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Luo Q, Zhang S, Yang F, Feng R, Xu Q, Chen X, Yang S. Role of ADP ribosylation factor guanylate kinase 1 in the malignant biological behavior of gastric cancer. Heliyon 2024; 10:e33255. [PMID: 39021998 PMCID: PMC11253526 DOI: 10.1016/j.heliyon.2024.e33255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/29/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Aim This study aims to investigate the influence of ASAP1 (ADP ribosylation factor guanylate kinase 1) on the malignant behavior of gastric cancer (GC) cells and to elucidate the potential molecular mechanisms involved in cancer development and progression. Methods We assessed the impact of ASAP1 overexpression and knockdown on GC cell malignancy using CCK8, colony formation, flow cytometry (Annexin V/propidium iodide), Transwell migration, invasion, and scratch assays. Western blot analysis was used to assess the effects of ASAP1 on angiogenesis, matrix metalloproteinases (MMPs), apoptotic proteins, epithelial-mesenchymal transition (EMT)-related proteins, as well as AKT and p-AKT. The influence of ASAP1 knockdown was also evaluated in nude mice bearing BGC823 cell-derived tumors. Results Our findings revealed that ASAP1 was significantly overexpressed in GC cells, enhancing their proliferation, invasion, and migration, while reducing apoptosis. Conversely, ASAP1 knockdown reversed these effects, markedly increasing the expression of cleaved-caspase 3 (Casp3), PARP, and the epithelial marker E-cadherin, and significantly decreasing MMP2, MMP9, VEGFA, and mesenchymal markers such as N-cadherin and vimentin. Additionally, it reduced AKT, and p-AKT levels (P < 0.01). Tumor growth in nude mice was suppressed following ASAP1 knockdown. Conclusion The overexpression of ASAP1 significantly promotes malignant behaviors in GC cells, whereas its knockdown diminishes these effects. This modulation is potentially through the downregulation of VEGFA, leading to reduced angiogenesis, Cleaved-Casp3 and Cleaved-PARP overexpression, and a decrease in MMPs, EMT, AKT, and p-AKT activity.
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Affiliation(s)
- Qiong Luo
- Departments of Oncology, Fuzhou, Fujian 350001, PR China
| | - Suyun Zhang
- Departments of Oncology, Fuzhou, Fujian 350001, PR China
| | - Fan Yang
- Departments of Pulmonary and Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, PR China
| | - Rui Feng
- Departments of Oncology, Fuzhou, Fujian 350001, PR China
| | - Qian Xu
- Departments of Oncology, Fuzhou, Fujian 350001, PR China
| | - Xiangqi Chen
- Departments of Pulmonary and Critical Care Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, PR China
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Fuzhou, Fujian 350001, PR China
| | - Sheng Yang
- Departments of Oncology, Fuzhou, Fujian 350001, PR China
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Fuzhou, Fujian 350001, PR China
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Jia Q, Ding Q, Shao K, Dang J, Zhang F. Research progress regarding CYP3A gene family in gastric cancer. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2023; 48:1874-1881. [PMID: 38448381 PMCID: PMC10930750 DOI: 10.11817/j.issn.1672-7347.2023.230150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Indexed: 03/08/2024]
Abstract
Cytochrome P450 family 3 subfamily A (CYP3A), a major member of cytochrome P450 (CYP) family, is one of the most important drug metabolizing enzymes in human. CYP3A includes 4 gene subtypes (CYP3A4, CYP3A5, CYP3A7, and CYP3A43), which is involved in 60% of drug metabolism in the human. It is not only widely distributed in normal tissues, but also significantly overexpressed in various tumor tissues. Recently, CYP3A has attracted great attention due to its involvement in the progression from chronic atrophic gastritis to gastric cancer, as well as the differential metabolism and resistance of chemotherapeutic drugs. Targeting CYP3A gene mediated-prodrug provides new ideas for the treatment of gastric cancer and is expected to become a new target for the diagnosis and treatment of gastric cancer.
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Affiliation(s)
- Qi Jia
- Second Clinical Medical School, Lanzhou University, Lanzhou 730030.
| | - Qingsong Ding
- Second Clinical Medical School, Lanzhou University, Lanzhou 730030
| | - Kangmei Shao
- Second Clinical Medical School, Lanzhou University, Lanzhou 730030
| | - Jianzhong Dang
- Department of Surgical Oncology, Second Hospital, Lanzhou University, Lanzhou 730030
| | - Fan Zhang
- Department of Surgical Oncology, Second Hospital, Lanzhou University, Lanzhou 730030.
- Frontiers Science Center for Rare Isotopes, Lanzhou University, Lanzhou 730000, China.
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3
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Wang D, Hao S, He H, Zhang J, You G, Wu X, Zhang R, Meng X, Cui X, Bai J, Fu S, Yu J. Contribution of PGAP3 co-amplified and co-overexpressed with ERBB2 at 17q12 involved poor prognosis in gastric cancer. J Cell Mol Med 2023; 27:2424-2436. [PMID: 37386793 PMCID: PMC10424286 DOI: 10.1111/jcmm.17828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/10/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
The locus at 17q12 erb-b2 receptor tyrosine kinase 2 (ERBB2) has been heavily amplificated and overexpressed in gastric cancer (GC), but it remains to be elucidated about the clinical significance of the co-amplification and co-overexpression of PGAP3 gene located around ERBB2 in GC. The profile of PGAP3 and ERBB2 in four GC cell lines and tissue microarrays containing 418 primary GC tissues was assessed to investigate the co-overexpression and clinical significance of the co-amplified genes, and to evaluate the impact of the co-amplified genes on the malignancy of GC. Co-amplification of PGAP3 and ERBB2 accompanied with co-overexpression was observed in a haploid chromosome 17 of NCI-N87 cells with double minutes (DMs). PGAP3 and ERBB2 were overexpressed and positively correlated in 418 GC patients. Co-overexpression of the PGAP3 and ERBB2 was correlated with T stage, TNM stage, tumour size, intestinal histological type and poor survival proportion in 141 GC patients. In vitro, knockdown of the endogenous PGAP3 or ERBB2 decreased cell proliferation and invasion, increased G1 phase accumulation and induced apoptosis in NCI-N87 cells. Furthermore, combined silencing of PGAP3 and ERBB2 showed an additive effect on resisting proliferation of NCI-N87 cells compared with targeting ERBB2 or PGAP3 alone. Taken together, the co-overexpression of PGAP3 and ERBB2 may be crucial due to its significant correlation with clinicopathological factors of GC. Haploid gain of PGAP3 co-amplified with ERBB2 is sufficient to facilitate the malignancy and progression of GC cells in a synergistic way.
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Affiliation(s)
- Dong Wang
- Scientific Research CentreThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Siyu Hao
- Scientific Research CentreThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Hongjie He
- Scientific Research CentreThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Jian Zhang
- Scientific Research CentreThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Ge You
- Scientific Research CentreThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Xin Wu
- Scientific Research CentreThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Rui Zhang
- Scientific Research CentreThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
| | - Xiangning Meng
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University)Ministry of EducationHarbinChina
| | - Xiaobo Cui
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University)Ministry of EducationHarbinChina
| | - Jing Bai
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University)Ministry of EducationHarbinChina
| | - Songbin Fu
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University)Ministry of EducationHarbinChina
| | - Jingcui Yu
- Scientific Research CentreThe Second Affiliated Hospital of Harbin Medical UniversityHarbinChina
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China (Harbin Medical University)Ministry of EducationHarbinChina
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Rivera-Yañez N, Ruiz-Hurtado PA, Rivera-Yañez CR, Arciniega-Martínez IM, Yepez-Ortega M, Mendoza-Arroyo B, Rebollar-Ruíz XA, Méndez-Cruz AR, Reséndiz-Albor AA, Nieto-Yañez O. The Role of Propolis as a Natural Product with Potential Gastric Cancer Treatment Properties: A Systematic Review. Foods 2023; 12:foods12020415. [PMID: 36673507 PMCID: PMC9858610 DOI: 10.3390/foods12020415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Gastric cancer is one of the most common, aggressive, and invasive types of malignant neoplasia. It ranks fifth for incidence and fourth for prevalence worldwide. Products of natural origin, such as propolis, have been assessed for use as new complementary therapies to combat cancer. Propolis is a bee product with antiproliferative and anticancer properties. The concentrations and types of secondary metabolites contained in propolis mainly vary according to the geographical region, the season of the year, and the species of bees that make it. The present study is a systematic review of the main articles related to the effects of propolis against gastric cancer published between 2011 and 2021 in the PubMed and Science Direct databases. Of 1305 articles published, only eight studies were selected; among their principal characteristics was the use of in vitro analysis with cell lines from gastric adenocarcinoma and in vivo murine models of the application of propolis treatments. These studies suggest that propolis arrests the cell cycle and inhibits proliferation, prevents the release of oxidizing agents, and promotes apoptosis. In vivo assays showed that propolis decreased the number of tumors by regulating the cell cycle and the expression of proteins related to apoptosis.
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Affiliation(s)
- Nelly Rivera-Yañez
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
- División de Investigación y Posgrado, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
| | - Porfirio Alonso Ruiz-Hurtado
- Laboratorio de Toxicología de Productos Naturales, Departamento de Farmacia, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Av. Wilfrido Massieu, Esq. Manuel L. Stampa s/n, Gustavo A. Madero, Ciudad de México 07738, Mexico
- Laboratorio de Toxicología Molecular y Celular, Departamento de Farmacia, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Av. Wilfrido Massieu, Esq. Manuel L. Stampa s/n, Gustavo A. Madero, Ciudad de México 07738, Mexico
| | - Claudia Rebeca Rivera-Yañez
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
- Laboratorio de Inmunología, Unidad de Morfofisiología y Función, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
| | - Ivonne Maciel Arciniega-Martínez
- Laboratorio de Inmunonutrición, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis esq. Salvador Díaz Mirón s/n, Ciudad de México 11340, Mexico
| | - Mariazell Yepez-Ortega
- Laboratorio de Inmunonutrición, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis esq. Salvador Díaz Mirón s/n, Ciudad de México 11340, Mexico
| | - Belén Mendoza-Arroyo
- Laboratorio de Inmunidad de Mucosas, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis esq. Salvador Díaz Mirón s/n, Ciudad de México 11340, Mexico
| | - Xóchitl Abril Rebollar-Ruíz
- Laboratorio de Inmunonutrición, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis esq. Salvador Díaz Mirón s/n, Ciudad de México 11340, Mexico
| | - Adolfo René Méndez-Cruz
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
- Laboratorio de Inmunología, Unidad de Morfofisiología y Función, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
| | - Aldo Arturo Reséndiz-Albor
- Laboratorio de Inmunidad de Mucosas, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis esq. Salvador Díaz Mirón s/n, Ciudad de México 11340, Mexico
- Correspondence: (A.A.R.-A.); (O.N.-Y.); Tel.: +52-5521-327-136 (O.N.-Y.)
| | - Oscar Nieto-Yañez
- Carrera de Médico Cirujano, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla 54090, Mexico
- Correspondence: (A.A.R.-A.); (O.N.-Y.); Tel.: +52-5521-327-136 (O.N.-Y.)
