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Davidson BSA, Arcila-Galvis JE, Trevisan-Herraz M, Mikulasova A, Brackley CA, Russell LJ, Rico D. Evolutionarily conserved enhancer-associated features within the MYEOV locus suggest a regulatory role for this non-coding DNA region in cancer. Front Cell Dev Biol 2024; 12:1294510. [PMID: 39139450 PMCID: PMC11319300 DOI: 10.3389/fcell.2024.1294510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 07/01/2024] [Indexed: 08/15/2024] Open
Abstract
The myeloma overexpressed gene (MYEOV) has been proposed to be a proto-oncogene due to high RNA transcript levels found in multiple cancers, including myeloma, breast, lung, pancreas and esophageal cancer. The presence of an open reading frame (ORF) in humans and other primates suggests protein-coding potential. Yet, we still lack evidence of a functional MYEOV protein. It remains undetermined how MYEOV overexpression affects cancerous tissues. In this work, we show that MYEOV has likely originated and may still function as an enhancer, regulating CCND1 and LTO1. Firstly, MYEOV 3' enhancer activity was confirmed in humans using publicly available ATAC-STARR-seq data, performed on B-cell-derived GM12878 cells. We detected enhancer histone marks H3K4me1 and H3K27ac overlapping MYEOV in multiple healthy human tissues, which include B cells, liver and lung tissue. The analysis of 3D genome datasets revealed chromatin interactions between a MYEOV-3'-putative enhancer and the proto-oncogene CCND1. BLAST searches and multi-sequence alignment results showed that DNA sequence from this human enhancer element is conserved from the amphibians/amniotes divergence, with a 273 bp conserved region also found in all mammals, and even in chickens, where it is consistently located near the corresponding CCND1 orthologues. Furthermore, we observed conservation of an active enhancer state in the MYEOV orthologues of four non-human primates, dogs, rats, and mice. When studying this homologous region in mice, where the ORF of MYEOV is absent, we not only observed an enhancer chromatin state but also found interactions between the mouse enhancer homolog and Ccnd1 using 3D-genome interaction data. This is similar to the interaction observed in humans and, interestingly, coincides with CTCF binding sites in both species. Taken together, this suggests that MYEOV is a primate-specific gene with a de novo ORF that originated at an evolutionarily older enhancer region. This deeply conserved putative enhancer element could regulate CCND1 in both humans and mice, opening the possibility of studying MYEOV regulatory functions in cancer using non-primate animal models.
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Affiliation(s)
| | | | | | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Chris A. Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh, United Kingdom
| | - Lisa J. Russell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- CABIMER, CSIC-Universidad de Sevilla-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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Ou D, Wu Y, Zhang J, Liu J, Liu Z, Shao M, Guo X, Cui S. MYEOV with High Frequencies of Mutations in Head and Neck Cancers Facilitates Cancer Cell Malignant Behaviors. Biochem Genet 2024; 62:1657-1674. [PMID: 37667096 DOI: 10.1007/s10528-023-10484-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/06/2023] [Indexed: 09/06/2023]
Abstract
Cancer driver genes (CDGs) and the driver mutations disrupt the homeostasis of numerous critical cell activities, thereby playing a critical role in tumor initiation and progression. In this study, integrative bioinformatics analyses were performed based on a series of online databases, aiming to identify driver genes with high frequencies of mutations in head and neck cancers. Higher myeloma overexpressed (MYEOV) genetic variation frequency and expression level were connected to a poorer prognosis in head and neck cancer patients. MYEOV was dramatically upregulated within head and neck tumor samples and cells. Consistently, MYEOV overexpression remarkably enhanced the aggressiveness of head and neck cancer cells by promoting colony formation, cell invasion, and cell migration. Conversely, MYEOV knockdown attenuated cancer cell aggressiveness and inhibited tumor growth and metastasis in the oral orthotopic tumor model. In conclusion, MYEOV is overexpressed in head and neck cancer, with greater mutation frequencies correlating to a poorer prognosis in head and neck cancer patients. MYEOV serves as an oncogene in head and neck cancer through the promotion of tumor cell colony formation, invasion, and migration, as well as promoting tumor growth and metastasis in the oral orthotopic tumor model.
