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PANAGOPOULOS IOANNIS, HEIM SVERRE. Neoplasia-associated Chromosome Translocations Resulting in Gene Truncation. Cancer Genomics Proteomics 2022; 19:647-672. [PMID: 36316036 PMCID: PMC9620447 DOI: 10.21873/cgp.20349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/27/2022] Open
Abstract
Chromosomal translocations in cancer as well as benign neoplasias typically lead to the formation of fusion genes. Such genes may encode chimeric proteins when two protein-coding regions fuse in-frame, or they may result in deregulation of genes via promoter swapping or translocation of the gene into the vicinity of a highly active regulatory element. A less studied consequence of chromosomal translocations is the fusion of two breakpoint genes resulting in an out-of-frame chimera. The breaks then occur in one or both protein-coding regions forming a stop codon in the chimeric transcript shortly after the fusion point. Though the latter genetic events and mechanisms at first awoke little research interest, careful investigations have established them as neither rare nor inconsequential. In the present work, we review and discuss the truncation of genes in neoplastic cells resulting from chromosomal rearrangements, especially from seemingly balanced translocations.
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Affiliation(s)
- IOANNIS PANAGOPOULOS
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - SVERRE HEIM
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Panagopoulos I, Heim S. Interstitial Deletions Generating Fusion Genes. Cancer Genomics Proteomics 2021; 18:167-196. [PMID: 33893073 DOI: 10.21873/cgp.20251] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
A fusion gene is the physical juxtaposition of two different genes resulting in a structure consisting of the head of one gene and the tail of the other. Gene fusion is often a primary neoplasia-inducing event in leukemias, lymphomas, solid malignancies as well as benign tumors. Knowledge about fusion genes is crucial not only for our understanding of tumorigenesis, but also for the diagnosis, prognostication, and treatment of cancer. Balanced chromosomal rearrangements, in particular translocations and inversions, are the most frequent genetic events leading to the generation of fusion genes. In the present review, we summarize the existing knowledge on chromosome deletions as a mechanism for fusion gene formation. Such deletions are mostly submicroscopic and, hence, not detected by cytogenetic analyses but by array comparative genome hybridization (aCGH) and/or high throughput sequencing (HTS). They are found across the genome in a variety of neoplasias. As tumors are increasingly analyzed using aCGH and HTS, it is likely that more interstitial deletions giving rise to fusion genes will be found, significantly impacting our understanding and treatment of cancer.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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Zhao Y, Zhao Q, Kaboli PJ, Shen J, Li M, Wu X, Yin J, Zhang H, Wu Y, Lin L, Zhang L, Wan L, Wen Q, Li X, Cho CH, Yi T, Li J, Xiao Z. m1A Regulated Genes Modulate PI3K/AKT/mTOR and ErbB Pathways in Gastrointestinal Cancer. Transl Oncol 2019; 12:1323-1333. [PMID: 31352195 PMCID: PMC6661385 DOI: 10.1016/j.tranon.2019.06.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND: Gene expression can be posttranscriptionally regulated by a complex network of proteins. N1-methyladenosine (m1A) is a newly validated RNA modification. However, little is known about both its influence and biogenesis in tumor development. METHODS: This study analyzed TCGA data of patients with five kinds of gastrointestinal (GI) cancers. Using data from cBioPortal, molecular features of the nine known m1A-related enzymes in GI cancers were investigated. Using a variety of bioinformatics approach, the impact of m1A regulators on its downstream signaling pathway was studied. To further confirm this regulation, the effect of m1A writer ALKBH3 knockdown was studied using RNA-seq data from published database. RESULTS: Dysregulation and multiple types of genetic alteration of putative m1A-related enzymes in tumor samples were observed. The ErbB and mTOR pathways with ErbB2, mTOR, and AKT1S1 hub genes were identified as being regulated by m1A-related enzymes. The expression of both ErbB2 and AKT1S1 was decreased after m1A writer ALKBH3 knockdown. Furthermore, Gene Ontology analysis revealed that m1A downstream genes were associated with cell proliferation, and the results showed that m1A genes are reliably linked to mTOR. CONCLUSION: This study demonstrated for the first time the dysregulation of m1A regulators in GI cancer and its signaling pathways and will contribute to the understanding of RNA modification in cancer.
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Affiliation(s)
- Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Qijie Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Jianhua Yin
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Hanyu Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Yuanlin Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Ling Lin
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Lingling Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Lin Wan
- Department of Hematology and Oncology, The Children's Hospital of Soochow, Jiangsu, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Luzhou Medical College, Luzhou, Sichuan 646000, PR China
| | - Xiang Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China
| | - Tao Yi
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Jing Li
- Department of Oncology and Hematology, Hospital (T.C.M) Affiliated to Southwest Medical University, Luzhou, Sichuan, China.
