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Nair NU, Schäffer AA, Gertz EM, Cheng K, Zerbib J, Sahu AD, Leor G, Shulman ED, Aldape KD, Ben-David U, Ruppin E. Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576103. [PMID: 38313282 PMCID: PMC10836086 DOI: 10.1101/2024.01.17.576103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
The co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas is the most frequent loss-gain co-aneuploidy pair in human cancers, a phenomenon that has been investigated without resolution since the late 1980s. Expanding beyond previous gene-centric studies, we investigate the co-occurrence in a genome-wide manner taking an evolutionary perspective. First, by mining large tumor aneuploidy data, we predict that the more likely order is 10 loss followed by 7 gain. Second, by analyzing extensive genomic and transcriptomic data from both patients and cell lines, we find that this co-occurrence can be explained by functional rescue interactions that are highly enriched on 7, which can possibly compensate for any detrimental consequences arising from the loss of 10. Finally, by analyzing transcriptomic data from normal, non-cancerous, human brain tissues, we provide a plausible reason why this co-occurrence happens preferentially in cancers originating in certain regions of the brain.
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Karami Fath M, Akbari Oryani M, Ramezani A, Barjoie Mojarad F, Khalesi B, Delazar S, Anjomrooz M, Taghizadeh A, Taghizadeh S, Payandeh Z, Pourzardosht N. Extra chromosomal DNA in different cancers: Individual genome with important biological functions. Crit Rev Oncol Hematol 2021; 166:103477. [PMID: 34534658 DOI: 10.1016/j.critrevonc.2021.103477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 12/21/2022] Open
Abstract
Cancer can be caused by various factors, including the malfunction of tumor suppressor genes and the hyper-activation of proto-oncogenes. Tumor-associated extrachromosomal circular DNA (eccDNA) has been shown to adversely affect human health and accelerate malignant actions. Whole-genome sequencing (WGS) on different cancer types suggested that the amplification of ecDNA has increased the oncogene copy number in various cancers. The unique structure and function of ecDNA, its profound significance in cancer, and its help in the comprehension of current cancer genome maps, renders it as a hotspot to explore the tumor pathogenesis and evolution. Illumination of the basic mechanisms of ecDNA may provide more insights into cancer therapeutics. Despite the recent advances, different features of ecDNA require further elucidation. In the present review, we primarily discussed the characteristics, biogenesis, genesis, and origin of ecDNA and later highlighted its functions in both tumorigenesis and therapeutic resistance of different cancers.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mahsa Akbari Oryani
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arefeh Ramezani
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Barjoie Mojarad
- Department of Radiology, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Sina Delazar
- Department of Radiology, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehran Anjomrooz
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Arvin Taghizadeh
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Taghizadeh
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran.
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Hong DS, LoRusso P, Hamid O, Janku F, Kittaneh M, Catenacci DVT, Chan E, Bekaii-Saab T, Gadgeel SM, Loberg RD, Amore BM, Hwang YC, Tang R, Ngarmchamnanrith G, Kwak EL. Phase I Study of AMG 337, a Highly Selective Small-molecule MET Inhibitor, in Patients with Advanced Solid Tumors. Clin Cancer Res 2019; 25:2403-2413. [PMID: 30425090 PMCID: PMC6892342 DOI: 10.1158/1078-0432.ccr-18-1341] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/28/2018] [Accepted: 11/08/2018] [Indexed: 12/25/2022]
Abstract
PURPOSE This first-in-human, open-label phase I study evaluated AMG 337, an oral, highly selective small-molecule inhibitor of MET in advanced solid tumors.Patients and Methods: Patients enrolled into dose-escalation cohorts received AMG 337 up to 400 mg once daily or up to 250 mg twice daily, following a modified 3+3+3 design. Dose expansion was conducted in MET-amplified patients at the maximum tolerated dose (MTD). Primary endpoints included assessment of adverse events (AEs), establishment of the MTD, and pharmacokinetics; clinical response was a secondary endpoint. RESULTS The safety analysis set included 111 patients who received ≥1 dose of AMG 337. Thirteen patients had ≥1 AE qualifying as dose-limiting toxicity. The MTD was determined to be 300 mg once daily; the MTD for twice-daily dosing was not reached. Most frequent treatment-related AEs were headache (63%) and nausea (31%). Grade ≥3 treatment-related AEs occurred in 23 patients (21%), most commonly headache (n = 6) and fatigue (n = 5). Maximum plasma concentration occurred at 3.0 hours following 300-mg once-daily dosing, indicating AMG 337 absorption soon after treatment. Objective response rate was 9.9% (11/111; 95% CI, 5.1%-17.0%) in all patients and 29.6% (8/27; 95% CI, 13.8%-50.2%) in MET-amplified patients; median (range) duration of response was 202 (51-1,430+) days in all patients and 197 (64-1,430+) days in MET-amplified patients. CONCLUSIONS Oral AMG 337 was tolerated with manageable toxicities, with an MTD and recommended phase II dose of 300 mg once daily. The promising response rate observed in patients with heavily pretreated MET-amplified tumors warrants further investigation.See related commentary by Ma, p. 2375.
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Affiliation(s)
- David S Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | | | - Omid Hamid
- Melanoma Center, The Angeles Clinic and Research Institute, Los Angeles, California
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Muaiad Kittaneh
- Hematology/Oncology, Loyola University Chicago Stritch School of Medicine, Chicago, Illinois
| | | | - Emily Chan
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | | | - Shirish M Gadgeel
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Thoracic Oncology, Karmanos Cancer Institute, Detroit, Michigan
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan
| | | | - Benny M Amore
- Clinical Pharmacology, Modeling and Simulation, Amgen Inc., South San Francisco, California
| | - Yuying C Hwang
- Global Biostatistical Sciences, Amgen Inc., Thousand Oaks, California
| | - Rui Tang
- Global Biostatistical Sciences, Amgen Inc., Thousand Oaks, California
| | | | - Eunice L Kwak
- Hematology/Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts
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4
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Van Cutsem E, Karaszewska B, Kang YK, Chung HC, Shankaran V, Siena S, Go NF, Yang H, Schupp M, Cunningham D. A Multicenter Phase II Study of AMG 337 in Patients with MET-Amplified Gastric/Gastroesophageal Junction/Esophageal Adenocarcinoma and Other MET-Amplified Solid Tumors. Clin Cancer Res 2018; 25:2414-2423. [PMID: 30366938 DOI: 10.1158/1078-0432.ccr-18-1337] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 09/26/2018] [Accepted: 10/22/2018] [Indexed: 12/18/2022]
Abstract
PURPOSE MET gene amplification is associated with poor prognosis in gastric/gastroesophageal junction/esophageal (G/GEJ/E) cancers. We determined antitumor activity, safety, and pharmacokinetics of the small-molecule MET inhibitor AMG 337 in MET-amplified G/GEJ/E adenocarcinoma or other solid tumors.Patients and Methods: In this phase II, single-arm study, adults with MET-amplified G/GEJ/E adenocarcinoma (cohort 1) or other MET-amplified solid tumors (cohort 2) received AMG 337 300 mg/day orally in 28-day cycles. The primary endpoint was objective response rate (ORR; cohort 1). Secondary endpoints included ORR (cohort 2), progression-free survival (PFS), overall survival (OS), and safety. RESULTS Of 2101 patients screened for MET amplification, 132 were MET-amplified and 60 were enrolled: 45 in cohort 1, and 15 in cohort 2. Fifty-six patients (97%) had metastatic disease; 57 had prior lines of therapy (1 prior line, 29%; ≥2 prior lines, 69%). A protocol-permitted review showed efficacy that was lower-than-expected based on preliminary data from a first-in-human study, and enrollment was stopped. Fifty-eight patients received ≥1 AMG 337 dose. ORR in cohort 1 was 18% (8 partial responses). No responses were observed in cohort 2. Of 54 evaluable patients, median (95% CI) PFS and OS were 3.4 (2.2-5.0) and 7.9 (4.8-10.9) months, respectively. The most frequent adverse events (AEs) were headache (60%), nausea (38%), vomiting (38%), and abdominal pain, decreased appetite, and peripheral edema (33% each); 71% had grade ≥3 AEs and 59% had serious AEs. CONCLUSIONS AMG 337 showed antitumor activity in MET-amplified G/GEJ/E adenocarcinoma but not in MET-amplified non-small-cell lung cancer.See related commentary by Ma, p. 2375.