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Zou Y, Cao C, Wang Y, Zhou Y, Yao S, Zhang L, Zheng K, Zhang H, Qin W, Qin K, Xiong H, Yuan X, Fu S, Wang Y, Xiong H. Multi-omics consensus portfolio to refine the classification of lung adenocarcinoma with prognostic stratification, tumor microenvironment, and unique sensitivity to first-line therapies. Transl Lung Cancer Res 2022; 11:2243-2260. [PMID: 36519025 PMCID: PMC9742627 DOI: 10.21037/tlcr-22-775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/21/2022] [Indexed: 09/09/2023]
Abstract
BACKGROUND Molecular classification of lung adenocarcinoma (LUAD) based on transcriptomic features has been widely studied. The complementarity of data obtained from multilayer molecular biology could help the LUAD classification via combining multi-omics information. METHODS We successfully divided samples from the The Cancer Genome Atlas (TCGA) (n=437) into four subtypes (CS1, CS2, CS3 and CS4) by 10 comprehensive multi-omics clustering methods in the "movics" R package. Meanwhile, external validation sets from different sequencing technologies proved the robustness of the grouping model. The relationship between subtypes, prognosis, molecular features, tumor microenvironment and response to first-line therapy was further analyzed. Next we used univariate Cox regression analysis and Lasso regression analysis to explore the application of biomarkers in clinical prognosis and constructed a prognostic model. RESULTS CS1 showed the worst overall survival (OS) among all four clusters, possibly related to its poor immune infiltration, higher tumor mutation and worse chromosomal stability. Patients in different subtypes differed significantly in cancer stem cell characteristics, activation of cancer-related pathways, sensitivity to chemotherapy and immunotherapy. The prognostic model showed good predictive performance. The 1-, 2- and 3-year areas under the curve of risk score were 0.779, 0.742 and 0.678, respectively. Seven genes (DKK1, TSPAN7, ID1, DLGAP5, HHIPL2, CD40 and SEMA3C) used to build the model may be potential therapeutic targets for LUAD. CONCLUSIONS Four LUAD subtypes with different molecular characteristics and clinical implications were identified successfully through bioinformatic analysis. Our results may contribute to precision medicine and inform the development of rational clinical strategies for targeted and immune therapies.
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Affiliation(s)
- Yanmei Zou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenlin Cao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yilu Zhou
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Shuo Yao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lili Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Zheng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengling Fu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yihua Wang
- Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Hua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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6
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Huang Y, Qiu L, Liang X, Zhao J, Chen H, Luo Z, Li W, Lin X, Jin J, Huang J, Zhang G. Identifying a 6-Gene Prognostic Signature for Lung Adenocarcinoma Based on Copy Number Variation and Gene Expression Data. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6962163. [PMID: 36211815 PMCID: PMC9535135 DOI: 10.1155/2022/6962163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 11/20/2022]
Abstract
The occurrence of lung adenocarcinoma (LUAD) is a complicated process, involving the genetic and epigenetic changes of proto-oncogenes and oncogenes. The objective of this study was to establish new predictive signatures of lung adenocarcinoma based on copy number variations (CNVs) and gene expression data. Next-generation sequencing was implemented to obtain gene expression and CNV information. According to univariate, multivariate survival Cox regression analysis, and LASSO analysis, the expression profiles of lung adenocarcinoma patients were screened and a risk score formula was established and experimentally validated in a local cohort. The model was evaluated by three independent cohorts (TCGA-LUAD, GSE31210, and GSE30219), and then validated by clinical samples from LUAD patients. A total of 844 CNV-related differentially expressed genes (CNV-related DEGs) were identified. These genes are significantly associated with the imbalance of various oxidative stress pathways. A CNV-associated-six gene signature was dramatically linked to overall survival in lung adenocarcinoma samples from both training and validation groups. Functional enrichment analysis further revealed involvement of genes in p53 signaling pathway and cell cycle as well as the mismatch repair pathway. Risk score is an independent marker considering clinical parameters and had better prediction in clinical subpopulation. The same signature also classified tumor tissues of clinical patients with CNV detected from their corresponding nontumorous tissues with an accuracy of 0.92. In conclusion, we identified a new class of 6 CNV-related gene markers that may act as efficient prognostic predictors of lung adenocarcinoma, thus contributing to individualized treatment decisions in patients.
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Affiliation(s)
- Yisheng Huang
- Postdoctoral Innovation Center of Zhongshan Chenxinghai Hospital, Jinan University, Guangzhou, China
- Department of Oncology, Maoming People's Hospital, Maoming City, China
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Liling Qiu
- Department of Endocrinology, Zhongshan Hospital of Sun Yat-Sen University, Zhongshan City People's Hospital, Zhongshan City, China
| | - Xiaoye Liang
- Department of Oncology, Maoming People's Hospital, Maoming City, China
| | - Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Haoting Chen
- Translational Medicine Center, Key Laboratory of Molecular Target and Clinical Pharmacology, School of Pharmaceutical Sciences, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhiqiang Luo
- Department of Thoracic Surgery, Maoming People's Hospital, Maoming City, China
| | - Wanzhen Li
- Department of Oncology, Maoming People's Hospital, Maoming City, China
| | - Xiaohua Lin
- Department of Oncology, Maoming People's Hospital, Maoming City, China
| | - Jingjie Jin
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Jian Huang
- Department of Thoracic Surgery, Maoming People's Hospital, Maoming City, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
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7
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Li Q, Wang Y, Li Z, Su M, Song Y, Hu Q, Zhou B, Zhang L. Association of oncostatin M receptor polymorphisms with clinical recurrence of ovarian cancer in the Chinese Han population. Biomark Med 2022; 16:461-471. [PMID: 35321549 DOI: 10.2217/bmm-2021-0989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: Ovarian cancer (OC) is a gynecological malignancy with a challenging judgment of prognosis due to complicated etiology and high recurrence rate. The oncostatin M receptor (OSMR) from members of the IL-6 receptor family is associated with tumor development. This study aims to explore the correlations between OSMR gene polymorphisms (rs2278329 [G/A, missense, Asp553Asn], rs2292016 [G/T, promoter, -100G/T]) and OC. Methods: This study enrolled 160 OC patients and 397 healthy controls. Genotypes of two single-nucleotide polymorphisms were distinguished using TaqMan SNP Genotyping Assay, and statistical analysis was performed using SPSS software. Results: A significantly decreased overall survival rate was found in serous OC patients carrying rs2278329 GA/AA genotypes. Meanwhile, TT genotype carriers of rs2292016 had an improved relapse rate, and the GT genotype showed a definitive correlation with a lower relapse rate. Conclusion: OSMR gene polymorphisms may be related to recurrence and overall survival of serous OC patients.
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Affiliation(s)
- Qin Li
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects & Related Diseases of Women & Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, PR, 610041, China
| | - Yanyun Wang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects & Related Diseases of Women & Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, PR, 610041, China
| | - Zhilong Li
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects & Related Diseases of Women & Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, PR, 610041, China
| | - Min Su
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects & Related Diseases of Women & Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, PR, 610041, China
| | - Yaping Song
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects & Related Diseases of Women & Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, PR, 610041, China
| | - Qian Hu
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects & Related Diseases of Women & Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, PR, 610041, China
| | - Bin Zhou
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects & Related Diseases of Women & Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, PR, 610041, China
| | - Lin Zhang
- Laboratory of Molecular Translational Medicine, Center for Translational Medicine, Key Laboratory of Birth Defects & Related Diseases of Women & Children (Sichuan University), Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, PR, 610041, China
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8
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Patel V, Szász I, Koroknai V, Kiss T, Balázs M. Molecular Alterations Associated with Acquired Drug Resistance during Combined Treatment with Encorafenib and Binimetinib in Melanoma Cell Lines. Cancers (Basel) 2021; 13:cancers13236058. [PMID: 34885166 PMCID: PMC8656772 DOI: 10.3390/cancers13236058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022] Open
Abstract
Combination treatment using BRAF/MEK inhibitors is a promising therapy for patients with advanced BRAFV600E/K mutant melanoma. However, acquired resistance largely limits the clinical efficacy of this drug combination. Identifying resistance mechanisms is essential to reach long-term, durable responses. During this study, we developed six melanoma cell lines with acquired resistance for BRAFi/MEKi treatment and defined the molecular alterations associated with drug resistance. We observed that the invasion of three resistant cell lines increased significantly compared to the sensitive cells. RNA-sequencing analysis revealed differentially expressed genes that were functionally linked to a variety of biological functions including epithelial-mesenchymal transition, the ROS pathway, and KRAS-signalling. Using proteome profiler array, several differentially expressed proteins were detected, which clustered into a unique pattern. Galectin showed increased expression in four resistant cell lines, being the highest in the WM1617E+BRes cells. We also observed that the resistant cells behaved differently after the withdrawal of the inhibitors, five were not drug addicted at all and did not exhibit significantly increased lethality; however, the viability of one resistant cell line (WM1617E+BRes) decreased significantly. We have selected three resistant cell lines to investigate the protein expression changes after drug withdrawal. The expression patterns of CapG, Enolase 2, and osteopontin were similar in the resistant cells after ten days of "drug holiday", but the Snail protein was only expressed in the WM1617E+BRes cells, which showed a drug-dependent phenotype, and this might be associated with drug addiction. Our results highlight that melanoma cells use several types of resistance mechanisms involving the altered expression of different proteins to bypass drug treatment.
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Affiliation(s)
- Vikas Patel
- Doctoral School of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary;
| | - István Szász
- MTA-DE Public Health Research Group, University of Debrecen, 4032 Debrecen, Hungary; (I.S.); (V.K.)
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Viktória Koroknai
- MTA-DE Public Health Research Group, University of Debrecen, 4032 Debrecen, Hungary; (I.S.); (V.K.)
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Tímea Kiss
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Margit Balázs
- MTA-DE Public Health Research Group, University of Debrecen, 4032 Debrecen, Hungary; (I.S.); (V.K.)
- Department of Public Health and Epidemiology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Correspondence:
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9
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Copy number alteration profiling facilitates differential diagnosis between ossifying fibroma and fibrous dysplasia of the jaws. Int J Oral Sci 2021; 13:21. [PMID: 34188021 PMCID: PMC8242074 DOI: 10.1038/s41368-021-00127-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/22/2022] Open
Abstract
Ossifying fibroma (OF) and fibrous dysplasia (FD) are two fibro-osseous lesions with overlapping clinicopathological features, making diagnosis challenging. In this study, we applied a whole-genome shallow sequencing approach to facilitate differential diagnosis via precise profiling of copy number alterations (CNAs) using minute amounts of DNA extracted from morphologically correlated microdissected tissue samples. Freshly frozen tissue specimens from OF (n = 29) and FD (n = 28) patients were obtained for analysis. Lesion fibrous tissues and surrounding normal tissues were obtained by laser capture microdissection (LCM), with ~30–50 cells (5 000–10 000 µm2) per sample. We found that the rate of recurrent CNAs in OF cases was much higher (44.8%, 13 of 29) than that in FD cases (3.6%, 1 of 28). Sixty-nine percent (9 of 13) of the CNA-containing OF cases involved segmental amplifications and deletions on Chrs 7 and 12. We also identified eight CNA-associated genes (HILPDA, CALD1, C1GALT1, MICALL2, PHF14, AIMP2, MDM2, and CDK4) with amplified expression, which was consistent with the copy number changes. We further confirmed a jaw lesion with a previous uncertain diagnosis due to its ambiguous morphological features and the absence of GNAS mutation as OF based on the typical Chr 12 amplification pattern in its CNA profile. Moreover, analysis of a set of longitudinal samples collected from an individual with a cellular lesion in suspicion of OF at the first surgery, recurrence and the latest malignant transformation revealed identical CNA patterns at the three time points, suggesting that copy number profiling can be used as an important tool to identify borderline lesions or lesions with malignant potential. Overall, CNA profiling of fibro-osseous lesions can greatly improve differential diagnosis between OF and FD and help predict disease progression.
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10
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Clerici SP, Oliveira PFDS, Akagi EM, Cordeiro HG, Azevedo-Martins JM, Faria AVDS, Ferreira-Halder CV. A comprehensive review on the role of protein tyrosine phosphatases in gastric cancer development and progression. Biol Chem 2021; 402:663-674. [PMID: 33544466 DOI: 10.1515/hsz-2020-0355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/15/2021] [Indexed: 12/09/2022]
Abstract
The main post-translational reversible modulation of proteins is phosphorylation and dephosphorylation, catalyzed by protein kinases (PKs) and protein phosphatases (PPs) which is crucial for homeostasis. Imbalance in this crosstalk can be related to diseases, including cancer. Plenty of evidence indicates that protein tyrosine phosphatases (PTPs) can act as tumor suppressors and tumor promoters. In gastric cancer (GC), there is a lack of understanding of the molecular aspects behind the tumoral onset and progression. Here we describe several members of the PTP family related to gastric carcinogenesis. We discuss the associated molecular mechanisms which support the down or up modulation of different PTPs. We emphasize the Helicobacter pylori (H. pylori) virulence which is in part associated with the activation of PTP receptors. We also explore the involvement of intracellular redox state in response to H. pylori infection. In addition, some PTP members are under influence by genetic mutations, epigenetics mechanisms, and miRNA modulation. The understanding of multiple aspects of PTPs in GC may provide new targets and perspectives on drug development.
