpression of its encoded mRNA transcripts and high levels of expression of E2F3 protein. Immunohistochemical analyses of E2F3 protein levels have established that around one-third (33/101) of primary transitional cell carcinomas of the bladder overexpress nuclear E2F3 protein, with the proportion of tumours containing overexpressed nuclear E2F3 increasing with tumour stage and grade. When considered together with the established role of E2F3 in cell cycle progression, these results suggest that the E2F3 gene represents a candidate bladder cancer oncogene that is activated by DNA amplification and overexpression.
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Affiliation(s)
- Andrew Feber
- Section of Molecular Carcinogenesis and Male Urological Cancer Research, Centre, Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
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Zhang DH, Salto-Tellez M, Chiu LL, Shen L, Koay ESC. Tissue microarray study for classification of breast tumors. Life Sci 2003; 73:3189-99. [PMID: 14561524 DOI: 10.1016/j.lfs.2003.05.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Clinical and pathological heterogeneity of breast cancer hinders selection of appropriate treatment for individual cases. Molecular profiling at gene or protein levels may elucidate the biological variance of tumors and provide a new classification system that correlates better with biological, clinical and prognostic parameters. We studied the immunohistochemical profile of a panel of seven important biomarkers using tumor tissue arrays. The tumor samples were then classified with a monothetic (binary variables) clustering algorithm. Two distinct groups of tumors are characterized by the estrogen receptor (ER) status and tumor grade (p = 0.0026). Four biomarkers, c-erbB2, Cox-2, p53 and VEGF, were significantly overexpressed in tumors with the ER-negative (ER-) phenotype. Eight subsets of tumors were further identified according to the expression status of VEGF, c-erbB2 and p53. The malignant potential of the ER-/VEGF+ subgroup was associated with the strong correlations of Cox-2 and c-erbB2 with VEGF. Our results indicate that this molecular classification system, based on the statistical analysis of immunohistochemical profiling, is a useful approach for tumor grouping. Some of these subgroups have a relative genetic homogeneity that may allow further study of specific genetically-controlled metabolic pathways. This approach may hold great promise in rationalizing the application of different therapeutic strategies for different subgroups of breast tumors.
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Affiliation(s)
- Dao-Hai Zhang
- Department of Laboratory Medicine, Molecular Diagnosis Centre, National University Hospital, Singapore
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Lu YJ, Williamson D, Wang R, Summersgill B, Rodriguez S, Rogers S, Pritchard-Jones K, Campbell C, Shipley J. Expression profiling targeting chromosomes for tumor classification and prediction of clinical behavior. Genes Chromosomes Cancer 2003; 38:207-14. [PMID: 14506694 DOI: 10.1002/gcc.10276] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Tumors are associated with altered or deregulated gene products that affect critical cellular functions. Here we assess the use of a global expression profiling technique that identifies chromosome regions corresponding to differential gene expression, termed comparative expressed sequence hybridization (CESH). CESH analysis was performed on a total of 104 tumors with a diagnosis of rhabdomyosarcoma, leiomyosarcoma, prostate cancer, and favorable-histology Wilms tumors. Through the use of the chromosome regions identified as variables, support vector machine analysis was applied to assess classification potential, and feature selection (recursive feature elimination) was used to identify the best discriminatory regions. We demonstrate that the CESH profiles have characteristic patterns in tumor groups and were also able to distinguish subgroups of rhabdomyosarcoma. The overall CESH profiles in favorable-histology Wilms tumors were found to correlate with subsequent clinical behavior. Classification by use of CESH profiles was shown to be similar in performance to previous microarray expression studies and highlighted regions for further investigation. We conclude that analysis of chromosomal expression profiles can group, subgroup, and even predict clinical behavior of tumors to a level of performance similar to that of microarray analysis. CESH is independent of selecting sequences for interrogation and is a simple, rapid, and widely accessible approach to identify clinically useful differential expression.
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Affiliation(s)
- Yong-Jie Lu
- Molecular Cytogenetics, Section of Molecular Carcinogenesis, Institute of Cancer Research, Sutton, Surrey, United Kingdom
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Al-Mulla F, Al-Maghrebi M, Varadharaj G. Expressive genomic hybridisation: gene expression profiling at the cytogenetic level. Mol Pathol 2003; 56:210-7. [PMID: 12890742 PMCID: PMC1187323 DOI: 10.1136/mp.56.4.210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AIMS To describe a cytogenetic technique suitable for the rapid assessment of global gene expression that is based on comparative genomic hybridisation (CGH), and to use it to understand the relation between genetic amplifications and gene expression. METHODS Whereas traditional CGH uses DNA as test and reference in hybridisations, expressive genomic hybridisation (EGH) uses globally amplified mRNA as test and normal DNA as reference. EGH is a rapid and powerful tool for localising and studying global gene expression profiles and correlating them with loci of genetic amplifications using traditional CGH. RESULTS EGH was used to correlate genetic amplifications detected by CGH with the expression profile of two independent cell lines-Colo320 and T47D. Although many amplifications resulted in overexpression, other amplifications were partially or completely silenced at the cytogenetic level. CONCLUSION This technique will assist in the analysis of overexpressed genes within amplicons and could resolve a controversial issue in cancer cytogenetics; namely, the relation between genetic amplifications and overexpression.
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Affiliation(s)
- F Al-Mulla
- Department of Pathology, Molecular Pathology Unit, Kuwait University, Faculty of Medicine, PO Box 24923, Safat, Kuwait 13110.
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Abstract
DNA microarray technology is revolutionizing many aspects of biological research, allowing the expression of many thousands of gene transcripts to be monitored simultaneously. This provides powerful tools for the genome-wide correlation of gene transcript levels with physiological responses and alterations in physiological states. To date, microarray analyses have been applied almost exclusively to a few model species for which the abundant gene sequence data permit the fabrication of whole-genome microarrays. However, many interesting physiological traits and responses are poorly expressed or absent in model species and may be better illustrated in nonmodel organisms. Comparative approaches to understanding function traditionally focus on species that by virtue of their unusual adaptations, lifestyles, and phylogeny are particularly suited to address a specific biological process or problem. In this review, we show that microarray technology can be successfully applied to these nonmodel species and used to generate new insights of comparative and evolutionary significance into animal function.
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Affiliation(s)
- Andrew Y Gracey
- Laboratory for Environmental Gene Regulation, School of Biological Sciences, University of Liverpool, Liverpool L69 3BX, United Kingdom.
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