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Affiliation(s)
- Eric Van Cutsem
- Department of Digestive Oncology, University Hospitals Gasthuisberg, Leuven, and KU Leuven, Leuven, Belgium.
| | | | - Yoon-Koo Kang
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Hyun Cheol Chung
- Department of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, South Korea
| | - Veena Shankaran
- Division of Medical Oncology, University of Washington, Seattle, Washington
| | - Salvatore Siena
- Department of Hematology and Oncology, Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Dipartimento di Oncologia and Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | - Ning F Go
- Clinical Biomarkers and Diagnostics, Amgen Inc., Thousand Oaks, California
| | - Hui Yang
- Global Biostatistical Sciences, Amgen Inc., Thousand Oaks, California
| | - Marco Schupp
- Global Development, Amgen (Europe) GmbH, Zug, Switzerland
| | - David Cunningham
- Department of Medicine, Royal Marsden Hospital, London, United Kingdom
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Raghav K, Bailey AM, Loree JM, Kopetz S, Holla V, Yap TA, Wang F, Chen K, Salgia R, Hong D. Untying the gordion knot of targeting MET in cancer. Cancer Treat Rev 2018; 66:95-103. [PMID: 29730462 DOI: 10.1016/j.ctrv.2018.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 01/30/2023]
Abstract
Despite compelling evidence backing the crucial role of a dysregulated MET axis in cancer and a myriad of agents targeting this pathway in active clinical development, the therapeutic value of MET inhibition in cancer oncology remains to be established. Although a series of disappointing clinical trials, at first, lessened fervor for targeting this pathway, investigations continue unabated with a number of novel active compounds entering clinical trials. Suboptimal designs which lacked biomarker selection have been the main reason for these early failures and this has stimulated a more biomarker enriched approach lately. Fresh insights into the mechanics of diverse MET aberrations (amplifications and mutations) have allowed trial enrichment for appropriate patients in appropriate disease settings. Development of MET inhibition as a therapeutic strategy in cancer has been a lesson in itself reflecting the challenging opportunities enclosed in the genetic landscape of cancer. Here, we will review the status of MET targeted therapy in development as it stands today, discuss emerging paradigms in MET inhibition and theorize on concepts for future development. We venture to propose that in spite of early disappointments, the future of this therapeutic strategy is promising with use of appropriate predictive biomarker in the right clinical context.
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Affiliation(s)
- Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ann Marie Bailey
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jonathan M Loree
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Vijaykumar Holla
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Timothy Anthony Yap
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Fang Wang
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ken Chen
- Department of Bioinformatics & Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ravi Salgia
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, United States
| | - David Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.
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6
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Yasui H, Go N, Yang H, Amore BM, Jung AS, Doi T. A Phase 1 study evaluating AMG 337 in Asian patients with advanced solid tumors. Jpn J Clin Oncol 2017; 47:772-776. [PMID: 28582510 DOI: 10.1093/jjco/hyx067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/22/2017] [Indexed: 11/12/2022] Open
Abstract
AMG 337, a selective small-molecule MET inhibitor, was evaluated in Asian patients with advanced solid tumors. Eligible patients orally self-administered AMG 337; the initial dose of 150 mg once daily (QD) was escalated to 300 mg QD (modified 3+3+3 design). Treatment continued until disease progression, intolerability, or death. The primary endpoint was adverse events (AEs) and clinical abnormalities defined as dose-limiting toxicities (DLTs). Secondary endpoints included other AEs, pharmacokinetics and tumor response. Eleven patients were enrolled. No DLTs occurred. The most common treatment-emergent AEs were headache (73%) and nausea (45%). Cmax and AUC0-24 exposures increased proportionally with dose; t1/2 was comparable between groups; plasma accumulation was minimal over 28 days. One patient (150 mg) had partial response; one patient (300 mg) had stable disease. Safety, tolerability, pharmacokinetics and efficacy of AMG 337 in Asian patients were consistent with those observed in Western patient populations. The study was terminated early.
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Affiliation(s)
| | - Ning Go
- Amgen Inc., Thousand Oaks, CA, USA
| | - Hui Yang
- Amgen Inc., Thousand Oaks, CA, USA
| | | | | | - Toshihiko Doi
- National Cancer Center Hospital East, Kashiwa, Chiba, Japan
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7
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Lee J, Tran P, Klempner SJ. Targeting the MET Pathway in Gastric and Oesophageal Cancers: Refining the Optimal Approach. Clin Oncol (R Coll Radiol) 2016; 28:e35-44. [PMID: 26880063 DOI: 10.1016/j.clon.2016.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/09/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022]
Abstract
Gastric and oesophageal cancers are a major cause of global cancer-related morbidity and mortality. Improvements in treatment for locoregional and metastatic gastric and oesophageal cancer have been incremental and the overall prognosis remains poor. Increasingly, molecular classification has identified recurrent, therapeutically relevant, somatic alterations in gastroesophageal malignancies. However, other than ERBB2 amplification, molecularly directed therapies have not translated to improved survival. Amplification of the receptor tyrosine kinase MET is found in about 5% of gastroesophageal cancers and represents an oncogenic driver and therapeutic target. Small series have shown activity of MET-directed tyrosine kinase inhibitors, but the clinical benefit of anti-MET antibodies has been disappointing. Here we discuss the MET pathway in gastroesophageal cancers, the clinical data for MET small molecule tyrosine kinase inhibitors, anti-MET antibodies and future clinical directions for targeting MET in gastric and oesophageal cancers. To our knowledge, this is the most comprehensive review of the clinical experience with MET-directed therapies in gastric and oesophageal cancers.
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Affiliation(s)
- J Lee
- Department of Medicine, University of California Irvine, Orange, CA, USA
| | - P Tran
- Division of Hematology-Oncology, University of California Irvine, Orange, CA, USA
| | - S J Klempner
- Division of Hematology-Oncology, University of California Irvine, Orange, CA, USA.
