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Mallick S, Choi Y, Taylor AM, Cosper PF. Human Papillomavirus-Induced Chromosomal Instability and Aneuploidy in Squamous Cell Cancers. Viruses 2024; 16:501. [PMID: 38675844 PMCID: PMC11053578 DOI: 10.3390/v16040501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Chromosomal instability (CIN) and aneuploidy are hallmarks of cancer. CIN is defined as a continuous rate of chromosome missegregation events over the course of multiple cell divisions. CIN causes aneuploidy, a state of abnormal chromosome content differing from a multiple of the haploid. Human papillomavirus (HPV) is a well-known cause of squamous cancers of the oropharynx, cervix, and anus. The HPV E6 and E7 oncogenes have well-known roles in carcinogenesis, but additional genomic events, such as CIN and aneuploidy, are often required for tumor formation. HPV+ squamous cancers have an increased frequency of specific types of CIN, including polar chromosomes. CIN leads to chromosome gains and losses (aneuploidies) specific to HPV+ cancers, which are distinct from HPV- cancers. HPV-specific CIN and aneuploidy may have implications for prognosis and therapeutic response and may provide insight into novel therapeutic vulnerabilities. Here, we review HPV-specific types of CIN and patterns of aneuploidy in squamous cancers, as well as how this impacts patient prognosis and treatment.
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Affiliation(s)
- Samyukta Mallick
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032, USA
| | - Yeseo Choi
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Cancer Biology Graduate Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Alison M. Taylor
- Department of Pathology and Cell Biology at the Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Pippa F. Cosper
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI 53705, USA
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2
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SALL Proteins; Common and Antagonistic Roles in Cancer. Cancers (Basel) 2021; 13:cancers13246292. [PMID: 34944911 PMCID: PMC8699250 DOI: 10.3390/cancers13246292] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary Transcription factors play essential roles in regulating gene expression, impacting the cell phenotype and function, and in the response of cells to environmental conditions. Alterations in transcription factors, including gene amplification or deletion, point mutations, and expression changes, are implicated in carcinogenesis, cancer progression, metastases, and resistance to cancer treatments. Not surprisingly, transcription factor activity is altered in numerous cancers, representing a unique class of cancer drug targets. This review updates and integrates information on the SALL family of transcription factors, highlighting the synergistic and/or antagonistic functions they perform in various cancer types. Abstract SALL proteins are a family of four conserved C2H2 zinc finger transcription factors that play critical roles in organogenesis during embryonic development. They regulate cell proliferation, survival, migration, and stemness; consequently, they are involved in various human genetic disorders and cancer. SALL4 is a well-recognized oncogene; however, SALL1–3 play dual roles depending on the cancer context and stage of the disease. Current reviews of SALLs have focused only on SALL2 or SALL4, lacking an integrated view of the SALL family members in cancer. Here, we update the recent advances of the SALL members in tumor development, cancer progression, and therapy, highlighting the synergistic and/or antagonistic functions they perform in similar cancer contexts. We identified common regulatory mechanisms, targets, and signaling pathways in breast, brain, liver, colon, blood, and HPV-related cancers. In addition, we discuss the potential of the SALL family members as cancer biomarkers and in the cancer cells’ response to therapies. Understanding SALL proteins’ function and relationship will open new cancer biology, clinical research, and therapy perspectives.
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3
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Moritz S, Krause M, Schlatter J, Cordes N, Vehlow A. Lamellipodin-RICTOR Signaling Mediates Glioblastoma Cell Invasion and Radiosensitivity Downstream of EGFR. Cancers (Basel) 2021; 13:5337. [PMID: 34771501 PMCID: PMC8582497 DOI: 10.3390/cancers13215337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Glioblastoma is a tumor type of unmet need despite the development of multimodal treatment strategies. The main factors contributing to the poor prognosis of glioblastoma patients are diverse genetic and epigenetic changes driving glioblastoma persistence and recurrence. Complemented are these factors by extracellular cues mediated through cell surface receptors, which further aid in fostering pro-invasion and pro-survival signaling contributing to glioblastoma therapy resistance. The underlying mechanisms conferring this therapy resistance are poorly understood. Here, we show that the cytoskeleton regulator Lamellipodin (Lpd) mediates invasiveness, proliferation and radiosensitivity of glioblastoma cells. Phosphoproteome analysis identified the epidermal growth factor receptor (EGFR) signaling axis commonly hyperactive in glioblastoma to depend on Lpd. Mechanistically, EGFR signaling together with an interaction between Lpd and the Rapamycin-insensitive companion of mammalian target of rapamycin (RICTOR) jointly regulate glioblastoma radiosensitivity. Collectively, our findings demonstrate an essential function of Lpd in the radiation response and invasiveness of glioblastoma cells. Thus, we uncover a novel Lpd-driven resistance mechanism, which adds an additional critical facet to the complex glioblastoma resistance network.
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Affiliation(s)
- Stefanie Moritz
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine, Technische Universität Dresden, Fetscherstraße 74, PF 41, 01307 Dresden, Germany; (S.M.); (N.C.)
| | - Matthias Krause
- Randall Centre of Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, King’s College London, London SE1 1UL, UK; (M.K.); (J.S.)
| | - Jessica Schlatter
- Randall Centre of Cell and Molecular Biophysics, New Hunt’s House, Guy’s Campus, King’s College London, London SE1 1UL, UK; (M.K.); (J.S.)
| | - Nils Cordes
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine, Technische Universität Dresden, Fetscherstraße 74, PF 41, 01307 Dresden, Germany; (S.M.); (N.C.)
- Institute of Radiooncology-OncoRay, Helmholtz-Zentrum Dresden-Rossendorf, Bautzner Landstraße 400, 01328 Dresden, Germany
- Department of Radiotherapy and Radiation Oncology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstraße 74, PF 50, 01307 Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69192 Heidelberg, Germany
| | - Anne Vehlow
- OncoRay-National Center for Radiation Research in Oncology, Faculty of Medicine, Technische Universität Dresden, Fetscherstraße 74, PF 41, 01307 Dresden, Germany; (S.M.); (N.C.)
- German Cancer Consortium (DKTK), Partner Site Dresden, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69192 Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Partner Site Dresden, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69192 Heidelberg, Germany
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4
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Griess B, Klinkebiel D, Kueh A, Desler M, Cowan K, Fitzgerald M, Teoh-Fitzgerald M. Association ofSOD3 promoter DNA methylation with its down-regulation in breast carcinomas. Epigenetics 2020; 15:1325-1335. [PMID: 32508251 DOI: 10.1080/15592294.2020.1777666] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Superoxide dismutase 3 (SOD3) is a secreted antioxidant enzyme that regulates reactive oxygen species in the microenvironment. It is also a potential tumour suppressor gene that is significantly downregulated in breast cancer. We have previously shown that its mRNA expression is inversely correlated with relapse free survival in breast cancer patients. This study aimed to investigate the correlation of SOD3 promoter DNA methylation with its expression in different molecular subtypes of breast carcinoma. We found that SOD3 expression was significantly reduced in breast carcinoma samples compared to normal tissues with the lowest levels observed in Luminal B subtype. Pyrosequencing analysis showed significant increase in methylation levels in the SOD3 promoter region (-108 and -19 from the TSS) in tumours vs normal tissues (53.6% vs 25.2%). The highest degree of correlation between methylation and SOD3 expression levels was observed in Luminal B subtype (Spearman's R = -0.540, P < 0.00093). In this subtype, the -78 CpG position is the most significantly methylated site. The Spearman's coefficient analysis also indicated the most significant correlation of DNA methylation at this site with SOD3 gene expression levels in tumours vs. normal tissues (R = -0.5816, P < 6.9E-12). Moreover, copy number variation analysis of TCGA database revealed that the more aggressive Triple Negative and Her2+ subtypes had higher levels of SOD3 gene deletion. The predominantly down-regulated expression pattern of SOD3 and the various genetic and epigenetic deregulations of its expression suggest that loss of this antioxidant promotes an advantageous tumour-promoting microenvironment in breast cancer.
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Affiliation(s)
- Brandon Griess
- Department of Biochemistry and Molecular Biology, Fred and Pamela Buffett Cancer Center, College of Medicine, University of Nebraska Medical Center , Omaha, NE, USA
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, Fred and Pamela Buffett Cancer Center, College of Medicine, University of Nebraska Medical Center , Omaha, NE, USA
| | - Alice Kueh
- Eppley Institute for Cancer Research, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center , Omaha, NE, USA
| | - Michelle Desler
- Eppley Institute for Cancer Research, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center , Omaha, NE, USA
| | - Kenneth Cowan
- Eppley Institute for Cancer Research, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center , Omaha, NE, USA
| | - Matthew Fitzgerald
- College of Nursing, University of Nebraska Medical Center , Omaha, NE, USA
| | - Melissa Teoh-Fitzgerald
- Department of Biochemistry and Molecular Biology, Fred and Pamela Buffett Cancer Center, College of Medicine, University of Nebraska Medical Center , Omaha, NE, USA
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5
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Guan Y, Wang G, Fails D, Nagarajan P, Ge Y. Unraveling cancer lineage drivers in squamous cell carcinomas. Pharmacol Ther 2020; 206:107448. [PMID: 31836455 PMCID: PMC6995404 DOI: 10.1016/j.pharmthera.2019.107448] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022]
Abstract
Cancer hijacks embryonic development and adult wound repair mechanisms to fuel malignancy. Cancer frequently originates from de-regulated adult stem cells or progenitors, which are otherwise essential units for postnatal tissue remodeling and repair. Cancer genomics studies have revealed convergence of multiple cancers across organ sites, including squamous cell carcinomas (SCCs), a common group of cancers arising from the head and neck, esophagus, lung, cervix and skin. In this review, we summarize our current knowledge on the molecular drivers of SCCs, including these five major organ sites. We especially focus our discussion on lineage dependent driver genes and pathways, in the context of squamous development and stratification. We then use skin as a model to discuss the notion of field cancerization during SCC carcinogenesis, and cancer as a wound that never heals. Finally, we turn to the idea of context dependency widely observed in cancer driver genes, and outline literature support and possible explanations for their lineage specific functions. Through these discussions, we aim to provide an up-to-date summary of molecular mechanisms driving tumor plasticity in squamous cancers. Such basic knowledge will be helpful to inform the clinics for better stratifying cancer patients, revealing novel drug targets and providing effective treatment options.