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, 646000, Sichuan, PR China; South Sichuan Institution for Translational Medicine, Luzhou, 646000, Sichuan, PR China.
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Barasch N, Gong X, Kwei KA, Varma S, Biscocho J, Qu K, Xiao N, Lipsick JS, Pelham RJ, West RB, Pollack JR. Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma. PLoS One 2017; 12:e0171265. [PMID: 28212443 PMCID: PMC5315303 DOI: 10.1371/journal.pone.0171265] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 01/17/2017] [Indexed: 12/22/2022] Open
Abstract
Pathogenic gene fusions have been identified in several histologic types of salivary gland neoplasia, but not previously in acinic cell carcinoma (AcCC). To discover novel gene fusions, we performed whole-transcriptome sequencing surveys of three AcCC archival cases. In one specimen we identified a novel HTN3-MSANTD3 gene fusion, and in another a novel PRB3-ZNF217 gene fusion. The structure of both fusions was consistent with the promoter of the 5’ partner (HTN3 or PRB3), both highly expressed salivary gland genes, driving overexpression of full-length MSANTD3 or ZNF217. By fluorescence in situ hybridization of an expanded AcCC case series, we observed MSANTD3 rearrangements altogether in 3 of 20 evaluable cases (15%), but found no additional ZNF217 rearrangements. MSANTD3 encodes a previously uncharacterized Myb/SANT domain-containing protein. Immunohistochemical staining demonstrated diffuse nuclear MSANTD3 expression in 8 of 27 AcCC cases (30%), including the three cases with MSANTD3 rearrangement. MSANTD3 displayed heterogeneous expression in normal salivary ductal epithelium, as well as among other histologic types of salivary gland cancer though without evidence of translocation. In a broader survey, MSANTD3 showed variable expression across a wide range of normal and neoplastic human tissue specimens. In preliminary functional studies, engineered MSANTD3 overexpression in rodent salivary gland epithelial cells did not enhance cell proliferation, but led to significant upregulation of gene sets involved in protein synthesis. Our findings newly identify MSANTD3 rearrangement as a recurrent event in salivary gland AcCC, providing new insight into disease pathogenesis, and identifying a putative novel human oncogene.
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Affiliation(s)
- Nicholas Barasch
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Xue Gong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kevin A. Kwei
- Genomic Health, Redwood City, California, United States of America
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jewison Biscocho
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kunbin Qu
- Genomic Health, Redwood City, California, United States of America
| | - Nan Xiao
- Arthur A. Dugoni School of Dentistry, University of the Pacific, San Francisco, California, United States of America
| | - Joseph S. Lipsick
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert J. Pelham
- Genomic Health, Redwood City, California, United States of America
| | - Robert B. West
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (RBW); (JRP)
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (RBW); (JRP)
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Murata S, Zhang C, Finch N, Zhang K, Campo L, Breuer EK. Predictors and Modulators of Synthetic Lethality: An Update on PARP Inhibitors and Personalized Medicine. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2346585. [PMID: 27642590 PMCID: PMC5013223 DOI: 10.1155/2016/2346585] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/28/2016] [Indexed: 12/18/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors have proven to be successful agents in inducing synthetic lethality in several malignancies. Several PARP inhibitors have reached clinical trial testing for treatment in different cancers, and, recently, Olaparib (AZD2281) has gained both United States Food and Drug Administration (USFDA) and the European Commission (EC) approval for use in BRCA-mutated advanced ovarian cancer treatment. The need to identify biomarkers, their interactions in DNA damage repair pathways, and their potential utility in identifying patients who are candidates for PARP inhibitor treatment is well recognized. In this review, we detail many of the biomarkers that have been investigated for their ability to predict both PARP inhibitor sensitivity and resistance in preclinical studies as well as the results of several clinical trials that have tested the safety and efficacy of different PARP inhibitor agents in BRCA and non-BRCA-mutated cancers.