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8
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Activating MET kinase rearrangements in melanoma and Spitz tumours. Nat Commun 2015; 6:7174. [PMID: 26013381 PMCID: PMC4446791 DOI: 10.1038/ncomms8174] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 04/14/2015] [Indexed: 12/11/2022] Open
Abstract
Oncogenic gene fusions have been identified in many cancers and many serve as biomarkers or targets for therapy. Here we identify six different melanocytic tumors with genomic rearrangements of MET fusing the kinase domain of MET in-frame to six different N-terminal partners. These tumors lack activating mutations in other established melanoma oncogenes. We functionally characterize two of the identified fusion proteins (TRIM4-MET and ZKSCAN1-MET) and find that they constitutively activate the mitogen-activated protein kinase (MAPK), phosphoinositol-3 kinase (PI3K), and phospholipase C gamma 1 (PLCγ1) pathways. The MET inhibitors cabozantinib (FDA-approved for progressive medullary thyroid cancer) and PF-04217903 block their activity at nanomolar concentrations. MET fusion kinases thus provide a potential therapeutic target for a rare subset of melanoma for which currently no targeted therapeutic options currently exist.
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Camacho CV, Todorova PK, Gillam MC, Tomimatsu N, del Alcazar CRG, Ilcheva M, Mukherjee B, McEllin B, Vemireddy V, Hatanpaa K, Story MD, Habib AA, Murty VV, Bachoo R, Burma S. DNA double-strand breaks cooperate with loss of Ink4 and Arf tumor suppressors to generate glioblastomas with frequent Met amplification. Oncogene 2015; 34:1064-72. [PMID: 24632607 PMCID: PMC4167163 DOI: 10.1038/onc.2014.29] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/31/2013] [Accepted: 01/01/2014] [Indexed: 12/15/2022]
Abstract
Glioblastomas (GBM) are highly radioresistant and lethal brain tumors. Ionizing radiation (IR)-induced DNA double-strand breaks (DSBs) are a risk factor for the development of GBM. In this study, we systematically examined the contribution of IR-induced DSBs to GBM development using transgenic mouse models harboring brain-targeted deletions of key tumor suppressors frequently lost in GBM, namely Ink4a, Ink4b, Arf and/or PTEN. Using low linear energy transfer (LET) X-rays to generate simple breaks or high LET HZE particles (Fe ions) to generate complex breaks, we found that DSBs induce high-grade gliomas in these mice which, otherwise, do not develop gliomas spontaneously. Loss of Ink4a and Arf was sufficient to trigger IR-induced glioma development but additional loss of Ink4b significantly increased tumor incidence. We analyzed IR-induced tumors for copy number alterations to identify oncogenic changes that were generated and selected for as a consequence of stochastic DSB events. We found Met amplification to be the most significant oncogenic event in these radiation-induced gliomas. Importantly, Met activation resulted in the expression of Sox2, a GBM cancer stem cell marker, and was obligatory for tumor formation. In sum, these results indicate that radiation-induced DSBs cooperate with loss of Ink4 and Arf tumor suppressors to generate high-grade gliomas that are commonly driven by Met amplification and activation.
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Affiliation(s)
- Cristel V. Camacho
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Pavlina K. Todorova
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Molly C. Gillam
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Nozomi Tomimatsu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Mariya Ilcheva
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Bipasha Mukherjee
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Brian McEllin
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Vamsidhara Vemireddy
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kimmo Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Michael D. Story
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Amyn A. Habib
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
- VA North Texas Health Care System, Dallas, TX
| | - Vundavalli V. Murty
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
| | - Robert Bachoo
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sandeep Burma
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX
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10
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Smyth EC, Sclafani F, Cunningham D. Emerging molecular targets in oncology: clinical potential of MET/hepatocyte growth-factor inhibitors. Onco Targets Ther 2014; 7:1001-14. [PMID: 24959087 PMCID: PMC4061165 DOI: 10.2147/ott.s44941] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The MET/hepatocyte growth-factor (HGF) signaling pathway plays a key role in the processes of embryogenesis, wound healing, and organ regeneration. Aberrant activation of MET/HGF occurs through multiple mechanisms including gene amplification, mutation, protein overexpression, and abnormal gene splicing interrupting autocrine and paracrine regulatory feedback mechanisms. In many cancers including non-small-cell lung cancer, colorectal, gastric, renal, and hepatocellular cancer, dysregulation of MET may lead to a more aggressive cancer phenotype and may be a negative prognostic indicator. Successful therapeutic targeting of the MET/HGF pathway has been achieved using monoclonal antibodies against the MET receptor and its ligand HGF in addition to MET-specific and multitargeted small-molecule tyrosine-kinase inhibitors with several drugs in late-phase clinical trials including onartuzumab, rilotumumab, tivantinib, and cabozantinib. MET frequently interacts with other key oncogenic tyrosine kinases including epidermal growth-factor receptor (EGFR) and HER-3 and these interactions may be responsible for resistance to anti-EGFR therapies. Similarly, resistance to MET inhibition may be mediated through EGFR activation, or alternatively by increasing levels of MET amplification or acquisition of novel "gatekeeper" mutations. In order to optimize development of effective inhibitors of the MET/HGF pathway clinical trials must be enriched for patients with demonstrable MET-pathway dysregulation for which robustly standardized and validated assays are required.
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Affiliation(s)
- Elizabeth C Smyth
- Department of Gastrointestinal Oncology, Royal Marsden Hospital, Sutton, UK
| | - Francesco Sclafani
- Department of Gastrointestinal Oncology, Royal Marsden Hospital, Sutton, UK
| | - David Cunningham
- Department of Gastrointestinal Oncology, Royal Marsden Hospital, Sutton, UK
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11
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Lai AZ, Cory S, Zhao H, Gigoux M, Monast A, Guiot MC, Huang S, Tofigh A, Thompson C, Naujokas M, Marcus VA, Bertos N, Sehat B, Perera RM, Bell ES, Page BDG, Gunning PT, Ferri LE, Hallett M, Park M. Dynamic reprogramming of signaling upon met inhibition reveals a mechanism of drug resistance in gastric cancer. Sci Signal 2014; 7:ra38. [PMID: 24757178 DOI: 10.1126/scisignal.2004839] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Met receptor tyrosine kinase is activated or genetically amplified in some gastric cancers, but resistance to small-molecule inhibitors of Met often emerges in patients. We found that Met abundance correlated with a proliferation marker in patient gastric tumor sections, and gastric cancer cell lines that have MET amplifications depended on Met for proliferation and anchorage-independent growth in culture. Inhibition of Met induced temporal changes in gene expression in the cell lines, initiated by a rapid decrease in the expression of genes encoding transcription factors, followed by those encoding proteins involved in epithelial-mesenchymal transition, and finally those encoding cell cycle-related proteins. In the gastric cancer cell lines, microarray and chromatin immunoprecipitation analysis revealed considerable overlap between genes regulated in response to Met stimulation and those regulated by signal transducer and activator of transcription 3 (STAT3). The activity of STAT3, extracellular signal-regulated kinase (ERK), and the kinase Akt was decreased by Met inhibition, but only inhibitors of STAT3 were as effective as the Met inhibitor in decreasing tumor cell proliferation in culture and in xenografts, suggesting that STAT3 mediates the pro-proliferative program induced by Met. However, the phosphorylation of ERK increased after prolonged Met inhibition in culture, correlating with decreased abundance of the phosphatases DUSP4 and DUSP6, which inhibit ERK. Combined inhibition of Met and the mitogen-activated protein kinase kinase (MEK)-ERK pathway induced greater cell death in cultured gastric cancer cells than did either inhibitor alone. These findings indicate combination therapies that may counteract resistance to Met inhibitors.