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Affiliation(s)
- Yinglu Guan
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Guan Wang
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Danielle Fails
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Priyadharsini Nagarajan
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Yejing Ge
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
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6
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Mukohda M, Fang S, Wu J, Agbor LN, Nair AR, Ibeawuchi SRC, Hu C, Liu X, Lu KT, Guo DF, Davis DR, Keen HL, Quelle FW, Sigmund CD. RhoBTB1 protects against hypertension and arterial stiffness by restraining phosphodiesterase 5 activity. J Clin Invest 2019; 129:2318-2332. [PMID: 30896450 DOI: 10.1172/jci123462] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mice selectively expressing PPARγ dominant negative mutation in vascular smooth muscle exhibit RhoBTB1-deficiency and hypertension. Our rationale was to employ genetic complementation to uncover the mechanism of action of RhoBTB1 in vascular smooth muscle. Inducible smooth muscle-specific restoration of RhoBTB1 fully corrected the hypertension and arterial stiffness by improving vasodilator function. Notably, the cardiovascular protection occurred despite preservation of increased agonist-mediated contraction and RhoA/Rho kinase activity, suggesting RhoBTB1 selectively controls vasodilation. RhoBTB1 augmented the cGMP response to nitric oxide by restraining the activity of phosphodiesterase 5 (PDE5) by acting as a substrate adaptor delivering PDE5 to the Cullin-3 E3 Ring ubiquitin ligase complex for ubiquitination inhibiting PDE5. Angiotensin-II infusion also caused RhoBTB1-deficiency and hypertension which was prevented by smooth muscle specific RhoBTB1 restoration. We conclude that RhoBTB1 protected from hypertension, vascular smooth muscle dysfunction, and arterial stiffness in at least two models of hypertension.
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Affiliation(s)
- Masashi Mukohda
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Shi Fang
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Department of Physiology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jing Wu
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Department of Physiology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Larry N Agbor
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Anand R Nair
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Stella-Rita C Ibeawuchi
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Chunyan Hu
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Xuebo Liu
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ko-Ting Lu
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Department of Physiology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Deng-Fu Guo
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Deborah R Davis
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Henry L Keen
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Frederick W Quelle
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Curt D Sigmund
- Department of Pharmacology, UIHC Center for Hypertension Research, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA.,Department of Physiology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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7
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Cao Y, Song J, Chen J, Xiao J, Ni J, Wu C. Overexpression of NEK3 is associated with poor prognosis in patients with gastric cancer. Medicine (Baltimore) 2018; 97:e9630. [PMID: 29504992 PMCID: PMC5779761 DOI: 10.1097/md.0000000000009630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The NIMA-related kinase 3 (NEK3) plays an important role in cell migration, cell proliferation, and cell viability. Recently, NEK3 was reported to enhance the malignancy of breast cancer. However, its role in gastric cancer has not been completely characterized. In this study, we explored the prognostic significance of NEK3 in human gastric cancer. Reverse transcription-polymerase chain reaction and western blot were performed to detect the NEK3 mRNA and protein expression in 6 paired fresh human gastric cancer tissues and surrounding normal tissues. NEK3 levels in gastric cancer and its adjacent normal samples of 168 cases were detected by immunohistochemistry, and the relationships between the NEK3 level and various clinicopathological features were analyzed. NEK3 mRNA and protein were significantly overexpressed in gastric cancer tissues, compared with adjacent normal tissues. Immunohistochemistry staining assay showed the percentage of high NEK3 expression in gastric cancer samples was higher than that in adjacent normal samples. NEK3 overexpression was significantly correlated with pT stage, pathologic TNM stage, lymph node metastasis, and poor prognosis of gastric cancer. Cox multivariate regression analyses suggested that NEK3 was an independent prognostic factor for survival of patients with gastric cancer. The data demonstrate that NEK3 is overexpressed in gastric cancer, which promotes the malignancy of gastric cancer. NEK3 may be as a prognostic biomarker and a potential therapeutic target for gastric cancer.
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Affiliation(s)
- Yongfeng Cao
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou
- Department of Oncology, The Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jiaye Song
- Department of Oncology, The Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jia Chen
- Department of Oncology, The Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jinzhang Xiao
- Department of Oncology, The Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Jingyi Ni
- Department of Oncology, The Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Changping Wu
- Department of Oncology, The Third Affiliated Hospital of Soochow University, Changzhou
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8
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Griess B, Tom E, Domann F, Teoh-Fitzgerald M. Extracellular superoxide dismutase and its role in cancer. Free Radic Biol Med 2017; 112:464-479. [PMID: 28842347 PMCID: PMC5685559 DOI: 10.1016/j.freeradbiomed.2017.08.013] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 12/19/2022]
Abstract
Reactive oxygen species (ROS) are increasingly recognized as critical determinants of cellular signaling and a strict balance of ROS levels must be maintained to ensure proper cellular function and survival. Notably, ROS is increased in cancer cells. The superoxide dismutase family plays an essential physiological role in mitigating deleterious effects of ROS. Due to the compartmentalization of ROS signaling, EcSOD, the only superoxide dismutase in the extracellular space, has unique characteristics and functions in cellular signal transduction. In comparison to the other two intracellular SODs, EcSOD is a relatively new comer in terms of its tumor suppressive role in cancer and the mechanisms involved are less well understood. Nevertheless, the degree of differential expression of this extracellular antioxidant in cancer versus normal cells/tissues is more pronounced and prevalent than the other SODs. A significant association of low EcSOD expression with reduced cancer patient survival further suggests that loss of extracellular redox regulation promotes a conducive microenvironment that favors cancer progression. The vast array of mechanisms reported in mediating deregulation of EcSOD expression, function, and cellular distribution also supports that loss of this extracellular antioxidant provides a selective advantage to cancer cells. Moreover, overexpression of EcSOD inhibits tumor growth and metastasis, indicating a role as a tumor suppressor. This review focuses on the current understanding of the mechanisms of deregulation and tumor suppressive function of EcSOD in cancer.
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Affiliation(s)
- Brandon Griess
- Department of Biochemistry and Molecular Biology, Buffett Cancer Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Eric Tom
- Department of Biochemistry and Molecular Biology, Buffett Cancer Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Frederick Domann
- Free Radical and Radiation Biology Program, Radiation Oncology, University of Iowa, Iowa, IA 52242, United States
| | - Melissa Teoh-Fitzgerald
- Department of Biochemistry and Molecular Biology, Buffett Cancer Center, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, United States.
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9
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Türke C, Horn S, Petto C, Labudde D, Lauer G, Wittenburg G. Loss of heterozygosity in FANCG, FANCF and BRIP1 from head and neck squamous cell carcinoma of the oral cavity. Int J Oncol 2017; 50:2207-2220. [PMID: 28440438 DOI: 10.3892/ijo.2017.3974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/28/2017] [Indexed: 01/10/2023] Open
Abstract
Recent advances have been made in the understanding of Fanconi anemia (FA), a hereditary disease that increases the risk for head and neck squamous cell carcinomas (HNSCC) by 500- to 700-fold. FA patients harbour germline mutations in genes of cellular DNA repair pathways that are assumed to facilitate the accumulation of mutations during HNSCC development. Mutations in these FA genes may also contribute to HNSCC in general. In the present study, we analysed three FA genes; FANCF, FANCG and BRIP1, that are involved in the repair of DNA inter strand cross-links, in HNSCC and their potential role for patient survival. We measured loss of heterozygosity (LOH) mutations at eight microsatellite loci flanking three FA genes in 54 HNSCC of the oral cavity and corresponding blood samples. Survival analyses were carried out using mutational data and clinical variables. LOH was present in 17% (FANCF region), 41% (FANCG region) and 11% (BRIP1 region) of the patients. Kaplan-Meier survival curves and log-rank tests indicated strong clinical predictors (lymph node stages with decreased survival: p=2.69e-12; surgery with improved survival: p=0.0005). LOH in the FANCF region showed a weaker association with decreased overall survival (p=0.006), which however, did not hold in multivariate analyses. LOH may predominantly indicate copy number gains in FANCF and losses in FANCG and BRIP1. Integration of copy number data and gene expression proved difficult as the available sample sets did not overlap. In conclusion, LOH in FA genes appears to be a common feature of HNSCC development seen here in 57% of patients and other mutation types may increase this mutation frequency. We suggest larger patient cohorts would be needed to test the observed association of LOH in FANCF and patient survival comprehensively.
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Affiliation(s)
- Christin Türke
- Department for Oral and Maxillofacial Surgery, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Susanne Horn
- Department of Dermatology, University Hospital, West German Cancer Center, University Duisburg-Essen, and German Consortium for Translational Cancer Research (DKTK), Essen, Germany
| | - Carola Petto
- Department for Oral and Maxillofacial Surgery, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Dirk Labudde
- Department of Bioinformatics, University of Applied Sciences Mittweida, Mittweida, Germany
| | - Günter Lauer
- Department for Oral and Maxillofacial Surgery, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Gretel Wittenburg
- Department for Oral and Maxillofacial Surgery, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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10
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Mahas A, Potluri K, Kent MN, Naik S, Markey M. Copy number variation in archival melanoma biopsies versus benign melanocytic lesions. Cancer Biomark 2017; 16:575-97. [PMID: 27002761 DOI: 10.3233/cbm-160600] [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] [Indexed: 12/25/2022]
Abstract
BACKGROUND Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations. OBJECTIVE This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi. METHODS Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi. RESULTS We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis. CONCLUSIONS Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.