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Affiliation(s)
- Stefano Piatto Clerici
- Department of Biochemistry and Tissue Biology, University of Campinas, UNICAMP, Rua Monteiro Lobato 255, 13083-862Campinas, São Paulo, Brazil
| | | | - Erica Mie Akagi
- Department of Biochemistry and Tissue Biology, University of Campinas, UNICAMP, Rua Monteiro Lobato 255, 13083-862Campinas, São Paulo, Brazil
| | - Helon Guimarães Cordeiro
- Department of Biochemistry and Tissue Biology, University of Campinas, UNICAMP, Rua Monteiro Lobato 255, 13083-862Campinas, São Paulo, Brazil
| | - Jordana Maria Azevedo-Martins
- Department of Biochemistry and Tissue Biology, University of Campinas, UNICAMP, Rua Monteiro Lobato 255, 13083-862Campinas, São Paulo, Brazil
| | - Alessandra Valéria de Sousa Faria
- Department of Biochemistry and Tissue Biology, University of Campinas, UNICAMP, Rua Monteiro Lobato 255, 13083-862Campinas, São Paulo, Brazil
| | - Carmen Veríssima Ferreira-Halder
- Department of Biochemistry and Tissue Biology, University of Campinas, UNICAMP, Rua Monteiro Lobato 255, 13083-862Campinas, São Paulo, Brazil
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11
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Zhu X, Yan S, Xiao S, Xue M. Knockdown of ALPK2 inhibits the development and progression of Ovarian Cancer. Cancer Cell Int 2020; 20:267. [PMID: 32595416 PMCID: PMC7313216 DOI: 10.1186/s12935-020-01347-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 06/15/2020] [Indexed: 01/28/2023] Open
Abstract
Background Alpha protein kinase 2 (ALPK2) was known to play a vital role in cancer by regulating cell cycle and DNA repair. Ovarian cancer (OC) is one of the most lethal malignancies in the female reproductive system. The emphasis of this study is to explore the role of ALPK2 in OC. Methods Firstly, tumor and normal tissues were collected for detecting expression of ALPK2 in OC. Lentivirus-mediated shRNA knockdown of ALPK2 was used to construct OC cell model, which was verified by qRT-PCR and Western blot. The cell proliferation was detected by MTT, cell cycle and apoptosis were measured through flow cytometry. Wound-healing assay was conducted to detect the migration of OC cells. Results It was proved that the expression of ALPK2 in OC tissues was significantly higher than that in normal ovarian tissues. Moreover, knockdown of ALPK2 could inhibit proliferation, migration and promote apoptosis, arrested cell cycle of OC cells. It was also found that ALPK2 knockdown inhibited tumor growth in xenograft mice in vivo. Furthermore, ALPK2 was involved in OC cells via regulating EMT-related proteins (N-cadherin, Vimentin and Snail), inhibiting apoptosis-related proteins (Bcl-2, Bcl-w, HSP27, HSP60, IGF-I, IGF-1sR, Survivin and XIAP), as well as the regulation of downstream pathways (Akt, p-Akt, Cyclin D1, CDK6 and PIK3CA). Conclusions In conclusion, ALPK2 might serve as an optional target for prognosis and therapeutic of OC patients.
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Affiliation(s)
- Xiaogang Zhu
- Department of Obstetrics and Gynecology, the Third Xiangya Hospital of Central South University, Changsha, 410013 Hunan China
| | - Siqi Yan
- Department of radiation oncology, Hunan Academy of traditional Chinese medicine affiliated hospital, Changsha, Hunan 410007 China
| | - Songshu Xiao
- Department of Obstetrics and Gynecology, the Third Xiangya Hospital of Central South University, Changsha, 410013 Hunan China
| | - Min Xue
- Department of Obstetrics and Gynecology, the Third Xiangya Hospital of Central South University, Changsha, 410013 Hunan China
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12
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Zhang F, Wang F, Chen C, Wang T, Hu J, Su R, Li X, Gu B, Tang S, Chen H, Li Y. Prediction of progression of chronic atrophic gastritis with Helicobacter pylori and poor prognosis of gastric cancer by CYP3A4. J Gastroenterol Hepatol 2020; 35:425-432. [PMID: 31441961 DOI: 10.1111/jgh.14844] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM It has been well documented that Helicobacter pylori (H. pylori) infection is a risk factor for aggravating gastric mucosal atrophy. However, the exact molecular mechanism mediating this process is not fully elucidated. The purpose of this study was to identify biomarkers, which may predict the risk for progression of chronic atrophic gastritis (CAG) with H. pylori. METHODS GSE27411 was downloaded from the Gene Expression Omnibus. The differentially expressed genes (DEGs) between H. pylori-infected samples without CAG and H. pylori-infected CAG samples were analyzed. Gene Ontology and pathway enrichment analyses were performed, followed by protein-protein interaction network construction. We used immunohistochemistry analysis to identify DEGs in 20 chronic gastritis, 20 CAG, and 22 gastric cancer (GC) specimens. RESULTS A total of 303 upregulated and 26 downregulated DEGs were identified. The pathways enriched by upregulated DEGs were mainly related to fat digestion and absorption, peroxisome proliferator-activated receptor signaling pathway, and chemical carcinogenesis. Cytochrome P450, family 3, subfamily A, polypeptide 4 (CYP3A4) had the highest degrees in protein-protein interaction network. Moreover, the positive rates of CYP3A4 protein expression in chronic gastritis, CAG, and GC were 10% (2/20), 55% (11/20), and 77.3% (17/22), respectively (P < 0.001). The Kaplan-Meier analysis revealed that elevated expression of CYP3A4 was significantly associated with worse overall survival and first progression, respectively (P < 0.0001). CONCLUSION According to the findings of this study, the expression of CYP3A4 might be related to the potential carcinogenic transformation of CAG to GC. Therefore, CYP3A4 may be biomarkers to predict progression of CAG and poor prognosis of gastric cancer.
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Affiliation(s)
- Fan Zhang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Furong Wang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Cong Chen
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Tianyu Wang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Jike Hu
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Ruiliang Su
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Xuemei Li
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Baohong Gu
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Shaojun Tang
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, District of Columbia, USA.,Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Hao Chen
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Yumin Li
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
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13
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Evaluation of Epithelial-Mesenchymal Transition Genes Involved in Iranian Gastric Cancer Patients via Transcriptome Analysis. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2019. [DOI: 10.5812/ijcm.94924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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14
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Feng Y, Shi C, Wang D, Wang X, Chen Z. Integrated Analysis of DNA Copy Number Changes and Gene Expression Identifies Key Genes in Gastric Cancer. J Comput Biol 2019; 27:877-887. [PMID: 31545074 DOI: 10.1089/cmb.2019.0149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This study was aimed at identifying differentially expressed genes (DEGs) with copy number changes in gastric cancer (GC) pathogenesis. Microarray data GSE33429, including array-based comparative genomic hybridization and gene expression profiles, were obtained. DEGs were screened between GC and adjacent noncancerous tissues. Genes located at Minimum Common Regions (MCRs) were identified, and overlapped genes between DEGs and genes with amplification or deletion were identified. Gene Ontology function and pathway enrichment analysis of DEGs were performed. A protein-protein interaction network for DEGs was built, and significant modules were mined from the network. Functional annotation of genes in modules was also performed. A total of 677 up- and 583 downregulated DEGs were identified, including 37 overexpressed genes located at gained MCRs and 28 downregulated genes located at deleted MCRs. In significant modules, upregulated genes with amplification, including DSN1 (MIS12 kinetochore complex component), MAPRE1 (microtubule-associated protein, RP/EB family, member 1), TPX2 (microtubule-associated), UBE2C (ubiquitin-conjugating enzyme E2C), and MYBL2 (v-myb avian myeloblastosis viral oncogene homolog-like 2), were associated with cell cycle, but downregulated genes with deletion, including UGT2B15 (UDP glucuronosyltransferase 2 family, polypeptide B15), UGT2B17 (UDP glucuronosyltransferase 2 family, polypeptide B17), ADH1B (alcohol dehydrogenase 1B), and ADH1A (alcohol dehydrogenase 1A), were related to metabolism. The identified genes DSN1, MAPRE1, TPX2, UBE2C, and MYBL2 located at gained MCRs and UGT2B15, UGT2B17, ADH1B, and ADH1A located at deleted MCRs may play an important role in GC progression through regulating cell cycle and metabolism.
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Affiliation(s)
- Ye Feng
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Chunyu Shi
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Dayu Wang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xuefeng Wang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhi Chen
- Department of Nephrology, First Hospital of Jilin University, Changchun, China
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15
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Yu Z, Li Z, Wang C, Pan T, Chang X, Wang X, Zhou Q, Wu X, Li J, Zhang J, Liu B, Zhu Z, Su L. Oncostatin M receptor, positively regulated by SP1, promotes gastric cancer growth and metastasis upon treatment with Oncostatin M. Gastric Cancer 2019; 22:955-966. [PMID: 30778797 DOI: 10.1007/s10120-019-00934-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 01/31/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Oncostatin M receptor (OSMR) is a member of the interleukin 6 (IL-6) receptor family that transduces signaling events of Oncostatin M (OSM). OSM-OSMR signaling plays a key role in inflammation and cancer progression. However, the role of OSM-OSMR in gastric cancer (GC) is still unknown. METHODS OSMR expression in GC was determined by real-time PCR (RT-PCR), immunohistochemistry (IHC) and Western blot. The effects of OSM-OSMR on GC cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in vitro and metastasis in vivo were examined. The pathways underlying OSM-OSMR signaling were explored by Western blot. Regulatory mechanism between SP1 and OSMR was explored in vitro. RESULTS OSMR was highly expressed in GC tissues and its expression level was closely associated with age, T stage, Lauren classification, lymph node metastasis, TNM stage and worse prognosis of patients with GC. Knockdown of OSMR expression in GC cells significantly inhibited cell proliferation, migration, invasion, and EMT in vitro, as well as tumorigenesis and peritoneal metastasis in vivo induced by OSM. These effects mediated by OSM-OSMR were dependent on the activation of STAT3/FAK/Src signaling. SP1 could bind to the promoter region of human OSMR gene from - 255 to - 246 bp, and transcriptionally regulated OSMR overexpression in GC cells. CONCLUSIONS OSM-OSMR contributes to GC progression through activating STAT3/FAK/Src signaling, and OSMR is transcriptionally activated by SP1.
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Affiliation(s)
- Zhenjia Yu
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhen Li
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chenchen Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Tao Pan
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xinyu Chang
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaofeng Wang
- Department of General Surgery, First People's Hospital, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Quan Zhou
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiongyan Wu
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianfang Li
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jinping Zhang
- Institute of Biology and Medical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
| | - Bingya Liu
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhenggang Zhu
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Liping Su
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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16
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Newton R, Wernisch L. A meta-analysis of multiple matched aCGH/expression cancer datasets reveals regulatory relationships and pathway enrichment of potential oncogenes. PLoS One 2019; 14:e0213221. [PMID: 31335867 PMCID: PMC6650054 DOI: 10.1371/journal.pone.0213221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022] Open
Abstract
The copy numbers of genes in cancer samples are often highly disrupted and form a natural amplification/deletion experiment encompassing multiple genes. Matched array comparative genomics and transcriptomics datasets from such samples can be used to predict inter-chromosomal gene regulatory relationships. Previously we published the database METAMATCHED, comprising the results from such an analysis of a large number of publically available cancer datasets. Here we investigate genes in the database which are unusual in that their copy number exhibits consistent heterogeneous disruption in a high proportion of the cancer datasets. We assess the potential relevance of these genes to the pathology of the cancer samples, in light of their predicted regulatory relationships and enriched biological pathways. A network-based method was used to identify enriched pathways from the genes’ inferred targets. The analysis predicts both known and new regulator-target interactions and pathway memberships. We examine examples in detail, in particular the gene POGZ, which is disrupted in many of the cancer datasets and has an unusually large number of predicted targets, from which the network analysis predicts membership of cancer related pathways. The results suggest close involvement in known cancer pathways of genes exhibiting consistent heterogeneous copy number disruption. Further experimental work would clarify their relevance to tumor biology. The results of the analysis presented in the database METAMATCHED, and included here as an R archive file, constitute a large number of predicted regulatory relationships and pathway memberships which we anticipate will be useful in informing such experiments.