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Affiliation(s)
- Stephen Murata
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Catherine Zhang
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Nathan Finch
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Kevin Zhang
- Department of Otorhinolaryngology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Loredana Campo
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Eun-Kyoung Breuer
- Department of Radiation Oncology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
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Peng Z, Yuan C, Zellmer L, Liu S, Xu N, Liao DJ. Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers. J Cancer 2015; 6:555-67. [PMID: 26000048 PMCID: PMC4439942 DOI: 10.7150/jca.11997] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
Recent RNA-sequencing technology and associated bioinformatics have led to identification of tens of thousands of putative human chimeric RNAs, i.e. RNAs containing sequences from two different genes, most of which are derived from neighboring genes on the same chromosome. In this essay, we redefine "two neighboring genes" as those producing individual transcripts, and point out two known mechanisms for chimeric RNA formation, i.e. transcription from a fusion gene or trans-splicing of two RNAs. By our definition, most putative RNA chimeras derived from canonically-defined neighboring genes may either be technical artifacts or be cis-splicing products of 5'- or 3'-extended RNA of either partner that is redefined herein as an unannotated gene, whereas trans-splicing events are rare in human cells. Therefore, most authentic chimeric RNAs result from fusion genes, about 1,000 of which have been identified hitherto. We propose a hypothesis of "consecutive reverse transcriptions (RTs)", i.e. another RT reaction following the previous one, for how most spurious chimeric RNAs, especially those containing a short homologous sequence, may be generated during RT, especially in RNA-sequencing wherein RNAs are fragmented. We also point out that RNA samples contain numerous RNA and DNA shreds that can serve as endogenous random primers for RT and ensuing polymerase chain reactions (PCR), creating artifacts in RT-PCR.
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Affiliation(s)
- Zhiyu Peng
- 1. Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen 518083, P. R. China
| | - Chengfu Yuan
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Lucas Zellmer
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
| | - Siqi Liu
- 3. CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Ningzhi Xu
- 4. Laboratory of Cell and Molecular Biology, Cancer Institute, Chinese Academy of Medical Science, Beijing 100021, P. R. China
| | - D Joshua Liao
- 2. Hormel Institute, University of Minnesota, Austin, MN 55912, USA
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7
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Targeted radiosensitization of ETS fusion-positive prostate cancer through PARP1 inhibition. Neoplasia 2014; 15:1207-17. [PMID: 24204199 DOI: 10.1593/neo.131604] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/01/2013] [Accepted: 10/01/2013] [Indexed: 12/12/2022] Open
Abstract
ETS gene fusions, which result in overexpression of an ETS transcription factor, are considered driving mutations in approximately half of all prostate cancers. Dysregulation of ETS transcription factors is also known to exist in Ewing's sarcoma, breast cancer, and acute lymphoblastic leukemia. We previously discovered that ERG, the predominant ETS family member in prostate cancer, interacts with the DNA damage response protein poly (ADP-ribose) polymerase 1 (PARP1) in human prostate cancer specimens. Therefore, we hypothesized that the ERG-PARP1 interaction may confer radiation resistance by increasing DNA repair efficiency and that this radio-resistance could be reversed through PARP1 inhibition. Using lentiviral approaches, we established isogenic models of ERG overexpression in PC3 and DU145 prostate cancer cell lines. In both cell lines, ERG overexpression increased clonogenic survival following radiation by 1.25 (±0.07) fold (mean ± SEM) and also resulted in increased PARP1 activity. PARP1 inhibition with olaparib preferentially radiosensitized ERG-positive cells by a factor of 1.52 (±0.03) relative to ERG-negative cells (P < .05). Neutral and alkaline COMET assays and immunofluorescence microscopy assessing γ-H2AX foci showed increased short- and long-term efficiencies of DNA repair, respectively, following radiation that was preferentially reversed by PARP1 inhibition. These findings were verified in an in vivo xenograft model. Our findings demonstrate that ERG overexpression confers radiation resistance through increased efficiency of DNA repair following radiation that can be reversed through inhibition of PARP1. These results motivate the use of PARP1 inhibitors as radiosensitizers in patients with localized ETS fusion-positive cancers.
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Nambiar M, Raghavan SC. Chromosomal translocations among the healthy human population: implications in oncogenesis. Cell Mol Life Sci 2013; 70:1381-92. [PMID: 22948164 PMCID: PMC11113647 DOI: 10.1007/s00018-012-1135-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 08/04/2012] [Accepted: 08/13/2012] [Indexed: 01/01/2023]
Abstract
Chromosomal translocations are characteristic features of many cancers, especially lymphoma and leukemia. However, recent reports suggest that many chromosomal translocations can be found in healthy individuals, although the significance of this observation is still not clear. In this review, we summarize recent studies on chromosomal translocations in healthy individuals carried out in different geographical areas of the world and discuss the relevance of the observation with respect to oncogenesis.