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Affiliation(s)
- Ahmed Mahas
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Keerti Potluri
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael N Kent
- Department of Dermatology, Wright State University Boonshoft School of Medicine, Dayton, OH, USA.,Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Sameep Naik
- Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Michael Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
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11
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Borczuk AC, Pei J, Taub RN, Levy B, Nahum O, Chen J, Chen K, Testa JR. Genome-wide analysis of abdominal and pleural malignant mesothelioma with DNA arrays reveals both common and distinct regions of copy number alteration. Cancer Biol Ther 2016; 17:328-35. [PMID: 26853494 DOI: 10.1080/15384047.2016.1145850] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Malignant mesothelioma (MM) is an aggressive tumor arising from mesothelial linings of the serosal cavities. Pleural space is the most common site, accounting for about 80% of cases, while peritoneum makes up the majority of the remaining 20%. While histologically similar, tumors from these sites are epidemiologically and clinically distinct and their attribution to asbestos exposure differs. We compared DNA array-based findings from 48 epithelioid peritoneal MMs and 41 epithelioid pleural MMs to identify similarities and differences in copy number alterations (CNAs). Losses in 3p (BAP1 gene), 9p (CDKN2A) and 22q (NF2) were seen in tumors from both tumor sites, although CDKN2A and NF2 losses were seen at a higher rate in pleural disease (p<0.01). Overall, regions of copy number gain were more common in peritoneal MM, whereas losses were more common in pleural MM, with regions of loss containing known tumor suppressor genes and regions of gain encompassing genes encoding receptor tyrosine kinase pathway members. Cases with known asbestos causation (n = 32 ) were compared with those linked to radiation exposure (n = 9 ). Deletions in 6q, 14q, 17p and 22q, and gain of 17q were seen in asbestos-associated but not radiation-related cases. As reported in post-radiation sarcoma, gains outnumbered losses in radiation-associated MM. The patterns of genomic imbalances suggest overlapping and distinct molecular pathways in MM of the pleura and peritoneum, and that differences in causation (i.e., asbestos vs. radiation) may account for some of these site-dependent differences.
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Affiliation(s)
- Alain C Borczuk
- a Department of Pathology and Medicine , Weill Cornell Medicine , New York , USA
| | - Jianming Pei
- b Cancer Biology Program and Genomics Facility, Fox Chase Cancer Center , Philadelphia , USA
| | - Robert N Taub
- c Department of Medicine , Division of Hematology and Oncology
| | - Brynn Levy
- d Department of Pathology and Cell Biology , Columbia University Medical Center , New York , USA
| | - Odelia Nahum
- d Department of Pathology and Cell Biology , Columbia University Medical Center , New York , USA
| | - Jinli Chen
- d Department of Pathology and Cell Biology , Columbia University Medical Center , New York , USA
| | - Katherine Chen
- a Department of Pathology and Medicine , Weill Cornell Medicine , New York , USA
| | - Joseph R Testa
- b Cancer Biology Program and Genomics Facility, Fox Chase Cancer Center , Philadelphia , USA
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12
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Chen C, Zhang Y, Loomis MM, Upton MP, Lohavanichbutr P, Houck JR, Doody DR, Mendez E, Futran N, Schwartz SM, Wang P. Genome-Wide Loss of Heterozygosity and DNA Copy Number Aberration in HPV-Negative Oral Squamous Cell Carcinoma and Their Associations with Disease-Specific Survival. PLoS One 2015; 10:e0135074. [PMID: 26247464 PMCID: PMC4527746 DOI: 10.1371/journal.pone.0135074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 07/17/2015] [Indexed: 01/15/2023] Open
Abstract
Oral squamous cell cancer of the oral cavity and oropharynx (OSCC) is associated with high case-fatality. For reasons that are largely unknown, patients with the same clinical and pathologic staging have heterogeneous response to treatment and different probability of recurrence and survival, with patients with Human Papillomavirus (HPV)-positive oropharyngeal tumors having the most favorable survival. To gain insight into the complexity of OSCC and to identify potential chromosomal changes that may be associated with OSCC mortality, we used Affymtrix 6.0 SNP arrays to examine paired DNA from peripheral blood and tumor cell populations isolated by laser capture microdissection to assess genome-wide loss of heterozygosity (LOH) and DNA copy number aberration (CNA) and their associations with risk factors, tumor characteristics, and oral cancer-specific mortality among 75 patients with HPV-negative OSCC. We found a highly heterogeneous and complex genomic landscape of HPV-negative tumors, and identified regions in 4q, 8p, 9p and 11q that seem to play an important role in oral cancer biology and survival from this disease. If confirmed, these findings could assist in designing personalized treatment or in the creation of models to predict survival in patients with HPV-negative OSCC.
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Affiliation(s)
- Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Yuzheng Zhang
- Program in Biostatistics and Biomathematics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Melissa M. Loomis
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Melissa P. Upton
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Pawadee Lohavanichbutr
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John R. Houck
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David R. Doody
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eduardo Mendez
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Neal Futran
- Department of Otolaryngology–Head and Neck Surgery, University of Washington, Seattle, Washington, United States of America
| | - Stephen M. Schwartz
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Pei Wang
- Program in Biostatistics and Biomathematics, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genetics and Genomics Sciences, Mt. Sinai School of Medicine, New York, New York, United States of America
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13
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Amplification and deletion of the RAPH1 gene in breast cancer patients. Mol Biol Rep 2013; 40:6613-7. [PMID: 24057252 DOI: 10.1007/s11033-013-2774-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
Abstract
Lamellipodin protein (Lpd), encoded by the RAPH1 gene, modulates the assembly of actin cytoskeleton through its binding to the Ena/VASPs proteins, and acts in cellular motility and lamelipodial protrusion. The region where RAPH1 gene is located (2q33) is deleted in various types of cancer and the gene expression changes in tumors when compared to normal tissues. Amplifications and deletions of the RAPH1 gene were investigated in breast carcinoma samples, in order to determine the possible relationship of the gene with breast cancer tumorigenesis and lymph node metastasis. RAPH1 gene alterations were determined by relative quantification, standard curve method using Real-time PCR technique in samples of tumor and peripheral blood from 52 patients. Regression and correlation analyses were conducted using gene alterations and clinicopathological data. All samples analyzed were altered, with 63.5 % deletion cases and 36.5 % amplification cases. The logistic regression and correlation analysis with clinicopathological data did not show significant results. The results suggest that although the RAPH1 gene was deleted or amplified in all samples, the Lpd does not seem to play a major role in tumorigenesis of mammary carcinomas and probably other proteins, also involved in the process of cellular motility and metastasis, are acting more effectively for or against the migration of breast tumor cells.
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14
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di Martino E, Taylor CF, Roulson JA, Knowles MA. An integrated genomic, transcriptional and protein investigation of FGFRL1 as a putative 4p16.3 deletion target in bladder cancer. Genes Chromosomes Cancer 2013; 52:860-71. [PMID: 23775577 DOI: 10.1002/gcc.22082] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 05/16/2013] [Indexed: 11/08/2022] Open
Abstract
Loss of heterozygosity (LOH) of chromosome arm 4p is a common event in bladder and other malignancies. At least three distinct regions of deletion have been identified, but the deletion targets have so far remained elusive. In this study, we have identified a novel region of deletion mapping to 4p16.3 spanning 0-2.1 Mb, in 15% of bladder tumors and 24% of bladder cancer cell lines. FGFRL1, which maps within this region, was investigated as putative deletion target. The retained FGFRL1 allele was not mutated in cell lines and tumors with LOH, although in patients heterozygous for the rs4647930 functional polymorphism, the common allele was preferentially lost in tumor tissue. Epigenetic silencing of the retained allele was also excluded as levels of FGFRL1 mRNA and protein were similar in cell lines and tumors with and without 4p16.3 loss. However, while FGFRL1 protein was moderately expressed in all layers of the normal bladder epithelium, the majority of tumors showed areas of downregulation. Overall, average FGFRL1 protein expression was significantly lower in bladder tumors compared to normal tissue, but downregulation was independent from 4p16.3 LOH status, FGFR3 mutation, and tumor grade and stage. In conclusion, although we found no evidence supporting a "two-hit" inactivation of FGFRL1 in bladder carcinogenesis, the effect of heterozygous deletion coupled with functional polymorphisms, and the role of post-transcriptional downregulation deserves further investigation.