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Affiliation(s)
- Richard Newton
- MRC Biostatistics Unit, Cambridge University, Cambridge, United Kingdom
- * E-mail:
| | - Lorenz Wernisch
- MRC Biostatistics Unit, Cambridge University, Cambridge, United Kingdom
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17
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Zhang J, Wang L. The Emerging World of TCR-T Cell Trials Against Cancer: A Systematic Review. Technol Cancer Res Treat 2019; 18:1533033819831068. [PMID: 30798772 PMCID: PMC6391541 DOI: 10.1177/1533033819831068] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 12/20/2018] [Accepted: 01/22/2019] [Indexed: 12/28/2022] Open
Abstract
T-cell receptor-engineered T-cell therapy and chimeric antigen receptor T-cell therapy are 2 types of adoptive T-cell therapy that genetically modify natural T cells to treat cancers. Although chimeric antigen receptor T-cell therapy has yielded remarkable efficacy for hematological malignancies of the B-cell lineages, most solid tumors fail to respond significantly to chimeric antigen receptor T cells. T-cell receptor-engineered T-cell therapy, on the other hand, has shown unprecedented promise in treating solid tumors and has attracted growing interest. In order to create an unbiased, comprehensive, and scientific report for this fast-moving field, we carefully analyzed all 84 clinical trials using T-cell receptor-engineered T-cell therapy and downloaded from ClinicalTrials.gov updated by June 11, 2018. Informative features and trends were observed in these clinical trials. The number of trials initiated each year is increasing as expected, but an interesting pattern is observed. NY-ESO-1, as the most targeted antigen type, is the target of 31 clinical trials; melanoma is the most targeted cancer type and is the target of 33 clinical trials. Novel antigens and underrepresented cancers remain to be targeted in future studies and clinical trials. Unlike chimeric antigen receptor T-cell therapy, only about 16% of the 84 clinical trials target against hematological malignancies, consistent with T-cell receptor-engineered T-cell therapy's high potential for solid tumors. Six pharma/biotech companies with novel T-cell receptor-engineered T-cell ideas and products were examined in this review. Multiple approaches have been utilized in these companies to increase the T-cell receptor's affinity and efficiency and to minimize cross-reactivity. The major challenges in the development of the T-cell receptor-engineered T-cell therapy due to tumor microenvironment were also discussed here.
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Affiliation(s)
- Jianxiang Zhang
- The High School Affiliated to Renmin University, Beijing, People’s Republic of China
| | - Lingyu Wang
- Department of Biology, Duke University, Durham, NC, USA
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18
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Enah overexpression is correlated with poor survival and aggressive phenotype in gastric cancer. Cell Death Dis 2018; 9:998. [PMID: 30250066 PMCID: PMC6155292 DOI: 10.1038/s41419-018-1031-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/25/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022]
Abstract
Enabled homolog (Enah), which is a member of the Ena/VASP family that also includes VASP (vasodilator-stimulated phosphoprotein) and Ena/VASP like, is a mammalian ortholog of Drosophila Enabled (Ena). An increasing number of studies demonstrated Enah overexpression is involved in human colorectal carcinomas, breast cancers and hepatocellular carcinoma. However, the significance of Enah expression in gastric cancer (GC) is poorly elucidated. Here, we demonstrate that Enah is upregulated in GC and associated with AJCC stage, depth of invasion and poor overall survival (OS). Knockdown of Enah inhibited GC cell proliferation and metastasis and vice versa. Further experiments suggested that p-Erk1/2, p-AKT, p-p65, Vimentin and Fibronectin were downregulated and E-cadherin was upregulated after Enah silencing, implicating altered functions in GC proliferation and metastasis. Thus, our study suggests that Enah is a harmful factor for GC and a novel target for GC treatment.
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19
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Integrated Genome-Wide Analysis of Gene Expression and DNA Copy Number Variations Highlights Stem Cell-Related Pathways in Small Cell Esophageal Carcinoma. Stem Cells Int 2018; 2018:3481783. [PMID: 30228821 PMCID: PMC6136462 DOI: 10.1155/2018/3481783] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 07/02/2018] [Indexed: 12/21/2022] Open
Abstract
Purpose/Objectives. Primary small cell esophageal carcinoma (SCEC) represents a rare and aggressive malignancy without any prospective clinical trial or established treatment strategy at present. Although previous studies have indicated similarities between SCEC and small cell lung cancer (SCLC) in terms of their clinical manifestations, pathology, and morphology, very little genetic information is available on this highly malignant tumor. At present, patients with SCEC are staged and treated according to the guidelines established for SCLC. However, early recurrence and distant metastasis are common, and long-time survivors are rare. Current options available for patients with relapsed SCEC are fairly unsatisfactory, and their prognosis is generally poor. Novel therapeutic approaches against SCEC are therefore urgently needed and require a deeper understanding of the underlying genetic mechanisms. The current investigation aims to characterize the gene expression profile and copy number variations (CNVs) in SCEC to clarify molecular markers and pathways that may possess clinical significance. Materials/Methods. De novo expression array was carried out on three matched sets of primary SCEC and adjacent normal tissue samples procured from the institutional tissue bank, utilizing the Affymetrix HG U133 Plus 2.0 Array. After individual tissue normalization, the statistical software GeneSpring GX 12.5 was used to determine differentially expressed genes (DEGs) in the tumors relative to their paired normal tissues. Gene enrichments in addition to functional annotation and gene interaction networks were performed using DAVID 6.8 and STRING 10.0, respectively. A gene alteration was determined to be recurrent if it was observed in at least 2 samples. Chromosomes X and Y were not included in calculations as gender differences are a known source of analysis bias. The DEGs of at least one SCEC sample could be mapped to the CNV regions (fold change (FC) ≥ 2 and false discovery rate (FDR) < 0.01) after gene expression profiling by RefSeq Transcript ID. These overlapped genes were subjected to the functional annotation using DAVID 6.8. In order to elucidate the effect of CNV on mRNA expression, we integrated the genome-wide copy number data and gene expression in 3 paired samples. CNV-associated gene expression aberration (CNV-FC) was calculated for the recurrent DEGs using previously published integrated microarray data as reference. Pearson's correlation coefficient was employed to determine if there was a statistical correlation between the gene expression log2 ratios and their copy numbers using the SPSS 19.0 software. Genes that possessed CNV-FC ≥ 2 and r ≥ 0.6 (p < 0.05) were determined to be genes potentially associated with cancer. Results. High-quality DNA and total RNA were first extracted from both SCEC and normal tissues. Microarray data showed significant upregulation in WNT gene sets and downregulation in the PTEN and notch gene sets in SCEC. Functional annotation showed that genes associated with DNA replication, mitosis, cell cycle, DNA repair, telomere maintenance, RB, and p53 pathways were significantly altered in SCEC compared to corresponding noncancerous tissues (Benjamini p < 0.05). Thirteen recurrent CNVs were found in all SCEC samples by array CGH. Chromosomal regions with gain were located in 14q11.2, and regions with loss were located in 4q22.3-23.3, 3q25.31-q29, 5p15.31-15.2, 8q21.11-24.3, and 9p23-13.1 in all samples. In two samples, the 14q11.2-32.33 region was amplified, whereas 3p26.3-25.3, 4p16.3-11, 4q11-22.3, 4q23-25, 8p23.3, and 16p13.3 were deleted. We further identified 306 genes that consistently differed in copy number and expression (194 upregulated and 112 downregulated) between the SCEC and noncancerous tissues in all three samples. These genes were significantly enriched with those involved in cell cycle, mitosis, DNA repair, P53 pathway, and RB pathway, according to their functional annotation. These 306 DEGs also included network genes of the above pathways such as NUF2, CCNE2, NFIB, ETV5, KLF5, ATAD2, NDC80, and ZWINT. In addition, 39 individual DEGs demonstrated a minimum 2-fold copy number-associated expression change (median: 5.35, 95% CI: 4.53–16.98) and Pearson's correlation coefficient ≥ 0.6 (p < 0.05), of which PTP4A3 showed the highest correlation (CNV-FC = 21362.13; Pearson's correlation coefficient = 0.9983; p = 0.037). Two distinct groups of genes belonging to each SCEC and nonmalignant tissues were observed upon unsupervised two-way (genes and samples) hierarchical clustering. Conclusions. The current investigation is the first to produce data regarding the genomic signature of SCEC at the transcription level and in relation to CNVs. Our preliminary data indicate possible key roles of WNT and notch signaling in SCEC and overexpressed PTP4A3 as a potential therapeutic target. Further validation of our findings is warranted.
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20
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Wang P, Wang Y, Hang B, Zou X, Mao JH. A novel gene expression-based prognostic scoring system to predict survival in gastric cancer. Oncotarget 2018; 7:55343-55351. [PMID: 27419373 PMCID: PMC5342421 DOI: 10.18632/oncotarget.10533] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Accepted: 05/26/2016] [Indexed: 01/29/2023] Open
Abstract
Analysis of gene expression patterns in gastric cancer (GC) can help to identify a comprehensive panel of gene biomarkers for predicting clinical outcomes and to discover potential new therapeutic targets. Here, a multi-step bioinformatics analytic approach was developed to establish a novel prognostic scoring system for GC. We first identified 276 genes that were robustly differentially expressed between normal and GC tissues, of which, 249 were found to be significantly associated with overall survival (OS) by univariate Cox regression analysis. The biological functions of 249 genes are related to cell cycle, RNA/ncRNA process, acetylation and extracellular matrix organization. A network was generated for view of the gene expression architecture of 249 genes in 265 GCs. Finally, we applied a canonical discriminant analysis approach to identify a 53-gene signature and a prognostic scoring system was established based on a canonical discriminant function of 53 genes. The prognostic scores strongly predicted patients with GC to have either a poor or good OS. Our study raises the prospect that the practicality of GC patient prognosis can be assessed by this prognostic scoring system.
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Affiliation(s)
- Pin Wang
- Department of Gastroenterology, Drum Tower Clinical Medical School Of Nanjing Medical University, Nanjing, Jiangsu 210008, China
| | - Yunshan Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,International Biotechnology R&D Center, Shandong University School of Ocean, Weihai, Shandong 264209, China
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Xiaoping Zou
- Department of Gastroenterology, Drum Tower Clinical Medical School Of Nanjing Medical University, Nanjing, Jiangsu 210008, China
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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21
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Kwon MJ, Kim RN, Song K, Jeon S, Jeong HM, Kim JS, Han J, Hong S, Oh E, Choi JS, An J, Pollack JR, Choi YL, Park CK, Shin YK. Genes co-amplified with ERBB2 or MET as novel potential cancer-promoting genes in gastric cancer. Oncotarget 2017; 8:92209-92226. [PMID: 29190909 PMCID: PMC5696175 DOI: 10.18632/oncotarget.21150] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/27/2017] [Indexed: 12/18/2022] Open
Abstract
Gastric cancer (GC), one of the most common cancers worldwide, has a high mortality rate due to limited treatment options. Identifying novel and promising molecular targets is a major challenge that must be overcome if treatment of advanced GC is to be successful. Here, we used comparative genomic hybridization and gene expression microarrays to examine genome-wide DNA copy number alterations (CNAs) and global gene expression in 38 GC samples from old and young patients. We identified frequent CNAs, which included copy number gains on chromosomes 3q, 7p, 8q, 20p, and 20q and copy number losses on chromosomes 19p and 21p. The most frequently gained region was 7p21.1 (55%), whereas the most frequently deleted region was 21p11.1 (50%). Recurrent highly amplified regions 17q12 and 7q31.1-7q31.31 harbored two well-known oncogenes: ERBB2 and MET. Correlation analysis of CNAs and gene expression levels identified CAPZA2 (co-amplified with MET) and genes GRB7, MIEN1, PGAP3, and STARD3 (co-amplified with ERBB2) as potential candidate cancer-promoting genes (CPGs). Public dataset analysis confirmed co-amplification of these genes with MET or ERBB2 in GC tissue samples, and revealed that high expression (except for PGAP3) was significantly associated with shorter overall survival. Knockdown of these genes using small interfering RNA led to significant suppression of GC cell proliferation and migration. Reduced GC cell proliferation mediated by CAPZA2 knockdown was attributable to attenuated cell cycle progression and increased apoptosis. This study identified novel candidate CPGs co-amplified with MET or ERBB2, and suggests that they play a functional role in GC.
