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Wang Z, Wu J. Causal inference of the effect of blood proteome on the risk of head and neck cancer: two-sample Mendelian randomization. Discov Oncol 2024; 15:277. [PMID: 38985358 PMCID: PMC11236829 DOI: 10.1007/s12672-024-01128-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/27/2024] [Indexed: 07/11/2024] Open
Abstract
Early diagnosis of head and neck cancer can improve therapeutic outcomes but remains a challenge. The blood proteome can comprise a key source of biomarkers that enable the early diagnosis and precision medicine in head and neck cancer, but blood protein biomarkers of head and neck cancer are not well delineated. Here we applied two-sample Mendelian randomization to a GWAS dataset of 1478 blood proteins and large dataset of head and neck cancer cases and controls to identify blood proteome traits associated with head and neck cancer. Multiple two-sample Mendelian randomization (MR) methods were used to assess causal effects of the exposures, including: Inverse-variance weighted (IVW), Mendelian randomization-Egger method, Weight Median method, simple mode, weight mode. Sensitivity analysis was performed by using heterogeneity test, pleiotropy test and one-by-one exclusion test. Multivariable MR analyses were performed to assess the effects of obesity, diabetes mellitus, and smoking. A significant causal association between A Disintegrin and metalloproteinase domain-containing protein 23 (ADAM23) and head and neck cancer was noted. The sensitivity analysis indicated no significant bias. Multivariate analysis showed that the effect for ADAM23 remained significant after adjusting for the indirect effects of obesity, diabetes mellitus and smoking. In sum, this study showed a significant causal role of genetically dysregulated ADAM23 protein with head and neck cancer risk. The specific mechanisms underlying the role of ADAM23 in mediating head and neck cancer risk, and its role as a potential therapeutic target and biomarker, need further investigation.
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Affiliation(s)
- Zhen Wang
- Department of Stomatology, The Quzhou Affiliated Hospital of Wenzhou Medical University (Quzhou People's Hospital), Kecheng District, Minjiang Avenue No. 100, Quzhou, 332400, Zhejiang Province, China
| | - Jianhao Wu
- Department of Stomatology, The Quzhou Affiliated Hospital of Wenzhou Medical University (Quzhou People's Hospital), Kecheng District, Minjiang Avenue No. 100, Quzhou, 332400, Zhejiang Province, China.
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Multi-Objective Artificial Bee Colony Algorithm Based on Scale-Free Network for Epistasis Detection. Genes (Basel) 2022; 13:genes13050871. [PMID: 35627256 PMCID: PMC9140669 DOI: 10.3390/genes13050871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/30/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
In genome-wide association studies, epistasis detection is of great significance for the occurrence and diagnosis of complex human diseases, but it also faces challenges such as high dimensionality and a small data sample size. In order to cope with these challenges, several swarm intelligence methods have been introduced to identify epistasis in recent years. However, the existing methods still have some limitations, such as high-consumption and premature convergence. In this study, we proposed a multi-objective artificial bee colony (ABC) algorithm based on the scale-free network (SFMOABC). The SFMOABC incorporates the scale-free network into the ABC algorithm to guide the update and selection of solutions. In addition, the SFMOABC uses mutual information and the K2-Score of the Bayesian network as objective functions, and the opposition-based learning strategy is used to improve the search ability. Experiments were performed on both simulation datasets and a real dataset of age-related macular degeneration (AMD). The results of the simulation experiments showed that the SFMOABC has better detection power and efficiency than seven other epistasis detection methods. In the real AMD data experiment, most of the single nucleotide polymorphism combinations detected by the SFMOABC have been shown to be associated with AMD disease. Therefore, SFMOABC is a promising method for epistasis detection.
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Li C, Liu T, Liu Y, Zhang J, Zuo D. Prognostic value of tumour microenvironment-related genes by TCGA database in rectal cancer. J Cell Mol Med 2021; 25:5811-5822. [PMID: 33949771 PMCID: PMC8184694 DOI: 10.1111/jcmm.16547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Rectal cancer is a common malignant tumour and the progression is highly affected by the tumour microenvironment (TME). This study intended to assess the relationship between TME and prognosis, and explore prognostic genes of rectal cancer. The gene expression profile of rectal cancer was obtained from TCGA and immune/stromal scores were calculated by Estimation of Stromal and Immune cells in Malignant Tumors using Expression data (ESTIMATE) algorithm. The correlation between immune/stromal scores and survival time as well as clinical characteristics were evaluated. Differentially expressed genes (DEGs) were identified according to the stromal/immune scores, and the functional enrichment analyses were conducted to explore functions and pathways of DEGs. The survival analyses were conducted to clarify the DEGs with prognostic value, and the protein‐protein interaction (PPI) network was performed to explore the interrelation of prognostic DEGs. Finally, we validated prognostic DEGs using data from the Gene Expression Omnibus (GEO) database by PrognoScan, and we verified these genes at the protein levels using the Human Protein Atlas (HPA) databases. We downloaded gene expression profiles of 83 rectal cancer patients from The Cancer Genome Atlas (TCGA) database. The Kaplan‐Meier plot demonstrated that low‐immune score was associated with worse clinical outcome (P = .034), metastasis (M1 vs. M0, P = .031) and lymphatic invasion (+ vs. ‐, P < .001). A total of 540 genes were screened as DEGs with 539 up‐regulated genes and 1 down‐regulated gene. In addition, 60 DEGs were identified associated with overall survival. Functional enrichment analyses and PPI networks showed that the DEGs are mainly participated in immune process, and cytokine‐cytokine receptor interaction. Finally, 19 prognostic genes were verified by GSE17536 and GSE17537 from GEO, and five genes (ADAM23, ARHGAP20, ICOS, IRF4,MMRN1) were significantly different in tumour tissues compared with normal tissues at the protein level. In summary, our study demonstrated the associations between TME and prognosis as well as clinical characteristics of rectal cancer. Moreover, we explored and verified microenvironment‐related genes, which may be the potential key prognostic genes of rectal cancer. Further clinical samples and functional studies are needed to validate this finding.
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Affiliation(s)
- Chao Li
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Tao Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yi Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jiantao Zhang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Didi Zuo
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, China
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4
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Schumacher N, Rose-John S, Schmidt-Arras D. ADAM-Mediated Signalling Pathways in Gastrointestinal Cancer Formation. Int J Mol Sci 2020; 21:ijms21145133. [PMID: 32698506 PMCID: PMC7404302 DOI: 10.3390/ijms21145133] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
Tumour growth is not solely driven by tumour cell-intrinsic mechanisms, but also depends on paracrine signals provided by the tumour micro-environment. These signals comprise cytokines and growth factors that are synthesized as trans-membrane proteins and need to be liberated by limited proteolysis also termed ectodomain shedding. Members of the family of A disintegrin and metalloproteases (ADAM) are major mediators of ectodomain shedding and therefore initiators of paracrine signal transduction. In this review, we summarize the current knowledge on how ADAM proteases on tumour cells but also on cells of the tumour micro-environment contribute to the formation of gastrointestinal tumours, and discuss how these processes can be exploited pharmacologically.
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5
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Zmetakova I, Kalinkova L, Smolkova B, Horvathova Kajabova V, Cierna Z, Danihel L, Bohac M, Sedlackova T, Minarik G, Karaba M, Benca J, Cihova M, Buocikova V, Miklikova S, Mego M, Fridrichova I. A disintegrin and metalloprotease 23 hypermethylation predicts decreased disease-free survival in low-risk breast cancer patients. Cancer Sci 2019; 110:1695-1704. [PMID: 30815959 PMCID: PMC6500989 DOI: 10.1111/cas.13985] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/13/2019] [Accepted: 02/24/2019] [Indexed: 01/06/2023] Open
Abstract
A Disintegrin And Metalloprotease 23 (ADAM23), a member of the ADAM family, is involved in neuronal differentiation and cancer. ADAM23 is considered a possible tumor suppressor gene and is frequently downregulated in various types of malignancies. Its epigenetic silencing through promoter hypermethylation was observed in breast cancer (BC). In the present study, we evaluated the prognostic significance of ADAM23 promoter methylation for hematogenous spread and disease-free survival (DFS). Pyrosequencing was used to quantify ADAM23 methylation in tumors of 203 BC patients. Presence of circulating tumor cells (CTC) in their peripheral blood was detected by quantitative RT-PCR. Expression of epithelial (KRT19) or mesenchymal (epithelial-mesenchymal transition [EMT]-inducing transcription factors TWIST1, SNAI1, SLUG and ZEB1) mRNA transcripts was examined in CD45-depleted peripheral blood mononuclear cells. ADAM23 methylation was significantly lower in tumors of patients with the mesenchymal CTC (P = .006). It positively correlated with Ki-67 proliferation, especially in mesenchymal CTC-negative patients (P = .001). In low-risk patients, characterized by low Ki-67 and mesenchymal CTC absence, ADAM23 hypermethylation was an independent predictor of DFS (P = .006). Our results indicate that ADAM23 is likely involved in BC progression and dissemination of mesenchymal CTC. ADAM23 methylation has the potential to function as a novel prognostic marker and therapeutic target.