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Affiliation(s)
- Mridula Nambiar
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012 India
| | - Sathees C. Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560 012 India
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Bell D, El-Naggar AK. Molecular heterogeneity in mucoepidermoid carcinoma: conceptual and practical implications. Head Neck Pathol 2013; 7:23-7. [PMID: 23459841 PMCID: PMC3597160 DOI: 10.1007/s12105-013-0432-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 02/27/2013] [Indexed: 01/19/2023]
Abstract
Mucoepidermoid carcinoma (MEC), the most common salivary gland malignancy of the upper aerodigestive tract and tracheobronchial tree, is also known for its considerable cellular heterogeneity including epidermoid, intermediate and mucin producing cells. Despite this structural and cellular heterogeneity, MEC is uniquely characterized by a specific translocation t(11; 19) (q12; p13), resulting in a fusion between the MECT1 and the MAML2 genes. Although the incidence of this fusion in MEC varies, it is generally accepted that more than 50 % of this entity manifest the MECT1-MAML2. Fusion-positive cases showed significantly better survival than fusion-negative cases, suggesting that MECT1-MAML2 represents a specific prognostic molecular marker in MEC. We contend that fusion in MEC represents a distinct mechanism in the development of this entity. In that context, fusion positive MEC, regardless of grade, manifest a more stable genome and better clinical behaviour, while fusion negative MEC represent a distinctly different pathway characterized by marked genomic instability and relatively aggressive tumors.
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Affiliation(s)
- Diana Bell
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 USA
| | - Adel K. El-Naggar
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030 USA
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10
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Abstract
Salivary gland carcinomas are a heterogeneous group of tumors with different biologic behavior. Given the lack of large randomized studies, there is no standard treatment for advanced and/or metastatic salivary gland tumors, and systemic therapy is empirically based. Tumor-specific recurrent chromosomal translocations and fusion oncogenes in aggressive head and neck malignancies have diagnostic, therapeutic, and prognostic implications. Pathognomonic fusion transcripts have been identified in subsets of mucoepidermoid carcinoma and adenoid cystic carcinoma. These translocations target 1) transcription factors involved in growth factor signaling and cell cycle regulation, 2) transcriptional co-activators, and 3) tyrosine kinase receptors. Prioritizing studies with a translational component to advance the molecular understanding of these cancers and molecular-targeted therapy clinical trials is critical.
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Affiliation(s)
- Diana Bell
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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11
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Brenner JC, Feng FY, Han S, Patel S, Goyal SV, Bou-Maroun LM, Liu M, Lonigro R, Prensner JR, Tomlins SA, Chinnaiyan AM. PARP-1 inhibition as a targeted strategy to treat Ewing's sarcoma. Cancer Res 2012; 72:1608-13. [PMID: 22287547 PMCID: PMC3319786 DOI: 10.1158/0008-5472.can-11-3648] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Ewing's sarcoma family of tumors (ESFT) refers to aggressive malignancies which frequently harbor characteristic EWS-FLI1 or EWS-ERG genomic fusions. Here, we report that these fusion products interact with the DNA damage response protein and transcriptional coregulator PARP-1. ESFT cells, primary tumor xenografts, and tumor metastases were all highly sensitive to PARP1 inhibition. Addition of a PARP1 inhibitor to the second-line chemotherapeutic agent temozolamide resulted in complete responses of all treated tumors in an EWS-FLI1-driven mouse xenograft model of ESFT. Mechanistic investigations revealed that DNA damage induced by expression of EWS-FLI1 or EWS-ERG fusion genes was potentiated by PARP1 inhibition in ESFT cell lines. Notably, EWS-FLI1 fusion genes acted in a positive feedback loop to maintain the expression of PARP1, which was required for EWS-FLI-mediated transcription, thereby enforcing oncogene-dependent sensitivity to PARP-1 inhibition. Together, our findings offer a strong preclinical rationale to target the EWS-FLI1:PARP1 intersection as a therapeutic strategy to improve the treatment of ESFTs.
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Affiliation(s)
- J Chad Brenner
- Michigan Center for Translational Pathology, Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
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Oncogene-specific activation of tyrosine kinase networks during prostate cancer progression. Proc Natl Acad Sci U S A 2012; 109:1643-8. [PMID: 22307624 DOI: 10.1073/pnas.1120985109] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Dominant mutations or DNA amplification of tyrosine kinases are rare among the oncogenic alterations implicated in prostate cancer. We demonstrate that castration-resistant prostate cancer (CRPC) in men exhibits increased tyrosine phosphorylation, raising the question of whether enhanced tyrosine kinase activity is observed in prostate cancer in the absence of specific tyrosine kinase mutation or DNA amplification. We generated a mouse model of prostate cancer progression using commonly perturbed non-tyrosine kinase oncogenes and pathways and detected a significant up-regulation of tyrosine phosphorylation at the carcinoma stage. Phosphotyrosine peptide enrichment and quantitative mass spectrometry identified oncogene-specific tyrosine kinase signatures, including activation of EGFR, ephrin type-A receptor 2 (EPHA2), and JAK2. Kinase:substrate relationship analysis of the phosphopeptides also revealed ABL1 and SRC tyrosine kinase activation. The observation of elevated tyrosine kinase signaling in advanced prostate cancer and identification of specific tyrosine kinase pathways from genetically defined tumor models point to unique therapeutic approaches using tyrosine kinase inhibitors for advanced prostate cancer.