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Affiliation(s)
- Deming Ou
- Department of Stomatology, Panyu Central Hospital, Guangzhou, 511400, China.
| | - Ying Wu
- Department of Stomatology, Foshan Hospital of Traditional Chinese Medicine, Foshan, 528000, China
| | - Jibin Zhang
- Department of Stomatology, Panyu Central Hospital, Guangzhou, 511400, China
| | - Jun Liu
- Department of Stomatology, Panyu Central Hospital, Guangzhou, 511400, China
| | - Zeyu Liu
- Department of Stomatology, Panyu Central Hospital, Guangzhou, 511400, China
| | - Minfeng Shao
- Department of Stomatology, Panyu Central Hospital, Guangzhou, 511400, China
| | - Xiaoying Guo
- Department of Stomatology, Panyu Central Hospital, Guangzhou, 511400, China
| | - Shiman Cui
- Department of Stomatology, Panyu Central Hospital, Guangzhou, 511400, China
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Luo S, Luo Y, Wang Z, Yin H, Wu Q, Du X, Xie X. Super-enhancer mediated upregulation of MYEOV suppresses ferroptosis in lung adenocarcinoma. Cancer Lett 2024; 589:216811. [PMID: 38490328 DOI: 10.1016/j.canlet.2024.216811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/02/2024] [Accepted: 03/09/2024] [Indexed: 03/17/2024]
Abstract
Super-enhancers (SEs) exerted a crucial role in regulating the transcription of oncogenes across various malignancies while the roles of SEs driven genes and the core regulatory elements remain elusive in LUAD. In this study, cancer-specific-SE-genes of lung adenocarcinoma (LUAD) were profiled through H3K27ac ChIP-seq data of cancer cell lines and normal lung tissues, which enriched in in biological processes and pathways integral to the pathophysiology of LUAD. Based on this study, LUAD cells were susceptible to SEs inhibitors, with a reduction of cell proliferation as well as an elevation of apoptosis upon JQ1 or THZ1 intervention. Moreover, the integration of SEs landscapes, CRISPRi, ChIP-PCR, Hi-C data analysis and dual-luciferase reporter assays revealed that myeloma overexpressed gene (MYEOV) was aberrantly overexpressed in LUAD via transcriptional activation by the core SE elements. Functionally, the knockdown of MYEOV undermined cell proliferation in vitro and tumor growth in vivo. In addition, the knockdown of MYEOV generated a prominent ferroptotic phenotype, characterized by elevation of intracellular ferrous iron, reactive oxygen species and lipid peroxidation, together with alteration in marker proteins (SLC7A11, GPX4, FTH1, and ACSL4). Instead, the overexpression of MYEOV accelerated cell proliferation and abrogated ferroptosis. Clinically, the overexpression of MYEOV was observed in LUAD tissues indicating a poor prognosis in patients with LUAD. Mechanistically, SMPD1-induced autophagic degradation of GPX4 assumed a crucial role in the process of ferroptosis triggered by MYEOV knockdown. Serving as an oncogene repressing ferroptosis, promoting proliferation as well as shortening survival in LUAD, SEs-mediated activation of MYEOV might distinguish as a promising therapeutic target.
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Affiliation(s)
- Shuimei Luo
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China; Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Yang Luo
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China; Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Ziming Wang
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China; Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Haofeng Yin
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China; Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Qing Wu
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China; Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xiaowei Du
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China; Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Xianhe Xie
- Department of Oncology, Molecular Oncology Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China; Department of Oncology, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China; Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China.