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Affiliation(s)
- Andrea Z Lai
- 1Department of Biochemistry, McGill University, Montréal, Québec H3A 0G4, Canada
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12
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Fischer U, Rheinheimer S, Krempler A, Löbrich M, Meese E. Glioma-amplified sequence KUB3 influences double-strand break repair after ionizing radiation. Int J Oncol 2013; 43:50-6. [PMID: 23670597 PMCID: PMC3742159 DOI: 10.3892/ijo.2013.1937] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/05/2013] [Indexed: 01/06/2023] Open
Abstract
Human glioblastomas are characterized by frequent DNA amplifications most often at chromosome regions 7p11.2 and 12q13-15. Although amplification is a well-known hallmark of glioblastoma genetics the function of most amplified genes in glioblastoma biology is not understood. Previously, we cloned Ku70-binding protein 3 (KUB3) from the amplified domain at 12q13-15. Here, we report that glioblastoma cell cultures with endogenous KUB3 gene amplification and with elevated KUB3 protein expression show an efficient double-strand break (DSB) repair after being irradiated with 1 Gy. A significantly less efficient DSB repair was found in glioma cell cultures without KUB3 amplification and expression. Furthermore, we found that a siRNA-mediated reduction of the endogenous KUB3 expression in glioblastoma cells resulted in a reduction of the repair efficiency. HeLa cells transfected with KUB3 showed an increased DSB repair in comparison to untreated HeLa cells. In addition, KUB3 seems to influence DSB efficiency via the DNA-PK-dependent repair pathway as shown by simultaneous inhibition of KUB3 and DNA-PK. The data provide the first evidence for a link between the level of KUB3 amplification and expression in glioma and DSB repair efficiency.
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Affiliation(s)
- Ulrike Fischer
- Department of Human Genetics, Medical School, Saarland University, D-66421 Homburg/Saar, Germany.
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Abstract
Glioblastoma multiforme is a histopathologically heterogeneous disease with few treatment options. Therapy based on genomic alterations is rapidly gaining popularity because of the high response rate and high specificity. DNA copy number and exon-sequencing studies of glioblastoma multiforme samples have revealed recurrent genomic alterations in genes such as TP53, EGFR, and IDH1, but to date, this has not resulted in novel glioblastoma multiforme therapies. Identification of expression subtypes has resulted in new insights such as the association between genomic abnormalities and expression signatures. This review describes the types of genomic studies that have been performed and that are underway, the most prominent results, and the implications of genomic research for the development of clinical treatment modalities.
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Abstract
INTRODUCTION The aberrantly upregulated c-mesenchymal-epithelia transition factor (c-MET) signaling pathway has been considered to be an attractive target for cancer intervention owing to the important roles it plays in tumor formation, progression, metastasis, angiogenesis and drug resistance. Based on the historical preclinical evidence, a number of c-MET pathway targeted agents are being developed in the clinic, and recent clinical data have begun to provide some insight into which tumor types and patient populations a c-MET pathway inhibitor may be beneficial for. AREAS COVERED Through reviewing recent publications in the literature and information disclosed in other public forums, we describe the current understanding of c-MET biology in human malignancies and discuss the latest progress in the development of c-MET pathway inhibitors for cancer treatment. EXPERT OPINION The c-MET pathway inhibitors currently being evaluated in the clinic have demonstrated compelling evidence of clinical activity in different cancer types and may provide significant therapeutic opportunities. The challenges, however, are to identify the tumor types and patient populations that benefit most, and find the most effective combinations of therapies while minimizing potential toxicity.
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Affiliation(s)
- Xiangdong Liu
- Incyte Corporation, Experimental Station, Wilmington, DE 19880, USA.
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15
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Ward SJ, Karakoula K, Phipps KP, Harkness W, Hayward R, Thompson D, Jacques TS, Harding B, Darling JL, Thomas DGT, Warr TJ. Cytogenetic analysis of paediatric astrocytoma using comparative genomic hybridisation and fluorescence in-situ hybridisation. J Neurooncol 2010; 98:305-18. [DOI: 10.1007/s11060-009-0081-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Accepted: 11/30/2009] [Indexed: 11/29/2022]
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16
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Neyns B, Sadones J, Joosens E, Bouttens F, Verbeke L, Baurain JF, D'Hondt L, Strauven T, Chaskis C, In't Veld P, Michotte A, De Greve J. Stratified phase II trial of cetuximab in patients with recurrent high-grade glioma. Ann Oncol 2009; 20:1596-1603. [PMID: 19491283 DOI: 10.1093/annonc/mdp032] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND To evaluate the antitumor activity and toxicity of single-agent cetuximab in patients with recurrent high-grade glioma (HGG) after failure of surgery, radiation therapy, and chemotherapy. PATIENTS AND METHODS In this two-arm, open-label, phase II study patients were stratified according to their epidermal growth factor receptor (EGFR) gene amplification status. Cetuximab was administered intravenously at a dose of 400 mg/m(2) on week 1 followed by weekly dose of 250 mg/m(2). The primary end point for this study was the response rate in both study arms separately. RESULTS Fifty-five eligible patients (28 with and 27 without EGFR amplification) tolerated cetuximab well. Three patients (5.5%) had a partial response and 16 patients (29.6%) had stable disease. The median time to progression was 1.9 months [95% confidence interval (CI) 1.6-2.2 months]. Whereas the progression-free survival (PFS) was <6 months in the majority (n = 50/55) of patients, five patients (9.2%) had a PFS on cetuximab of >9 months. Median overall survival was 5.0 months (95% CI 4.2-5.9 months). No significant correlation was found between response, survival and EGFR amplification. CONCLUSIONS Cetuximab was well tolerated but had limited activity in this patient population with progressive HGG. A minority of patients may derive a more durable benefit but were not prospectively identified by EGFR gene copy number.
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Affiliation(s)
- B Neyns
- Department of Medical Oncology, UZ Brussel, Brussels.
| | - J Sadones
- Department of Medical Oncology, UZ Brussel, Brussels
| | - E Joosens
- Department of Medical Oncology, ZNA Middelheim, Antwerp
| | - F Bouttens
- Department of Radiation therapy, AZ St Lucas, Ghent
| | - L Verbeke
- Department of Radiation therapy, OLV Aalst, Aalst
| | - J-F Baurain
- Department of Medical Oncology, Cliniques Universitaires St Luc, Brussels
| | - L D'Hondt
- Department of Medical Oncology, Centre Hospitalier Notre-Dame et Reine Fabiola, Charleroi
| | - T Strauven
- Department of Neurology, Sint-Augustinus, Antwerp
| | | | | | - A Michotte
- Department of Neurology; Department of Neuropathology, UZ Brussel, Brussels, Belgium
| | - J De Greve
- Department of Medical Oncology, UZ Brussel, Brussels
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17
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A novel multipurpose monoclonal antibody for evaluating human c-Met expression in preclinical and clinical settings. Appl Immunohistochem Mol Morphol 2009; 17:57-67. [PMID: 18815565 DOI: 10.1097/pai.0b013e3181816ae2] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The inappropriate expression of the c-MET cell surface receptor in many human solid tumors necessitates the development of companion diagnostics to identify those patients who could benefit from c-MET targeted therapies. Tumor tissues are formalin fixed and paraffin embedded (FFPE) for histopathologic evaluation, making the development of an antibody against c-MET that accurately and reproducibly detects the protein in FFPE samples an urgent need. We have developed a monoclonal antibody (mAb), designated MET4, from a panel of MET-avid mAbs, based on its specific staining pattern in FFPE preparations. The accuracy of MET4 immunohistochemistry (MET4-IHC) was assessed by comparing MET4-IHC in FFPE cell pellets with immunoblotting analysis. The technical reproducibility of MET4-IHC possessed a percentage coefficient of variability of 6.25% in intra-assay and interassay testing. Comparison with other commercial c-MET antibody detection reagents demonstrated equal specificity and increased sensitivity for c-MET detection in prostate tissues. In cohorts of ovarian cancers and gliomas, MET4 reacted with ovarian cancers of all histologic subtypes (strong staining in 25%) and with 63% of gliomas. In addition, MET4 bound c-MET on the surfaces of cultured human cancer cells and tumor xenografts. In summary, the MET4 mAb accurately and reproducibly measures c-MET expression by IHC in FFPE tissues and can be used for molecular imaging in vivo. These properties encourage further development of MET4 as a multipurpose molecular diagnostics reagent to help to guide appropriate selection of patients being considered for treatment with c-MET-antagonistic drugs.