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Affiliation(s)
- Iveta Zmetakova
- Cancer Research InstituteBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovakia
| | - Lenka Kalinkova
- Cancer Research InstituteBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovakia
| | - Bozena Smolkova
- Cancer Research InstituteBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovakia
| | | | - Zuzana Cierna
- Department of PathologyFaculty of MedicineComenius UniversityBratislavaSlovakia
| | - Ludovit Danihel
- Department of PathologyFaculty of MedicineComenius UniversityBratislavaSlovakia
| | - Martin Bohac
- 2nd Department of OncologyFaculty of MedicineNational Cancer InstituteComenius UniversityBratislavaSlovakia
| | - Tatiana Sedlackova
- Institute of Molecular BiomedicineFaculty of MedicineComenius UniversityBratislavaSlovakia
| | - Gabriel Minarik
- Institute of Molecular BiomedicineFaculty of MedicineComenius UniversityBratislavaSlovakia
| | - Marian Karaba
- 2nd Department of OncologyFaculty of MedicineNational Cancer InstituteComenius UniversityBratislavaSlovakia
- Department of OncosurgeryNational Cancer InstituteBratislavaSlovakia
| | - Juraj Benca
- Department of OncosurgeryNational Cancer InstituteBratislavaSlovakia
- Department of MedicineSt. Elizabeth UniversityBratislavaSlovakia
| | - Marina Cihova
- Cancer Research InstituteBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovakia
| | - Verona Buocikova
- Cancer Research InstituteBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovakia
| | - Svetlana Miklikova
- Cancer Research InstituteBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovakia
| | - Michal Mego
- 2nd Department of OncologyFaculty of MedicineNational Cancer InstituteComenius UniversityBratislavaSlovakia
| | - Ivana Fridrichova
- Cancer Research InstituteBiomedical Research CenterSlovak Academy of SciencesBratislavaSlovakia
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6
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McGrath-Morrow SA, Ndeh R, Collaco JM, Rothblum-Oviatt C, Wright J, O’Reilly MA, Singer BD, Lederman HM. Inflammation and transcriptional responses of peripheral blood mononuclear cells in classic ataxia telangiectasia. PLoS One 2018; 13:e0209496. [PMID: 30586396 PMCID: PMC6306200 DOI: 10.1371/journal.pone.0209496] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/06/2018] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Classic ataxia telangiectasia (A-T) is an autosomal recessive disease characterized by early onset ataxia, immune deficiency, sino-pulmonary disease, lymphoid/solid malignancies and telangiectasias. Prior studies have suggested that chronic inflammation and premature aging may contribute to the development of malignancy and pulmonary disease in people with A-T. To further examine the link between A-T and inflammation, we hypothesized that subjects with classic A-T would have greater enrichment of inflammatory pathways in peripheral blood mononuclear cells (PBMCs) compared to non A-T age-matched controls. To test this hypothesis we used RNAseq as an unsupervised approach to identify biological processes altered in people with classic A-T. METHODS PBMCs were isolated from subjects with classic A-T and compared to non-A-T age-matched healthy controls. RNAseq with differential gene expression analyses was then performed. Selected genes were validated by RT-qPCR using cohorts of subjects consisting of classic A-T, mild A-T or non-A-T controls. Subjects with mild A-T were characterized by later onset/mild neurologic features and normal/near normal immune status. RESULTS RNAseq revealed 310 differentially expressed genes (DEGs) including genes involved in inflammation, immune regulation, and cancer. Using gene set enrichment analysis, A-T subjects were found to have biological processes enriched for inflammatory and malignancy pathways. In examining a cohort of A-T subjects in which baseline serum IL8 and IL6 levels were measured previously, an association was found between higher serum IL8 levels and higher likelihood of developing malignancy and/or death in a subsequent 4-6 year period. CONCLUSION RNAseq using PBMCs from subjects with classic A-T uncovered differential expression of immune response genes and biological processes associated with inflammation, immune regulation, and cancer. Follow-up of A-T subjects over a 4-6 year period revealed an association between higher baseline serum IL8 levels and malignancy/death. These findings support a role for inflammation as a contributing factor in A-T phenotypes.
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Affiliation(s)
- Sharon A. McGrath-Morrow
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Roland Ndeh
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Joseph M. Collaco
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | | | - Jennifer Wright
- Eudowood Division of Pediatric, Allergy and Immunology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Michael A. O’Reilly
- Department of Pediatrics, School of Medicine and Dentistry, The University of Rochester, Rochester, New York, United States of America
| | - Benjamin D. Singer
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Howard M. Lederman
- Eudowood Division of Pediatric, Allergy and Immunology, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
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Borgonovo ZL, Ribeiro CF, Costa MD, Souza IL, Rossi GR, Alcantara MV, Ingberman M, Braga LG, Mercadante AF, Nakao LS, Zanata SM. Monoclonal Antibody DL11C8 Identifies ADAM23 as a Component of Lipid Raft Microdomains. Neuroscience 2018; 384:165-177. [DOI: 10.1016/j.neuroscience.2018.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/25/2018] [Accepted: 05/13/2018] [Indexed: 11/16/2022]
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Abstract
The peritoneum protects the intraabdominal organs. This function is exploited by aggressive cancers originating from organs within the abdomen, resulting in peritoneal metastasis. We discuss genomic variants that may lead to peritoneal metastasis from multiple cancers. Peritoneal malignancies are attributed to epithelial-mesenchymal transition. These metastatic lesions harbor similar genetic mutations to the primary tumor yet may manifest clone-specific aberrations that promote propagation. Peritoneal metastasis are increasingly being treated with surgical resection as an adjunct to radiation, chemotherapy, and other biologic therapies. We describe genetic and genomic variances that are predictive markers for metastasis and burgeoning indicators for peritoneal malignancies.
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Affiliation(s)
- Enusha Karunasena
- Department of Oncology, GI Clinical Cancer Research and Cancer Immunology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institute, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Jonathan Sham
- Department of Surgery, Johns Hopkins Medical Institute, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Kevin Wyatt McMahon
- Department of Surgery, Johns Hopkins Medical Institute, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Nita Ahuja
- Department of Surgery, Johns Hopkins Medical Institute, 600 North Wolfe Street, Baltimore, MD 21287, USA; Cancer Biology, Department of Oncology, Sidney Kimmel Comprehensive Cancer, Johns Hopkins Medical Institute, 600 North Wolfe Street, Baltimore, MD 21287, USA; Department of Surgery, Yale School of Medicine, PO Box 208062, New Haven, CT 06520-8062, USA.
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Ma R, Tang Z, Sun K, Ye X, Cheng H, Chang X, Cui H. Low levels of ADAM23 expression in epithelial ovarian cancer are associated with poor survival. Pathol Res Pract 2018; 214:1115-1122. [PMID: 29921495 DOI: 10.1016/j.prp.2018.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 05/30/2018] [Accepted: 06/08/2018] [Indexed: 12/28/2022]
Abstract
BACKGROUND ADAM23, a member of the disintegrin and metalloprotease (ADAM) family, has been reported to be expressed in several types of tumours. Nevertheless, the exact role of ADAM23 in epithelial ovarian cancer (EOC) remains unclear. The aim of this study was to investigate ADAM23 expression in EOC and evaluate its clinicopathological and prognostic significance. METHODS Immunohistochemistry (IHC), western blot and real-time PCR (RT-PCR) were used to analyse ADAM23 expression in 133 EOC, 42 benign ovarian tumour and 35 healthy control samples. Moreover, we evaluated the expression of ADAM23 in both public database (Oncomine and Kaplan-Meier plotter). The association between ADAM23 expression and various clinicopathological parameters was analysed. RESULTS The levels of ADAM23 mRNA and protein expression were significantly lower in EOC tissues than in corresponding control tissues and benign ovarian tumours, verifying results from the Oncomine databases. The loss of ADAM23 expression was significantly correlated with an advanced International Federation of Gynecology and Obstetrics (FIGO) stage and lymph node metastasis. The IHC data in the EOC samples correlated with the RT-PCR data. Furthermore, patients with low ADAM23 expression had shorter progression-free survival (PFS) and overall survival (OS) than patients with high ADAM23 expression. The multivariate analysis indicated that ADAM23 was an independent predictor in patients with EOC. CONCLUSIONS Our results demonstrate that ADAM23 expression is likely involved in the progression of EOC and may provide potential diagnostic and prognostic information regarding EOC.
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Affiliation(s)
- Ruiqiong Ma
- Gynaecologic Oncology Centre, Peking University People's Hospital, No. 11, Xizhimen nan Road, XiCheng District, Beijing, 100044, People's Republic of China
| | - Zhijian Tang
- Gynaecologic Oncology Centre, Peking University People's Hospital, No. 11, Xizhimen nan Road, XiCheng District, Beijing, 100044, People's Republic of China
| | - Kunkun Sun
- Department of Pathology, Peking University People's Hospital, No. 11, Xizhimen nan Road, XiCheng District, Beijing, 100044, People's Republic of China
| | - Xue Ye
- Gynaecologic Oncology Centre, Peking University People's Hospital, No. 11, Xizhimen nan Road, XiCheng District, Beijing, 100044, People's Republic of China
| | - Hongyan Cheng
- Gynaecologic Oncology Centre, Peking University People's Hospital, No. 11, Xizhimen nan Road, XiCheng District, Beijing, 100044, People's Republic of China.
| | - Xiaohong Chang
- Gynaecologic Oncology Centre, Peking University People's Hospital, No. 11, Xizhimen nan Road, XiCheng District, Beijing, 100044, People's Republic of China
| | - Heng Cui
- Gynaecologic Oncology Centre, Peking University People's Hospital, No. 11, Xizhimen nan Road, XiCheng District, Beijing, 100044, People's Republic of China.
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Li Z, Li AD, Xu L, Bai DW, Hou KZ, Zheng HC, Qu XJ, Liu YP. SPARC expression in gastric cancer predicts poor prognosis: Results from a clinical cohort, pooled analysis and GSEA assay. Oncotarget 2018; 7:70211-70222. [PMID: 28053291 PMCID: PMC5342547 DOI: 10.18632/oncotarget.12191] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 09/02/2016] [Indexed: 12/18/2022] Open
Abstract
Background The prognostic role of Secreted Protein Acidic and Rich in Cysteine (SPARC) in gastric cancer (GC) remains controversial. We investigated the clinical significance, the survival relevance, and potential function of SPARC in GC with resected samples, online gene set GSE62254, and cell line SGC7901. Results High immunostaining of SPARC significantly correlated with tumor differentiation (P = 0.004), and independently predicted shorter overall survival (OS) (HR = 1.446, P = 0.022), based on the current IHC evaluation. The accuracy of the results was further validated with 1000 times bootstrapping and the time-dependent receiver-operating characteristics (ROC) curves. The meta-analysis (pooled HR = 1.60, 95% CI: 1.01−2.53) confirmed SPARC as the predictor for reduced OS in GC. Moreover, the association between enhanced SPARC expression and Adriamycin (Adr) sensitivity was revealed by GSEA, and then confirmed by comparative cellular experiments, such as the protein level analysis of SGC7901and SGC7901/Adr cell line. Materials and Methods Immunohistochemistry (IHC) method was used to detect SPARC expression in 137 GC cases. Meta-analysis was performed based on 5 studies published in English on PubMed up to March 2016. GSEA was performed using online data set GSE62254 and GC-related functional gene sets derived from molecular signatures database (MSigDB). Western Blot was carried out to compare protein-level differences between gastric carcinoma SGC7901 cell line and Adr resistant SGC7901/Adr cell line. MTT assay was done to confirm the induction of SPARC on Adr sensitivity Conclusions Increased SPARC expression in GC led to a worse clinical outcome of patients and might induce Adr sensitivity of GC cells.