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Affiliation(s)
- Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University, Daegu, Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Korea
| | - Ryong Nam Kim
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Korea
| | - Kyoung Song
- R&D center, ABION Inc., Guro-gu, Seoul, Korea
| | - Sinyoung Jeon
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hae Min Jeong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Joo Seok Kim
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Jinil Han
- Gencurix, Inc., Guro-gu, Seoul, Korea
| | - Sungyoul Hong
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Ensel Oh
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Sun Choi
- The Center for Anti-cancer Companion Diagnostics, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea
| | - Jungsuk An
- Department of Pathology, Gachon University Gil Medical Center, Incheon, Korea
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Yoon-La Choi
- Laboratory of Cancer Genomics and Molecular Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.,Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Korea
| | - Cheol-Keun Park
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young Kee Shin
- Laboratory of Molecular Pathology and Cancer Genomics, College of Pharmacy, Seoul National University, Seoul, Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Korea.,The Center for Anti-cancer Companion Diagnostics, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Korea
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22
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Davis LE, Jeng S, Svalina MN, Huang E, Pittsenbarger J, Cantor EL, Berlow N, Seguin B, Mansoor A, McWeeney SK, Keller C. Integration of genomic, transcriptomic and functional profiles of aggressive osteosarcomas across multiple species. Oncotarget 2017; 8:76241-76256. [PMID: 29100308 PMCID: PMC5652702 DOI: 10.18632/oncotarget.19532] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/11/2017] [Indexed: 01/14/2023] Open
Abstract
In complex, highly unstable genomes such as in osteosarcoma, targeting aberrant checkpoint processes (metabolic, cell cycle or immune) may prove more successful than targeting specific kinase or growth factor signaling pathways. Here, we establish a comparative oncology approach characterizing the most lethal osteosarcomas identified in a biorepository of tumors from three different species: human, mouse and canine. We describe the development of a genetically-engineered mouse model of osteosarcoma, establishment of primary cell cultures from fatal human tumors, and a biorepository of osteosarcoma surgical specimens from pet dogs. We analyzed the DNA mutations, differential RNA expression and in vitro drug sensitivity from two phenotypically-distinct cohorts: tumors with a highly aggressive biology resulting in death from rapidly progressive, refractory metastatic disease, and tumors with a non-aggressive, curable phenotype. We identified ARK5 (AMPK-Related Protein Kinase 5, also referred to as NUAK Family Kinase 1) as a novel metabolic target present in all species, and independent analyses confirmed glucose metabolism as the most significantly aberrant cellular signaling pathway in a model system for highly metastatic tumors. Pathway integration analysis identified Polo Like Kinase 1 (PLK1)-mediated checkpoint adaptation as critical to the survival of a distinctly aggressive osteosarcoma. The tumor-associated macrophage cytokine CCL18 (C-C Motif Chemokine Ligand 18) was significantly over-expressed in aggressive human osteosarcomas, and a clustering of mutations in the BAGE (B Melanoma Antigen) tumor antigen gene family was found. The theme of these features of high risk osteosarcoma is checkpoint adaptations, which may prove both prognostic and targetable.
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Affiliation(s)
- Lara E Davis
- Knight Cancer Institute, Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health and Sciences University, Portland, Oregon, USA.,Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Sophia Jeng
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Matthew N Svalina
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Elaine Huang
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Janét Pittsenbarger
- Knight Cancer Institute, Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Emma L Cantor
- Department of Pediatrics, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Noah Berlow
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
| | - Bernard Seguin
- Flint Animal Cancer Center, Colorado State University, Fort Collins, Colorado, USA
| | - Atiya Mansoor
- Department of Pathology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Shannon K McWeeney
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Sciences University, Portland, Oregon, USA
| | - Charles Keller
- Children's Cancer Therapy Development Institute, Beaverton, Oregon, USA
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23
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Gigek CO, Calcagno DQ, Rasmussen LT, Santos LC, Leal MF, Wisnieski F, Burbano RR, Lourenço LG, Lopes-Filho GJ, Smith MAC. Genetic variants in gastric cancer: Risks and clinical implications. Exp Mol Pathol 2017; 103:101-111. [PMID: 28736214 DOI: 10.1016/j.yexmp.2017.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/03/2017] [Accepted: 07/19/2017] [Indexed: 12/14/2022]
Abstract
Cancer is a multifactorial disease that involves many molecular alterations. Gastric cancer (GC) is the third leading cause of cancer death worldwide. GC is a highly heterogeneous disease with different molecular and genetics features. Therefore, this review focuses on an overview of the genetic aspects of gastric cancer by highlighting the important impact and role of deletions and/or duplications of chromosomal segments, genomic variants, H. pylori infection and interleukin variants, as found in gene expression and newly proposed molecular classification studies. The challenge is to better understand the mechanisms and different pathways that lead to the development and progression of GC.
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Affiliation(s)
- Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), CEP 04023-900 São Paulo, Brazil; Disciplina de Gastroenterologia Cirúrgica, Universidade Federal de São Paulo (UNIFESP), CEP: 04024-002 São Paulo, Brazil.
| | - Danielle Queiroz Calcagno
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará (UFPA), CEP: 66073-000 Belém, Pará, Brazil
| | | | - Leonardo Caires Santos
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), CEP 04023-900 São Paulo, Brazil
| | - Mariana Ferreira Leal
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), CEP 04023-900 São Paulo, Brazil; Departamento de Ortopedia e Traumatologia, Universidade Federal de São Paulo (UNIFESP), CEP 04038-032 São Paulo, Brazil
| | - Fernanda Wisnieski
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), CEP 04023-900 São Paulo, Brazil
| | | | - Laercio Gomes Lourenço
- Disciplina de Gastroenterologia Cirúrgica, Universidade Federal de São Paulo (UNIFESP), CEP: 04024-002 São Paulo, Brazil
| | - Gaspar Jesus Lopes-Filho
- Disciplina de Gastroenterologia Cirúrgica, Universidade Federal de São Paulo (UNIFESP), CEP: 04024-002 São Paulo, Brazil
| | - Marilia Arruda Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), CEP 04023-900 São Paulo, Brazil
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24
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Gu Z, Fang X, Li C, Chen C, Liang G, Zheng X, Fan Q. Increased PTPRA expression leads to poor prognosis through c-Src activation and G1 phase progression in squamous cell lung cancer. Int J Oncol 2017; 51:489-497. [PMID: 28656243 PMCID: PMC5505127 DOI: 10.3892/ijo.2017.4055] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/19/2017] [Indexed: 01/02/2023] Open
Abstract
PTPRA is reported to be involved in cancer development and progression through activating the Src family kinase (SFK) signaling pathways, however, the roles of PTPRA in the squamous cell lung cancer (SCC) development are unclear. The purpose of this study was to clarify the clinical relevance and biological roles of PTPRA in SCC. We found that PTPRA was upregulated in squamous cell lung cancer compared to matched normal tissues at the mRNA (N=20, P=0.004) and protein expression levels (N=75, P<0.001). Notably, high mRNA level of PTPRA was significantly correlated with poorer prognosis in 675 SCC patients from the Kaplan-Meier plotter database. With 75 cases, we found that PTPRA protein expression was significantly correlated with tumor size (P=0.002), lymph node metastasis (P=0.008), depth of tumor invasion (P<0.001) and clinical stage (P<0.001). The Kaplan-Meier plot suggested that high expression of PTPRA had poorer overall survival in SCC patients (P=0.009). Multivariate Cox regression analysis suggested that PTPRA expression was an independent prognostic factor in SCC patients. In the cellular models, PTPRA promotes SCC cell proliferation through modulating Src activation as well as cell cycle progression. In conclusion, higher PTPRA level was associated with worse prognosis of SCC patients and PTPRA could promote the cell cycle progression through stimulating the c-Src signaling pathways.
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Affiliation(s)
- Zhidong Gu
- Department of Clinical Medicine, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai 200025, P.R. China
| | - Xuqian Fang
- Department of Clinical Medicine, Ruijin Hospital North, Jiaotong University School of Medicine, Shanghai 201801, P.R. China
| | - Chang Li
- Department of Clinical Medicine, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai 200025, P.R. China
| | - Changqiang Chen
- Department of Clinical Medicine, Ruijin Hospital North, Jiaotong University School of Medicine, Shanghai 201801, P.R. China
| | - Guangshu Liang
- Department of Clinical Medicine, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai 200025, P.R. China
| | - Xinming Zheng
- Department of Clinical Medicine, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai 200025, P.R. China
| | - Qishi Fan
- Department of Clinical Medicine, Ruijin Hospital North, Jiaotong University School of Medicine, Shanghai 201801, P.R. China
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25
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Mamlouk S, Childs LH, Aust D, Heim D, Melching F, Oliveira C, Wolf T, Durek P, Schumacher D, Bläker H, von Winterfeld M, Gastl B, Möhr K, Menne A, Zeugner S, Redmer T, Lenze D, Tierling S, Möbs M, Weichert W, Folprecht G, Blanc E, Beule D, Schäfer R, Morkel M, Klauschen F, Leser U, Sers C. DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer. Nat Commun 2017; 8:14093. [PMID: 28120820 PMCID: PMC5288500 DOI: 10.1038/ncomms14093] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 11/28/2016] [Indexed: 02/06/2023] Open
Abstract
Genetic heterogeneity between and within tumours is a major factor determining cancer progression and therapy response. Here we examined DNA sequence and DNA copy-number heterogeneity in colorectal cancer (CRC) by targeted high-depth sequencing of 100 most frequently altered genes. In 97 samples, with primary tumours and matched metastases from 27 patients, we observe inter-tumour concordance for coding mutations; in contrast, gene copy numbers are highly discordant between primary tumours and metastases as validated by fluorescent in situ hybridization. To further investigate intra-tumour heterogeneity, we dissected a single tumour into 68 spatially defined samples and sequenced them separately. We identify evenly distributed coding mutations in APC and TP53 in all tumour areas, yet highly variable gene copy numbers in numerous genes. 3D morpho-molecular reconstruction reveals two clusters with divergent copy number aberrations along the proximal-distal axis indicating that DNA copy number variations are a major source of tumour heterogeneity in CRC.