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18
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Liu X, Yao W, Newton RC, Scherle PA. Targeting the c-MET signaling pathway for cancer therapy. Expert Opin Investig Drugs 2008; 17:997-1011. [DOI: 10.1517/13543784.17.7.997] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiangdong Liu
- Incyte Corporation, Experimental Station, Rt. 141 & Henry Clay Road, Wilmington, DE 19880, USA ;
| | - Wenqing Yao
- Incyte Corporation, Experimental Station, Rt. 141 & Henry Clay Road, Wilmington, DE 19880, USA ;
| | - Robert C Newton
- Incyte Corporation, Experimental Station, Rt. 141 & Henry Clay Road, Wilmington, DE 19880, USA ;
| | - Peggy A Scherle
- Incyte Corporation, Experimental Station, Rt. 141 & Henry Clay Road, Wilmington, DE 19880, USA ;
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19
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Idbaih A, Crinière E, Marie Y, Rousseau A, Mokhtari K, Kujas M, El Houfi Y, Carpentier C, Paris S, Boisselier B, Laigle-Donadey F, Thillet J, Sanson M, Hoang-Xuan K, Delattre JY. Gene amplification is a poor prognostic factor in anaplastic oligodendrogliomas. Neuro Oncol 2008; 10:540-7. [PMID: 18544654 DOI: 10.1215/15228517-2008-022] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Various gene amplifications have been observed in gliomas. Prognostic-genomic correlations testing simultaneously all these amplified genes have never been conducted in anaplastic oligodendrogliomas. A set of 38 genes that have been reported to be amplified in gliomas and investigated as the main targets of amplicons were studied in a series of 52 anaplastic oligodendrogliomas using bacterial artificial chromosome-array based comparative genomic hybridization and quantitative polymerase chain reaction. Among the 38 target genes, 15 were found to be amplified in at least one tumor. Overall, 27% of anaplastic oligodendrogliomas exhibited at least one gene amplification. The most frequently amplified genes were epidermal growth factor receptor (EGFR) and cyclin-dependent kinase 4/sarcoma amplified sequence (CDK4/SAS) in 17% and 8% of anaplastic oligodendrogliomas, respectively. Gene amplification and codeletion of chromosome arms 1p/19q were perfectly exclusive (p = 0.005). In uni- and multivariate analyses, gene amplification was a negative prognostic factor for progression-free survival and overall survival in anaplastic oligodendrogliomas, providing complementary information to the classic prognostic factors identified in anaplastic oligodendrogliomas (extent of surgery, KPS, and chromosome arms 1p/19q status).
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Affiliation(s)
- Ahmed Idbaih
- Institut National de la Santé et de la Recherche Médicale, U711, Université Pierre et Marie Curie, Hôpital Pitié-Salpêtrière, Paris, France.
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20
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Eckerich C, Zapf S, Fillbrandt R, Loges S, Westphal M, Lamszus K. Hypoxia can induce c-Met expression in glioma cells and enhance SF/HGF-induced cell migration. Int J Cancer 2007; 121:276-83. [PMID: 17372907 DOI: 10.1002/ijc.22679] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The c-Met receptor and its ligand scatter factor/hepatocyte growth factor (SF/HGF) are strongly overexpressed in malignant gliomas. Signaling through c-Met as well as exposure to hypoxia can stimulate glioma cell migration and invasion. In several cancer cell types, hypoxia was shown to activate the c-met promoter, which contains hypoxia inducible factor-1 (HIF-1) binding sites. We hypothesized that hypoxia might upregulate c-Met also in glioma cells. Analyzing 18 different glioblastoma cell lines and 10 glioblastoma primary cultures, we found that in 50% of both the cell lines and the primary cultures c-Met protein levels were increased following exposure to hypoxia. Upregulation of c-met in response to hypoxia was also detected at the transcriptional level. In all primary cultures and in 16 of the 18 cell lines (89%), HIF-1 alpha levels were increased by hypoxia. Transfection of siRNA against HIF-1 alpha abgrogated the hypoxic induction of c-Met, suggesting that c-Met expression is upregulated by a HIF-1 alpha-dependent mechanism. Hypoxia sensitized glioblastoma cell lines which showed hypoxic induction of c-Met to the motogenic effects of SF/HGF. These findings suggest that approximately half of all human glioblastomas respond to hypoxia with an induction of c-Met, which can enhance the stimulating effect of SF/HGF on tumor cell migration.
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Affiliation(s)
- Carmen Eckerich
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Germany
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21
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Nakahara Y, Shiraishi T, Okamoto H, Mineta T, Oishi T, Sasaki K, Tabuchi K. Detrended fluctuation analysis of genome-wide copy number profiles of glioblastomas using array-based comparative genomic hybridization. Neuro Oncol 2004; 6:281-9. [PMID: 15494095 PMCID: PMC1872007 DOI: 10.1215/s1152851703000632)] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We examined whole genomic aberrations of biopsied samples from 19 independent glioblastomas by array-based comparative genomic hybridization analysis. The highest frequencies of copy number gains were observed on RFC2 (73.3%), EGFR (63.2%), and FGR, ELN, CDKN1C , FES, TOP2A, and ARSA (57.9% each). The highest frequencies of copy number losses were detected on TBR1 (52.6%), BMI1 (52.6%), EGR2 (47.4%), DMBT1 (47.4%), MTAP (42.1%), and FGFR2 (42.1%). The copy number gains of CDKN1C and INS and the copy number losses of TBR1 were significantly correlated with longer survival of patients. High-level amplifications were identified on EGFR, SAS/CDK4, PDGFRA, MDM2, and ARSA. These genes are assumed to be involved in tumorigenesis or progression of glioblastomas. The first attempts to apply detrended fluctuation analysis to copy number profiles by considering the reading direction as the time axis demonstrated that higher long-term fractal scaling exponents (alpha2) correlated well with longer survival of glioblastoma patients. The present study indicates that array-based comparative genomic hybridization analysis has great potential for assessment of copy number changes and altered chromosomal regions of brain tumors. Furthermore, we show that nonlinear analysis methods of whole genome copy number profiles may provide prognostic information about glioblastoma patients.