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Affiliation(s)
- Zhi Li
- Department of Medical Oncology, The First Hospital, China Medical University, Shenyang, Liaoning Province, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province
| | - Ao-Di Li
- Department of Medical Oncology, The First Hospital, China Medical University, Shenyang, Liaoning Province, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province
| | - Lu Xu
- Department of Medical Oncology, The First Hospital, China Medical University, Shenyang, Liaoning Province, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province
| | - De-Wei Bai
- Department of Medical Oncology, The First Hospital, China Medical University, Shenyang, Liaoning Province, China.,Department of Cell Biological Treatment Ward, Dalian Centre Hospital, Dalian, Liaoning Province, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province
| | - Ke-Zuo Hou
- Department of Medical Oncology, The First Hospital, China Medical University, Shenyang, Liaoning Province, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province
| | - Hua-Chuan Zheng
- Life Science Institute of Jinzhou Medical University, Jinzhou, Liaoning Province, China
| | - Xiu-Juan Qu
- Department of Medical Oncology, The First Hospital, China Medical University, Shenyang, Liaoning Province, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province
| | - Yun-Peng Liu
- Department of Medical Oncology, The First Hospital, China Medical University, Shenyang, Liaoning Province, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province
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Ota M, Mochizuki S, Shimoda M, Abe H, Miyamae Y, Ishii K, Kimura H, Okada Y. ADAM23 is downregulated in side population and suppresses lung metastasis of lung carcinoma cells. Cancer Sci 2016; 107:433-43. [PMID: 26800504 PMCID: PMC4832861 DOI: 10.1111/cas.12895] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/06/2016] [Accepted: 01/17/2016] [Indexed: 01/06/2023] Open
Abstract
Cancer cells contain a small population of cancer stem cells or cancer initiating cells, which can be enriched in the side population (SP) after fluorescence activated cell sorting. To examine the members of the ADAM, ADAMTS and MMP gene families related to phenotypes of the SP and the main population (MP), we screened the expression of all the members in the propagated SP and MP of A549 lung adenocarcinoma cells, and found that the relative expression ratio of ADAM23 in the MP to the SP is most highly increased, but none of them are increased in the SP. A similar result on the ADAM23 expression was obtained with another cell line, Calu‐3 cells. Overexpression of ADAM23 inhibited colony formation, cell adhesion and migration, and knockdown of ADAM23 by shRNA showed the reverse effects. ADAM23‐mediated suppression of colony formation, cell adhesion and migration was greatly reduced by treatment with neutralizing anti‐ADAM23 antibody, anti‐αvβ3 integrin antibody and/or ADAM23 disintegrin peptide. Expression of cancer stem cell‐related genes, including AKRC1/2, TM4SF1 and NR0B1, was increased by knockdown of ADAM23. In addition, lung metastasis of A549 transfectants with different levels of ADAM23 expression was negatively regulated by the ADAM23 expression levels. Our data provide evidence that ADAM23 plays a role in suppression of cancer cell progression through interaction with αvβ3 integrin, and suggest that downregulation of ADAM23 in SP cells may contribute toward providing a cancer stem cell phenotype by facilitating the activity of integrin αvβ3.
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Affiliation(s)
- Masahide Ota
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan.,Second Department of Internal Medicine and Respiratory Medicine, Nara Medical University, Kashihara, Japan
| | - Satsuki Mochizuki
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Masayuki Shimoda
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Hitoshi Abe
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yuka Miyamae
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Ken Ishii
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Kimura
- Second Department of Internal Medicine and Respiratory Medicine, Nara Medical University, Kashihara, Japan
| | - Yasunori Okada
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan.,Department of Pathophysiology for Locomotive and Neoplastic Diseases, Juntendo University Graduate School of Medicine, Tokyo, Japan
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12
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Ras oncogene-mediated progressive silencing of extracellular superoxide dismutase in tumorigenesis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:780409. [PMID: 26550576 PMCID: PMC4624945 DOI: 10.1155/2015/780409] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/31/2015] [Indexed: 02/03/2023]
Abstract
Extracellular superoxide dismutase (SOD3) is a secreted enzyme that uses superoxide anion as a substrate in a dismutase reaction that results in the formation of hydrogen peroxide. Both of these reactive oxygen species affect growth signaling in cells. Although SOD3 has growth-supporting characteristics, the expression of SOD3 is downregulated in epithelial cancer cells. In the current work, we studied the mechanisms regulating SOD3 expression in vitro using thyroid cell models representing different stages of thyroid cancer. We demonstrate that a low level of RAS activation increases SOD3 mRNA synthesis that then gradually decreases with increasing levels of RAS activation and the decreasing degree of differentiation of the cancer cells. Our data indicate that SOD3 regulation can be divided into two classes. The first class involves RAS–driven reversible regulation of SOD3 expression that can be mediated by the following mechanisms: RAS GTPase regulatory genes that are responsible for SOD3 self-regulation; RAS-stimulated p38 MAPK activation; and RAS-activated increased expression of the mir21 microRNA, which inversely correlates with sod3 mRNA expression. The second class involves permanent silencing of SOD3 mediated by epigenetic DNA methylation in cells that represent more advanced cancers. Therefore, the work suggests that SOD3 belongs to the group of ras oncogene-silenced genes.
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13
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Li Y, Liang J, Hou P. Hypermethylation in gastric cancer. Clin Chim Acta 2015; 448:124-32. [PMID: 26148722 DOI: 10.1016/j.cca.2015.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 07/02/2015] [Accepted: 07/02/2015] [Indexed: 02/07/2023]
Abstract
Although gastric cancer (GC) is highly prevalent in China and is a leading cause of cancer-related death, major advances in early diagnostic and effective therapeutic strategies have not been made. GC patients are usually diagnosed at an advanced stage and the prognosis is still poor. Over the years, many efforts have been done on exploring the pathology of GC. In particular, genome-wide analysis tools have been widely used in the detection of genetic and epigenetic alterations in GC. For example, many tumor suppressor genes have been found to be aberrantly hypermethylated in GCs, and some even in gastric precancerous lesions, suggesting a role of this molecular event in early gastric tumorigenesis. In addition, accumulating evidences have demonstrated that some hypermethylated genes can be used as potential biomarkers for detection and diagnosis of GC in biopsy specimens and non-invasive body fluids. These exciting advances provide unprecedented opportunities for the development of molecular-based novel diagnostic, prognostic, and therapeutic strategies for GC. Here, we reviewed recent findings on the promoter hypermethylation of tumor suppressor genes in GC and aimed to provide better understanding of the contribution of this epigenetic event to gastric tumorigenesis.
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Affiliation(s)
- Yujun Li
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, People's Republic of China
| | - Junrong Liang
- Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, People's Republic of China
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, People's Republic of China.
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14
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Conceição ALG, Babeto E, Candido NM, Franco FC, de Campos Zuccari DAP, Bonilha JL, Cordeiro JA, Calmon MF, Rahal P. Differential Expression of ADAM23, CDKN2A (P16), MMP14 and VIM Associated with Giant Cell Tumor of Bone. J Cancer 2015; 6:593-603. [PMID: 26078788 PMCID: PMC4466407 DOI: 10.7150/jca.11238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 02/10/2015] [Indexed: 12/17/2022] Open
Abstract
Though benign, giant cell tumor of bone (GCTB) can become aggressive and can exhibit a high mitotic rate, necrosis and rarely vascular invasion and metastasis. GCTB has unique histologic characteristics, a high rate of multinucleated cells, a variable and unpredictable growth potential and uncertain biological behavior. In this study, we sought to identify genes differentially expressed in GCTB, thus building a molecular profile of this tumor. We performed quantitative real-time polymerase chain reaction (qPCR), immunohistochemistry and analyses of methylation to identify genes that are putatively associated with GCTB. The expression of the ADAM23 and CDKN2A genes was decreased in GCTB samples compared to normal bone tissue, measured by qPCR. Additionally, a high hypermethylation frequency of the promoter regions of ADAM23 and CDKN2A in GCTB was observed. The expression of the MAP2K3, MMP14, TIMP2 and VIM genes was significantly higher in GCTB than in normal bone tissue, a fact that was confirmed by qPCR and immunohistochemistry. The set of genes identified here furthers our understanding of the molecular basis of GCTB.
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Affiliation(s)
| | - Erica Babeto
- 1. Laboratory of Genomics Studies, UNESP, São José do Rio Preto, Brazil
| | | | | | | | | | - José Antônio Cordeiro
- 4. Department of Epidemiology and Collective Health, FAMERP, São José do Rio Preto, Brazil
| | | | - Paula Rahal
- 1. Laboratory of Genomics Studies, UNESP, São José do Rio Preto, Brazil
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15
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Lee B, Yoon K, Lee S, Kang JM, Kim J, Shim SH, Kim HM, Song S, Naka K, Kim AK, Yang HK, Kim SJ. Homozygous deletions at 3p22, 5p14, 6q15, and 9p21 result in aberrant expression of tumor suppressor genes in gastric cancer. Genes Chromosomes Cancer 2014; 54:142-55. [PMID: 25521327 DOI: 10.1002/gcc.22226] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 10/28/2014] [Indexed: 12/27/2022] Open
Abstract
Homozygous deletion is a frequent mutational mechanism of silencing tumor suppressor genes in cancer. Therefore, homozygous deletions have been analyzed for identification of tumor suppressor genes that can be utilized as biomarkers or therapeutic targets for cancer treatment. In this study, to elucidate potential tumor suppressor genes involved in gastric cancer (GC), we analyzed the entire set of large homozygous deletions in six human GC cell lines through genome- and transcriptome-wide approaches. We identified 51 genes in homozygous deletion regions of chromosomes and confirmed the deletion frequency in tumor tissues of 219 GC patients from The Cancer Genome Atlas database. We evaluated the effect of homozygous deletions on the mRNA level and found significantly affected genes in chromosome bands 9p21, 3p22, 5p14, and 6q15. Among the genes in 9p21, we investigated the potential tumor suppressive effect of KLHL9. We demonstrated that ectopic expression of KLHL9 inhibited cell proliferation and tumor formation in KLHL9-deficient SNU-16 cell line. In addition, we observed that homozygous focal deletions generated truncated transcripts of TGFBR2, CTNNA1, and STXBP5. Ectopic expression of two kinds of TGFBR2-reverse GADL1 fusion genes suppressed TGF-β signaling, which may lead to the loss of sensitivity to TGF-β tumor suppressive activity. In conclusion, our findings suggest that novel tumor suppressor genes that are aberrantly expressed through homozygous deletions may play important roles in gastric tumorigenesis.
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Affiliation(s)
- Bona Lee
- CHA Cancer Institute, CHA University, Seongnam-si, 463-400, Republic of Korea; College of Pharmacy, Sookmyung Women's University, Seoul, 140-742, Republic of Korea
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16
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Shi J, Qu YP, Hou P. Pathogenetic mechanisms in gastric cancer. World J Gastroenterol 2014; 20:13804-13819. [PMID: 25320518 PMCID: PMC4194564 DOI: 10.3748/wjg.v20.i38.13804] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/15/2014] [Accepted: 05/29/2014] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is a major public health issue as the fourth most common cancer and the second leading cause of cancer-related death. Recent advances have improved our understanding of its molecular pathogenesis, as best exemplified by elucidating the fundamental role of several major signaling pathways and related molecular derangements. Central to these mechanisms are the genetic and epigenetic alterations in these signaling pathways, such as gene mutations, copy number variants, aberrant gene methylation and histone modification, nucleosome positioning, and microRNAs. Some of these genetic/epigenetic alterations represent effective diagnostic and prognostic biomarkers and therapeutic targets for GC. This information has now opened unprecedented opportunities for better understanding of the molecular mechanisms of gastric carcinogenesis and the development of novel therapeutic strategies for this cancer. The pathogenetic mechanisms of GC are the focus of this review.