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Affiliation(s)
- Soulafa Mamlouk
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Liam Harold Childs
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Daniela Aust
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
- NCT Biobank Dresden, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Daniel Heim
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Friederike Melching
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Cristiano Oliveira
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Thomas Wolf
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, University of Heidelberg, Heidelberg 69120, Germany
| | - Pawel Durek
- Experimental Rheumatology, German Rheumatism Research Centre, Berlin 10117, Germany
| | - Dirk Schumacher
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Hendrik Bläker
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
| | | | - Bastian Gastl
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- BSIO Berlin School of Integrative Oncology, University Medicine Charité, Berlin 13353, Germany
| | - Kerstin Möhr
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Andrea Menne
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Silke Zeugner
- Institute for Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden 01307, Germany
| | - Torben Redmer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Dido Lenze
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Sascha Tierling
- Department of Genetics/Epigenetics, FR8.3 Life Sciences, Saarland University, Saarbrücken 66123, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- Institute of Pathology, Technical University Munich, Munich 81675, Germany
| | - Gunnar Folprecht
- University Hospital Carl Gustav Carus, University Cancer Center/Medical Dpt. I, Dresden 01307, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reinhold Schäfer
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
- German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Markus Morkel
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Ulf Leser
- Knowledge Management in Bioinformatics, Humboldt University of Berlin, Berlin 10099, Germany
| | - Christine Sers
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin 10117, Germany
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany
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26
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Juxtaposed genes in 7q21-22 amplicon contribute for two major gastric cancer sub-Types by mutual exclusive expression. Mol Carcinog 2016; 56:1239-1250. [DOI: 10.1002/mc.22586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/23/2016] [Accepted: 10/28/2016] [Indexed: 12/29/2022]
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27
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Abstract
Members of the ADP-ribosylation factor (Arf) family of small GTP-binding (G) proteins regulate several aspects of membrane trafficking, such as vesicle budding, tethering and cytoskeleton organization. Arf family members, including Arf-like (Arl) proteins have been implicated in several essential cellular functions, like cell spreading and migration. These functions are used by cancer cells to disseminate and invade the tissues surrounding the primary tumor, leading to the formation of metastases. Indeed, Arf and Arl proteins, as well as their guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs) have been found to be abnormally expressed in different cancer cell types and human cancers. Here, we review the current evidence supporting the involvement of Arf family proteins and their GEFs and GAPs in cancer progression, focusing on 3 different mechanisms: cell-cell adhesion, integrin internalization and recycling, and actin cytoskeleton remodeling.
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Affiliation(s)
- Cristina Casalou
- a CEDOC, NOVA Medical School - Faculdade de Ciências Médicas, Universidade NOVA de Lisboa , Lisbon , Portugal
| | - Alexandra Faustino
- a CEDOC, NOVA Medical School - Faculdade de Ciências Médicas, Universidade NOVA de Lisboa , Lisbon , Portugal.,b ProRegeM PhD Program, NOVA Medical School - Faculdade de Ciências Médicas, Universidade NOVA de Lisboa , Lisbon , Portugal
| | - Duarte C Barral
- a CEDOC, NOVA Medical School - Faculdade de Ciências Médicas, Universidade NOVA de Lisboa , Lisbon , Portugal
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Guo F, Ren X, Dong Y, Hu X, Xu D, Zhou H, Meng F, Tian W, Zhao Y. Constitutive expression of PPARγ inhibits proliferation and migration of gastric cancer cells and down-regulates Wnt/β-Catenin signaling pathway downstream target genes TERT and ENAH. Gene 2016; 584:31-37. [DOI: 10.1016/j.gene.2016.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 02/25/2016] [Accepted: 03/03/2016] [Indexed: 02/06/2023]
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Smirnikhina SA, Lavrov AV, Chelysheva EY, Adilgereeva EP, Shukhov OA, Turkina A, Kutsev SI. Whole-exome sequencing reveals potential molecular predictors of relapse after discontinuation of the targeted therapy in chronic myeloid leukemia patients. Leuk Lymphoma 2016; 57:1669-76. [PMID: 26759060 DOI: 10.3109/10428194.2015.1132420] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chronic myeloid leukemia (CML) is a myeloproliferative disease well treated by tyrosine kinase inhibitors (TKIs). The aim was to identify genes with a predictive value for relapse-free survival after TKI cessation in CML patients. We performed whole-exome sequencing of DNA from six CML patients in long-lasting deep molecular remission. Patients were divided into two groups with relapse (n = 3) and without relapse (n = 3) after TKI discontinuation. We found variants in genes CYP1B1, ALPK2, and IRF1 in group of patients with relapse and one variant in gene PARP9 in group of patients without relapse. We verified prognostic value of the found markers in a small group of patients with TKI discontinuation and demonstrated their high sensitivity (77%), specificity (86%), positive (85%), and negative (79%) predictive values. Thus we revealed genetic variants, which are potential markers of outcome prediction in CML patients after TKI discontinuation.
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Affiliation(s)
- Svetlana A Smirnikhina
- a Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russian Federation
| | - Alexander V Lavrov
- a Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russian Federation ;,b The Russian National Research Medical University Named after N.I. Pirogov , Moscow , Russian Federation
| | - Ekaterina Yu Chelysheva
- c Scientific and Advisory Department of Chemotherapy of Myeloproliferative Disorders , Federal State-Funded Institution "National Research Center for Hematology" of the Ministry of Healthcare of the Russian Federation , Moscow , Russian Federation
| | - Elmira P Adilgereeva
- a Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russian Federation
| | - Oleg A Shukhov
- c Scientific and Advisory Department of Chemotherapy of Myeloproliferative Disorders , Federal State-Funded Institution "National Research Center for Hematology" of the Ministry of Healthcare of the Russian Federation , Moscow , Russian Federation
| | - Anna Turkina
- c Scientific and Advisory Department of Chemotherapy of Myeloproliferative Disorders , Federal State-Funded Institution "National Research Center for Hematology" of the Ministry of Healthcare of the Russian Federation , Moscow , Russian Federation
| | - Sergey I Kutsev
- a Federal State Budgetary Institution "Research Centre for Medical Genetics" , Moscow , Russian Federation ;,b The Russian National Research Medical University Named after N.I. Pirogov , Moscow , Russian Federation
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Investigating inter-chromosomal regulatory relationships through a comprehensive meta-analysis of matched copy number and transcriptomics data sets. BMC Genomics 2015; 16:967. [PMID: 26581858 PMCID: PMC4650296 DOI: 10.1186/s12864-015-2100-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/15/2015] [Indexed: 12/16/2022] Open
Abstract
Background Gene regulatory relationships can be inferred using matched array comparative genomics and transcriptomics data sets from cancer samples. The way in which copy numbers of genes in cancer samples are often greatly disrupted works like a natural gene amplification/deletion experiment. There are now a large number of such data sets publicly available making a meta-analysis of the data possible. Results We infer inter-chromosomal acting gene regulatory relationships from a meta-analysis of 31 publicly available matched array comparative genomics and transcriptomics data sets in humans. We obtained statistically significant predictions of target genes for 1430 potential regulatory genes. The regulatory relationships being inferred are either direct relationships, of a transcription factor on its target, or indirect ones, through pathways containing intermediate steps. We analyse the predictions in terms of cocitations, both publications which cite a regulator with any of its inferred targets and cocitations of any genes in a target list. Conclusions The most striking observation from the results is the greater number of inter-chromosomal regulatory relationships involving repression compared to those involving activation. The complete results of the meta-analysis are presented in the database METAMATCHED. We anticipate that the predictions contained in the database will be useful in informing experiments and in helping to construct networks of regulatory relationships. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2100-5) contains supplementary material, which is available to authorized users.
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Tagliamonte M, Petrizzo A, Tornesello ML, Buonaguro FM, Buonaguro L. Antigen-specific vaccines for cancer treatment. Hum Vaccin Immunother 2015; 10:3332-46. [PMID: 25483639 DOI: 10.4161/21645515.2014.973317] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Vaccines targeting pathogens are generally effective and protective because based on foreign non-self antigens which are extremely potent in eliciting an immune response. On the contrary, efficacy of therapeutic cancer vaccines is still disappointing. One of the major reasons for such poor outcome, among others, is the difficulty of identifying tumor-specific target antigens which should be unique to the tumors or, at least, overexpressed on the tumors as compared to normal cells. Indeed, this is the only option to overcome the peripheral immune tolerance and elicit a non toxic immune response. New and more potent strategies are now available to identify specific tumor-associated antigens for development of cancer vaccine approaches aiming at eliciting targeted anti-tumor cellular responses. In the last years this aspect has been addressed and many therapeutic vaccination strategies based on either whole tumor cells or specific antigens have been and are being currently evaluated in clinical trials. This review summarizes the current state of cancer vaccines, mainly focusing on antigen-specific approaches.
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Key Words
- APCs, antigen-presenting cell
- BCG, Bacille Calmette-Guerin
- BCR, B-cell receptor
- CDCA1, cell division cycle associated 1
- CRC, colorectal cancer
- CT, Cancer-testis
- CTL, cytotoxic T-lympocites
- DCs, dendritic cells
- EGT, electro-gene-transfer
- FDA, Food & drug administration
- GB, glioblastoma
- GM-CSF, granulocyte macrophage-colony stimulating factor
- HER2, human epidermal growth factor receptor 2
- HLA, human leukocyte antigen
- HPV, human papillomavirus
- HSPs, stress/heat shock proteins
- IFNg, interferon gamma
- Ig Id, immunoglobulin idiotype
- LPs, long peptides
- MAGE-A1, Melanoma-associated antigen 1
- MHC, major histocompatibility complex
- MS, mass spectrometry
- MVA, modified vaccinia strain Ankara
- NSCLC, non-small-cell lung carcinoma
- PAP, prostatic acid phosphatase
- PRRs, Pattern Recognition Receptors
- PSA, Prostate-specific antigen
- RCR, renal cell cancer
- SSX-2, Synovial sarcoma X breakpoint 2
- TAAs, tumor-associated antigens
- TACAs, Tumor-associated carbohydrate antigens
- TARP, T-cell receptor gamma alternate reading frame protein
- TLRs, Toll-Like Receptors
- TPA, transporter associated with antigen processing
- WES, whole exome sequencing
- WGS, whole genome sequencing
- cancer vaccine
- clinical trials
- epitopes
- hTERT, human Telomerase reverse transcriptase
- immunotherapeutics
- mCRPC, metastatic castrate-resistant prostate cancer
- tumor-associated antigens
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Affiliation(s)
- Maria Tagliamonte
- a Laboratory of Molecular Biology and Viral Oncology; Department of Experimental Oncology; Istituto Nazionale per lo Studio e la Cura dei Tumori; "Fondazione Pascale" - IRCCS ; Naples , Italy
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Kit OI, Vodolazhsky DI, Kutilin DS, Gudueva EN. Changes in the number of copies of genetic loci in gastric cancer. Mol Biol 2015. [DOI: 10.1134/s0026893315040093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tamilzhalagan S, Muthuswami M, Periasamy J, Lee MH, Rha SY, Tan P, Ganesan K. Upregulated, 7q21–22 amplicon candidate gene SHFM1 confers oncogenic advantage by suppressing p53 function in gastric cancer. Cell Signal 2015; 27:1075-86. [DOI: 10.1016/j.cellsig.2015.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/28/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022]
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Anderson KS, Cramer DW, Sibani S, Wallstrom G, Wong J, Park J, Qiu J, Vitonis A, LaBaer J. Autoantibody signature for the serologic detection of ovarian cancer. J Proteome Res 2014; 14:578-86. [PMID: 25365139 PMCID: PMC4334299 DOI: 10.1021/pr500908n] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sera from patients with ovarian cancer contain autoantibodies (AAb) to tumor-derived proteins that are potential biomarkers for early detection. To detect AAb, we probed high-density programmable protein microarrays (NAPPA) expressing 5177 candidate tumor antigens with sera from patients with serous ovarian cancer (n = 34 cases/30 controls) and measured bound IgG. Of these, 741 antigens were selected and probed with an independent set of ovarian cancer sera (n = 60 cases/60 controls). Twelve potential autoantigens were identified with sensitivities ranging from 13 to 22% at >93% specificity. These were retested using a Luminex bead array using 60 cases and 60 controls, with sensitivities ranging from 0 to 31.7% at 95% specificity. Three AAb (p53, PTPRA, and PTGFR) had area under the curve (AUC) levels >60% (p < 0.01), with the partial AUC (SPAUC) over 5 times greater than for a nondiscriminating test (p < 0.01). Using a panel of the top three AAb (p53, PTPRA, and PTGFR), if at least two AAb were positive, then the sensitivity was 23.3% at 98.3% specificity. AAb to at least one of these top three antigens were also detected in 7/20 sera (35%) of patients with low CA 125 levels and 0/15 controls. AAb to p53, PTPRA, and PTGFR are potential biomarkers for the early detection of ovarian cancer.