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Affiliation(s)
- Erica di Martino
- Section of Experimental Oncology, Leeds Institute of Cancer and Pathology, University of Leeds, St James's University Hospital, Leeds LS9 7TF, UK
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15
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Lee SM, Park JY, Kim DS. Methylation of TMEFF2 gene in tissue and serum DNA from patients with non-small cell lung cancer. Mol Cells 2012; 34:171-6. [PMID: 22814847 PMCID: PMC3887809 DOI: 10.1007/s10059-012-0083-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 05/31/2012] [Indexed: 12/31/2022] Open
Abstract
Lung cancer remains a global health problem with a high mortality rate. CpG island methylation is a common aberration frequently associated with gene silencing in multiple tumor types, emerging as a highly promising biomarker. The transmembrane protein with a single EGF-like and two follistatin domains (TMEFF2) is epigenetically silenced in numerous tumor types, suggesting a potential role as a potential tumor suppressor. However, the role of TMEFF2 in lung cancer remains to be fully elucidated. We explored the methylation status of TMEFF2 gene in 139 patients with non-small cell lung cancer (NSCLC) and the feasibility of detecting circulating methylated DNA as a screening tool for NSCLC using methylation-specific PCR in 316 patients and 50 age-matched health controls. TMEFF2 methylation in tumor tissues was found in 73 of the 139 NSCLCs (52.5%) and was related to gene expression. The frequency of TMEFF2 methylation was higher in females and never-smokers than in males and smokers with borderline significance (65.8% vs 47.8%, p = 0.06; 65.7% vs 48.1%, p = 0.07). Notably, in adenocarcinomas, TMEFF2 methylation was significantly more frequent in tumors without EGFR mutation than those with EGFR mutation (adjusted odds ratio = 7.13, 95% confidence interval = 2.05-24.83, P = 0.002). Furthermore, TMEFF2 methylation was exclusively detected in the serum of NSCLC patients at a frequency of 9.2% (29/316). These findings suggest that methylation-associated down-regulation of TMEFF2 gene may be involved in lung tumorigenesis and TMEFF2 methylation can serve as a specific blood-based biomarker for NSCLC.
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Affiliation(s)
- Su Man Lee
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu 702-422,
Korea
| | - Jae Yong Park
- Internal Medicine, School of Medicine, Kyungpook National University, Daegu 702-422,
Korea
| | - Dong Sun Kim
- Department of Anatomy, School of Medicine, Kyungpook National University, Daegu 702-422,
Korea
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16
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Abstract
Translational research refers to the interfaces between preclinical research and targeted short- and medium-term developments through to clinical standards. There are two distinct groups of oropharyngeal malignancies: those caused by tobacco and alcohol abuse and those caused by HPV infection. Although the prognosis of patients in the latter group is significantly better, this is not taken into consideration in the choice of treatment. However, less intensive use of radiotherapy, chemotherapy, or surgery, as well as targeted multimodal therapeutic approaches, is under research. This article summarizes the main events in the HPV life cycle, with emphasis on carcinogenic mechanisms and potential new molecular targets. Identifying distinct tumor entities of the oropharynx enables the design and development of new preventive and therapeutic strategies to reduce the incidence and mortality of HPV-associated oropharyngeal cancers in the near future.
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17
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Kasamatsu A, Uzawa K, Usukura K, Koike K, Nakashima D, Ishigami T, Fushimi K, Ogawara K, Shiiba M, Tanzawa H. Loss of heterozygosity in oral cancer. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/s1348-8643(11)00027-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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18
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Bebek G, Orloff M, Eng C. Microenvironmental genomic alterations reveal signaling networks for head and neck squamous cell carcinoma. J Clin Bioinforma 2011; 1:21. [PMID: 21884569 PMCID: PMC3170587 DOI: 10.1186/2043-9113-1-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 08/02/2011] [Indexed: 01/04/2023] Open
Abstract
Background Advanced stage head and neck squamous cell carcinoma (HNSCC) is an aggressive cancer with low survival rates. Loss-of-heterozygosity/allelic imbalance (LOH/AI) analysis has been widely used to identify genomic alterations in solid tumors and the tumor microenvironment (stroma). We hypothesize that these identified alterations can point to signaling networks functioning in HNSCC epithelial-tumor and surrounding stroma (tumor microenvironment). Results Under the assumption that genes in proximity to identified LOH/AI regions are correlated with the tumorigenic phenotype, we mined publicly available biological information to identify pathway segments (signaling proteins connected to each other in a network) and identify the role of tumor microenvironment in HNSCC. Across both neoplastic epithelial cells and the surrounding stromal cells, genetic alterations in HNSCC were successfully identified, and 75 markers were observed to have significantly different LOH/AI frequencies in these compartments (p < 0.026). We applied a network identification approach to the genes in proximity to these 75 markers in cancer epithelium and stroma in order to identify biological networks that can describe functional associations amongst these marker-associated genes. Conclusions We verified the involvement of T-cell receptor signaling pathways in HNSCC as well as associated oncogenes such as LCK and PLCB1, and tumor suppressors such as STAT5A, PTPN6, PARK2. We identified expression levels of genes within significant LOH/AI regions specific to stroma networks that correlate with better outcome in radiation therapy. By integrating various levels of high-throughput data, we were able to precisely focus on specific proteins and genes that are germane to HNSCC.
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Affiliation(s)
- Gurkan Bebek
- Genomic Medicine Institute, Cleveland Clinic, 9500 Euclid Avenue, Mailstop NE-50 Cleveland, OH 44195, USA.
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19
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Chien HT, Liao CT, Huang SF, Chen IH, Liu TY, Jou YS, Wang HM, Hsieh LL. Clinical significance of genome-wide minimally deleted regions in oral squamous cell carcinomas. Genes Chromosomes Cancer 2011; 50:358-69. [PMID: 21344537 DOI: 10.1002/gcc.20861] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/18/2011] [Accepted: 01/18/2011] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) has the highest rate of increase among male cancers in Taiwan. An understanding of the molecular pathogenesis of this disease as well as the development of prognostic markers for the clinical management of this disease is very important. Thus, a systematic loss of heterozygosity (LOH) analysis was performed to define minimally deleted regions (MDRs) in 63 male OSCCs using 400 polymorphic microsatellite markers. For increasing reliability, genomic DNA was extracted from >90% tumor cells that had been purified by LCM, and only when a microsatellite marker provided LOH information in >30% of the OSCCs was there considered to be successful allelotyping. A correlation of the various MDRs with clinicopathological parameters and prognosis was carried out. In total, 32 MDRs were identified and ten were noted as novel. In addition, six MDRs were found to be associated with cigarette smoking. Among these markers, a loss of MDR c7r2 (7q32.2-q35) was significantly associated with poor disease-free survival (DFS) and ten MDRs were associated with allelic imbalance (AI) in tumors. Among the latter, a loss of MDR c14r1 (14q24.2-q32.12) and c11r1 (11q13.4-q25) had a synergistic effect on poor DFS and were able to reduce further the DFS rate in patients with MDR c7r2 loss. Taken together, the results generated in this study provide new insights that help with exploring the molecular mechanisms associated with OSCC tumorigenesis and cigarette smoking. They also should aid the development of potential prognostic markers for the clinical management of OSCC.
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Affiliation(s)
- Huei-Tzu Chien
- Graduate Institute of Biomedical Sciences, Chang Gung University, Tao-Yuan, Taiwan
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20
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Libório TN, Acquafreda T, Matizonkas-Antonio LF, Silva-Valenzuela MG, Ferraz AR, Nunes FD. In situ hybridization detection of homeobox genes reveals distinct expression patterns in oral squamous cell carcinomas. Histopathology 2011; 58:225-33. [DOI: 10.1111/j.1365-2559.2011.03751.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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21
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Jovanovic L, Delahunt B, McIver B, Eberhardt NL, Bhattacharya A, Lea R, Grebe SKG. Distinct genetic changes characterise multifocality and diverse histological subtypes in papillary thyroid carcinoma. Pathology 2011; 42:524-33. [PMID: 20854070 DOI: 10.3109/00313025.2010.508780] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIMS This study was undertaken to investigate the genetic factors underlying the development of multifocality and phenotypic diversity in multifocal papillary thyroid carcinoma (mPTC). METHODS Loss of heterozygosity (LOH) and BRAF(V600E) mutation status were analysed in a total of 55 individual tumour foci from 18 cases of mPTC. The genetic findings and morphology of tumour foci were then compared. RESULTS Multifocal PTC LOH rates were higher than observed previously in solitary PTC. Different patterns of LOH and BRAF(V600E) positivity separated follicular variant tumours and tumour foci from other PTC histological subtypes. In five cases, genetic alterations were detected in morphologically normal thyroid epithelium. CONCLUSIONS These findings support the concept that multifocal PTCs develop through clonal selection from a field of pre-neoplastic cells, with morphotype differentiation correlating with specific tumour-genetic alterations. The relatively high genetic disarray in multifocal PTC may underlie their ability to spread throughout the thyroid gland.
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Affiliation(s)
- Lidija Jovanovic
- Department of Pathology and Molecular Medicine, Wellington School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
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22
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Abstract
Head and neck squamous cell carcinomas (HNSCCs) are caused by tobacco and alcohol consumption and by infection with high-risk types of human papillomavirus (HPV). Tumours often develop within preneoplastic fields of genetically altered cells. The persistence of these fields after treatment presents a major challenge, because it might lead to local recurrences and second primary tumours that are responsible for a large proportion of deaths. Aberrant signalling pathways have been identified in HNSCCs and inhibition of epidermal growth factor receptor (EGFR) has proved a successful therapeutic strategy. In this Review, we discuss the recent literature on tumour heterogeneity, field cancerization, molecular pathogenesis and the underlying causative cancer genes that can be exploited for novel and personalized treatments of patients with HNSCC.
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Affiliation(s)
- C René Leemans
- Department of Otolaryngology-Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.
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23
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Abstract
Head and neck squamous cell carcinomas (HNSCCs) are caused by tobacco and alcohol consumption and by infection with high-risk types of human papillomavirus (HPV). Tumours often develop within preneoplastic fields of genetically altered cells. The persistence of these fields after treatment presents a major challenge, because it might lead to local recurrences and second primary tumours that are responsible for a large proportion of deaths. Aberrant signalling pathways have been identified in HNSCCs and inhibition of epidermal growth factor receptor (EGFR) has proved a successful therapeutic strategy. In this Review, we discuss the recent literature on tumour heterogeneity, field cancerization, molecular pathogenesis and the underlying causative cancer genes that can be exploited for novel and personalized treatments of patients with HNSCC.