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17
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Hosoda F, Arai Y, Okada N, Shimizu H, Miyamoto M, Kitagawa N, Katai H, Taniguchi H, Yanagihara K, Imoto I, Inazawa J, Ohki M, Shibata T. Integrated genomic and functional analyses reveal glyoxalase I as a novel metabolic oncogene in human gastric cancer. Oncogene 2014; 34:1196-206. [PMID: 24662817 DOI: 10.1038/onc.2014.57] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 11/15/2013] [Accepted: 12/16/2013] [Indexed: 02/07/2023]
Abstract
Chromosomal abnormalities are good guideposts when hunting for cancer-related genes. We analyzed copy number alterations of 163 primary gastric cancers using array-based comparative genomic hybridization and simultaneously performed a genome-wide integrated analysis of copy number and gene expression using microarray data for 58 tumors. We showed that chromosome 6p21 amplification frequently occurred secondary to ERBB2 amplification, was associated with poorer prognosis and caused overexpression of half of the genes mapped. A comprehensive small interfering RNA knockdown of 58 genes overexpressed in tumors identified 32 genes that reduced gastric cancer cell growth. Enforced expression of 16 of these genes promoted cell growth in vitro, and six genes showing more than two-fold activity conferred tumor-forming ability in vivo. Among these six candidates, GLO1, encoding a detoxifying enzyme glyoxalase I (GLO1), exhibited the strongest tumor-forming activity. Coexpression of other genes with GLO1 enhanced growth-stimulating activity. A GLO1 inhibitor, S-p-bromobenzyl glutathione cyclopentyl diester, inhibited the growth of two-thirds of 24 gastric cancer cell lines examined. The efficacy was found to be associated with the mRNA expression ratio of GLO1 to GLO2, encoding glyoxalase II (GLO2), another constituent of the glyoxalase system. GLO1 downregulation affected cell growth through inactivating central carbon metabolism and reduced the transcriptional activities of nuclear factor kappa B and activator protein-1. Our study demonstrates that GLO1 is a novel metabolic oncogene of the 6p21 amplicon, which promotes tumor growth and aberrant transcriptional signals via regulating cellular metabolic activities for energy production and could be a potential therapeutic target in gastric cancer.
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Affiliation(s)
- F Hosoda
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Y Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - N Okada
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - H Shimizu
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - M Miyamoto
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - N Kitagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - H Katai
- Division of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - H Taniguchi
- Division of Clinical Laboratory, National Cancer Center Hospital, Tokyo, Japan
| | - K Yanagihara
- Division of Translational Research, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - I Imoto
- 1] Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan [2] Department of Human Genetics and Public Health, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - J Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - M Ohki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - T Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
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18
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Costa ET, Barnabé GF, Li M, Dias AAM, Machado TR, Asprino PF, Cavalher FP, Ferreira EN, Del Mar Inda M, Nagai MH, Malnic B, Duarte ML, Leite KRM, de Barros ACSD, Carraro DM, Chammas R, Armelin HA, Cavenee W, Furnari F, Camargo AA. Intratumoral heterogeneity of ADAM23 promotes tumor growth and metastasis through LGI4 and nitric oxide signals. Oncogene 2014; 34:1270-9. [PMID: 24662834 DOI: 10.1038/onc.2014.70] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 01/06/2014] [Accepted: 01/14/2014] [Indexed: 12/22/2022]
Abstract
Intratumoral heterogeneity (ITH) represents an obstacle for cancer diagnosis and treatment, but little is known about its functional role in cancer progression. The A Desintegrin And Metalloproteinase 23 (ADAM23) gene is epigenetically silenced in different types of tumors, and silencing is often associated with advanced disease and metastasis. Here, we show that invasive breast tumors exhibit significant ADAM23-ITH and that this heterogeneity is critical for tumor growth and metastasis. We demonstrate that while loss of ADAM23 expression enhances invasion, it causes a severe proliferative deficiency and is not itself sufficient to trigger metastasis. Rather, we observed that, in ADAM23-heterotypic environments, ADAM23-negative cells promote tumor growth and metastasis by enhancing the proliferation and invasion of adjacent A23-positive cells through the production of LGI4 (Leucine-rich Glioma Inactivated 4) and nitric oxide (NO). Ablation of LGI4 and NO in A23-negative cells significantly attenuates A23-positive cell proliferation and invasion. Our work denotes a driving role of ADAM23-ITH during disease progression, shifting the malignant phenotype from the cellular to the tissue level. Our findings also provide insights for therapeutic intervention, enforcing the need to ascertain ITH to improve cancer diagnosis and therapy.
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Affiliation(s)
- E T Costa
- 1] Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, Brazil [2] Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
| | - G F Barnabé
- 1] Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, Brazil [2] Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
| | - M Li
- Ludwig Institute for Cancer Research (LICR), University of California, San Diego, CA, USA
| | - A A M Dias
- Departamento de Biologia Geral (ICB), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - T R Machado
- Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
| | - P F Asprino
- 1] Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, Brazil [2] Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
| | - F P Cavalher
- Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
| | - E N Ferreira
- Centro Internacional de Pesquisa, Hospital AC Camargo, São Paulo, Brazil
| | - M Del Mar Inda
- Ludwig Institute for Cancer Research (LICR), University of California, San Diego, CA, USA
| | - M H Nagai
- Departamento de Bioquímica (IQ), Universidade de São Paulo, São Paulo, Brazil
| | - B Malnic
- Departamento de Bioquímica (IQ), Universidade de São Paulo, São Paulo, Brazil
| | - M L Duarte
- 1] Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, Brazil [2] Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
| | - K R M Leite
- Departamento de Urologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - A C S D de Barros
- Departamento de Mastologia, Hospital Sírio Libanês, São Paulo, Brazil
| | - D M Carraro
- Centro Internacional de Pesquisa, Hospital AC Camargo, São Paulo, Brazil
| | - R Chammas
- Departamento de Urologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - H A Armelin
- 1] Departamento de Bioquímica (IQ), Universidade de São Paulo, São Paulo, Brazil [2] Instituto Butantan, São Paulo, Brazil
| | - W Cavenee
- Ludwig Institute for Cancer Research (LICR), University of California, San Diego, CA, USA
| | - F Furnari
- Ludwig Institute for Cancer Research (LICR), University of California, San Diego, CA, USA
| | - A A Camargo
- 1] Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, Brazil [2] Ludwig Institute for Cancer Research (LICR), São Paulo, Brazil
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19
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Cifola I, Pietrelli A, Consolandi C, Severgnini M, Mangano E, Russo V, De Bellis G, Battaglia C. Comprehensive genomic characterization of cutaneous malignant melanoma cell lines derived from metastatic lesions by whole-exome sequencing and SNP array profiling. PLoS One 2013; 8:e63597. [PMID: 23704925 PMCID: PMC3660556 DOI: 10.1371/journal.pone.0063597] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/04/2013] [Indexed: 02/08/2023] Open
Abstract
Cutaneous malignant melanoma is the most fatal skin cancer and although improved comprehension of its pathogenic pathways allowed to realize some effective molecular targeted therapies, novel targets and drugs are still needed. Aiming to add genetic information potentially useful for novel targets discovery, we performed an extensive genomic characterization by whole-exome sequencing and SNP array profiling of six cutaneous melanoma cell lines derived from metastatic patients. We obtained a total of 3,325 novel coding single nucleotide variants, including 2,172 non-synonymous variants. We catalogued the coding mutations according to Sanger COSMIC database and to a manually curated list including genes involved in melanoma pathways identified by mining recent literature. Besides confirming the presence of known melanoma driver mutations (BRAF(V600E), NRAS(Q61R) ), we identified novel mutated genes involved in signalling pathways crucial for melanoma pathogenesis and already addressed by current targeted therapies (such as MAPK and glutamate pathways). We also identified mutations in four genes (MUC19, PAICS, RBMXL1, KIF23) never reported in melanoma, which might deserve further investigations. All data are available to the entire research community in our Melanoma Exome Database (at https://155.253.6.64/MExDB/). In summary, these cell lines are valuable biological tools to improve the genetic comprehension of this complex cancer disease and to study functional relevance of individual mutational events, and these findings could provide insights potentially useful for identification of novel therapeutic targets for cutaneous malignant melanoma.
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Affiliation(s)
- Ingrid Cifola
- Institute for Biomedical Technologies, National Research Council, Milan, Italy.
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20
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Calcagno DQ, Gigek CO, Chen ES, Burbano RR, Smith MDAC. DNA and histone methylation in gastric carcinogenesis. World J Gastroenterol 2013; 19:1182-92. [PMID: 23482412 PMCID: PMC3587474 DOI: 10.3748/wjg.v19.i8.1182] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/13/2012] [Accepted: 06/28/2012] [Indexed: 02/06/2023] Open
Abstract
Epigenetic alterations contribute significantly to the development and progression of gastric cancer, one of the leading causes of cancer death worldwide. Epigenetics refers to the number of modifications of the chromatin structure that affect gene expression without altering the primary sequence of DNA, and these changes lead to transcriptional activation or silencing of the gene. Over the years, the study of epigenetic processes has increased, and novel therapeutic approaches that target DNA methylation and histone modifications have emerged. A greater understanding of epigenetics and the therapeutic potential of manipulating these processes is necessary for gastric cancer treatment. Here, we review recent research on the effects of aberrant DNA and histone methylation on the onset and progression of gastric tumors and the development of compounds that target enzymes that regulate the epigenome.
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21
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Kim HA, Park WJ, Jeong HS, Lee HE, Lee SH, Kwon NS, Baek KJ, Kim DS, Yun HY. Leucine-rich glioma inactivated 3 regulates adipogenesis through ADAM23. Biochim Biophys Acta Mol Cell Biol Lipids 2012; 1821:914-22. [PMID: 22405860 DOI: 10.1016/j.bbalip.2012.02.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 02/10/2012] [Accepted: 02/15/2012] [Indexed: 12/19/2022]
Abstract
Leucine-rich glioma inactivated 3 (LGI3) is a secreted protein and a member of LGI/epitempin family. We previously showed that LGI3 was highly expressed in brain and played regulatory roles in neuronal exocytosis and differentiation. Besides the nervous system, LGI3 was shown to be expressed in diverse tissues. In this study, we found that LGI3 and its receptor candidate ADAM23 were expressed in adipose tissues and 3T3-L1 cells. 3T3-L1 preadipocytes secreted a 60-kDa protein, a major secreted form of LGI3, which declined with adipocyte differentiation. LGI3 was also expressed in adipose tissue macrophages in the ob/ob mice and in macrophage cell line. The 60-kDa LGI3 protein was selectively increased in the ob/ob adipose tissues comparing with the lean mice. Pull-down experiments, coimmunoprecipitation and immunocytochemistry indicated that LGI3 associated with ADAM23 in adipose tissues and 3T3-L1 cells. Knockdown of LGI3 or ADAM23 by siRNA increased adipogenesis in 3T3-L1 cells. Treatment with LGI3 protein did not affect preadipocyte proliferation but attenuated adipogenesis and this effect was reversed by siRNA-mediated knockdown of ADAM23. Taken together, we propose that LGI3 may be a candidate adipokine that is perturbed in obesity and suppresses adipogenesis through its receptor, ADAM23.