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Tange S, Hirano T, Idogawa M, Hirata E, Imoto I, Tokino T. MYEOV overexpression induced by demethylation of its promoter contributes to pancreatic cancer progression via activation of the folate cycle/c-Myc/mTORC1 pathway. BMC Cancer 2023; 23:85. [PMID: 36698109 PMCID: PMC9875418 DOI: 10.1186/s12885-022-10433-6] [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: 06/15/2022] [Accepted: 12/12/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND While molecular targeted drugs and other therapies are being developed for many tumors, pancreatic cancer is still considered to be the malignant tumor with the worst prognosis. We started this study to identify prognostic genes and therapeutic targets of pancreatic cancer. METHODS To comprehensively identify prognostic genes in pancreatic cancer, we investigated the correlation between gene expression and cancer-specific prognosis using transcriptome and clinical information datasets from The Cancer Genome Atlas (TCGA). In addition, we examined the effects of the suppression of candidate prognostic genes in pancreatic cancer cell lines. RESULT We found that patients with high expression levels of MYEOV, a primate-specific gene with unknown function, had significantly shorter disease-specific survival times than those with low expression levels. Cox proportional hazards analysis revealed that high expression of MYEOV was significantly associated with poor survival and was an independent prognostic factor for disease-specific survival in pancreatic cancer patients. Analysis of multiple cancer samples revealed that the MYEOV promoter region is methylated in noncancer tissues but is demethylated in tumors, causing MYEOV overexpression in tumors. Notably, the knockdown of MYEOV suppressed the expression of MTHFD2 and other folate metabolism-related enzyme genes required for the synthesis of amino acids and nucleic acids and also restored the expression of c-Myc and mTORC1 repressors. CONCLUSION There is a significant correlation between elevated MYEOV expression and poor disease-specific survival in pancreatic cancer patients. MYEOV enhances the activation of several oncogenic pathways, resulting in the induction of pancreatic cancer cell proliferation. Overall, MYEOV acts as an oncogene in pancreatic cancer. Furthermore, MYEOV may be a prognostic biomarker and serve as an 'actionable' therapeutic target for pancreatic cancers.
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Affiliation(s)
- Shoichiro Tange
- grid.263171.00000 0001 0691 0855Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, S1W17, Chuo-ku, Sapporo, 060-8556 Japan
| | - Tomomi Hirano
- grid.263171.00000 0001 0691 0855Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, S1W17, Chuo-ku, Sapporo, 060-8556 Japan
| | - Masashi Idogawa
- grid.263171.00000 0001 0691 0855Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, S1W17, Chuo-ku, Sapporo, 060-8556 Japan ,grid.263171.00000 0001 0691 0855Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, S1W16, Chuo-ku, Sapporo, 060-8543 Japan
| | - Eishu Hirata
- grid.9707.90000 0001 2308 3329Division of Tumor Cell Biology and Bioimaging, Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192 Japan
| | - Issei Imoto
- grid.410800.d0000 0001 0722 8444Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya, 464-8681 Japan
| | - Takashi Tokino
- grid.263171.00000 0001 0691 0855Department of Medical Genome Sciences, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, S1W17, Chuo-ku, Sapporo, 060-8556 Japan
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Jia E, Ren N, Guo B, Cui Z, Zhang B, Xue J. Construction and validation of a novel prognostic model for lung squamous cell cancer based on N6-methyladenosine-related genes. World J Surg Oncol 2022; 20:59. [PMID: 35220962 PMCID: PMC8883700 DOI: 10.1186/s12957-022-02509-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/01/2022] [Indexed: 12/24/2022] Open
Abstract
Background N6-methyladenosine (m6A) is the most prevalent modification in mRNA in biological processes and associated with various malignant tumor initiation and progression. The present study aimed to construct a prognostic risk model based on m6A-related genes (the downstream genes influenced by m6A modulators) for LUSC. Methods Based on TCGA, we stratified LUSC patients with and without genetic alteration of m6A modulators into altered and unaltered groups. Using univariate Cox and Lasso regression analyses, we identified prognostic m6A-related genes to construct a prognostic risk model. We then applied a multivariate Cox proportional regression model and the survival analysis to evaluate the risk model. Moreover, we performed the Receiver operating characteristic curve to assess the efficiency of the prognostic model based on TCGA and GSE43131. We analyzed the characteristics of tumor-associated immune cell infiltration in LUSC through the CIBERSORT method. Results Three m6A-related genes (FAM71F1, MT1E, and MYEOV) were identified as prognostic genes for LUSC. A novel prognostic risk model based on the three m6A-related genes was constructed. The multivariate Cox analysis showed that the prognostic risk model was an independent risk factor (HR = 2.44, 95% CI = 1.21~3.56, p = 0.029). Patients with a high-risk group had worse overall survival both in TCGA (p = 0.018) and GSE43131 (p = 0.00017). The 1, 2, and 3-year AUC value in TCGA was 0.662, 0.662, and 0.655, respectively; The 1, 2, and 3-year AUC value in GSE43131 was 0.724, 0.724, and 0.722, respectively. The proportion of infiltrated neutrophils in the high-risk group was higher than that in the low-risk group (p = 0.028), whereas that of resting NK cells (p = 0.002) was lower. Conclusion A novel prognostic risk model based on three m6A-related genes for LUSC was generated in this study. Supplementary Information The online version contains supplementary material available at 10.1186/s12957-022-02509-1.