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13
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Leacock SW, Basse AN, Chandler GL, Kirk AM, Rakheja D, Amatruda JF. A zebrafish transgenic model of Ewing's sarcoma reveals conserved mediators of EWS-FLI1 tumorigenesis. Dis Model Mech 2011; 5:95-106. [PMID: 21979944 PMCID: PMC3255547 DOI: 10.1242/dmm.007401] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ewing’s sarcoma, a malignant bone tumor of children and young adults, is a member of the small-round-blue-cell tumor family. Ewing’s sarcoma family tumors (ESFTs), which include peripheral primitive neuroectodermal tumors (PNETs), are characterized by chromosomal translocations that generate fusions between the EWS gene and ETS-family transcription factors, most commonly FLI1. The EWS-FLI1 fusion oncoprotein represents an attractive therapeutic target for treatment of Ewing’s sarcoma. The cell of origin of ESFT and the molecular mechanisms by which EWS-FLI1 mediates tumorigenesis remain unknown, and few animal models of Ewing’s sarcoma exist. Here, we report the use of zebrafish as a vertebrate model of EWS-FLI1 function and tumorigenesis. Mosaic expression of the human EWS-FLI1 fusion protein in zebrafish caused the development of tumors with histology strongly resembling that of human Ewing’s sarcoma. The incidence of tumors increased in a p53 mutant background, suggesting that the p53 pathway suppresses EWS-FLI1-driven tumorigenesis. Gene expression profiling of the zebrafish tumors defined a set of genes that might be regulated by EWS-FLI1, including the zebrafish ortholog of a crucial EWS-FLI1 target gene in humans. Stable zebrafish transgenic lines expressing EWS-FLI1 under the control of the heat-shock promoter exhibit altered embryonic development and defective convergence and extension, suggesting that EWS-FLI1 interacts with conserved developmental pathways. These results indicate that functional targets of EWS-FLI1 that mediate tumorigenesis are conserved from zebrafish to human and provide a novel context in which to study the function of this fusion oncogene.
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Affiliation(s)
- Stefanie W Leacock
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-8534, USA
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Mitani Y, Rao PH, Futreal PA, Roberts DB, Stephens PJ, Zhao YJ, Zhang L, Mitani M, Weber RS, Lippman SM, Caulin C, El-Naggar AK. Novel chromosomal rearrangements and break points at the t(6;9) in salivary adenoid cystic carcinoma: association with MYB-NFIB chimeric fusion, MYB expression, and clinical outcome. Clin Cancer Res 2011; 17:7003-14. [PMID: 21976542 DOI: 10.1158/1078-0432.ccr-11-1870] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE To investigate the molecular genetic heterogeneity associated with the t(6:9) in adenoid cystic carcinoma (ACC) and correlate the findings with patient clinical outcome. EXPERIMENTAL DESIGN Multimolecular and genetic techniques complemented with massive pair-ended sequencing and single-nucleotide polymorphism array analyses were used on tumor specimens from 30 new and 52 previously analyzed fusion transcript-negative ACCs by reverse transcriptase PCR (RT-PCR). MYB mRNA expression level was determined by quantitative RT-PCR. The results of 102 tumors (30 new and 72 previously reported cases) were correlated with the clinicopathologic factors and patients' survival. RESULTS The FISH analysis showed 34 of 82 (41.5%) fusion-positive tumors and molecular techniques identified fusion transcripts in 21 of the 82 (25.6%) tumors. Detailed FISH analysis of 11 out the 15 tumors with gene fusion without transcript formation showed translocation of NFIB sequences to proximal or distal sites of the MYB gene. Massive pair-end sequencing of a subset of tumors confirmed the proximal translocation to an NFIB sequence and led to the identification of a new fusion gene (NFIB-AIG1) in one of the tumors. Overall, MYB-NFIB gene fusion rate by FISH was in 52.9% whereas fusion transcript forming incidence was 38.2%. Significant statistical association between the 5' MYB transcript expression and patient survival was found. CONCLUSIONS We conclude that: (i) t(6;9) results in complex genetic and molecular alterations in ACC, (ii) MYB-NFIB gene fusion may not always be associated with chimeric transcript formation, (iii) noncanonical MYB-NFIB gene fusions occur in a subset of tumors, (iv) high MYB expression correlates with worse patient survival.