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Affiliation(s)
- Hyun A Kim
- Department of Biochemistry, Chung-Ang University, College of Medicine, 84 Heukseok-ro, Seoul 156-861, Republic of Korea
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22
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Wang H, Wu J, Meng X, Ying X, Zuo Y, Liu R, Pan Z, Kang T, Huang W. MicroRNA-342 inhibits colorectal cancer cell proliferation and invasion by directly targeting DNA methyltransferase 1. Carcinogenesis 2011; 32:1033-42. [PMID: 21565830 DOI: 10.1093/carcin/bgr081] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Overexpressed DNA methyltransferase 1 (DNMT1) strongly contributes to tumor suppressor gene silencing in colorectal cancer (CRC). However, the underlying mechanism of DNMT1 overexpression is still unclear. MicroRNAs (miRNA) have been implicated as gene regulators controlling diverse biological processes, including carcinogenesis. In this study, we investigated whether some miRNA is involved in the regulation of DNMT1 and thus play a functional role in CRC. Our results showed that miR-342 was downregulated in CRC tissues and cell lines. Restoration of miR-342 resulted in a dramatic reduction of the expression of DNMT1 at both messenger RNA and protein levels by directly targeting its 3' untranslated region. This in turn reactivated ADAM23, Hint1, RASSF1A and RECK genes via promoter demethylation. Furthermore, the enhanced expression of miR-342 could significantly inhibit SW480 cell proliferation in vitro (P = 0.006). Further investigation demonstrated G(0)/G(1) cell cycle arrest in SW480 cells, which was associated with an upregulation of p21 and downregulation of cyclinE and CDK2. Overexpression of miR-342 also inhibited SW480 cell invasion. The in vivo antitumor effect was evaluated in SW480 cells with lentivirus-mediated expression of miR-342. Results showed that overexpression of miR-342 significantly inhibited tumor growth and lung metastasis in nude mice (P = 0.034). Our findings describe a new mechanism for the regulation of DNMT1 and aberrant DNA hypermethylation in CRC. This is also the first report to demonstrate that miR-342 may act as a tumor suppressor gene in CRC development. The newly identified miR-342/DNMT1 link provides a new, potential therapeutic target for the treatment of CRC.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, 651 Dongfeng Road, East, Guangzhou 510060, People's Republic of China
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23
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Gene expression profile of ADAMs and ADAMTSs metalloproteinases in normal and malignant plasma cells and in the bone marrow environment. Exp Hematol 2011; 39:546-557.e8. [DOI: 10.1016/j.exphem.2011.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 01/28/2011] [Accepted: 02/03/2011] [Indexed: 01/15/2023]
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24
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Hu C, Lv H, Pan G, Cao H, Deng Z, Hu C, Wen J, Zhou J. The expression of ADAM23 and its correlation with promoter methylation in non-small-cell lung carcinoma. Int J Exp Pathol 2011; 92:333-9. [PMID: 21429053 DOI: 10.1111/j.1365-2613.2011.00766.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
ADAM23, a member of a disintegrin and metalloprotease (ADAM) family, has been reported to be expressed in several types of tumours. The exact role of ADAM23 and the possible mechanisms in which it is involved in non-small-cell lung carcinoma (NSCLC) remains unclear. Therefore, this study was designed to explore the expression of ADAM23 and its correlation with promoter methylation in NSCLC. Immunohistochemistry and RT-PCR together with Western blotting methods were used to analyse the expression of ADAM23 in 52 cancer tissue samples and eight benign pulmonary lesions as well as four cell lines. The methylated status of ADAM23 gene was determined with methylation-specific PCR (MSP). The results of immunohistochemistry showed that the expression of ADAM23 protein was lower in NSCLC than that in corresponding normal tissues and benign pulmonary lesions (38.5%vs. 86.5% and 87.5%, P < 0.05), and decreased as NSCLC progressed. Meanwhile, methylation of ADAM23 gene was observed in 21 of 52 NSCLC tissues (40.4%), much higher than that of adjacent normal tissues (7.6%) and benign pulmonary lesions (0/8). In the cancer tissues of ADAM23-negative samples, the rate of ADAM23 gene methylation was 50.3% (17/32). ADAM23 expression and its promoter methylation were negatively associated (r = -0.328, P = 0.017). Moreover, weak expression of ADAM23 in methylated cancer cells increased after treatment with 5-aza-2'-deoxycytidine (5-Aza-2'-dC), confirming that methylation was responsible for the gene downregulation. Our results demonstrate that the expression level of ADAM23 is likely to be involved in the progression of NSCLC and its downregulation is probably correlated with promoter methylation. These findings may provide potential diagnostic and prognostic information about NSCLC.
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Affiliation(s)
- Chunyan Hu
- Department of Pathology, Xiangya Medical College, Central South University, Changsha, Hunan, China
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25
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Kim J, Kim MA, Min SY, Jee CD, Lee HE, Kim WH. Downregulation of methylthioadenosin phosphorylase by homozygous deletion in gastric carcinoma. Genes Chromosomes Cancer 2011; 50:421-33. [PMID: 21412930 DOI: 10.1002/gcc.20867] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 02/09/2011] [Indexed: 12/27/2022] Open
Abstract
The methylthioadenosine phosphorylase (MTAP) gene is located on 9p21 telomeric to the CDKN2A tumor suppressor gene. Loss of MTAP gene is frequently associated with CDKN2A homozygous deletion. Although the homozygous deletion of MTAP has been reported in various human cancers, its function in gastric carcinogenesis is unknown. Here, we determined the status of the MTAP gene by using a combination of array-based comparative genomic hybridization and oligonucleotide microarray. It was found that MTAP was deleted and downregulated in 2 of 10 gastric cancer cell lines. Of the 494 primary gastric carcinomas examined, MTAP expression at the protein level was reduced in 59 (11.9%). Furthermore, a lack of MTAP expression was found to be associated with poor survival (P = 0.038). The genomic loss of MTAP and CDKN2A in gastric carcinomas was investigated by quantitative real-time PCR. Among 20 gastric carcinomas, two cases showed deletion of both MTAP and CDKN2A, and three samples showed homozygous deletion of MTAP, but not of CDKN2A. An analysis of gastric carcinomas revealed that reduced MTAP expression correlated significantly with a genomic deletion. Furthermore, functional assays by transfecting the siRNA or the expressional cDNA into gastric cancer cell lines demonstrated that MTAP regulates cell growth and invasion. The present study suggests that MTAP plays an important role in the regulation of gastric carcinogenesis and, in particular, that MTAP loss is implicated in some way with tumor growth via the modulation of cellular properties, which, in turn, suggests that MTAP has therapeutic applications.
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Affiliation(s)
- Jin Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
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26
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Pan Q, Yang S, Wei Y, Sun F, Li Z. SP1 acts as a key factor, contributes to upregulation of ADAM23 expression under serum deprivation. Biochem Biophys Res Commun 2010; 401:306-12. [PMID: 20851106 DOI: 10.1016/j.bbrc.2010.09.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2010] [Accepted: 09/14/2010] [Indexed: 10/19/2022]
Abstract
ADAM23 modulates many cellular functions, alteration of expression causes a number of tumor types; however, the mechanisms controlling ADAM23 expression remain unknown. Here we have identified a SP1 binding site (-202/-190) that binds SP1 at the proximal promoter of human ADAM23 gene; furthermore, serum deprivation enhances open chromatin accessibility and help expose the SP1 binding site; finally, SP1 binding recruits RNA polymerase II, which in turn results in upregulation of endogenous ADAM23 expression. Therefore, the present study delineates the fundamental elements of a core promoter structure that will be helpful for future studies of the regulation of ADAM23 gene.
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Affiliation(s)
- Qiuhui Pan
- The Central Laboratory, People's 10th Hospital, Shanghai 200072, PR China
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Ding SZ, Goldberg JB, Hatakeyama M. Helicobacter pylori infection, oncogenic pathways and epigenetic mechanisms in gastric carcinogenesis. Future Oncol 2010; 6:851-62. [PMID: 20465395 DOI: 10.2217/fon.10.37] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chronic colonization of the human stomach by Helicobacter pylori, a Gram-negative bacterium, is the major cause of chronic gastritis, peptic ulcers and gastric cancer. Recent progress has elucidated important bacterial and host factors that are responsible for H. pylori-induced gastric inflammation and gastric malignancy. H. pylori cytotoxin-associated antigen A is the major oncogenic factor injected into host cells from bacteria and it disrupts epithelial cell functions. Together with H. pylori cag pathogenicity island, it causes general inflammatory stress within gastric mucosa and activates multiple oncogenic pathways in epithelial cells. A growing list of these pathways includes NF-kappaB, activator protein-1, PI3K, signal transducers and activators of transcription 3, Wnt/beta-catenin and cyclooxygenase 2. H. pylori induces epigenetic alterations, such as DNA methylation and histone modification, which play critical roles in oncogenic transformation. In addition, investigations into gastric stem cell or progenitor cell biology have shed light on the mechanisms through which gastric cancer may originate. Continued investigation in these areas will yield novel insights and help to elucidate the mechanisms of bacteria-induced carcinogenesis.
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Affiliation(s)
- Song-Ze Ding
- Department of Microbiology, University of Virginia Health System, Charlottesville, VA 22908, USA.
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Abstract
After the completion of the human genome, a need was identified by scientists to look for a functional map of the human genome. Epigenomics provided functional characteristics of genes identified in the genome. Epigenetics is the alteration in gene expression (function) without changing the nucleotide sequence. Both activation and inactivation of cancer-associated genes can occur by epigenetic mechanisms. The major players in epigenetic mechanisms of gene regulation are DNA methylation, histone deacetylation, chromatin remodeling, small noncoding RNA expression and gene imprinting. In the last few years, epigenetic mechanisms have been studied in a number of tumor types and epigenetic markers have been identified that are suitable for cancer detection, diagnosis, follow-up of treatment and screening high-risk populations. One interesting aspect of epigenetics is the reactivation of genes by successful reversion of some epigenetic changes using chemicals. The reversibility of epigenetic aberrations has made them attractive targets for cancer treatment with modulators that demethylate DNA and inhibit histone deacetylases, leading to the reactivation of silenced genes. In this article, we have described the current status of this powerful science and discussed the challenges in the clinical fields where epigenetic approaches in cancer are applied.
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Affiliation(s)
- Hirendra Nath Banerjee
- Department of Biology, Campus Box 930, Elizabeth City State University, 1704 Weeksville Road, Elizabeth City, NC 27909, USA.