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24
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Transcriptional repression of DLEC1 associates with the depth of tumor invasion in oral squamous cell carcinoma. Oral Oncol 2010; 46:874-9. [PMID: 20952247 DOI: 10.1016/j.oraloncology.2010.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 09/07/2010] [Accepted: 09/07/2010] [Indexed: 12/31/2022]
Abstract
The objective of this study was to clarify the expression and epigenetic regulation of DLEC1, a candidate tumor suppressor gene (TSG) located at 3p21.3-p22, in oral squamous cell carcinoma (OSCC) and the clinical relevance of its down-expression. Quantitative RT-PCR was performed to exam the expression level of DLEC1 in matched OSCC and normal oral samples from 57 prospectively enrolled patients (with additional matched leukoplakia samples from 9 patients). We defined DLEC1 down-expression as a 2-fold decrease in expression of DLEC1 between normal tissues and tumors, and determined its correlation with clinical characteristics. Methylation-specific PCR (MSP) and bisulfite sequencing were used to evaluate the promoter methylation status of DLEC1 in 19 OSCC, 19 oral leukoplakia (OL), and 17 normal oral tissues. A statistically significant association between DLEC1 down-expression and invasive depth of OSCC was observed (P=0.026). Besides, expression of DLEC1 decreased sequentially from normal tissues to OL and then to OSCC (P<0.05), which was inversely correlated with methylation status of the DLEC1 promoter. Promoter methylation of DLEC1 increased progressively among normal tissues, OL, and OSCC, as revealed by MSP, and confirmed by sequencing. Treatment of OSCC cell lines with 5-aza-2'-deoxycytidine (5-Aza-dC) reversed the methylation and restored DLEC1 expression. Our results demonstrating that down-expression and promoter methylation of DLEC1 increased from normal tissues to premalignancies and then to malignancies. Furthermore, its transcriptional repression is associated with the depth of tumor invasion.
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25
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Bilodeau E, Alawi F, Costello BJ, Prasad JL. Molecular diagnostics for head and neck pathology. Oral Maxillofac Surg Clin North Am 2010; 22:183-94. [PMID: 20159486 DOI: 10.1016/j.coms.2009.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Molecular diagnostic techniques are quickly finding a role in the detection and diagnosis of tumors, and in predicting their behavior. They may also prove useful in developing new therapeutic approaches to head and neck cancer. The surgeon working in the craniomaxillofacial region should have an understanding of these technologies, their availability in various settings, and how they affect various aspects of treatment, particularly in the detection and treatment of malignancies. This article offers an overview of recent advances in molecular diagnostic techniques, with their implications for diagnosis and management of head and neck tumors.
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Affiliation(s)
- Elizabeth Bilodeau
- Department of Oral and Maxillofacial Surgery, University of Pittsburgh School of Dental Medicine, 3501 Terrace Street, Pittsburgh, PA 15261, USA
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26
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Katase N, Gunduz M, Beder LB, Gunduz E, Al Sheikh Ali M, Tamamura R, Yaykasli KO, Yamanaka N, Shimizu K, Nagatsuka H. Frequent allelic loss of Dkk-1 locus (10q11.2) is related with low distant metastasis and better prognosis in head and neck squamous cell carcinomas. Cancer Invest 2010; 28:103-10. [PMID: 19995224 DOI: 10.3109/07357900903095680] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a frequently occurring cancer worldwide. Dickkopf (Dkk)-1 gene is suggested to function as tumor suppressor gene (TSG) in several kinds of malignancies. In this study, we performed loss of heterozygosity (LOH) analysis of Dkk-1 and examined the correlation between LOH status and clinicopathological parameters for the first time. A pretty high LOH ratio (50%) was detected. Interestingly, in the cases with Dkk-1 retention group showed less distant metastasis and a tendency of longer disease free survival. These results indicate that Dkk-1 can play a role in HNSCC carcinogenesis and it may also be related to distant metastasis.
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Affiliation(s)
- Naoki Katase
- Department of Oral pathology and Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Okayama 700-8525, Japan
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27
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Kruszyna Ł, Lianeri M, Rydzanicz M, Gajęcka M, Szyfter K, Jagodziński PP. Polymorphic variants of folate metabolism genes and the risk of laryngeal cancer. Mol Biol Rep 2009; 37:241-7. [DOI: 10.1007/s11033-009-9643-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 07/21/2009] [Indexed: 10/20/2022]
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28
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Gunduz E, Gunduz M, Ali MAS, Beder L, Tamamura R, Katase N, Tominaga S, Yamanaka N, Shimizu K, Nagatsuka H. Loss of Heterozygosity at the 9p21–24 Region and Identification of BRM as a Candidate Tumor Suppressor Gene in Head and Neck Squamous Cell Carcinoma. Cancer Invest 2009; 27:661-8. [DOI: 10.1080/07357900802563010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Klussmann JP, Mooren JJ, Lehnen M, Claessen SMH, Stenner M, Huebbers CU, Weissenborn SJ, Wedemeyer I, Preuss SF, Straetmans JMJAA, Manni JJ, Hopman AHN, Speel EJM. Genetic signatures of HPV-related and unrelated oropharyngeal carcinoma and their prognostic implications. Clin Cancer Res 2009; 15:1779-86. [PMID: 19223504 DOI: 10.1158/1078-0432.ccr-08-1463] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Patients with human papillomavirus (HPV)-containing oropharyngeal squamous cell carcinomas (OSCC) have a better prognosis than patients with HPV-negative OSCC. This may be attributed to different genetic pathways promoting cancer. EXPERIMENTAL DESIGN We used comparative genomic hybridization to identify critical genetic changes in 60 selected OSCC, 28 of which were associated with HPV-16 as determined by HPV-specific PCR and fluorescence in situ hybridization analysis and positive p16(INK4A) immunostaining. The results were correlated with HPV status and clinical data from patients. RESULTS Two thirds of OSCC harbored gain at 3q26.3-qter irrespective of HPV status. In HPV-negative tumors this alteration was associated with advanced tumor stage (P=0.013). In comparison with HPV-related OSCC, the HPV-negative tumors harbored: (a) a higher number of chromosomal alterations and amplifications (P=0.03 and 0.039, respectively); (b) significantly more losses at 3p, 5q, 9p, 15q, and 18q, and gains/amplifications at 11q13 (P=0.002, 0.03; <0.001, 0.02, 0.004, and 0.001, respectively); and (c) less often 16q losses and Xp gains (P=0.02 and 0.03). Survival analysis revealed a significantly better disease-free survival for HPV-related OSCC (P=0.02), whereas chromosome amplification was an unfavorable prognostic indicator for disease-free and overall survival (P=0.01 and 0.05, respectively). Interestingly, 16q loss, predominantly identified in HPV-related OSCC, was a strong indicator of favorable outcome (overall survival, P=0.008; disease-free survival, P=0.01) and none of these patients had a tumor recurrence. CONCLUSIONS Genetic signatures of HPV-related and HPV-unrelated OSCC are different and most likely underlie differences in tumor development and progression. In addition, distinct chromosomal alterations have prognostic significance.
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Affiliation(s)
- Jens P Klussmann
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Jean-Uhrmacher Institute, University of Cologne, Cologne, Germany.
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30
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Koy S, Plaschke J, Luksch H, Friedrich K, Kuhlisch E, Eckelt U, Martinez R. Microsatellite instability and loss of heterozygosity in squamous cell carcinoma of the head and neck. Head Neck 2008; 30:1105-13. [PMID: 18615731 DOI: 10.1002/hed.20857] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Microsatellite instability (MSI) in head and neck squamous cell carcinoma (HNSCC) has been reported with a wide range of frequencies. The aim of our study was to disclose the frequency and basis of MSI in HNSCC and to correlate MSI and findings on loss of heterozygosity (LOH) with the clinical data. METHODS We analyzed MSI and LOH in 91 tumors. All tumors presenting instability were analyzed for the expression of mismatch repair genes (MMR) proteins. RESULTS Low-level microsatellite instability (MSI-L) was seen in 7.7% of the HNSCC. None of the MSI-L tumors had aberrant MMR protein expression. LOH rates up to 57% were identified for different regions on chromosome 3p. For the marker D10S197, we found a significant correlation between LOH and tumor stage IV. CONCLUSION Our results indicate that MMR gene inactivation is rare among primary HNSCC. In contrast, the MSI-L phenotype plays a role in a small subset of tumors. LOH on chromosome arm 3p and 10p12 seems to be involved in tumorigenesis and progression HNSCC, respectively.
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Affiliation(s)
- Susanne Koy
- Department of Oral and Maxillofacial Surgery, University Hospital Carl Gustav Carus, Technical University Dresden, Fetscherstr. 74, 01307 Dresden, Germany.
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Abstract
For years, head and neck squamous cell carcinomas (HNSCC) have been among the leading cancers worldwide. Despite considerable efforts, the 5-year survival rate for HNSCC has not changed significantly. To improve this situation, it is necessary to understand the fundamental biological processes leading to the disease and its progression. In addition to known genetic changes in HNSCC, molecular cytogenetic investigations have identified chromosomal regions of gains and losses, but many of the responsible candidate genes have yet to be identified. Furthermore, recent results indicate the importance of epigenetic modifications in HNSCC, such as DNA methylation. Several genes, including the tumor suppressor CDKN2A and other candidates such as DAPK1, MGMT, TIMP3, TCF21, and C/EBPalpha, have been found to harbor hypermethylated regulatory sequences that lead to reduced expression or gene silencing. Hypermethylation in such genes could be used not only as biomarkers for the early detection of HNSCC but also to improve prevention strategies and therapy outcomes.