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Li S, Chen R, Luo W, Lin J, Chen Y, Wang Z, Lin W, Li B, Wang J, Yang J. Identification of a Four Cancer Stem Cell-Related Gene Signature and Establishment of a Prognostic Nomogram Predicting Overall Survival of Pancreatic Adenocarcinoma. Comb Chem High Throughput Screen 2022; 25:2070-2081. [PMID: 35048799 DOI: 10.2174/1386207325666220113142212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/10/2021] [Accepted: 11/19/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cancer stem cells (CSCs) are now being considered as the initial component in the development of pancreatic adenocarcinoma (PAAD). Our aim was to develop a CSCrelated signature to assess the prognosis of PAAD patients for the optimization of treatment. METHODS Differentially expressed genes (DEGs) between pancreatic tumor and normal tissue in the Cancer Genome Atlas (TCGA) were screened out, and the weighted gene correlation network analysis (WGCNA) was employed to identify the CSC-related gene sets. Then, univariate, Lasso Cox regression analyses and multivariate Cox regression were applied to construct a prognostic signature using the CSC-related genes. Its prognostic performance was validated in TCGA and ICGC cohorts. Furthermore, Univariate and multivariate Cox regression analyses were used to identify independent prognostic factors in PAAD, and a prognostic nomogram was established. RESULTS The Kaplan-Meier analysis, ROC curve and C-index indicated the good performance of the CSC-related signature at predicting overall survival (OS). Univariate Cox regression and multivariate Cox regression revealed that the CSC-related signature was an independent prognostic factor in PAAD. The nomogram was superior to the risk model and AJCC stage in predicting OS. In terms of mutation and tumor immunity, patients in the high-risk group had higher tumor mutation burden (TMB) scores than patients in the low-risk group, and the immune score and the ESTIMATE score were significantly lower in the high-risk group. Moreover, according to the results of principal component analysis (PCA) and Gene Set Enrichment Analysis (GSEA), the low-risk and high-risk groups displayed different stemness statuses based on the risk model. CONCLUSION Our study identified four CSC-related gene signatures and established a prognostic nomogram that reliably predicts OS in PAAD. The findings may support new ideas for screening therapeutic targets to inhibit stem characteristics and the development of PAAD.
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Affiliation(s)
- Shuanghua Li
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Rui Chen
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Wang Luo
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Jinyu Lin
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Yunlong Chen
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Zhuangxiong Wang
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Wenjun Lin
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Baihong Li
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Junfeng Wang
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
| | - Jian Yang
- Department of Hepatobiliary Surgery I, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Clinical and Engineering Center of Digital Medicine, Guangzhou, China
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Shen H, Ye F, Xu D, Fang L, Zhang X, Zhu J. The MYEOV-MYC association promotes oncogenic miR-17/93-5p expression in pancreatic ductal adenocarcinoma. Cell Death Dis 2021; 13:15. [PMID: 34930894 PMCID: PMC8688437 DOI: 10.1038/s41419-021-04387-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/18/2021] [Accepted: 10/29/2021] [Indexed: 12/21/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy worldwide. As metastasis and malignant progression are primarily responsible for the poor clinical outcomes of PDAC, identifying key genes involved in these processes and the underlying molecular mechanisms of PDAC is vital. In this study, by analyzing TCGA PDAC data and matched GTEx data, we found that MYEOV expression is associated with poor survival in PDAC patients and higher in carcinoma tissues than in healthy tissues. Elevated levels of MYEOV led to enhanced cell proliferation, invasion and migration in vitro and in vivo. Transcriptome analysis results revealed that MYEOV mediates global alterations in gene expression profiles in PDAC cells. MiRNA-seq analysis showed that MYEOV regulates the expression levels of miR-17-5p and miR-93-5p, and its depletion resulted in reduced cell proliferation, invasion and migration, as observed in MYEOV-knockdown PDAC cells. These effects are likely due to the ability of MYEOV to regulate enrichment of the transcription factor MYC at the gene promoter regions of the two miRNAs. Furthermore, we identified a complex containing MYEOV and MYC in the nucleus, providing additional evidence for the association of MYEOV with MYC. Taken together, our results suggest that MYEOV promotes oncogenic miR-17/93-5p expression by associating with MYC, contributing to PDAC progression.