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Affiliation(s)
- Karen S Anderson
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University , Tempe, Arizona 85287-6401, United States
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Du Y, Grandis JR. Receptor-type protein tyrosine phosphatases in cancer. CHINESE JOURNAL OF CANCER 2014; 34:61-9. [PMID: 25322863 PMCID: PMC4360074 DOI: 10.5732/cjc.014.10146] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play an important role in regulating cell signaling events in coordination with tyrosine kinases to control cell proliferation, apoptosis, survival, migration, and invasion. Receptor-type protein tyrosine phosphatases (PTPRs) are a subgroup of PTPs that share a transmembrane domain with resulting similarities in function and target specificity. In this review, we summarize genetic and epigenetic alterations including mutation, deletion, amplification, and promoter methylation of PTPRs in cancer and consider the consequences of PTPR alterations in different types of cancers. We also summarize recent developments using PTPRs as prognostic or predictive biomarkers and/or direct targets. Increased understanding of the role of PTPRs in cancer may provide opportunities to improve therapeutic approaches.
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Affiliation(s)
- Yu Du
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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Newton R, Wernisch L. A meta-analysis of multiple matched copy number and transcriptomics data sets for inferring gene regulatory relationships. PLoS One 2014; 9:e105522. [PMID: 25148247 PMCID: PMC4141782 DOI: 10.1371/journal.pone.0105522] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/21/2014] [Indexed: 12/25/2022] Open
Abstract
Inferring gene regulatory relationships from observational data is challenging. Manipulation and intervention is often required to unravel causal relationships unambiguously. However, gene copy number changes, as they frequently occur in cancer cells, might be considered natural manipulation experiments on gene expression. An increasing number of data sets on matched array comparative genomic hybridisation and transcriptomics experiments from a variety of cancer pathologies are becoming publicly available. Here we explore the potential of a meta-analysis of thirty such data sets. The aim of our analysis was to assess the potential of in silico inference of trans-acting gene regulatory relationships from this type of data. We found sufficient correlation signal in the data to infer gene regulatory relationships, with interesting similarities between data sets. A number of genes had highly correlated copy number and expression changes in many of the data sets and we present predicted potential trans-acted regulatory relationships for each of these genes. The study also investigates to what extent heterogeneity between cell types and between pathologies determines the number of statistically significant predictions available from a meta-analysis of experiments.
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Affiliation(s)
- Richard Newton
- Biostatistics Unit, Medical Research Council, Cambridge, United Kingdom
- * E-mail:
| | - Lorenz Wernisch
- Biostatistics Unit, Medical Research Council, Cambridge, United Kingdom
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Qu Y, Li J, Cai Q, Liu B. Hec1/Ndc80 is overexpressed in human gastric cancer and regulates cell growth. J Gastroenterol 2014; 49:408-18. [PMID: 23591767 DOI: 10.1007/s00535-013-0809-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/29/2013] [Indexed: 02/04/2023]
Abstract
BACKGROUND Chromosomal instability caused by abnormal cell division is a major cause of heterogeneity which evokes highly complex and malignant features of gastric cancer. Hec1/Ndc80 is critical in regulating proper cell division at the G2/M phase. The aim of our study is to investigate the in vitro and in vivo effects of Hec1 on gastric cancer cell growth. METHODS The mRNA levels of Hec1 in human normal and cancer tissues were analyzed using the Oncomine database. Hec1 mRNA and protein levels in human gastric cancer tissues were analyzed by quantitative realtime-PCR and immunohistochemical staining, respectively. The effects of Hec1 on cell growth were explored by Hec1 knockdown and Hec1 overexpression. Apoptosis and cell cycle distributions were analyzed by flow cytometry. In vivo tumorigenicity was performed by engrafting tumor cells into nude mice. RESULTS Hec1 mRNA and protein were broadly overexpressed in many human cancers including gastric cancer. Hec1 knockdown dramatically suppressed gastric cancer cell growth in vitro and in vivo, induced apoptosis, and arrested cell division at the G2/M phase. On the contrary, Hec1 overexpression moderately promoted gastric cancer cell growth in vivo. Hec1 overexpression induced asymmetrical chromosome alignments, abnormal cell division, and thus rendered chromosomal instability. CONCLUSIONS Hec1 is critical in maintaining the in vitro and in vivo growth of gastric cancer cells. Elevated Hec1 levels may occur at the early stage of gastric tumorigenesis.
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Affiliation(s)
- Ying Qu
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong University, 200025, Shanghai, People's Republic of China
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Xu R, Wang Q. An iterative searching and ranking algorithm for prioritising pharmacogenomics genes. INTERNATIONAL JOURNAL OF COMPUTATIONAL BIOLOGY AND DRUG DESIGN 2013; 6:18-31. [PMID: 23428471 PMCID: PMC6100784 DOI: 10.1504/ijcbdd.2013.052199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pharmacogenomics (PGx) studies are to identify genetic variants that may affect drug efficacy and toxicity. A machine understandable drug-gene relationship knowledge is important for many computational PGx studies and for personalised medicine. A comprehensive and accurate PGx-specific gene lexicon is important for automatic drug-gene relationship extraction from the scientific literature, rich knowledge source for PGx studies. In this study, we present a bootstrapping learning technique to rank 33,310 human genes with respect to their relevance to drug response. The algorithm uses only one seed PGx gene to iteratively extract and rank co-occurred genes using 20 million MEDLINE abstracts. Our ranking method is able to accurately rank PGx-specific genes highly among all human genes. Compared to randomly ranked genes (precision: 0.032, recall: 0.013, F1: 0.018), the algorithm has achieved significantly better performance (precision: 0.861, recall: 0.548, F1: 0.662) in ranking the top 2.5% of genes.
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Affiliation(s)
- Rong Xu
- Medical Informatics Division, Case Western Reserve University, Cleveland, OH 44106, USA
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Liu YY, Chen HY, Zhang ML, Tian D, Li S, Lee JY. Loss of fragile histidine triad and amplification of 1p36.22 and 11p15.5 in primary gastric adenocarcinomas. World J Gastroenterol 2012; 18:4522-32. [PMID: 22969225 PMCID: PMC3435777 DOI: 10.3748/wjg.v18.i33.4522] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/01/2012] [Accepted: 04/13/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the genomic copy number alterations that may harbor key driver genes in gastric tumorigenesis.
METHODS: Using high-resolution array comparative genomic hybridization (CGH), we investigated the genomic alterations of 20 advanced primary gastric adenocarcinomas (seventeen tubular and three mucinous) of Chinese patients from the Jilin province. Ten matching adjacent normal regions from the same patients were also studied.
RESULTS: The most frequent imbalances detected in these cancer samples were gains of 3q26.31-q27.2, 5p, 8q, 11p, 18p, 19q and 20q and losses of 3p, 4p, 18q and 21q. The use of high-resolution array CGH increased the resolution and sensitivity of the observed genomic changes and identified focal genetic imbalances, which included 54 gains and 16 losses that were smaller than 1 Mb in size. The most interesting focal imbalances were the intergenic loss/homozygous deletion of the fragile histidine triad gene and the amplicons 11q13, 18q11.2 and 19q12, as well as the novel amplicons 1p36.22 and 11p15.5.
CONCLUSION: These regions, especially the focal amplicons, may harbor key driver genes that will serve as biomarkers for either the diagnosis or the prognosis of gastric cancer, and therefore, a large-scale investigation is recommended.
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Tang W, Morgan DR, Meyers MO, Dominguez RL, Martinez E, Kakudo K, Kuan PF, Banet N, Muallem H, Woodward K, Speck O, Gulley ML. Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile. Infect Agent Cancer 2012; 7:21. [PMID: 22929309 PMCID: PMC3598565 DOI: 10.1186/1750-9378-7-21] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 08/22/2012] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND EBV DNA is found within the malignant cells of 10% of gastric cancers. Modern molecular technology facilitates identification of virus-related biochemical effects that could assist in early diagnosis and disease management. METHODS In this study, RNA expression profiling was performed on 326 macrodissected paraffin-embedded tissues including 204 cancers and, when available, adjacent non-malignant mucosa. Nanostring nCounter probes targeted 96 RNAs (20 viral, 73 human, and 3 spiked RNAs). RESULTS In 182 tissues with adequate housekeeper RNAs, distinct profiles were found in infected versus uninfected cancers, and in malignant versus adjacent benign mucosa. EBV-infected gastric cancers expressed nearly all of the 18 latent and lytic EBV RNAs in the test panel. Levels of EBER1 and EBER2 RNA were highest and were proportional to the quantity of EBV genomes as measured by Q-PCR. Among protein coding EBV RNAs, EBNA1 from the Q promoter and BRLF1 were highly expressed while EBNA2 levels were low positive in only 6/14 infected cancers. Concomitant upregulation of cellular factors implies that virus is not an innocent bystander but rather is linked to NFKB signaling (FCER2, TRAF1) and immune response (TNFSF9, CXCL11, IFITM1, FCRL3, MS4A1 and PLUNC), with PPARG expression implicating altered cellular metabolism. Compared to adjacent non-malignant mucosa, gastric cancers consistently expressed INHBA, SPP1, THY1, SERPINH1, CXCL1, FSCN1, PTGS2 (COX2), BBC3, ICAM1, TNFSF9, SULF1, SLC2A1, TYMS, three collagens, the cell proliferation markers MYC and PCNA, and EBV BLLF1 while they lacked CDH1 (E-cadherin), CLDN18, PTEN, SDC1 (CD138), GAST (gastrin) and its downstream effector CHGA (chromogranin). Compared to lymphoepithelioma-like carcinoma of the uterine cervix, gastric cancers expressed CLDN18, EPCAM, REG4, BBC3, OLFM4, PPARG, and CDH17 while they had diminished levels of IFITM1 and HIF1A. The druggable targets ERBB2 (Her2), MET, and the HIF pathway, as well as several other potential pharmacogenetic indicators (including EBV infection itself, as well as SPARC, TYMS, FCGR2B and REG4) were identified in some tumor specimens. CONCLUSION This study shows how modern molecular technology applied to archival fixed tissues yields novel insights into viral oncogenesis that could be useful in managing affected patients.
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Affiliation(s)
- Weihua Tang
- Department of Pathology & Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, 913 Brinkhous-Bullitt Building, Chapel Hill, NC, 27599-7525, USA.