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Takada H, Wakabayashi N, Dohi O, Yasui K, Sakakura C, Mitsufuji S, Taniwaki M, Yoshikawa T. Tissue factor pathway inhibitor 2 (TFPI2) is frequently silenced by aberrant promoter hypermethylation in gastric cancer. ACTA ACUST UNITED AC 2010; 197:16-24. [PMID: 20113832 DOI: 10.1016/j.cancergencyto.2009.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Revised: 10/04/2009] [Accepted: 11/02/2009] [Indexed: 12/16/2022]
Abstract
Aberrant methylation of promoter CpG islands is associated with transcriptional inactivation of tumor-suppressor genes in cancer. TFPI2, a Kunitz-type serine proteinase inhibitor, has been identified as a putative tumor-suppressor gene from genome-wide screening for aberrant methylation, using a microarray combined with the methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-dCyd) in various types of tumors. We assessed the methylation status of TFPI2 and investigated its expression pattern in human primary gastric cancer (GC) tissues and in GC cell lines. Hypermethylation of the promoter CpG island, which was observed in more or less all of GC cell lines, was prevalent in a high proportion of primary GC tissues (15/18, or 83%), compared with noncancerous (4/18, or 22%) or normal (0/3, or 0%) stomach tissues, and expression of TFPI2 mRNA was reduced in 7 of the 17 primary GC tissues (41%). Moreover, immunohistochemical analyses showed decreased levels of TFPI-2 protein, compared with adjacent noncancerous tissues in 8 of the 20 primary GC tissues examined (40%). TFPI2 mRNA expression was restored in gene-silenced GC cells after treatment with 5-aza-dCyd. Aberrant methylation of TFPI2 promoter CpG island occurred not only in GC cells but also in primary GC tissues at a high frequency, suggesting that epigenetic silencing of TFPI2 may contribute to gastric carcinogenesis.
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Affiliation(s)
- Hisashi Takada
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kawaramachi Hirokoji, Kamigyo-ku, Kyoto, Japan.
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Kim J, Kim MA, Jee CD, Jung EJ, Kim WH. Reduced expression and homozygous deletion of annexin A10 in gastric carcinoma. Int J Cancer 2009; 125:1842-50. [DOI: 10.1002/ijc.24541] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mita H, Toyota M, Aoki F, Akashi H, Maruyama R, Sasaki Y, Suzuki H, Idogawa M, Kashima L, Yanagihara K, Fujita M, Hosokawa M, Kusano M, Sabau SV, Tatsumi H, Imai K, Shinomura Y, Tokino T. A novel method, digital genome scanning detects KRAS gene amplification in gastric cancers: involvement of overexpressed wild-type KRAS in downstream signaling and cancer cell growth. BMC Cancer 2009; 9:198. [PMID: 19545448 PMCID: PMC2717977 DOI: 10.1186/1471-2407-9-198] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Accepted: 06/23/2009] [Indexed: 01/02/2023] Open
Abstract
Background Gastric cancer is the third most common malignancy affecting the general population worldwide. Aberrant activation of KRAS is a key factor in the development of many types of tumor, however, oncogenic mutations of KRAS are infrequent in gastric cancer. We have developed a novel quantitative method of analysis of DNA copy number, termed digital genome scanning (DGS), which is based on the enumeration of short restriction fragments, and does not involve PCR or hybridization. In the current study, we used DGS to survey copy-number alterations in gastric cancer cells. Methods DGS of gastric cancer cell lines was performed using the sequences of 5000 to 15000 restriction fragments. We screened 20 gastric cancer cell lines and 86 primary gastric tumors for KRAS amplification by quantitative PCR, and investigated KRAS amplification at the DNA, mRNA and protein levels by mutational analysis, real-time PCR, immunoblot analysis, GTP-RAS pull-down assay and immunohistochemical analysis. The effect of KRAS knock-down on the activation of p44/42 MAP kinase and AKT and on cell growth were examined by immunoblot and colorimetric assay, respectively. Results DGS analysis of the HSC45 gastric cancer cell line revealed the amplification of a 500-kb region on chromosome 12p12.1, which contains the KRAS gene locus. Amplification of the KRAS locus was detected in 15% (3/20) of gastric cancer cell lines (8–18-fold amplification) and 4.7% (4/86) of primary gastric tumors (8–50-fold amplification). KRAS mutations were identified in two of the three cell lines in which KRAS was amplified, but were not detected in any of the primary tumors. Overexpression of KRAS protein correlated directly with increased KRAS copy number. The level of GTP-bound KRAS was elevated following serum stimulation in cells with amplified wild-type KRAS, but not in cells with amplified mutant KRAS. Knock-down of KRAS in gastric cancer cells that carried amplified wild-type KRAS resulted in the inhibition of cell growth and suppression of p44/42 MAP kinase and AKT activity. Conclusion Our study highlights the utility of DGS for identification of copy-number alterations. Using DGS, we identified KRAS as a gene that is amplified in human gastric cancer. We demonstrated that gene amplification likely forms the molecular basis of overactivation of KRAS in gastric cancer. Additional studies using a larger cohort of gastric cancer specimens are required to determine the diagnostic and therapeutic implications of KRAS amplification and overexpression.
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Affiliation(s)
- Hiroaki Mita
- Department of Molecular Biology, Cancer Research Institute, Sapporo Medical University, Sapporo, Japan.
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Verbisck NV, Costa ÉT, Costa FF, Cavalher FP, Costa MD, Muras A, Paixão VA, Moura R, Granato MF, Ierardi DF, Machado T, Melo F, Ribeiro KB, Cunha IW, Lima VC, Maciel MDS, Carvalho AL, Soares FF, Zanata S, Sogayar MC, Chammas R, Camargo AA. ADAM23 Negatively Modulates αvβ3 Integrin Activation during Metastasis. Cancer Res 2009; 69:5546-52. [DOI: 10.1158/0008-5472.can-08-2976] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Watanabe Y, Kim HS, Castoro RJ, Chung W, Estecio MRH, Kondo K, Guo Y, Ahmed SS, Toyota M, Itoh F, Suk KT, Cho MY, Shen L, Jelinek J, Issa JPJ. Sensitive and specific detection of early gastric cancer with DNA methylation analysis of gastric washes. Gastroenterology 2009; 136:2149-58. [PMID: 19375421 PMCID: PMC2722957 DOI: 10.1053/j.gastro.2009.02.085] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 02/21/2009] [Accepted: 02/26/2009] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Aberrant DNA methylation is an early and frequent process in gastric carcinogenesis and could be useful for detection of gastric neoplasia. We hypothesized that methylation analysis of DNA recovered from gastric washes could be used to detect gastric cancer. METHODS We studied 51 candidate genes in 7 gastric cancer cell lines and 24 samples (training set) and identified 6 for further studies. We examined the methylation status of these genes in a test set consisting of 131 gastric neoplasias at various stages. Finally, we validated the 6 candidate genes in a different population of 40 primary gastric cancer samples and 113 nonneoplastic gastric mucosa samples. RESULTS Six genes (MINT25, RORA, GDNF, ADAM23, PRDM5, MLF1) showed frequent differential methylation between gastric cancer and normal mucosa in the training, test, and validation sets. GDNF and MINT25 were most sensitive molecular markers of early stage gastric cancer, whereas PRDM5 and MLF1 were markers of a field defect. There was a close correlation (r = 0.5-0.9, P = .03-.001) between methylation levels in tumor biopsy and gastric washes. MINT25 methylation had the best sensitivity (90%), specificity (96%), and area under the receiver operating characteristic curve (0.961) in terms of tumor detection in gastric washes. CONCLUSIONS These findings suggest MINT25 is a sensitive and specific marker for screening in gastric cancer. Additionally, we have developed a new method for gastric cancer detection by DNA methylation in gastric washes.
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Affiliation(s)
- Yoshiyuki Watanabe
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hyun Soo Kim
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Ryan J. Castoro
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Woonbok Chung
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | | | - Kimie Kondo
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Yi Guo
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Saira S. Ahmed
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Minoru Toyota
- First Department of Internal Medicine, Sapporo Medical University, Sapporo, Japan
| | - Fumio Itoh
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ki Tae Suk
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Mee-Yon Cho
- Department of Pathology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Lanlan Shen
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Jaroslav Jelinek
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | - Jean-Pierre J. Issa
- Department of Leukemia, The University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
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Choi JS, Kim KH, Jeon YK, Kim SH, Jang SG, Ku JL, Park JG. Promoter hypermethylation of the ADAM23 gene in colorectal cancer cell lines and cancer tissues. Int J Cancer 2009; 124:1258-62. [PMID: 19089928 DOI: 10.1002/ijc.24023] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Promoter hypermethylation of the ADAM23 gene, which is normally involved in cell-to-cell and cell-to matrix adhesion, has been reported in pancreatic, breast and brain cancer, and recently the role of this gene was examined in gastric cancer. In this study, we analyzed ADAM23 expression in colorectal cancer cell lines and examined its methylation by methylation-specific PCR (MSP) and bisulfate-modified DNA sequencing analysis. Methylated cells were treated with 5-aza-2'-deoxycytidine to restore the ADAM23 expression. We then examined ADAM23 methylation status in colorectal cancer tissues and their corresponding normal tissues. We found that ADAM23 was aberrantly silenced or expressed at very low levels in 28 of the 32 (88%) colorectal cancer cell lines. MSP analysis showed that ADAM23 was methylated in 29 of 32 (91%) colorectal cancer cell lines and attenuated expression of ADAM23 was found to be related to hypermethylation in its promoter region. Moreover, the CpG dinucleotide methylation threshold of 70-90% was found to be required for complete silencing. In addition, when some cell lines without ADAM23 expression were treated with 5-aza-2'-deoxycytidine, ADAM23 was reexpressed. In colorectal cancer tissues, the promoter region of ADAM23 was hypermethylated in 36 of 76 (47%). These results demonstrated that ADAM23 may be down-regulated by aberrant promoter hypermethylation during the progression of colorectal cancer.
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Affiliation(s)
- Jin-Sung Choi
- Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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Harada T, Chelala C, Crnogorac-Jurcevic T, Lemoine NR. Genome-wide analysis of pancreatic cancer using microarray-based techniques. Pancreatology 2008; 9:13-24. [PMID: 19077451 DOI: 10.1159/000178871] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND/AIMS Microarray-based comparative genomic hybridisation (CGH) has allowed high-resolution analysis of DNA copy number alterations across the entire cancer genome. Recent advances in bioinformatics tools enable us to perform a robust and highly sensitive analysis of array CGH data and facilitate the discovery of novel cancer-related genes. METHODS We analysed a total of 29 pancreatic ductal adenocarcinoma (PDAC) samples (6 cell lines and 23 microdissected tissue specimens) using 1-Mb-spaced CGH arrays. The transcript levels of all genes within the identified regions of genetic alterations were then screened using our Pancreatic Expression Database. RESULTS In addition to 238 high-level amplifications and 35 homozygous deletions, we identified 315 minimal common regions of 'non-random' genetic alterations (115 gains and 200 losses) which were consistently observed across our tumour samples. The small size of these aberrations (median size of 880 kb) contributed to the reduced number of candidate genes included (on average 12 Ensembl-annotated genes). The database has further specified the genes whose expression levels are consistent with their copy number status. Such genes were UQCRB, SQLE, DDEF1, SLA, ERICH1 and DLC1, indicating that these may be potential target candidates within regions of aberrations. CONCLUSION This study has revealed multiple novel regions that may indicate the locations of oncogenes or tumour suppressor genes in PDAC. Using the database, we provide a list of novel target genes whose altered DNA copy numbers could lead to significant changes in transcript levels in PDAC.