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Affiliation(s)
- P Schmezer
- Abteilung Toxikologie und Krebsrisikofaktoren, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg
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32
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Loss of heterozygosity at chromosome 14q is associated with poor prognosis in head and neck squamous cell carcinomas. J Cancer Res Clin Oncol 2008; 134:1267-76. [DOI: 10.1007/s00432-008-0423-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2008] [Accepted: 05/13/2008] [Indexed: 12/12/2022]
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Guled M, Myllykangas S, Frierson HF, Mills SE, Knuutila S, Stelow EB. Array comparative genomic hybridization analysis of olfactory neuroblastoma. Mod Pathol 2008; 21:770-8. [PMID: 18408657 DOI: 10.1038/modpathol.2008.57] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Olfactory neuroblastoma is an unusual neuroectodermal malignancy, which is thought to arise at the olfactory membrane of the sinonasal tract. Due to its rarity, little is understood regarding its molecular and cytogenetic abnormalities. The aim of the current study is to identify specific DNA copy number changes in olfactory neuroblastoma. Thirteen dissected tissue samples were analyzed using array comparative genomic hybridization. Our results show that gene copy number profiles of olfactory neuroblastoma samples are complex. The most frequent changes included gains at 7q11.22-q21.11, 9p13.3, 13q, 20p/q, and Xp/q, and losses at 2q31.1, 2q33.3, 2q37.1, 6q16.3, 6q21.33, 6q22.1, 22q11.23, 22q12.1, and Xp/q. Gains were more frequent than losses, and high-stage tumors showed more alterations than low-stage olfactory neuroblastoma. Frequent changes in high-stage tumors were gains at 13q14.2-q14.3, 13q31.1, and 20q11.21-q11.23, and loss of Xp21.1 (in 66% of cases). Gains at 5q35, 13q, and 20q, and losses at 2q31.1, 2q33.3, and 6q16-q22, were present in 50% of cases. The identified regions of gene copy number change have been implicated in a variety of tumors, especially carcinomas. In addition, our results indicate that gains in 20q and 13q may be important in the progression of this cancer, and that these regions possibly harbor genes with functional relevance in olfactory neuroblastoma.
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Affiliation(s)
- Mohamed Guled
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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Abstract
RhoBTB proteins constitute a subfamily of atypical members within the Rho family of small guanosine triphosphatases (GTPases). Their most salient feature is their domain architecture: a GTPase domain (in most cases, non-functional) is followed by a prolinerich region, a tandem of 2 broadcomplex, tramtrack, bric a brac (BTB) domains, and a conserved Cterminal region. In humans, the RhoBTB subfamily consists of 3 isoforms: RhoBTB1, RhoBTB2, and RhoBTB3. Orthologs are present in several other eukaryotes, such as Drosophila and Dictyostelium, but have been lost in plants and fungi. Interest in RhoBTB arose when RHOBTB2 was identified as the gene homozygously deleted in breast cancer samples and was proposed as a candidate tumor suppressor gene, a property that has been extended to RHOBTB1. The functions of RhoBTB proteins have not been defined yet, but may be related to the roles of BTB domains in the recruitment of cullin3, a component of a family of ubiquitin ligases. A model emerges in which RhoBTB proteins are required to maintain constant levels of putative substrates involved in cell cycle regulation or vesicle transport through targeting for degradation in the 26S proteasome. RhoBTB proteins are engrossing the list of Rho GTPases involved in tumorigenesis. Unlike typical Rho GTPases (usually overexpressed or hyperactive), RhoBTB proteins appear to play a part in the carcinogenic process through a mechanism that involves the decreased or abolished expression of the corresponding genes, or more rarely, mutations that result in impaired functioning of the protein, presumably leading to the accumulation of RhoBTB substrates and alterations of the cellular homeostasis.
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Affiliation(s)
- Jessica Berthold
- Centers for Biochemistry and Molecular Medicine, University of Cologne, Cologne, Germany
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35
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Gunduz M, Beder LB, Gunduz E, Nagatsuka H, Fukushima K, Pehlivan D, Cetin E, Yamanaka N, Nishizaki K, Shimizu K, Nagai N. Downregulation of ING3 mRNA expression predicts poor prognosis in head and neck cancer. Cancer Sci 2008; 99:531-8. [PMID: 18081876 PMCID: PMC11159728 DOI: 10.1111/j.1349-7006.2007.00708.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Revised: 11/07/2007] [Accepted: 11/13/2007] [Indexed: 06/09/2024] Open
Abstract
Although many clinical and pathological prognostic factors such as tumor stage and lymph-node involvement have been described, to date no reliable or clinically applicable marker or tumor aggressiveness has been identified for head and neck cancer. In an attempt to identify such a molecular prognostic marker, we analyzed the mRNA expression status of ING3 by quantitative reverse transcription-polymerase chain reaction. We also examined p53 mutation status and investigated its relationship with ING3, as well its clinicopathological characteristics. About half of the 71 tumor samples demonstrated downregulation of ING3 compared to their matched normal counterparts. Although most clinicopathological variables were not significantly related to ING3 downregulation or p53 mutation status, a significant relationship was detected in terms of overall survival between the cases with low and normal to high ING3 expression. At 5 years follow up, approximately 60% of the patients with normal to high ING3 expression survived, whereas this was 35% in the patients with low ING3 expression. Multivariate analysis also showed downregulation of ING3 as an independent prognostic factor for poor overall survival. These results reveal that ING3 would function as a potential tumor suppressor molecule and that low levels of ING3 may indicate an aggressive nature of head and neck cancer.
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Affiliation(s)
- Mehmet Gunduz
- Department of Oral Pathology and Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Shikatacho 2-5-1, Okayama, Japan.
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36
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Honjo N, Gunduz M, Fukushima K, Cengiz B, Beder LB, Gunduz E, Nagatsuka H, Xiao J, Shimizu K, Nishizaki K. Comprehensive loss of heterozygosity analysis and identification of a novel hotspot at 3p21 in salivary gland neoplasms. Otolaryngol Head Neck Surg 2007; 137:119-25. [PMID: 17599578 DOI: 10.1016/j.otohns.2007.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2006] [Accepted: 01/16/2007] [Indexed: 11/20/2022]
Abstract
OBJECTIVES We sought to assess loss of heterozygosity (LOH) profiles of 3p, 6q, 8q, 10q, 12q, 13q, and 17p and to identify the tumor suppressor genes involved in salivary gland neoplasms. STUDY DESIGN LOH analysis was performed using 26 microsatellite markers by polymerase chain reaction-polyacrylamide gel electrophoresis method in 20 benign and 6 malignant salivary gland tumors. RESULTS Overall, LOH was detected in at least one informative locus in 18 of 20 (90%) of benign tumors and in all of 6 cases of malignant tumors. High LOH frequencies were revealed at the loci D3S1307 (22%, 3p26), D3S966 (41%, 3p21), D6S255 (27%, 6q25), D8S166 (25%, 8q12), D8S199 (21%, 8q24), and D10S1765 (28%, 10q23) in benign tumors, defining the hotspot regions for putative tumor suppressor genes. CONCLUSIONS AND SIGNIFICANCE The hotspot regions defined by the present study suggest that new tumor suppressor genes related to the development of salivary gland tumors may reside at several chromosomal loci, including loci at 3p, 6q, 8q and 10q.
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MESH Headings
- Adenolymphoma/genetics
- Adenoma, Pleomorphic/genetics
- Adult
- Aged
- Carcinoma/genetics
- Carcinoma, Squamous Cell/genetics
- Chromosome Mapping
- Chromosomes, Human, Pair 10/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 3/genetics
- Chromosomes, Human, Pair 6/genetics
- Chromosomes, Human, Pair 8/genetics
- Female
- Genes, Tumor Suppressor
- Humans
- Loss of Heterozygosity/genetics
- Male
- Microsatellite Repeats/genetics
- Middle Aged
- Parotid Neoplasms/genetics
- Submandibular Gland Neoplasms/genetics
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Affiliation(s)
- Noriyasu Honjo
- Department of Otolaryngology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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37
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Huijsmans R, Damen J, van der Linden H, Hermans M. Single nucleotide polymorphism profiling assay to confirm the identity of human tissues. J Mol Diagn 2007; 9:205-13. [PMID: 17384212 PMCID: PMC1867440 DOI: 10.2353/jmoldx.2007.060059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To identify issues of sample mix-ups, various molecular techniques are currently used. These techniques, however, are time consuming and require experience and/or DNA sequencing equipment or have a relatively high risk of errors because of contamination. Therefore, a quick and straightforward single nucleotide polymorphism (SNP) profiling assay was developed to link human tissues to a source. SNPs are common sequence variations in the human genome, and each individual has a unique combination of these nucleotide variations. Using potentially mislabeled paraffin-embedded tissues, DNA was extracted and SNP profiles were determined by real-time polymerase chain reaction analysis of the purified DNA using a selection of 10 commercially available SNP amplification assays. These profiles were compared with profiles of the supposed owners. All issues (34 in total) of potential sample mix-ups during the last 3 years were adequately solved, with six cases described here. The SNP profiling assay provides a quick (within 24 hours), easy, and reliable way to link human samples to a source, without polymerase chain reaction postprocessing. The chance for two randomly chosen individuals to have an identical profile is 1 in 18,000. Solving potential sample mix-ups will secure downstream evaluations and critical decisions concerning the patients involved.