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Affiliation(s)
- Hongzhang Shen
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fuqiang Ye
- Huadong Research Institute for Medicine and Biotechniques, Nanjing, China
| | - Dongchao Xu
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liangliang Fang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China
| | - Xiaofeng Zhang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Juanjuan Zhu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.
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High expression of MYEOV reflects poor prognosis in non-small cell lung cancer. Gene 2020; 770:145337. [PMID: 33278551 DOI: 10.1016/j.gene.2020.145337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/09/2020] [Accepted: 11/27/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND The myeloma overexpressed gene (MYEOV) plays a critical role in tumorigenesis in a variety of cancers. However, little is known of the prognosis and immune infiltration associated with MYEOV in non-small cell lung cancer (NSCLC). METHODS We used several databases (Oncomine, TCGA, and GEO) to analysis the expression, prognosis, and immune infiltration, associated with MYEOV in NSCLC. We also used RT-qPCR and immunohistochemistry to investigate the expression and prognosis of MYEOV in NSCLC. RESULTS Compared with normal tissues, high MYEOV expression in NSCLC was observed in Oncomine database, and was validated in the TCGA database. High MYEOV expression was significantly associated with different subtypes of NSCLC. Moreover, high MYEOV expression was closely related with a poorer overall survival in NSCLC in TCGA cohort, and was validated in GEO database. Simultaneously, high expression of MYEOV correlates with clinical relevance of NSCLC. Specifically, MYEOV expression was negatively correlated with infiltrating levels of tumor purity and B cells in LUAD. MYEOV expression was negatively correlated with infiltrating levels of tumor purity, and positively associated with CD8 + T cells, CD4 + T cells, dendritic cells, and neutrophils in LUSC. GSEA also revealed that high MYEOV expression were enriched in certain cancer-specific pathways. In addition, RT-qPCR and immunohistochemistry showed MYEOV expression was higher in NSCLC compared to the normal tissues. Finally, high MYEOV expression was closely related with poorer overall survival of NSCLC in an independent validation cohort. CONCLUSION Our analyses indicate that MYEOV can be used as a prognostic biomarker for determining prognosis and immune infiltration in NSCLC.
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Luo H, Ma C. Identification of prognostic genes in uveal melanoma microenvironment. PLoS One 2020; 15:e0242263. [PMID: 33196683 PMCID: PMC7668584 DOI: 10.1371/journal.pone.0242263] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 10/30/2020] [Indexed: 12/22/2022] Open
Abstract
Background Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Many previous studies have demonstrated that the infiltrating of immune and stromal cells in the tumor microenvironment contributes significantly to prognosis. Methods Dataset TCGA-UVM, download from TCGA portal, was taken as the training cohort, and GSE22138, obtained from GEO database, was set as the validation cohort. ESTIMATE algorithm was applied to find intersection differentially expressed genes (DEGs) among tumor microenvironment. Kaplan-Meier analysis and univariate Cox regression model were performed on intersection DEGs to initial screen for potential prognostic genes. Then these genes entered into the validation cohort for validation using the same methods as that in the training cohort. Moreover, we conducted correlation analyses between the genes obtained in the validation cohort and the status of chromosome 3, chromosome 8q, and tumor metastasis to get prognosis genes. At last, the immune infiltration analysis was performed between the prognostic genes and 6 main kinds of tumor-infiltrating immune cells (TICs) for understanding the role of the genes in the tumor microenvironment. Results 959 intersection DEGs were found in the UM microenvironment. Kaplan-Meier and Cox analysis was then performed in the training and validation cohorts on these DEGs, and 52 genes were identified with potential prognostic value. After comparing the 52 genes to chromosome 3, chromosome 8q, and metastasis, we obtained 21 genes as the prognostic genes. The immune infiltration analysis showed that Neutrophil had the potential prognostic ability, and almost every prognostic gene we had identified was correlated with abundances of Neutrophil and CD8+ T Cell. Conclusions Identifying 21 prognosis genes (SERPINB9, EDNRB, RAPGEF3, HFE, RNF43, ZNF415, IL12RB2, MTUS1, NEDD9, ZNF667, AZGP1, WARS, GEM, RAB31, CALHM2, CA12, MYEOV, CELF2, SLCO5A1, ISM1, and PAPSS2) could accurately identify patients' prognosis and had close interactions with Neutrophil in the tumor environment, which may provide UM patients with personalized prognosis prediction and new treatment insights.