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Affiliation(s)
- Tomohiko Harada
- Centre for Molecular Oncology, Cancer Research UK, Institute of Cancer, Barts and The London School of Medicine and Dentistry, Queen Mary, University of London, London, UK
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Abstract
Over the last few years disintegrin metalloproteinases of the Adam (a disintegrin and metalloproteinase) family have been associated with the process of proteolytic 'shedding' of membrane-associated proteins and hence the rapid modulation of key cell signalling pathways in the tumour microenvironment. Furthermore, numerous members of the Adam family have been associated with tumorigenesis and tumour progression. The question now arises of whether pharmacological manipulation of their functions would be a useful adjunct to therapies targeting intercellular communications. To learn from the lessons of matrix metalloproteinase inhibitors as anticancer agents, there are many facets of the biological and clinical relevance of the ADAMs that need to be understood before embarking with confidence on such an approach.
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Affiliation(s)
- Gillian Murphy
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK.
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Wang FJ, Zhang Q, Yu HL, Li SL. Expression of ADAM23 gene and its significance in human colorectal cancer. Shijie Huaren Xiaohua Zazhi 2008; 16:3406-3409. [DOI: 10.11569/wcjd.v16.i30.3406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the expression of ADAM23 mRNA and protein in human colorectal cancer and its clinical significance.
METHODS: Forty-five cases with colorectal cancer undergoing surgical treatment in our hospital from 2007 to 2008 were collected. Reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemistry were performed to detect the expression of ADAM23 mRNA and protein respectively in tumor and paratumorous tissues.
RESULTS: The expression levels of ADAM23 mRNA and protein were significantly lower in tumor tissues than those in paratumorous tissues (37.8% vs 95.6%, 28.9% vs 86.7%; both P < 0.01). ADAM23 expression had no correlation with patients' age, sex and tumor size, but markedly related to tumor differentiation degree, infiltration depth, lymph node metastasis and clinical stages (χ2 = 5.688, 14.79, 11.8172, 11.8172; P < 0.01 or 0.05).
CONCLUSION: ADAM23, which is associated with partial biological behaviors, may be involved in the development of colorectal cancer, and it may serve as an important molecular biological indicator in diagnosing and predicting the biological behaviors of colorectal cancer.
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Kikuchi R, Tsuda H, Kozaki KI, Kanai Y, Kasamatsu T, Sengoku K, Hirohashi S, Inazawa J, Imoto I. Frequent inactivation of a putative tumor suppressor, angiopoietin-like protein 2, in ovarian cancer. Cancer Res 2008; 68:5067-75. [PMID: 18593905 DOI: 10.1158/0008-5472.can-08-0062] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Angiopoietin-like protein 2 (ANGPTL2) is a secreted protein belonging to the angiopoietin family, the members of which are implicated in various biological processes, although its receptor remains unknown. We identified a homozygous loss of ANGPTL2 (9q33.3) in the course of screening a panel of ovarian cancer (OC) cell lines for genomic copy-number aberrations using in-house array-based comparative genomic hybridization. ANGPTL2 mRNA expression was observed in normal ovarian tissue and immortalized normal ovarian epithelial cells, but was reduced in some OC lines without its homozygous deletion (18 of 23 lines) and restored after treatment with 5-aza 2'-deoxycytidine. The methylation status of sequences around the ANGPTL2 CpG-island with clear promoter activity inversely correlated with expression. ANGPTL2 methylation was frequently observed in primary OC tissues as well. In an immunohistochemical analysis of primary OCs, ANGPTL2 expression was frequently reduced (51 of 100 cases), and inversely correlated with methylation status. Patients with OC showing reduced ANGPTL2 immunoreactivity had significantly worse survival in the earlier stages (stages I and II), but better survival in advanced stages (stages III and IV). The restoration of ANGPTL2 expression or treatment with conditioned medium containing ANGPTL2 inhibited the growth of OC cells originally lacking the expression of this gene, whereas the knockdown of endogenous ANGPTL2 accelerated the growth of OC cells with the expression of ANGPTL2. These results suggest that, at least partly, epigenetic silencing by hypermethylation of the ANGPTL2 promoter leads to a loss of ANGPTL2 function, which may be a factor in the carcinogenesis of OC in a stage-dependent manner.
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Affiliation(s)
- Ryoko Kikuchi
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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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: 42] [Impact Index Per Article: 2.6] [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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Yang Y, Haitchi HM, Cakebread J, Sammut D, Harvey A, Powell RM, Holloway JW, Howarth P, Holgate ST, Davies DE. Epigenetic mechanisms silence a disintegrin and metalloprotease 33 expression in bronchial epithelial cells. J Allergy Clin Immunol 2008; 121:1393-9, 1399.e1-14. [PMID: 18423563 DOI: 10.1016/j.jaci.2008.02.031] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2007] [Revised: 02/25/2008] [Accepted: 02/26/2008] [Indexed: 10/22/2022]
Abstract
BACKGROUND A disintegrin and metalloprotease 33 (ADAM33) polymorphism is strongly associated with asthma and bronchial hyperresponsiveness. Although considered to be a mesenchymal cell-specific gene, recent reports have suggested epithelial expression of ADAM33 in patients with severe asthma. OBJECTIVES Because dysregulated expression of ADAM33 can contribute to disease pathogenesis, we characterized the mechanism or mechanisms that control its transcription and investigated ADAM33 expression in bronchial biopsy specimens and brushings from healthy and asthmatic subjects. METHODS The ADAM33 promoter and CpG island methylation were analyzed by using bioinformatics, luciferase reporters, and bisulfite sequencing of genomic DNA. Epithelial-mesenchymal transition was induced by using TGF-beta1. ADAM33 mRNA was scrutinized in bronchial biopsy specimens and brushings by using reverse transcriptase-quantitative polymerase chain reaction, melt-curve analysis, and direct sequencing. RESULTS The predicted ADAM33 promoter (-550 to +87) had promoter transcriptional activity. Bisulfite sequencing showed that the predicted promoter CpG island (-362 to +80) was hypermethylated in epithelial cells but hypomethylated in ADAM33-expressing fibroblasts. Treatment of epithelial cells with 5-aza-deoxycytidine caused demethylation of the CpG island and induced ADAM33 expression. In contrast, phenotypic transformation of epithelial cells through a TGF-beta-induced epithelial-mesenchymal transition was insufficient to induce ADAM33 expression. ADAM33 mRNA was confirmed in bronchial biopsy specimens, but no validated signal was detected in bronchial brushings from healthy or asthmatic subjects. CONCLUSION The ADAM33 gene contains a regulatory CpG island within its promoter, the methylation status of which tightly controls its expression in a cell type-specific manner. ADAM33 repression is a stable feature of airway epithelial cells, irrespective of disease.
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Affiliation(s)
- Youwen Yang
- Brooke Laboratories, Division of Infection, Inflammation and Repair, School of Medicine, University of Southampton, Southampton, United Kingdom
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Katoh H, Ojima H, Kokubu A, Saito S, Kondo T, Kosuge T, Hosoda F, Imoto I, Inazawa J, Hirohashi S, Shibata T. Genetically distinct and clinically relevant classification of hepatocellular carcinoma: putative therapeutic targets. Gastroenterology 2007; 133:1475-86. [PMID: 17983802 DOI: 10.1053/j.gastro.2007.08.038] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Accepted: 08/02/2007] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS The biological aggressiveness of hepatocellular carcinoma (HCC) and the lack of optimal therapeutic strategies have rendered the disease a major challenge. Highly heterogeneous genetic alteration profiles of HCC have made it difficult to identify effective tailor-made molecular therapeutic targets. Therefore, classification of HCC into genetically homogeneous subclasses would be of great worth to develop novel therapeutic strategies. METHODS We clarified genome-scale chromosomal copy number alteration profiles and mutational statuses of p53 and beta-catenin in 87 HCC tumors. We investigated the possibility that HCC might be classifiable into a number of homogeneous subclasses based solely on their genetic alteration profiles. We also explored putative molecular therapeutic targets specific for each HCC subgroup. RESULTS Unsupervised hierarchical cluster analysis based on chromosomal alteration profiles suggested that HCCs with heterogeneous genetic backgrounds are divisible into homogeneous subclasses that are highly associated with a range of clinicopathologic features of the tumors and moreover with clinical outcomes of the patients (P < .05). These genetically homogeneous subclasses could be characterized distinctively by pathognomonic chromosomal amplifications (eg, c-Myc-induced HCC, 6p/1q-amplified HCC, and 17q-amplified HCC). An in vitro experiment raised a possibility that Rapamycin would significantly inhibit the proliferative activities of HCCs with 17q amplification. CONCLUSIONS HCC is composed of several genetically homogeneous subclasses, each of which harbors characteristic genetic alterations that can be putative tailor-made molecular therapeutic targets for HCCs with specific genetic backgrounds. Our results offer an opportunity for developing novel individualized therapeutic modalities for distinctive genome types of HCC.
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Affiliation(s)
- Hiroto Katoh
- Cancer Genomics Project, National Cancer Center Research Institute, Tokyo, Japan; Pathology Division, National Cancer Center Research Institute, Tokyo, Japan
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Abstract
Proteases have long been associated with cancer progression because of their ability to degrade extracellular matrices, which facilitates invasion and metastasis. However, recent studies have shown that these enzymes target a diversity of substrates and favour all steps of tumour evolution. Unexpectedly, the post-trial studies have also revealed proteases with tumour-suppressive effects. These effects are associated with more than 30 different enzymes that belong to three distinct protease classes. What are the clinical implications of these findings?
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Affiliation(s)
- Carlos López-Otín
- Carlos López-Otín is at the Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain.
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Michels E, De Preter K, Van Roy N, Speleman F. Detection of DNA copy number alterations in cancer by array comparative genomic hybridization. Genet Med 2007; 9:574-84. [PMID: 17873645 DOI: 10.1097/gim.0b013e318145b25b] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Over the past few years, various reliable platforms for high-resolution detection of DNA copy number changes have become widely available. Together with optimized protocols for labeling and hybridization and algorithms for data analysis and representation, this has lead to a rapid increase in the application of this technology in the study of copy number variation in the human genome in normal cells and copy number imbalances in genetic diseases, including cancer. In this review, we briefly discuss specific technical issues relevant for array comparative genomic hybridization analysis in cancer tissues. We specifically focus on recent successes of array comparative genomic hybridization technology in the progress of our understanding of oncogenesis in a variety of cancer types. A third section highlights the potential of sensitive genome-wide detection of patterns of DNA imbalances or molecular portraits for class discovery and therapeutic stratification.