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Affiliation(s)
- Ronald Huijsmans
- Multidisciplinary Laboratory of Molecular Diagnostics, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
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38
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Yu Y, Baras AS, Shirasuna K, Frierson HF, Moskaluk CA. Concurrent loss of heterozygosity and copy number analysis in adenoid cystic carcinoma by SNP genotyping arrays. J Transl Med 2007; 87:430-9. [PMID: 17372589 DOI: 10.1038/labinvest.3700536] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Adenoid cystic carcinoma (ACC) is one of the most common malignancies to arise in the salivary glands, yet very little is known of the genetic alterations that are involved in the pathogenesis of this disease. To further examine the genetic changes that underlie ACC, we analyzed genomic DNA obtained from 22 primary ACC and two ACC-derived cell lines by high-density oligonucleotide single-nucleotide polymorphism genotyping arrays (Affymetrix GeneChip Human Mapping 100K Set). Allelotype calls were analyzed by the Haplotype Correction version of the Linkage Disequilibrium Hidden Markov Model to determine loss of heterozygosity using information derived only from tumor samples. Comparison of data obtained from matched tumor-normal samples suggested that only deletion calls of >3 Mb were reliable. Within these parameters, ACC samples revealed a mean of three deletions per tumor, and no consensus areas of deletion were observed across the majority of tumors. Similarly, copy number analysis of primary hybridization data revealed no consensus areas of gene amplification. This is in contrast to a much higher rate of genomic alterations detected in a cohort of squamous carcinomas analyzed by the same methods. Our data show that most ACC have predominantly stable genomes, which is consistent with the theory that telomere crisis does not play a significant role in early stages of ACC tumor progression. Our data suggest that gene mutation and/or epigenetic events that cannot be detected by assay of gross alteration of chromosomal structure are likely to underlie the malignant transformation events of this tumor type.
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Affiliation(s)
- Yongtao Yu
- Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA
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39
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Nakaya K, Yamagata HD, Arita N, Nakashiro KI, Nose M, Miki T, Hamakawa H. Identification of homozygous deletions of tumor suppressor gene FAT in oral cancer using CGH-array. Oncogene 2007; 26:5300-8. [PMID: 17325662 DOI: 10.1038/sj.onc.1210330] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Homozygous deletions (HD) provide an important resource for identifying the location of candidate tumor suppressor genes. To identify the tumor suppressor gene in oral cancer, we employed high-resolution comparative genomic hybridization (CGH)-array analysis. We identified a homozygous loss of FAT (4q35), a new member of the human cadherin superfamily, from genome-wide screening of copy number alterations in one primary oral cancer. This result was evaluated by genomic polymerase chain reaction in 13 oral cancer cell lines and 20 primary oral cancers and Southern blot in the cell lines. We found frequent exonic HD of FAT in the cell lines (3/13, 23%) and in primary oral cancers (16/20, 80%). FAT expression was absent in these cell lines. Homozygous deletion hot spots were observed in exon 1 (9/20, 45%) and exon 4 (7/20, 35%). Moreover, loss of gene expression was identified in other types of squamous cell carcinoma. The methylation status of the FAT CpG island in squamous cell carcinomas correlated negatively with its expression. Our results identify mutations in FAT as an important factor in the development of oral cancer and indicate the importance of FATs function in some squamous cell carcinomas.
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Affiliation(s)
- K Nakaya
- Department of Oral and Maxillofacial Surgery, Organ Function Regenerative and Reconstructive Surgery, Ehime University Graduate School of Medicine, Toon-city, Ehime, Japan
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40
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Hernández M, Almeida TA. Is there any association between nek3 and cancers with frequent 13q14 deletion? Cancer Invest 2007; 24:682-8. [PMID: 17118778 DOI: 10.1080/07357900600981364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromosomal region 13q14 is frequently deleted in prostate cancer. nek3, a protein kinase related gene, is located on this region. Analysis of the coding region of nek3 showed an A insertion/deletion polymorphism in a stretch of adenines at the end of exon 9, with 2 alleles showing either 7 or 8 adenines. In addition we found a variant human NEK3 transcript, which lacks the entire exon 10 due to alternative splicing. The frequency of A8 allele is statistically higher in prostate cancer samples (p < 0.001) than normal controls, indicating that tumor samples preferentially express a full length protein. On the contrary, normal samples have a higher frequency for the A7 allele, expressing preferentially a shorter protein. To test if this association is a common feature in cancers with frequent 13q14 alterations, we analyzed cell lines established from oral, lung, and hepatocellular cancers. An association between nek3 A insertion/deletion polymorphism and cancers with alterations at 13q14 is observed.
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Affiliation(s)
- M Hernández
- Universidad de La Laguna, Facultad de Biología, Departamento de Genética, Tenerife, Islas Canarias, Spain
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41
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Poetsch M, Kleist B. Loss of heterozygosity at 15q21.3 correlates with occurrence of metastases in head and neck cancer. Mod Pathol 2006; 19:1462-9. [PMID: 16906132 DOI: 10.1038/modpathol.3800666] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Deletions on the long arm of chromosome 15 suggesting the presence of potential tumor suppressor genes have been found in several tumors including carcinomas of the colorectum, urinary bladder, breast, lung, and head and neck. Here, we analyzed allelic imbalance on chromosome 15q in head and neck carcinomas and corresponding lymph node metastases to define common regions of aberrations with potential involvement in development and progression of these tumors. We studied a panel of 40 polymorphic microsatellite markers, spanning 15q13-15q26, in 63 head and neck carcinomas and 38 lymph node metastases. Loss of heterozygosity (LOH) could be demonstrated in 34 primary tumors (54%) and 35 metastases (92%). Aberration mapping defined three minimum regions of aberrations: a region between the markers D15S106 and D15S1029 in 15q21.3 (estimated as 3.9 Mb; region 1) was affected in the majority of tumors, whereas two other regions between D15S144 and D15S1040 in 15q13.3-14 (estimated as 2.4 Mb; region 2) and between D15S130 and D15S985 in 15q26.2-26.3 (estimated as 4.7 Mb; region 3) were less often involved. Allelic loss in region 1 correlated with T stages (P=0.0029) and metastatic potential (P=0.0018). LOH in regions 2 and 3 occurred predominantly in metastases (P=0.0129 and P=0.0013, respectively). No correlation with grading, localization, or clinical outcome could be established for any of the affected regions. Our data hint at aberrations in 15q21.3 as a possible important characteristic for head and neck squamous cell carcinomas with risk of progression.
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Affiliation(s)
- Micaela Poetsch
- Institute of Forensic Medicine, University of Greifswald, Greifswald, Germany.
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42
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Mitra S, Banerjee S, Misra C, Singh RK, Roy A, Sengupta A, Panda CK, Roychoudhury S. Interplay between human papilloma virus infection and p53 gene alterations in head and neck squamous cell carcinoma of an Indian patient population. J Clin Pathol 2006; 60:1040-7. [PMID: 17079356 PMCID: PMC1972436 DOI: 10.1136/jcp.2005.034835] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AIM To investigate the complex interplay between human papilloma virus (HPV) infection and p53 gene alteration in 92 head and neck squamous cell carcinoma (HNSCC) and 28 leukoplakia samples from eastern India. METHODS DNA isolated from the patient samples was subjected to HPV detection, loss of heterozygosity (LOH) analysis of the chromosome 17p region harbouring p53, genotyping at the p53 codon 72 locus and sequencing of the entire p53 gene to identify somatic mutations. Codon 72 heterozygotes carrying the p53 mutation were further cloned and resequenced to identify the allele harbouring the mutation. RESULTS HPV positivity in the HNSCC samples was 69%; 21% of the HNSCC were found to harbour p53 mutations in the coding region of the gene. The absence of the p53 mutation in HPV positive tumours was statistically significant compared to the HPV negative tumours (p = 0.01), but the same did not hold true for p53 LOH (p = 1.0). Among the germline p53 codon 72 heterozygotes, the Pro allele was preferentially lost (p = 0.02) while the Arg allele was mutated in the majority of cases. The risk of HPV mediated tumourigenesis increased with the increase in number of Arg alleles at the codon 72 locus. CONCLUSION It is proposed that genetic and epigenetic alteration of p53 follow distinct pathways during the development of HNSCC from normal epithelium via dysplasia. The p53 mutation and HPV mediated p53 inactivation possibly constitute two independent pathways of tumourigenesis.
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Affiliation(s)
- S Mitra
- Human Genetics and Genomics Division, Indian Institute of Chemical Biology, Kolkata, India
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43
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Sckolnick J, Murphy J, Hunt JL. Microsatellite Instability in Nasopharyngeal and Lymphoepithelial Carcinomas of the Head and Neck. Am J Surg Pathol 2006; 30:1250-3. [PMID: 17001155 DOI: 10.1097/01.pas.0000209829.16607.cd] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Lymphoepithelial carcinoma (LEC) is a descriptive diagnosis for an undifferentiated carcinoma that has a typical morphologic appearance of large vesicular cells with prominent nucleoli and infiltrating lymphocytes. Tumors with this histopathologic appearance in the head and neck can be categorized as either those that occur in endemic areas, such as Southeast Asia and are associated with Epstein-Barr virus (EBV) infection, or those that occur in other countries and are less commonly associated with EBV. The molecular changes in endemic EBV-related LEC have been fairly well studied and include both alterations in tumor suppressor genes and 1 report of high levels of microsatellite instability. In nonendemic LECs arising in western countries, there is very little data related to molecular mutational profiles. In this study, we examined 19 cases of LEC from the United States for evidence of microsatellite instability at the DNA level and for alterations in the DNA mismatch repair (MMR) system at the immunohistochemical staining level. Only 3/19 cases showed high-level microsatellite instability and only 1 of these showed an alteration in the DNA MMR protein expression hMLH1. These data suggest that alterations in DNA MMR system are not a common mechanism of tumorigenesis in LEC of the head and neck in a nonendemic country.