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Affiliation(s)
- Huan Luo
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and the Berlin Institute of Health, Berlin, Germany
- Klinik für Augenheilkunde, Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Chao Ma
- Charité–Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and the Berlin Institute of Health, Berlin, Germany
- BCRT—Berlin Institute of Health Center for Regenerative Therapies, Charité—Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
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Liang E, Lu Y, Shi Y, Zhou Q, Zhi F. MYEOV increases HES1 expression and promotes pancreatic cancer progression by enhancing SOX9 transactivity. Oncogene 2020; 39:6437-6450. [PMID: 32879444 DOI: 10.1038/s41388-020-01443-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/05/2020] [Accepted: 08/21/2020] [Indexed: 01/07/2023]
Abstract
Emerging evidence indicates that myeloma overexpressed (MYEOV) is an oncogene and plays crucial roles in multiple human cancers. However, its roles in the development of pancreatic ductal adenocarcinoma (PDAC) remain elusive. Here, we provide evidence of essential roles of MYEOV in the development and progression of PDAC. In tumor specimens derived from pancreatic cancer patients, MYEOV was overexpressed and associated with poor prognosis. In addition, MYEOV expression in PDAC was upregulated through promoter hypomethylation. MYEOV depletion impaired metastatic ability and proliferation of PDAC cells both in vitro and in vivo, whereas its overexpression had the opposite effect. Mechanistic investigations revealed that MYEOV interacted with SRY-Box Transcription Factor 9 (SOX9), a well-known oncogenic transcription factor in PDAC. This interaction occurred mainly in the nuclei of PDAC cells and increased transcriptional activity of SOX9. Furthermore, MYEOV promoted the expression of Hairy and enhancer of split homolog-1 (HES1), a SOX9 target gene, by enhancing SOX9 DNA-binding ability to the HES1 enhancer without affecting the protein level and subcellular localization of SOX9. HES1 knockdown partly abrogated the oncogenic effect of MYEOV. Our findings suggest that MYEOV could be a potential prognostic biomarker and therapeutic target for PDAC.
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Affiliation(s)
- Erbo Liang
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Yishi Lu
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Yanqiang Shi
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Qian Zhou
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China
| | - Fachao Zhi
- Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, 510515, Guangzhou, China.
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11
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Tang R, Ji J, Ding J, Huang J, Gong B, Zhang X, Li F. Overexpression of MYEOV predicting poor prognosis in patients with pancreatic ductal adenocarcinoma. Cell Cycle 2020; 19:1602-1610. [PMID: 32420813 PMCID: PMC7469688 DOI: 10.1080/15384101.2020.1757243] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 01/28/2023] Open
Abstract
Myeloma Overexpressed (MYEOV) is closely related to cell growth and differentiation in many cancer types. However, the role of this protein-coding gene in pancreatic ductal adenocarcinoma (PDAC) has rarely been investigated. In this study, we demonstrated that MYEOV was higher expressed in tumor tissues compared with adjacent normal pancreas tissues (ANPTs) both in mRNA and protein levels. We also performed bioinformatic analysis and found high MYEOV expression was positively correlated with tumor differentiation (P = 0.004), lymph node metastasis (P = 0.016) and TNM stage (P = 0.001). Moreover, Kaplan-Meier and Cox proportional-hazards analyses indicated that high MYEOV expression was significantly associated with poor survival in patients with PDAC and that MYEOV was an independent prognostic factor for overall survival in patients with PDAC. Geneset Enrichment Analysis (GSEA) result showed that high expression of MYEOV facilitates glycolysis of tumor cells in PDAC and validated in cellular assays. In conclusion, our results suggest that MYEOV acts as an oncogene in PDAC and can therefore serve as a biomarker for the prognosis of patients with PDAC.