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Affiliation(s)
- Yoshitsugu Mitani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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15
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Nambiar M, Raghavan SC. How does DNA break during chromosomal translocations? Nucleic Acids Res 2011; 39:5813-25. [PMID: 21498543 PMCID: PMC3152359 DOI: 10.1093/nar/gkr223] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 03/25/2011] [Accepted: 03/29/2011] [Indexed: 12/20/2022] Open
Abstract
Chromosomal translocations are one of the most common types of genetic rearrangements and are molecular signatures for many types of cancers. They are considered as primary causes for cancers, especially lymphoma and leukemia. Although many translocations have been reported in the last four decades, the mechanism by which chromosomes break during a translocation remains largely unknown. In this review, we summarize recent advances made in understanding the molecular mechanism of chromosomal translocations.
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Affiliation(s)
- Mridula Nambiar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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16
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Yan J, Diaz J, Jiao J, Wang R, You J. Perturbation of BRD4 protein function by BRD4-NUT protein abrogates cellular differentiation in NUT midline carcinoma. J Biol Chem 2011; 286:27663-75. [PMID: 21652721 DOI: 10.1074/jbc.m111.246975] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
NUT midline carcinoma (NMC) belongs to a class of highly lethal and poorly differentiated epithelial cancers arising mainly in human midline organs. NMC is caused by the chromosome translocation-mediated fusion of the NUT (nuclear protein in testis) gene on chromosome 15 to a few other genes, most frequently the BRD4 gene on chromosome 19. The mechanism by which the BRD4-NUT fusion product blocks NMC cellular differentiation and contributes to oncogenesis remains elusive. In this study, we show that BRD4-NUT and BRD4 colocalize in discrete nuclear foci that are hyperacetylated but transcriptionally inactive. BRD4-NUT recruits histone acetyltransferases to induce histone hyperacetylation in these chromatin foci, which provide docking sites for accumulation of additional BRD4 and associated P-TEFB (positive transcription elongation factor b) complexes in the transcriptionally inactive BRD4-NUT foci. These molecular events lead to repression of a BRD4·P-TEFB downstream target gene c-fos, a component of activator protein 1 (AP-1), that directly regulates epithelial differentiation. Knockdown of BRD4-NUT in NMC cells disperses the transcriptionally inactive chromatin foci and releases the transcriptional activators to stimulate c-fos expression, leading to restoration of cellular differentiation. Our study provides a novel mechanism by which the BRD4-NUT oncogene perturbs BRD4 functions to block cellular differentiation and to contribute to the oncogenic progression in the highly aggressive NMC.
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Affiliation(s)
- Junpeng Yan
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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17
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Brenner JC, Ateeq B, Li Y, Yocum AK, Cao Q, Asangani IA, Patel S, Wang X, Liang H, Yu J, Palanisamy N, Siddiqui J, Yan W, Cao X, Mehra R, Sabolch A, Basrur V, Lonigro RJ, Yang J, Tomlins SA, Maher CA, Elenitoba-Johnson KS, Hussain M, Navone NM, Pienta KJ, Varambally S, Feng FY, Chinnaiyan AM. Mechanistic rationale for inhibition of poly(ADP-ribose) polymerase in ETS gene fusion-positive prostate cancer. Cancer Cell 2011; 19:664-78. [PMID: 21575865 PMCID: PMC3113473 DOI: 10.1016/j.ccr.2011.04.010] [Citation(s) in RCA: 339] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 03/02/2011] [Accepted: 04/19/2011] [Indexed: 01/09/2023]
Abstract
Recurrent fusions of ETS genes are considered driving mutations in a diverse array of cancers, including Ewing's sarcoma, acute myeloid leukemia, and prostate cancer. We investigate the mechanisms by which ETS fusions mediate their effects, and find that the product of the predominant ETS gene fusion, TMPRSS2:ERG, interacts in a DNA-independent manner with the enzyme poly (ADP-ribose) polymerase 1 (PARP1) and the catalytic subunit of DNA protein kinase (DNA-PKcs). ETS gene-mediated transcription and cell invasion require PARP1 and DNA-PKcs expression and activity. Importantly, pharmacological inhibition of PARP1 inhibits ETS-positive, but not ETS-negative, prostate cancer xenograft growth. Finally, overexpression of the TMPRSS2:ERG fusion induces DNA damage, which is potentiated by PARP1 inhibition in a manner similar to that of BRCA1/2 deficiency.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Catalytic Domain
- Cell Line, Tumor
- Cell Movement
- Chick Embryo
- Chromatin Immunoprecipitation
- DNA Damage
- DNA-Activated Protein Kinase/metabolism
- Enzyme Inhibitors/pharmacology
- Gene Expression Regulation, Neoplastic
- Gene Fusion
- Genes, Reporter
- HEK293 Cells
- Humans
- Male
- Mass Spectrometry
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Mice, SCID
- Models, Molecular
- Neoplasm Invasiveness
- Oncogene Proteins, Fusion/chemistry
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Phthalazines/pharmacology