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Affiliation(s)
- Yukiko Nakahara
- Department of Neurosurgery, Faculty of Medicine, Saga University, Saga 849-850, Japan.
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22
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Nakahara Y, Shiraishi T, Okamoto H, Mineta T, Oishi T, Sasaki K, Tabuchi K. Detrended fluctuation analysis of genome-wide copy number profiles of glioblastomas using array-based comparative genomic hybridization. Neuro Oncol 2004. [PMID: 15494095 DOI: 10.1215/s1152851703000632] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We examined whole genomic aberrations of biopsied samples from 19 independent glioblastomas by array-based comparative genomic hybridization analysis. The highest frequencies of copy number gains were observed on RFC2 (73.3%), EGFR (63.2%), and FGR, ELN, CDKN1C , FES, TOP2A, and ARSA (57.9% each). The highest frequencies of copy number losses were detected on TBR1 (52.6%), BMI1 (52.6%), EGR2 (47.4%), DMBT1 (47.4%), MTAP (42.1%), and FGFR2 (42.1%). The copy number gains of CDKN1C and INS and the copy number losses of TBR1 were significantly correlated with longer survival of patients. High-level amplifications were identified on EGFR, SAS/CDK4, PDGFRA, MDM2, and ARSA. These genes are assumed to be involved in tumorigenesis or progression of glioblastomas. The first attempts to apply detrended fluctuation analysis to copy number profiles by considering the reading direction as the time axis demonstrated that higher long-term fractal scaling exponents (alpha2) correlated well with longer survival of glioblastoma patients. The present study indicates that array-based comparative genomic hybridization analysis has great potential for assessment of copy number changes and altered chromosomal regions of brain tumors. Furthermore, we show that nonlinear analysis methods of whole genome copy number profiles may provide prognostic information about glioblastoma patients.
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Affiliation(s)
- Yukiko Nakahara
- Department of Neurosurgery, Faculty of Medicine, Saga University, Saga 849-850, Japan.
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23
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Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, Liau LM, Mischel PS, Nelson SF. Gene expression profiling of gliomas strongly predicts survival. Cancer Res 2004; 64:6503-10. [PMID: 15374961 DOI: 10.1158/0008-5472.can-04-0452] [Citation(s) in RCA: 538] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In current clinical practice, histology-based grading of diffuse infiltrative gliomas is the best predictor of patient survival time. Yet histology provides little insight into the underlying biology of gliomas and is limited in its ability to identify and guide new molecularly targeted therapies. We have performed large-scale gene expression analysis using the Affymetrix HG U133 oligonucleotide arrays on 85 diffuse infiltrating gliomas of all histologic types to assess whether a gene expression-based, histology-independent classifier is predictive of survival and to determine whether gene expression signatures provide insight into the biology of gliomas. We found that gene expression-based grouping of tumors is a more powerful survival predictor than histologic grade or age. The poor prognosis samples could be grouped into three different poor prognosis groups, each with distinct molecular signatures. We further describe a list of 44 genes whose expression patterns reliably classify gliomas into previously unrecognized biological and prognostic groups: these genes are outstanding candidates for use in histology-independent classification of high-grade gliomas. The ability of the large scale and 44 gene set expression signatures to group tumors into strong survival groups was validated with an additional external and independent data set from another institution composed of 50 additional gliomas. This demonstrates that large-scale gene expression analysis and subset analysis of gliomas reveals unrecognized heterogeneity of tumors and is efficient at selecting prognosis-related gene expression differences which are able to be applied across institutions.
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Affiliation(s)
- William A Freije
- Department of Human Genetics, University of California at Los Angeles, Los Angeles, California 90095, USA
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24
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Hirose Y, Aldape KD, Chang S, Lamborn K, Berger MS, Feuerstein BG. Grade II astrocytomas are subgrouped by chromosome aberrations. CANCER GENETICS AND CYTOGENETICS 2003; 142:1-7. [PMID: 12660025 DOI: 10.1016/s0165-4608(02)00791-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Grade II astrocytoma is defined as a low-grade tumor, yet patients have a wide range of survival and tumors can quickly progress to high-grade astrocytoma/glioblastoma. Previous studies using comparative genomic hybridization (CGH) failed to demonstrate frequent copy number aberrations (CNA) in these tumors. This may be related to technical difficulties because infiltrating astrocytic tumors are often intermixed with normal brain tissue. We developed methods to exclude most normal tissue and use small amounts of DNA for CGH by microdissecting small regions of tumor from paraffin sections and amplifying extracted DNA using degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR). Using this method, we examined 30 grade II astrocytoma cases. We found CNA in 25 cases (83%), with a mean of two CNA per case. The most frequent CNA were gains on 7q (12 cases), 5p (5 cases), 9 (5 cases), and 19p (3 cases), and losses on 19q (7 cases), 1p (6 cases), and Xp (3 cases). Gain on 7q and losses on 1p/19q were mutually exclusive. This is the first report on the genetic characterization of low-grade astrocytomas using CGH from microdissected and formalin-fixed tissue. The comparatively large number of cases in this study allows us to suggest that these tumors are genetically subgrouped.
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Affiliation(s)
- Yuichi Hirose
- Department of Neurological Surgery, University of California, San Francisco, CA 94115, USA
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25
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Tchirkov A, Rolhion C, Bertrand S, Doré JF, Dubost JJ, Verrelle P. IL-6 gene amplification and expression in human glioblastomas. Br J Cancer 2001; 85:518-22. [PMID: 11506489 PMCID: PMC2364101 DOI: 10.1054/bjoc.2001.1942] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aggressiveness of human gliomas appears to be correlated with the upregulation of interleukin 6 (IL-6) gene. Using quantitative PCR methods, we detected amplification and expression of the IL-6 gene in 5 of 5 primary glioblastoma samples and in 4 of 5 glioblastoma cell lines. This finding suggests that the amplification of IL-6 gene may be a common feature in glioblastomas and may contribute to the IL-6 over-expression.
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Affiliation(s)
- A Tchirkov
- Centre Jean Perrin, 58 rue Montalembert, 63011 Clermont-Ferrand, France
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26
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Helou K, Walentinsson A, Kost-Alimova M, Levan G. Hgfr/Met oncogene acts as target for gene amplification in DMBA-induced rat sarcomas: free chromatin fluorescence in situ hybridization analysis of amplicon arrays in homogeneously staining regions. Genes Chromosomes Cancer 2001; 30:416-20. [PMID: 11241796 DOI: 10.1002/1098-2264(2001)9999:9999<::aid-gcc1109>3.0.co;2-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Analysis of chromosome rearrangements in tumors is an important means for revealing genetic pathways underlying tumorigenesis and tumor progression. In five of 17 DMBA-induced rat sarcomas, cytogenetic analysis had disclosed homogeneously staining regions (hsrs), which are generally accepted to be cytogenetic signs of gene amplification. Using comparative genomic hybridization (CGH), regional increases in DNA copy number of the proximal part of rat chromosome (RNO) 4 were detected in four of the tumors harboring hsrs. Amplification of the Hgfr/Met oncogene, located at RNO4q21.2, was detected by fluorescence in situ hybridization (FISH) in five tumors. In four of them, a number of flanking genes located in the close vicinity of Hgfr/Met, including Cav1 (q21.1), Wnt2 (q21.2-q21.3), and Cftr (q21.3), also were amplified, though amplification was seen in a lower fraction of the cells than was Hgfr/Met amplification. In the fifth tumor (BL150T), Hgfr/Met was amplified in all cells and was the sole amplified gene of those tested. In addition, the Hgfr/Met FISH signals in BL150T were tightly clustered and formed compact and intense spots compared with the signals seen in the other four tumors. Application of the free chromatin FISH technique to BL150T showed that the genomic Hgfr/Met probe stained the extended chromatin fibers of up to 1.5 Mb with an almost uninterrupted signal, indicating that the BL150T amplicon was build up solely of Hgfr/Met gene sequences. Our results suggest that the Hgfr/Met oncogene is the primary target for amplification in a subset of rat DMBA sarcomas.