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Park C, Ahn J, Yoon Y, Park S. Identification of functional CNV region networks using a CNV-gene mapping algorithm in a genome-wide scale. ACTA ACUST UNITED AC 2012; 28:2045-51. [PMID: 22652832 DOI: 10.1093/bioinformatics/bts318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MOTIVATION Identifying functional relation of copy number variation regions (CNVRs) and gene is an essential process in understanding the impact of genotypic variations on phenotype. There have been many related works, but only a few attempts were made to normal populations. RESULTS To analyze the functions of genome-wide CNVRs, we applied a novel correlation measure called Correlation based on Sample Set (CSS) to paired Whole Genome TilePath array and messenger RNA (mRNA) microarray data from 210 HapMap individuals with normal phenotypes and calculated the confident CNVR-gene relationships. Two CNVR nodes form an edge if they regulate a common set of genes, allowing the construction of a global CNVR network. We performed functional enrichment on the common genes that were trans-regulated from CNVRs clustered together in our CNVR network. As a result, we observed that most of CNVR clusters in our CNVR network were reported to be involved in some biological processes or cellular functions, while most CNVR clusters from randomly constructed CNVR networks showed no evidence of functional enrichment. Those results imply that CSS is capable of finding related CNVR-gene pairs and CNVR networks that have functional significance. AVAILABILITY http://embio.yonsei.ac.kr/~ Park/cnv_net.php. CONTACT sanghyun@cs.yonsei.ac.kr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chihyun Park
- Department of Computer Science, Yonsei University, South Korea, Seoul 120-749, South Korea
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Cheng L, Wang P, Yang S, Yang Y, Zhang Q, Zhang W, Xiao H, Gao H, Zhang Q. Identification of genes with a correlation between copy number and expression in gastric cancer. BMC Med Genomics 2012; 5:14. [PMID: 22559327 PMCID: PMC3441862 DOI: 10.1186/1755-8794-5-14] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Accepted: 03/27/2012] [Indexed: 12/11/2022] Open
Abstract
Background To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues. Methods We applied laser capture microdissection (LCM) to obtain samples for microarray experiments and profiled DNA copy number and gene expression using 244K CGH Microarray and Human Exon 1.0 ST Microarray. Results Obviously, gain at 8q was detected at the highest frequency (70%) and 20q at the second (63%). We also identified molecular genetic divergences for different TNM-stages or histological subtypes of gastric cancers. Interestingly, the C20orf11 amplification and gain at 20q13.33 almost separated moderately differentiated (MD) gastric cancers from poorly differentiated (PD) type. A set of 163 genes showing the correlations between gene copy number and expression was selected and the identified genes were able to discriminate matched adjacent noncancerous samples from gastric cancer samples in an unsupervised two-way hierarchical clustering. Quantitative RT-PCR analysis for 4 genes (C20orf11, XPO5, PUF60, and PLOD3) of the 163 genes validated the microarray results. Notably, some candidate genes (MCM4 and YWHAZ) and its adjacent genes such as PRKDC, UBE2V2, ANKRD46, ZNF706, and GRHL2, were concordantly deregulated by genomic aberrations. Conclusions Taken together, our results reveal diverse chromosomal region alterations for different TNM-stages or histological subtypes of gastric cancers, which is helpful in researching clinicopathological classification, and highlight several interesting genes as potential biomarkers for gastric cancer.
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Affiliation(s)
- Lei Cheng
- State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Fan B, Dachrut S, Coral H, Yuen ST, Chu KM, Law S, Zhang L, Ji J, Leung SY, Chen X. Integration of DNA copy number alterations and transcriptional expression analysis in human gastric cancer. PLoS One 2012; 7:e29824. [PMID: 22539939 PMCID: PMC3335165 DOI: 10.1371/journal.pone.0029824] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 12/03/2011] [Indexed: 12/16/2022] Open
Abstract
Background Genomic instability with frequent DNA copy number alterations is one of the key hallmarks of carcinogenesis. The chromosomal regions with frequent DNA copy number gain and loss in human gastric cancer are still poorly defined. It remains unknown how the DNA copy number variations contributes to the changes of gene expression profiles, especially on the global level. Principal Findings We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridization (aCGH). Statistical analysis was applied to correlate previously published gene expression data obtained from cDNA microarrays with corresponding DNA copy number variation data to identify candidate oncogenes and tumor suppressor genes. We found that gastric cancer samples showed recurrent DNA copy number variations, including gains at 5p, 8q, 20p, 20q, and losses at 4q, 9p, 18q, 21q. The most frequent regions of amplification were 20q12 (7/72), 20q12–20q13.1 (12/72), 20q13.1–20q13.2 (11/72) and 20q13.2–20q13.3 (6/72). The most frequent deleted region was 9p21 (8/72). Correlating gene expression array data with aCGH identified 321 candidate oncogenes, which were overexpressed and showed frequent DNA copy number gains; and 12 candidate tumor suppressor genes which were down-regulated and showed frequent DNA copy number losses in human gastric cancers. Three networks of significantly expressed genes in gastric cancer samples were identified by ingenuity pathway analysis. Conclusions This study provides insight into DNA copy number variations and their contribution to altered gene expression profiles during human gastric cancer development. It provides novel candidate driver oncogenes or tumor suppressor genes for human gastric cancer, useful pathway maps for the future understanding of the molecular pathogenesis of this malignancy, and the construction of new therapeutic targets.
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Affiliation(s)
- Biao Fan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
| | - Somkid Dachrut
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Ho Coral
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Siu Tsan Yuen
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Kent Man Chu
- Department of Surgery; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Simon Law
- Department of Surgery; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Lianhai Zhang
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
| | - Jiafu Ji
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
- * E-mail: (XC); (SYL); (JFJ)
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
- * E-mail: (XC); (SYL); (JFJ)
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (XC); (SYL); (JFJ)
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Abstract
Gastric cancer is the most common cancer in Korea, with an age-standardized rate of 61.2 in males and 23.9 in females (in 2007), one of the highest in the world. Using a large gastric tissue depository and the extensive clinical experience gained from gastric cancer surgery, we work as a 'translational researcher' to apply basic research tools and results to the clinical field. We are also interested in providing answers to the questions in the operating room using the methods of basic research. I would like to introduce our research activities in this review paper.
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Affiliation(s)
- Han-Kwang Yang
- Department of Surgery, Seoul National University College of Medicine and Gastric Cancer Center, Seoul National University Cancer Hospital, Korea.
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Holbrook JD, Parker JS, Gallagher KT, Halsey WS, Hughes AM, Weigman VJ, Lebowitz PF, Kumar R. Deep sequencing of gastric carcinoma reveals somatic mutations relevant to personalized medicine. J Transl Med 2011; 9:119. [PMID: 21781349 PMCID: PMC3152520 DOI: 10.1186/1479-5876-9-119] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 07/25/2011] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Globally, gastric cancer is the second most common cause of cancer-related death, with the majority of the health burden borne by economically less-developed countries. METHODS Here, we report a genetic characterization of 50 gastric adenocarcinoma samples, using affymetrix SNP arrays and Illumina mRNA expression arrays as well as Illumina sequencing of the coding regions of 384 genes belonging to various pathways known to be altered in other cancers. RESULTS Genetic alterations were observed in the WNT, Hedgehog, cell cycle, DNA damage and epithelial-to-mesenchymal-transition pathways. CONCLUSIONS The data suggests targeted therapies approved or in clinical development for gastric carcinoma would be of benefit to ~22% of the patients studied. In addition, the novel mutations detected here, are likely to influence clinical response and suggest new targets for drug discovery.
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Affiliation(s)
- Joanna D Holbrook
- Cancer Research, Oncology R&D, Glaxosmithkline R&D, Collegeville, USA.
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Gertler F, Condeelis J. Metastasis: tumor cells becoming MENAcing. Trends Cell Biol 2010; 21:81-90. [PMID: 21071226 DOI: 10.1016/j.tcb.2010.10.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 09/28/2010] [Accepted: 10/01/2010] [Indexed: 12/31/2022]
Abstract
During breast cancer metastasis cells emigrate from the primary tumor to the bloodstream, and this carries them to distant sites where they infiltrate and sometimes form metastases within target organs. These cells must penetrate the dense extracellular matrix comprising the basement membrane of the mammary duct/acinus and migrate toward blood and lymphatic vessels, processes that mammary tumor cells execute primarily using epidermal growth factor (EGF)-dependent protrusive and migratory activity. Here, we focus on how the actin regulatory protein Mena affects EGF-elicited movement, invasion and metastasis. Recent findings indicate that, in invasive migratory tumor cells, Mena isoforms that endow heightened sensitivity to EGF and increased protrusive and migratory abilities are upregulated, whereas other isoforms are selectively downregulated. This change in Mena isoform expression enables tumor cells to invade in response to otherwise benign EGF stimulus levels and could offer an opportunity to identify metastatic risk in patients.
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Affiliation(s)
- Frank Gertler
- Department of Biology and Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), 77 Massachusetts Ave, Cambridge, MA 02138, USA.
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48
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Translating tumor antigens into cancer vaccines. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2010; 18:23-34. [PMID: 21048000 DOI: 10.1128/cvi.00286-10] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Vaccines represent a strategic successful tool used to prevent or contain diseases with high morbidity and/or mortality. However, while vaccines have proven to be effective in combating pathogenic microorganisms, based on the immune recognition of these foreign antigens, vaccines aimed at inducing effective antitumor activity are still unsatisfactory. Nevertheless, the effectiveness of the two licensed cancer-preventive vaccines targeting tumor-associated viral agents (anti-HBV [hepatitis B virus], to prevent HBV-associated hepatocellular carcinoma, and anti-HPV [human papillomavirus], to prevent HPV-associated cervical carcinoma), along with the recent FDA approval of sipuleucel-T (for the therapeutic treatment of prostate cancer), represents a significant advancement in the field of cancer vaccines and a boost for new studies in the field. Specific active immunotherapies based on anticancer vaccines represent, indeed, a field in continuous evolution and expansion. Significant improvements may result from the selection of the appropriate tumor-specific target antigen (to overcome the peripheral immune tolerance) and/or the development of immunization strategies effective at inducing a protective immune response. This review aims to describe the vast spectrum of tumor antigens and strategies to develop cancer vaccines.
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Sayagués JM, Fontanillo C, Abad MDM, González-González M, Sarasquete ME, Chillon MDC, Garcia E, Bengoechea O, Fonseca E, Gonzalez-Diaz M, De Las Rivas J, Muñoz-Bellvis L, Orfao A. Mapping of genetic abnormalities of primary tumours from metastatic CRC by high-resolution SNP arrays. PLoS One 2010; 5:e13752. [PMID: 21060790 PMCID: PMC2966422 DOI: 10.1371/journal.pone.0013752] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 10/06/2010] [Indexed: 02/07/2023] Open
Abstract
Background For years, the genetics of metastatic colorectal cancer (CRC) have been studied using a variety of techniques. However, most of the approaches employed so far have a relatively limited resolution which hampers detailed characterization of the common recurrent chromosomal breakpoints as well as the identification of small regions carrying genetic changes and the genes involved in them. Methodology/Principal Findings Here we applied 500K SNP arrays to map the most common chromosomal lesions present at diagnosis in a series of 23 primary tumours from sporadic CRC patients who had developed liver metastasis. Overall our results confirm that the genetic profile of metastatic CRC is defined by imbalanced gains of chromosomes 7, 8q, 11q, 13q, 20q and X together with losses of the 1p, 8p, 17p and 18q chromosome regions. In addition, SNP-array studies allowed the identification of small (<1.3 Mb) and extensive/large (>1.5 Mb) altered DNA sequences, many of which contain cancer genes known to be involved in CRC and the metastatic process. Detailed characterization of the breakpoint regions for the altered chromosomes showed four recurrent breakpoints at chromosomes 1p12, 8p12, 17p11.2 and 20p12.1; interestingly, the most frequently observed recurrent chromosomal breakpoint was localized at 17p11.2 and systematically targeted the FAM27L gene, whose role in CRC deserves further investigations. Conclusions/Significance In summary, in the present study we provide a detailed map of the genetic abnormalities of primary tumours from metastatic CRC patients, which confirm and extend on previous observations as regards the identification of genes potentially involved in development of CRC and the metastatic process.
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Affiliation(s)
- José María Sayagués
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - Celia Fontanillo
- Grupo de Investigación en Bioinformática y Genómica Funcional, Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - María del Mar Abad
- Departamento de Patología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - María González-González
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - María Eugenia Sarasquete
- Servicio de Hematología, Hospital Universitario, Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Salamanca, Spain
| | - Maria del Carmen Chillon
- Servicio de Hematología, Hospital Universitario, Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Salamanca, Spain
| | - Eva Garcia
- Unidad de Genómica y Proteómica, Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - Oscar Bengoechea
- Departamento de Patología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Emilio Fonseca
- Servicio de Oncología Médica, Departamento de Cirugía, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Marcos Gonzalez-Diaz
- Servicio de Hematología, Hospital Universitario, Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Salamanca, Spain
| | - Javier De Las Rivas
- Grupo de Investigación en Bioinformática y Genómica Funcional, Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
| | - Luís Muñoz-Bellvis
- Unidad de Cirugía Hepatobiliopancreática, Departamento de Cirugía, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Servicio General de Citometría, Departamento de Medicina and Centro de Investigación del Cáncer (IBMCC-CSIC/USAL), Universidad de Salamanca, Salamanca, Spain
- * E-mail:
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