- Piperazines/pharmacology
- Poly (ADP-Ribose) Polymerase-1
- Poly(ADP-ribose) Polymerase Inhibitors
- Poly(ADP-ribose) Polymerases/genetics
- Poly(ADP-ribose) Polymerases/metabolism
- Prostatic Neoplasms/drug therapy
- Prostatic Neoplasms/enzymology
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/pathology
- Protein Conformation
- RNA Interference
- Recombinant Fusion Proteins/metabolism
- Time Factors
- Transcriptional Activation
- Transfection
- Tumor Burden
- Xenograft Model Antitumor Assays
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Affiliation(s)
- J. Chad Brenner
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Bushra Ateeq
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Yong Li
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Anastasia K. Yocum
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Qi Cao
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Irfan A. Asangani
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Sonam Patel
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Xiaoju Wang
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Hallie Liang
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Jindan Yu
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Medicine, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Nallasivam Palanisamy
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Medicine, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Wei Yan
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Howard Hughes Medical Institute, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Rohit Mehra
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Aaron Sabolch
- Department of Radiation Oncology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Venkatesha Basrur
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Robert J. Lonigro
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Jun Yang
- Department of Genitourinary Medical Oncology, and David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Christopher A. Maher
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Biology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Kojo S.J. Elenitoba-Johnson
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Maha Hussain
- Department of Medicine, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Nora M. Navone
- Department of Genitourinary Medical Oncology, and David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas M. D. Anderson Cancer Center, Houston, TX
| | - Kenneth J. Pienta
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Medicine, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Sooryanarayana Varambally
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Felix Y. Feng
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Radiation Oncology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Pathology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Howard Hughes Medical Institute, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Department of Urology, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Comprehensive Cancer Center, University of Michigan 1400 E. Medical Center Drive, 5316 CCGC, Ann Arbor, MI 48109, USA
- Corresponding author. Tel.: + 734 615-4062, (A.Chinnaiyan), URL: http://www.pathology.med.umich.edu/dynamo/chinnaiyan/index.jsp
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18
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The role of mechanistic factors in promoting chromosomal translocations found in lymphoid and other cancers. Adv Immunol 2010; 106:93-133. [PMID: 20728025 DOI: 10.1016/s0065-2776(10)06004-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recurrent chromosomal abnormalities, especially chromosomal translocations, are strongly associated with certain subtypes of leukemia, lymphoma and solid tumors. The appearance of particular translocations or associated genomic alterations can be important indicators of disease prognosis, and in some cases, certain translocations may indicate appropriate therapy protocols. To date, most of our knowledge about chromosomal translocations has derived from characterization of the highly selected recurrent translocations found in certain cancers. Until recently, mechanisms that promote or suppress chromosomal translocations, in particular, those responsible for their initiation, have not been addressed. For translocations to occur, two distinct chromosomal loci must be broken, brought together (synapsed) and joined. Here, we discuss recent findings on processes and pathways that influence the initiation of chromosomal translocations, including the generation fo DNA double strand breaks (DSBs) by general factors or in the context of the Lymphocyte-specific V(D)J and IgH class-switch recombination processes. We also discuss the role of spatial proximity of DSBs in the interphase nucleus with respect to how DSBs on different chromosomes are justaposed for joining. In addition, we discuss the DNA DSB response and its role in recognizing and tethering chromosomal DSBs to prevent translocations, as well as potential roles of the classical and alternative DSB end-joining pathways in suppressing or promoting translocations. Finally, we discuss the potential roles of long range regulatory elements, such as the 3'IgH enhancer complex, in promoting the expression of certain translocations that are frequent in lymphomas and, thereby, contributing to their frequent appearance in tumors.