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Affiliation(s)
- K Helou
- Department of Cell and Molecular Biology-Genetics, Lundberg Laboratory, Göteborg University, Sweden.
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27
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Wallenius V, Hisaoka M, Helou K, Levan G, Mandahl N, Meis-Kindblom JM, Kindblom LG, Jansson JO. Overexpression of the hepatocyte growth factor (HGF) receptor (Met) and presence of a truncated and activated intracellular HGF receptor fragment in locally aggressive/malignant human musculoskeletal tumors. THE AMERICAN JOURNAL OF PATHOLOGY 2000; 156:821-9. [PMID: 10702398 PMCID: PMC1876854 DOI: 10.1016/s0002-9440(10)64950-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/29/1999] [Indexed: 01/08/2023]
Abstract
Enhanced hepatocyte growth factor (HGF) receptor (Met) signaling has been suggested to play an important role in the development and progression of various epithelial and nonepithelial tumors. N-terminally truncated forms of the HGF receptor have been shown to be constitutively activated and tumorigenic in animal experiments. In the present study, 102 benign and malignant human musculoskeletal tumors were examined for expression of the HGF receptor by Western blotting and/or immunohistochemistry. A clear predominance of HGF receptor expression was seen in malignant as compared to benign tumors (Western blotting, P < 0.001; immunohistochemistry, P < 0.02). For the first time we show HGF receptor expression in the following four tumor types: dermatofibrosarcoma protuberans, clear cell sarcoma of tendons, malignant primitive neuroectodermal tumor, and benign fibrous histiocytoma. In three cases of sarcoma with high HGF receptor expression by Western blotting, we found indications of a short 85-kd N-terminally truncated HGF receptor that was tyrosine phosphorylated and located in the cytoplasm. Although fragments of this length were seen in 18 of 65 tumors, most were not tyrosine-phosphorylated. Northern blotting revealed only the 7.5-kb full-length HGF receptor transcript, suggesting that the 85-kd fragment is generated by an alternative initiation of translation or by proteolytic cleavage. Southern blotting detected no amplification of the Hgfr/Met gene in the 35 tumors examined, in contrast to our recent report of Hgfr/Met gene amplification in 7, 12-dimethylbenz(a)anthracene (DMBA)-induced rat sarcomas. The present data suggest that the locally aggressive and malignant properties of human mesenchymal tumors maybe related, in part, to high levels of full-length HGF receptors, and in some cases to the occurrence of N-terminally truncated HGF receptors, activated independently of HGF.
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MESH Headings
- Blotting, Western
- Bone Neoplasms/chemistry
- Bone Neoplasms/metabolism
- Bone Neoplasms/pathology
- Dermatofibrosarcoma/chemistry
- Dermatofibrosarcoma/metabolism
- Dermatofibrosarcoma/pathology
- Hepatocyte Growth Factor/biosynthesis
- Histiocytoma, Benign Fibrous/chemistry
- Histiocytoma, Benign Fibrous/metabolism
- Histiocytoma, Benign Fibrous/pathology
- Humans
- Neuroectodermal Tumors, Primitive/chemistry
- Neuroectodermal Tumors, Primitive/metabolism
- Neuroectodermal Tumors, Primitive/pathology
- Peptide Fragments/analysis
- Proto-Oncogene Proteins c-met/biosynthesis
- Receptor Protein-Tyrosine Kinases/biosynthesis
- Receptors, Cell Surface/biosynthesis
- Sarcoma, Clear Cell/chemistry
- Sarcoma, Clear Cell/metabolism
- Sarcoma, Clear Cell/pathology
- Soft Tissue Neoplasms/chemistry
- Soft Tissue Neoplasms/metabolism
- Soft Tissue Neoplasms/pathology
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Affiliation(s)
- V Wallenius
- Research Center for Endocrinology and Metabolism (RCEM), Department of Internal Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden.
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Forozan F, Veldman R, Ammerman CA, Parsa NZ, Kallioniemi A, Kallioniemi OP, Ethier SP. Molecular cytogenetic analysis of 11 new breast cancer cell lines. Br J Cancer 1999; 81:1328-34. [PMID: 10604729 PMCID: PMC2362964 DOI: 10.1038/sj.bjc.6695007] [Citation(s) in RCA: 159] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We describe a survey of genetic changes by comparative genomic hybridization (CGH) in 11 human breast cancer cell lines recently established in our laboratory. The most common gains took place at 8q (73%), 1 q (64%), 7q (64%), 3q (45%) and 7p (45%), whereas losses were most frequent at Xp (54%), 8p (45%), 18q (45%) and Xq (45%). Many of the cell lines displayed prominent, localized DNA amplifications by CGH. One-third of these loci affected breast cancer oncogenes, whose amplifications were validated with specific probes: 17q12 (two cell lines with ERBB2 amplifications), 11q13 (two with cyclin-D1), 8p11-p12 (two with FGFR1) and 10q25 (one with FGFR2). Gains and amplifications affecting 8q were the most common genetic alterations in these cell lines with the minimal, common region of involvement at 8q22-q23. No high-level MYC (at 8q24) amplifications were found in any of the cell lines. Two-thirds of the amplification sites took place at loci not associated with established oncogenes, such as 1q41-q43, 7q21-q22, 7q31, 8q23, 9p21-p23, 11p12-p14, 15q12-q14, 16q13-q21, 17q23, 20p11-p12 and 20q13. Several of these locations have not been previously reported and may harbour important genes whose amplification is selected for during cancer development. In summary, this set of breast cancer cell lines displaying prominent DNA amplifications should facilitate discovery and functional analysis of genes and signal transduction pathways contributing to breast cancer development.