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Affiliation(s)
- Rui Tang
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Jianmei Ji
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Jun Ding
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Jinxin Huang
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Biao Gong
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Xiwen Zhang
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
| | - Fu Li
- Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, P.R. China
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12
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Gao M, Kong W, Huang Z, Xie Z. Identification of Key Genes Related to Lung Squamous Cell Carcinoma Using Bioinformatics Analysis. Int J Mol Sci 2020; 21:ijms21082994. [PMID: 32340320 PMCID: PMC7215920 DOI: 10.3390/ijms21082994] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/10/2020] [Accepted: 04/21/2020] [Indexed: 01/30/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is often diagnosed at the advanced stage with poor prognosis. The mechanisms of its pathogenesis and prognosis require urgent elucidation. This study was performed to screen potential biomarkers related to the occurrence, development and prognosis of LUSC to reveal unknown physiological and pathological processes. Using bioinformatics analysis, the lung squamous cell carcinoma microarray datasets from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were analyzed to identify differentially expressed genes (DEGs). Furthermore, PPI and WGCNA network analysis were integrated to identify the key genes closely related to the process of LUSC development. In addition, survival analysis was performed to achieve a prognostic model that accomplished good prediction accuracy. Three hundred and thirty–seven up–regulated and 119 down-regulated genes were identified, in which four genes have been found to play vital roles in LUSC development, namely CCNA2, AURKA, AURKB, and FEN1. The prognostic model contained 5 genes, which were all detrimental to prognosis. The AUC of the established prognostic model for predicting the survival of patients at 1, 3, and 5 years was 0.692, 0.722, and 0.651 in the test data, respectively. In conclusion, this study identified several biomarkers of significant interest for additional investigation of the therapies and methods of prognosis of lung squamous cell carcinoma.
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Affiliation(s)
- Miaomiao Gao
- Peking University International Cancer Institute and Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Weikaixin Kong
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhuo Huang
- Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
- Correspondence: (Z.H.); (Z.X.)
| | - Zhengwei Xie
- Peking University International Cancer Institute and Department of Pharmacology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- Correspondence: (Z.H.); (Z.X.)
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13
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Wang J, Zhang X, Yao H, Le Y, Zhou W, Li J, Lu L, Chen M, Li X. MiR-490-5p functions as tumor suppressor in childhood neuroblastoma by targeting MYEOV. Hum Cell 2020; 33:261-271. [DOI: 10.1007/s13577-019-00302-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/11/2019] [Indexed: 12/24/2022]
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14
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Fang L, Wu S, Zhu X, Cai J, Wu J, He Z, Liu L, Zeng M, Song E, Li J, Li M, Guan H. MYEOV functions as an amplified competing endogenous RNA in promoting metastasis by activating TGF-β pathway in NSCLC. Oncogene 2018; 38:896-912. [PMID: 30181549 PMCID: PMC6756124 DOI: 10.1038/s41388-018-0484-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/06/2018] [Accepted: 08/10/2018] [Indexed: 01/13/2023]
Abstract
Non-small cell lung cancer (NSCLC) remains a major cause of death worldwide. As metastatic disease is primarily responsible for the poor clinical outcome of NSCLC, it is important to understand the process, and its underlying molecular mechanism as well, via which NSCLC cells disseminate. In this study, we identified a new competing endogenous RNA (ceRNA), namely, the MYEOV transcript, and found that it is upregulated in NSCLC and associated with a poor prognosis of the disease. We further uncovered that the MYEOV ceRNA plays a critical role in the invasion and metastasis of NSCLC cells. Intriguingly, the MYEOV ceRNA exerted its pro-metastatic function independent of its protein-coding capacity, but in a miR-30c-2-3p binding-dependent manner. Further experiments demonstrated that the MYEOV ceRNA sequestered miR-30c-2-3p from binding its targets TGFBR2 and USP15 mRNAs, which in turn leading to constitutive activation of TGF-β signaling and tumor progression in NSCLC. By identifying a new layer of regulatory modality for TGF-β signaling, our findings extend the current understanding on the molecular mechanism mediating NSCLC progression and highlight a potential role of MYEOV transcript to serve as the therapeutic target.
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Affiliation(s)
- Lishan Fang
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Central Laboratory of The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shanshan Wu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xun Zhu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, China
| | - Junchao Cai
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Jueheng Wu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhenjian He
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Lei Liu
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.,Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Musheng Zeng
- State Key Laboratory of Oncology in South China, Department of Experimental Research, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Erwei Song
- Department of Breast Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jun Li
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Mengfeng Li
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China. .,Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.