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19
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Mitani Y, Li J, Rao PH, Zhao YJ, Bell D, Lippman SM, Weber RS, Caulin C, El-Naggar AK. Comprehensive analysis of the MYB-NFIB gene fusion in salivary adenoid cystic carcinoma: Incidence, variability, and clinicopathologic significance. Clin Cancer Res 2010; 16:4722-31. [PMID: 20702610 DOI: 10.1158/1078-0432.ccr-10-0463] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The objectives of this study were to determine the incidence of the MYB-NFIB fusion in salivary adenoid cystic carcinoma (ACC), to establish the clinicopathologic significance of the fusion, and to analyze the expression of MYB in ACCs in the context of the MYB-NFIB fusion. EXPERIMENTAL DESIGN We did an extensive analysis involving 123 cancers of the salivary gland, including primary and metastatic ACCs, and non-ACC salivary carcinomas. MYB-NFIB fusions were identified by reverse transcriptase-PCR (RT-PCR) and sequencing of the RT-PCR products, and confirmed by fluorescence in situ hybridization. MYB RNA expression was determined by quantitative RT-PCR and protein expression was analyzed by immunohistochemistry. RESULTS The MYB-NFIB fusion was detected in 28% primary and 35% metastatic ACCs, but not in any of the non-ACC salivary carcinomas analyzed. Different exons in both the MYB and NFIB genes were involved in the fusions, resulting in expression of multiple chimeric variants. Notably, MYB was overexpressed in the vast majority of the ACCs, although MYB expression was significantly higher in tumors carrying the MYB-NFIB fusion. The presence of the MYB-NFIB fusion was significantly associated (P = 0.03) with patients older than 50 years of age. No correlation with other clinicopathologic markers, factors, and survival was found. CONCLUSIONS We conclude that the MYB-NFIB fusion characterizes a subset of ACCs and contributes to MYB overexpression. Additional mechanisms may be involved in MYB overexpression in ACCs lacking the MYB-NFIB fusion. These findings suggest that MYB may be a specific novel target for tumor intervention in patients with ACC.
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Affiliation(s)
- Yoshitsugu Mitani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, 77030-4009, USA
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20
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Weigelt B, Geyer FC, Reis-Filho JS. Histological types of breast cancer: how special are they? Mol Oncol 2010; 4:192-208. [PMID: 20452298 PMCID: PMC5527938 DOI: 10.1016/j.molonc.2010.04.004] [Citation(s) in RCA: 284] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 04/11/2010] [Accepted: 04/12/2010] [Indexed: 12/16/2022] Open
Abstract
Breast cancer is a heterogeneous disease, comprising multiple entities associated with distinctive histological and biological features, clinical presentations and behaviours and responses to therapy. Microarray-based technologies have unravelled the molecular underpinning of several characteristics of breast cancer, including metastatic propensity and histological grade, and have led to the identification of prognostic and predictive gene expression signatures. Furthermore, a molecular taxonomy of breast cancer based on transcriptomic analysis has been proposed. However, microarray studies have primarily focused on invasive ductal carcinomas of no special type. Owing to the relative rarity of special types of breast cancer, information about the biology and clinical behaviour of breast cancers conveyed by histological type has not been taken into account. Histological special types of breast cancer account for up to 25% of all invasive breast cancers. Recent studies have provided direct evidence of the existence of genotypic-phenotypic correlations. For instance, secretory carcinomas of the breast consistently harbour the t(12;15) translocation that leads to the formation of the ETV6-NTRK3 fusion gene, adenoid cystic carcinomas consistently display the t(6;9) MYB-NFIB translocation and lobular carcinomas consistently show inactivation of the CDH1 gene through multiple molecular mechanisms. Furthermore, histopathological and molecular analysis of tumours from conditional mouse models has provided direct evidence for the causative role of specific genes in the genesis of specific histological special types of breast cancer. Here we review the associations between the molecular taxonomy of breast cancer and histological special types, discuss the possible origins of the heterogeneity of breast cancer and propose an approach for the identification of novel therapeutic targets based on the study of histological special types of breast cancer.
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Affiliation(s)
- Britta Weigelt
- Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, London WC2A 3PX, UK
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Chari R, Thu KL, Wilson IM, Lockwood WW, Lonergan KM, Coe BP, Malloff CA, Gazdar AF, Lam S, Garnis C, MacAulay CE, Alvarez CE, Lam WL. Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer. Cancer Metastasis Rev 2010; 29:73-93. [PMID: 20108112 DOI: 10.1007/s10555-010-9199-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Advances in high-throughput, genome-wide profiling technologies have allowed for an unprecedented view of the cancer genome landscape. Specifically, high-density microarrays and sequencing-based strategies have been widely utilized to identify genetic (such as gene dosage, allelic status, and mutations in gene sequence) and epigenetic (such as DNA methylation, histone modification, and microRNA) aberrations in cancer. Although the application of these profiling technologies in unidimensional analyses has been instrumental in cancer gene discovery, genes affected by low-frequency events are often overlooked. The integrative approach of analyzing parallel dimensions has enabled the identification of (a) genes that are often disrupted by multiple mechanisms but at low frequencies by any one mechanism and (b) pathways that are often disrupted at multiple components but at low frequencies at individual components. These benefits of using an integrative approach illustrate the concept that the whole is greater than the sum of its parts. As efforts have now turned toward parallel and integrative multidimensional approaches for studying the cancer genome landscape in hopes of obtaining a more insightful understanding of the key genes and pathways driving cancer cells, this review describes key findings disseminating from such high-throughput, integrative analyses, including contributions to our understanding of causative genetic events in cancer cell biology.
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Affiliation(s)
- Raj Chari
- Genetics Unit - Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada.
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