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Affiliation(s)
- Evi Michels
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
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Shinoda Y, Kozaki KI, Imoto I, Obara W, Tsuda H, Mizutani Y, Shuin T, Fujioka T, Miki T, Inazawa J. Association of KLK5 overexpression with invasiveness of urinary bladder carcinoma cells. Cancer Sci 2007; 98:1078-86. [PMID: 17459052 PMCID: PMC11158320 DOI: 10.1111/j.1349-7006.2007.00495.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Array-based comparative genomic hybridization (array-CGH) has powerful potential for high-throughput identification of genetic aberrations in cell genomes. We identified high-level amplification of kallikrein (KLK) genes, which are mapped to 19q13.3 and belong to the serine protease family, in the course of a program to screen a panel of urinary bladder carcinoma cell lines for genomic copy number aberrations using our in-house CGH-array. Expression levels of KLK5, -6, -8 and -9 were significantly increased in three cell lines with copy number gains of these KLK genes. Knockdown of these KLK transcripts by specific small interfering RNA significantly inhibited the invasion of a bladder carcinoma cell line through Matrigel in vitro. Reverse transcription-polymerase chain reaction analysis of 42 primary bladder tumor samples showed that increased expression of KLK5 was frequently observed in invasive tumors (pT2-pT4) (14.3%, 6/42) compared with superficial tumors (pTa, pT1) (0%, 0/42; P = 0.0052), and expression levels of KLK5, -6, -8 and -9 mRNA were higher in invasive tumors than in superficial tumors (P < 0.0001, P = 0.0043, P = 0.0790 and P = 0.0037, respectively). These observations indicate that KLK5, -6, -8 and -9 may be the most likely targets of the 19q13.3 amplification, and may play a crucial role in promoting cancer-cell invasion in bladder tumor.
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Affiliation(s)
- Yasuo Shinoda
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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Kawanishi H, Takahashi T, Ito M, Matsui Y, Watanabe J, Ito N, Kamoto T, Kadowaki T, Tsujimoto G, Imoto I, Inazawa J, Nishiyama H, Ogawa O. Genetic analysis of multifocal superficial urothelial cancers by array-based comparative genomic hybridisation. Br J Cancer 2007; 97:260-6. [PMID: 17579624 PMCID: PMC2360305 DOI: 10.1038/sj.bjc.6603850] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The purpose of this study was to investigate the accumulation of genetic alterations during metachronous and/or synchronous development of multifocal low-grade superficial urothelial tumours in the same patient, by using array-based comparative genomic hybridisation (array-CGH) and FGFR mutation analysis. We analysed 24 tumours (pTa-1 G1-2) from five patients. We had previously identified a clonal relationship among the tumours of each patient by microsatellite analysis. This time, unsupervised hierarchical cluster analysis revealed that the tumours from each patient were clustered together independently of the tumours from the other patients. All of the tumours from a single patient showed a set of 2–7 identical regional or whole-arm chromosomal changes. In addition, several individual alterations were also found. Cladistic diagrams revealed that the accumulation of genetic alterations could not be explained by a linear model, and the existence of a hypothetical precursor cell was assumed in four patients. In some cases, FGFR mutation seemed to occur later during multifocal tumour development. Taken together, these findings suggest that low-grade superficial urothelial tumours accumulate minor genetic alterations during multifocal development, although these tumours are genetically stable.
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Affiliation(s)
- H Kawanishi
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - T Takahashi
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - M Ito
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Y Matsui
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - J Watanabe
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - N Ito
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - T Kamoto
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - T Kadowaki
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
- Eisai Co. Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - G Tsujimoto
- Department of Genomic Drug Discovery Science, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - I Imoto
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Core Research for Evolutional Science and Technology of Japan Science and Technology Corporation, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - J Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Core Research for Evolutional Science and Technology of Japan Science and Technology Corporation, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
- 21st Century Center of Excellence (COE) Program for Molecular Destruction and Reconstitution of Tooth and Bone, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - H Nishiyama
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - O Ogawa
- Department of Urology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
- E-mail:
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Suzuki E, Imoto I, Pimkhaokham A, Nakagawa T, Kamata N, Kozaki KI, Amagasa T, Inazawa J. PRTFDC1, a possible tumor-suppressor gene, is frequently silenced in oral squamous-cell carcinomas by aberrant promoter hypermethylation. Oncogene 2007; 26:7921-32. [PMID: 17599052 DOI: 10.1038/sj.onc.1210589] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Array-based comparative genomic hybridization (array-CGH) has good potential for the high-throughput identification of genetic aberrations in cell genomes. In the course of a program to screen a panel of oral squamous-cell carcinoma (OSCC), cell lines for genomic copy-number aberrations by array-CGH using our in-house arrays, we identified a 3-Mb homozygous deletion at 10p12 in 1 of 18 cell lines (5.6%). Among seven genes located within this region, expression of PRTFDC1 mRNA was not detected in 50% (9/18) or decreased in 5.6% (1/18) of OSCC cell lines, but detected in normal oral epithelia and restored in gene-silenced OSCC cells without its homozygous loss after treatment with 5-aza-2'-deoxycytidine. Among 17 cell lines without a homozygous deletion, the hypermethylation of the PRTFDC1 CpG island, which showed promoter activity, was observed in all nine cell lines with no or reduced PRTFDC1 expression (52.9%). Methylation of this CpG island was also observed in primary OSCC tissues (8/47, 17.0%). In addition, restoration of PRTFDC1 in OSCC cells lacking its expression inhibited cell growth in colony-formation assays, whereas knockdown of PRTFDC1 expression in OSCC cells expressing the gene promoted cell growth. These results suggest that epigenetic silencing of PRTFDC1 by hypermethylation of the CpG island leads to a loss of PRTFDC1 function, which might be involved in squamous cell oral carcinogenesis.
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Affiliation(s)
- E Suzuki
- Department of Molecular Cytogenetics, Medical Research Institute and School of Biomedical Science, Tokyo Medical and Dental University, Tokyo, Japan
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Calmon MF, Colombo J, Carvalho F, Souza FP, Filho JFG, Fukuyama EE, Camargo AA, Caballero OLS, Tajara EH, Cordeiro JA, Rahal P. Methylation profile of genes CDKN2A (p14 and p16), DAPK1, CDH1, and ADAM23 in head and neck cancer. ACTA ACUST UNITED AC 2007; 173:31-7. [PMID: 17284367 DOI: 10.1016/j.cancergencyto.2006.09.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 08/07/2006] [Accepted: 09/08/2006] [Indexed: 11/21/2022]
Abstract
Hypermethylation in the promoter region has been associated with a loss of gene function that may give a selective advantage to neoplastic cells. In this study, the methylation pattern of genes CDKN2A (alias p14, p14(ARF), p16, p16(INK4a)), DAPK1, CDH1, and ADAM23 was analyzed in 43 samples of head and neck tumors using methylation-specific polymerase chain reaction. In the oropharynx, there was a statistically significant association between hypermethylation of the DAPK1 gene and the occurrence of lymph node metastases, and in the larynx there was statistically significant evidence of an association between hypermethylation of the ADAM23 gene and advanced stages of the tumors. Thus, a correlation was observed between hypermethylation of the promoter region of genes DAPK1 and ADAM23 and the progression of head and neck cancer.
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Affiliation(s)
- Marilia F Calmon
- Department of Biology, UNESP-IBILCE, Rua Cristovão Colombo, 2265, Jardim Nazareth, CEP: 15054-000, São José do Rio Preto, SP, Brazil
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48
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Current World Literature. Curr Opin Oncol 2007; 19:65-9. [PMID: 17133115 DOI: 10.1097/cco.0b013e328012d5fa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ng G, Huang J, Roberts I, Coleman N. Defining ploidy-specific thresholds in array comparative genomic hybridization to improve the sensitivity of detection of single copy alterations in cell lines. J Mol Diagn 2006; 8:449-58. [PMID: 16931585 PMCID: PMC1867620 DOI: 10.2353/jmoldx.2006.060033] [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: 12/21/2022] Open
Abstract
Array comparative genomic hybridization (CGH) is being widely used to screen for recurrent genomic copy number alterations in neoplasms, with imbalances typically detected through the application of gain and loss thresholds. Review of array CGH publications for the year 2005 showed that a wide range of thresholds are used. However, the effect of sample ploidy on the sensitivity of these thresholds for single copy alterations (SCAs) has not been evaluated. Here, we describe a method to evaluate the detection accuracy of thresholds for detecting SCAs in cell line array CGH data. By applying a hidden Markov model-based method, we segmented array CGH data from well-karyotyped cell lines and generated ploidy-specific sensitivity-specificity plots, from which we identified optimum thresholds relevant to sample ploidy. We demonstrate that commonly used nonploidy-specific thresholds are suboptimal in their ability to call SCAs, particularly when applied to hypertriploid or tetraploid cell lines. We conclude that the use of ploidy-specific thresholds improves the sensitivity of thres-hold-based array CGH for detecting SCAs in cell lines. Because polyploidy is a common feature of cancer cells, the application of ploidy-specific thresholds to cell lines (and potentially to clinical samples) may improve the detection sensitivity of SCAs of biological significance.
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Affiliation(s)
- Grace Ng
- Medical Research Council Cancer Cell Unit, Hutchison/MRC Research Centre, Box 197, Hills Rd., Cambridge CB2 2XZ, UK
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Yu W, Imoto I, Inoue J, Onda M, Emi M, Inazawa J. A novel amplification target, DUSP26, promotes anaplastic thyroid cancer cell growth by inhibiting p38 MAPK activity. Oncogene 2006; 26:1178-87. [PMID: 16924234 DOI: 10.1038/sj.onc.1209899] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Anaplastic thyroid cancer (ATC) is one of the most lethal of all human tumors, but cytogenetic information concerning ATC is extremely limited. Using our in-house array-based comparative genomic hybridization and 14 ATC cell lines with further fluorescence in situ hybridization analysis, we demonstrated amplification of the DUSP26 gene, known by another report as MAP kinase phosphatase-8. DUSP26 was overexpressed in ATC cell lines and primary ATC tumor samples. When overexpressed, either exogenously or endogenously, DUSP26 promoted growth of the ATC cells. DUSP26 encodes a protein containing a dual-specificity phosphatase domain that can dephosphorylate itself. DUSP26 effectively dephosphorylates p38 and has a little effect on extracellular signal-regulated kinase in ATC cells. DUSP26 protein formed a physical complex with p38, and promoted survival of ATC cells by inhibiting p38-mediated apoptosis. Our findings suggest that DUSP26 may act as an oncogene in ATC, and might be a useful diagnostic marker and therapeutic target of this disease.
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Affiliation(s)
- W Yu
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Biomedical Science, Tokyo, Japan
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