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Affiliation(s)
- Joshua Sckolnick
- Department of Otolaryngology, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
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44
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Cengiz B, Gunduz M, Nagatsuka H, Beder L, Gunduz E, Tamamura R, Mahmut N, Fukushima K, Ali MAS, Naomoto Y, Shimizu K, Nagai N. Fine deletion mapping of chromosome 2q21-37 shows three preferentially deleted regions in oral cancer. Oral Oncol 2006; 43:241-7. [PMID: 16857411 DOI: 10.1016/j.oraloncology.2006.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 03/10/2006] [Accepted: 03/10/2006] [Indexed: 11/30/2022]
Abstract
We analysed the loss of heterozygosity (LOH) of long arm of chromosome 2 by using 16 polymorphic microsatellite markers in 39 matched oral normal and cancer tissues, and defined the deletional mapping of the region with putative tumor suppressor genes. LOH was detected at least one location in 33 of 39 (85%) tumor tissues. Frequent deletions were detected at the locations of microsatellite markers, D2S2304 (35%), D2S111 (40%), D2S155 (35%), D2S1327 (29%), D2S164 (29%), D2S125 (68%) and D2S140 (32%). Three preferentially deleted regions at 2q21-24, 2q33-35 and 2q37.3 were observed. Several candidate tumor suppressor genes in these regions such as LRP1B, CASP8, CASP10, BARD1, ILKAP, PPP1R7, and ING5, are located. Further molecular analysis of each gene should be performed to clarify their roles in oral carcinogenesis.
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Affiliation(s)
- Beyhan Cengiz
- Department of Oral Pathology and Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayamashi 700-8525, Japan
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45
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Smeets SJ, Braakhuis BJM, Abbas S, Snijders PJF, Ylstra B, van de Wiel MA, Meijer GA, Leemans CR, Brakenhoff RH. Genome-wide DNA copy number alterations in head and neck squamous cell carcinomas with or without oncogene-expressing human papillomavirus. Oncogene 2006; 25:2558-64. [PMID: 16314836 DOI: 10.1038/sj.onc.1209275] [Citation(s) in RCA: 196] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Oncogene-expressing human papillomavirus type 16 (HPV16) is found in a subset of head and neck squamous cell carcinomas (HNSCC). HPV16 drives carcinogenesis by inactivating p53 and pRb with the viral oncoproteins E6 and E7, paralleled by a low level of mutations in TP53 and allelic loss at 3p, 9p, and 17p, genetic changes frequently found in HNSCCs of nonviral etiology. We hypothesize that two pathways to HNSCC exist: one determined by HPV16 and the other by environmental carcinogens. To define the critical genetic events in these two pathways, we now present a detailed genome analysis of HNSCC with and without HPV16 involvement by employing high-resolution microarray comparative genomic hybridization. Four regions showed alterations in HPV-negative tumors that were absent in HPV-positive tumors: losses at 3p11.2-26.3, 5q11.2-35.2, and 9p21.1-24, and gains/amplifications at 11q12.1-13.4. Also, HPV16-negative tumors demonstrated loss at 18q12.1-23, in contrast to gain in HPV16-positive tumors. Seven regions were altered at high frequency (>33%) in both groups: gains at 3q22.2-qter, 5p15.2-pter, 8p11.2-qter, 9q22-34.1, and 20p-20q, and losses at 11q14.1-qter and 13q11-33. These data show that HNSCC arising by environmental carcinogens are characterized by genetic alterations that differ from those observed in HPV16-induced HNSCC, and most likely occur early in carcinogenesis. A number of genetic changes are shared in both tumor groups and can be considered crucial in the later stages of HNSCC progression.
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Affiliation(s)
- S J Smeets
- Department of Otolaryngology/Head-Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands
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46
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Brieger J, Kastner J, Gosepath J, Mann WJ. Evaluation of microsatellite amplifications at chromosomal locus 3q26 as surrogate marker for premalignant changes in mucosa surrounding head and neck squamous cell carcinoma. ACTA ACUST UNITED AC 2006; 167:26-31. [PMID: 16682282 DOI: 10.1016/j.cancergencyto.2005.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 10/25/2005] [Accepted: 11/11/2005] [Indexed: 10/24/2022]
Abstract
We analyzed tumor and surrounding mucosal samples of head and neck squamous cell carcinoma by fragment analysis for gain of genomic material as a potential indicator for oncogenic transformation. Our aim was to evaluate the potential value of this fast and sensitive polymerase chain reaction (PCR)-based method for intra-operative detection of chromosomal aberrations as a surrogate marker for incomplete tumor resection. Biopsies of the primary tumors and adjacent macroscopically nonmalignant mucosa 1 and 2 cm away from the tumor margins were collected from 20 patients. DNA were isolated, and 11 microsatellite markers at loci 3q25.31 approximately 3q28 were amplified by PCR. Allelic losses or gains were analyzed by capillary electrophoresis. Imbalanced alleles were common in the samples evaluated. In the median gains of the informative loci were detected in 67% of the primary tumors, 22% of the samples taken at 1 cm and 15% of the samples taken at 2 cm distance. We observed gains of 3q at least in one microsatellite in all primary tumors, in 15 (1 cm) and 12 (2 cm) nonmalignant mucosa samples. Gain of genetic material is frequent in tumor-surrounding mucosa. Detection of small chromosomal aberrations is possible using the PCR-based, highly sensitive, and fast-to-perform fragment analysis technique. The value for the diagnosis and prognosis will have to be proven in follow-up studies.
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Affiliation(s)
- Jürgen Brieger
- Department of Otorhinolaryngology, Mainz Medical School, Building 102, Lagenbeckstrasse 1, Mainz 55101, Germany.
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Kempski HM, Austin N, Chatters SJ, Toomey SM, Chalker J, Anderson J, Sebire NJ. Previously unidentified complex cytogenetic changes found in a pediatric case of solid-pseudopapillary neoplasm of the pancreas. ACTA ACUST UNITED AC 2006; 164:54-60. [PMID: 16364763 DOI: 10.1016/j.cancergencyto.2005.06.017] [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] [Received: 03/31/2005] [Revised: 06/07/2005] [Accepted: 06/17/2005] [Indexed: 12/28/2022]
Abstract
Solid pseudopapillary neoplasm of the pancreas (SPNP) is a rare tumor with low malignant potential found in adolescent girls and young women. The pathogenesis of SPNP remains uncertain and its management is controversial. Genetic changes associated with SPNP have seldom been reported. We describe here the cytogenetic investigation of a case of SPNP in a 13-year-old girl whose tumor cells revealed two unrelated clones: one clone characterized by complex karyotypic changes, including breakpoints in two common fragile sites at chromosome 2, band q33, and chromosome 4, band q31, and the second clone defined by partial monosomy for chromosome X. Loss of heterozygosity for HRAS was also identified by array comparative genomic hybridization (a-CGH). These cumulative changes seem insufficient for activation of cell transformation, but could possibly play a role in priming the cell for future mutagenic events.
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Affiliation(s)
- H M Kempski
- Paediatric Malignancy Cytogenetics Unit, Great Ormond Street Hospital for Children, London, UK.
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Hernández M, Papadopoulos N, Almeida TA. Absence of mutations in DICE1/DDX26 gene in human cancer cell lines with frequent 13q14 deletions. ACTA ACUST UNITED AC 2006; 163:91-2. [PMID: 16271964 DOI: 10.1016/j.cancergencyto.2005.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Revised: 04/14/2005] [Accepted: 04/21/2005] [Indexed: 10/25/2022]
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Gunduz E, Gunduz M, Nagatsuka H, Beder L, Tamamura R, Katase N, Mahmut N, Cengiz B, Fukushima K, Nishizaki K, Shimizu K, Nagai N. Frequent Deletion of BRG1 Locus at 19p13 Predicts Recurrence and Previous Cancer History in Oral Squamous Cell Carcinomas. J HARD TISSUE BIOL 2006. [DOI: 10.2485/jhtb.15.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Braakhuis BJM, Brakenhoff RH, Leemans CR. Second field tumors: a new opportunity for cancer prevention? Oncologist 2005; 10:493-500. [PMID: 16079316 DOI: 10.1634/theoncologist.10-7-493] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recent molecular genetic studies provide evidence that the majority of, if not all, head and neck squamous cell carcinomas (HNSCCs) develop within a contiguous field of preneoplastic cells. Cells of a field show genetic alterations associated with the process of carcinogenesis. A subclone in a field gives rise to an invasive carcinoma. An important implication of this knowledge is that, after surgery of the initial carcinoma, part of the field may remain in the patient. A field with preneoplastic cells that share genetic alterations with cells of the excised tumor has been detected in the resection margins of at least 25% of patients, indicating that this frequently occurs. Fields can be much larger than the actual carcinoma, sometimes having a diameter >7 cm. When a field remains after resection of the tumor, the risk for another carcinoma, designated as a second field tumor (SFT), is considerably greater. It is important to realize that an SFT develops from preneoplastic cells clonally related to the initial tumor. In this respect, it should be discriminated from a recurrent carcinoma that has developed from minimal residual cancer that was left behind and from a second primary tumor that independently develops from the initial carcinoma. Patients at risk for SFTs belong to a unique patient group for whom intense surveillance is indicated and chemoprevention is an attractive option. The priorities are to identify the patients in whom a remaining field will progress to cancer and to find the genes involved. With this knowledge, highly efficient clinical prevention trials, including those using the local application of therapeutic agents, can be designed. It is important to note that SFTs also may occur after treatment of various other cancers, including those of the bladder, skin, esophagus, lung, cervix, breast, and colon.
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Affiliation(s)
- Boudewijn J M Braakhuis
- Department of Otolaryngology/Head and Neck Surgery, Room 1D 116, VU University Medical Center, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.
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