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Affiliation(s)
- F Forozan
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-4470, USA
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29
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Helou K, Wallenius V, Qiu Y, Ohman F, Ståhl F, Klinga-Levan K, Kindblom LG, Mandahl N, Jansson JO, Levan G. Amplification and overexpression of the hepatocyte growth factor receptor (HGFR/MET) in rat DMBA sarcomas. Oncogene 1999; 18:3226-34. [PMID: 10359528 DOI: 10.1038/sj.onc.1202658] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the present study subcutaneous fibrosarcomas were induced by the carcinogen 7,12-dimethylbenz(a)anthracene (DMBA) in rats from F1 generation cross breedings of two different inbred strains. Comparative genomic hybridization (CGH) analysis, which allows detection of DNA sequence copy changes, was applied to one of the tumors and it was found that there were increased copy numbers of sequences at chromosome 4q12-q21 in this tumor. We have previously determined that the loci for the hepatocyte growth factor (Hgf) and hepatocyte growth factor receptor (Hgfr/Met), a protooncogene, are situated in this particular chromosome region. Using probes for the two genes in FISH (fluorescence in situ hybridization) and in Southern blots we found that the Hgfr/Met gene was amplified in five of the 19 sarcomas studied, and that the Hgf gene was coamplified in two of them. Northern and Western blots and tyrosine phosphorylation analysis showed that the HGF receptor was overexpressed and functional in all five tumors, as well as in two additional tumors. In summary, both amplification and overexpression of the Hgfr/Met gene was found in about 25% of DMBA-induced experimental rat sarcomas, and HGF receptor overexpression alone was seen in two additional tumors. Possibly this reflects an involvement in paracrine or autocrine stimulation of growth and invasiveness by HGF. Our finding could provide a rodent model system to increased knowledge about causality and therapy, which may be applicable to the sizeable fraction of human musculoskeletal tumors displaying MET overexpression.
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Affiliation(s)
- K Helou
- Department of Cell and Molecular Biology-Genetics, Göteborg University, Gothenburg, Sweden
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Abstract
Over the past few years, although much has been learned about the molecular genetics of central nervous system (CNS) tumors, researchers and pathologists are only beginning to understand the scientific basis of the development of these tumors. Data accumulated so far support the division of glioblastoma into two clinical and molecular subsets. Primary or de novo glioblastomas occur in older patients, are clinically aggressive and exhibit epidermal growth factor receptor amplification or overexpression. Secondary glioblastomas develop from pre-existing low-grade astrocytomas, have a more protracted clinical course, and frequently contain p53 mutations. Both types of tumors show deletions of chromosome 10 and possibly mutations of the PTEN/MMAC1 gene as an endstage event. Oligodendrogliomas have been shown to have genetic abnormalities distinct from those of the astrocytic tumors, commonly involving chromosomes 1p and 19q. As regards meningiomas, loss of chromosome 22q and mutations of the neurofibromatosis type 2 gene are frequent events and loss of chromosome 14q and 10q may be seen in atypical or malignant transformation. Such genetic findings, apart from providing a better understanding of neoplastic transformation in brain tumors, are beginning to form the basis of a new approach to neuro-oncology.
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Affiliation(s)
- H K Ng
- Department of Anatomical & Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin
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Mohapatra G, Bollen AW, Kim DH, Lamborn K, Moore DH, Prados MD, Feuerstein BG. Genetic analysis of glioblastoma multiforme provides evidence for subgroups within the grade. Genes Chromosomes Cancer 1998. [DOI: 10.1002/(sici)1098-2264(199803)21:3<195::aid-gcc3>3.0.co;2-v] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Patel A, van Meyel DJ, Mohapatra G, Bollen A, Wrensch M, Cairncross JG, Feuerstein BG. Gliomas in families: chromosomal analysis by comparative genomic hybridization. CANCER GENETICS AND CYTOGENETICS 1998; 100:77-83. [PMID: 9406586 DOI: 10.1016/s0165-4608(97)00275-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Gliomas that aggregate in otherwise unremarkable families may have a heritable genetic basis. To determine the spectrum of genetic alterations in glioma-susceptible families, we examined tumor DNA from familial cases for regions of chromosomal gain or loss using comparative genomic hybridization (CGH). We compared chromosomal alterations within and among glioma families to those found in sporadic gliomas. A specific chromosomal abnormality common to the tumors of multiple unrelated probands with glioma or a specific chromosomal abnormality common to multiple affected persons in a single glioma-prone family would support the hypothesis of an inherited predisposition to glioma and at the same time identify specific regions of the genome harboring putative glioma susceptibility genes. Tumor DNA from 11 patients from seven families with two or more individuals with glioma was analyzed, including three members of a remarkable family having 10 affected individuals. We found no chromosomal abnormality common to all tumors of all probands nor did we find family-specific abnormalities in two of three glioma-prone kindreds. There were frequent copy number aberrations (CNAs) on chromosomes 7, 10, 19, and the sex chromosomes; other CNAs included +3q(13.3-29), -4q, +5q, -9q34, +12, -13q(21-->33), -15, -16p, +17qter, -18, -21, and -22. Amplifications occurred at +2 7p(11.1-->12), +2 7q(21.2-->33), +2 12q(13.2-->14), and +2 12p(11-->12). Although there were several novel CNAs [-16p, and +2 12p(11-p12)], none could readily explain the inheritance of these tumors.
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Affiliation(s)
- A Patel
- Department of Laboratory Medicine, University of California, San Francisco 94143-0808, USA
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Fischer U, Heckel D, Michel A, Janka M, Hulsebos T, Meese E. Cloning of a novel transcription factor-like gene amplified in human glioma including astrocytoma grade I. Hum Mol Genet 1997; 6:1817-22. [PMID: 9302258 DOI: 10.1093/hmg/6.11.1817] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Gene amplification, which is generally considered to occur late in tumor development, is a common feature of high grade glioma. Up until now, there have been no reports on amplification in astrocytoma grade I. In this study, we report cloning and sequencing of a cDNA termed glioma-amplified sequence (GAS41) which was identified recently in a glioblastoma cell line by microdissection-mediated cDNA capture. This technique is tailored to isolate amplified genes from human tumors. An increased copy number of GAS41 was found in glioblastoma multiforme and astrocytoma III, and at a high frequency in astrocytoma grades I and II. Sequence comparison indicates a high homology between the GAS41 protein, the yeast and human AF-9 and the human ENL proteins. Both AF-9 and ENL belong to a new class of transcription factors, indicating that GAS41 might also represent a transcription factor. With GAS41 being the first gene found with increased copy number in low grade glioma, this study provides the first evidence that gene amplification can occur in early tumor development.
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Affiliation(s)
- U Fischer
- Department of Human Genetics, Medical School, University Hospital, Homburg/Saar, Germany
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The molecular genetics of astrocytomas: current understanding and future applications. J Clin Neurosci 1997; 4:114-21. [DOI: 10.1016/s0967-5868(97)90060-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/1995] [Accepted: 03/05/1996] [Indexed: 11/21/2022]
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Van de Kelft E. Molecular pathogenesis of astrocytoma and glioblastoma multiforme. Acta Neurochir (Wien) 1997; 139:589-99. [PMID: 9265950 DOI: 10.1007/bf01411992] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Our understanding of the complexity of genetic abnormalities involved in the tumourigenesis of malignant gliomas is as yet rudimentary. However, we can discern distinctive patterns of loss of genetic material and amplification of chromosomal regions that characterize both the different types of gliomas as well as the different malignancy grades. In this review, we discuss through specific examples of recent work on astrocytomas and glioblastoma multiforme, the importance of several tumour suppressor genes and oncogenes in the development of these glial tumours. In conclusion it would seem that distinct genetic changes in different genes, the protein products of which interact in particular growth control mechanism may lead to the same cellular abnormality. It seems likely that many further genetic abnormalities affecting genes coding for proteins, either involved in the cellular mechanisms yet identified or in new growth control mechanisms. Will be found in the near future.
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Affiliation(s)
- E Van de Kelft
- Department of Neurosurgery, Universitair Ziekenhuis Antwerpen, University of Antwerp, Belgium
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