| | - Hongyu Guan
- Department of Endocrinology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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15
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Papamichos SI, Margaritis D, Kotsianidis I. Adaptive Evolution Coupled with Retrotransposon Exaptation Allowed for the Generation of a Human-Protein-Specific Coding Gene That Promotes Cancer Cell Proliferation and Metastasis in Both Haematological Malignancies and Solid Tumours: The Extraordinary Case of MYEOV Gene. SCIENTIFICA 2015; 2015:984706. [PMID: 26568894 PMCID: PMC4629056 DOI: 10.1155/2015/984706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/27/2015] [Indexed: 06/05/2023]
Abstract
The incidence of cancer in human is high as compared to chimpanzee. However previous analysis has documented that numerous human cancer-related genes are highly conserved in chimpanzee. Till date whether human genome includes species-specific cancer-related genes that could potentially contribute to a higher cancer susceptibility remains obscure. This study focuses on MYEOV, an oncogene encoding for two protein isoforms, reported as causally involved in promoting cancer cell proliferation and metastasis in both haematological malignancies and solid tumours. First we document, via stringent in silico analysis, that MYEOV arose de novo in Catarrhini. We show that MYEOV short-isoform start codon was evolutionarily acquired after Catarrhini/Platyrrhini divergence. Throughout the course of Catarrhini evolution MYEOV acquired a gradually elongated translatable open reading frame (ORF), a gradually shortened translation-regulatory upstream ORF, and alternatively spliced mRNA variants. A point mutation introduced in human allowed for the acquisition of MYEOV long-isoform start codon. Second, we demonstrate the precious impact of exonized transposable elements on the creation of MYEOV gene structure. Third, we highlight that the initial part of MYEOV long-isoform coding DNA sequence was under positive selection pressure during Catarrhini evolution. MYEOV represents a Primate Orphan Gene that acquired, via ORF expansion, a human-protein-specific coding potential.
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Affiliation(s)
- Spyros I. Papamichos
- Department of Haematology, School of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Dimitrios Margaritis
- Department of Haematology, School of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ioannis Kotsianidis
- Department of Haematology, School of Medicine, Democritus University of Thrace, 68100 Alexandroupolis, Greece
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16
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mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer. PLoS One 2015; 10:e0117818. [PMID: 25710561 PMCID: PMC4339844 DOI: 10.1371/journal.pone.0117818] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/30/2014] [Indexed: 12/30/2022] Open
Abstract
Intrinsic and acquired resistance to the monoclonal antibody drug trastuzumab is a major problem in the treatment of HER2-positive breast cancer. A deeper understanding of the underlying mechanisms could help to develop new agents. Our intention was to detect genes and single nucleotide polymorphisms (SNPs) affecting trastuzumab efficiency in cell culture. Three HER2-positive breast cancer cell lines with different resistance phenotypes were analyzed. We chose BT474 as model of trastuzumab sensitivity, HCC1954 as model of intrinsic resistance, and BTR50, derived from BT474, as model of acquired resistance. Based on RNA-Seq data, we performed differential expression analyses on these cell lines with and without trastuzumab treatment. Differentially expressed genes between the resistant cell lines and BT474 are expected to contribute to resistance. Differentially expressed genes between untreated and trastuzumab treated BT474 are expected to contribute to drug efficacy. To exclude false positives from the candidate gene set, we removed genes that were also differentially expressed between untreated and trastuzumab treated BTR50. We further searched for SNPs in the untreated cell lines which could contribute to trastuzumab resistance. The analysis resulted in 54 differentially expressed candidate genes that might be connected to trastuzumab efficiency. 90% of 40 selected candidates were validated by RT-qPCR. ALPP, CALCOCO1, CAV1, CYP1A2 and IGFBP3 were significantly higher expressed in the trastuzumab treated than in the untreated BT474 cell line. GDF15, IL8, LCN2, PTGS2 and 20 other genes were significantly higher expressed in HCC1954 than in BT474, while NCAM2, COLEC12, AFF3, TFF3, NRCAM, GREB1 and TFF1 were significantly lower expressed. Additionally, we inferred SNPs in HCC1954 for CAV1, PTGS2, IL8 and IGFBP3. The latter also had a variation in BTR50. 20% of the validated subset have already been mentioned in literature. For half of them we called and analyzed SNPs. These results contribute to a better understanding of trastuzumab action and resistance mechanisms.
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17
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Abstract
The mammalian genome is extensively transcribed, a large fraction of which is divergent transcription from promoters and enhancers that is tightly coupled with active gene transcription. Here, we propose that divergent transcription may shape the evolution of the genome by new gene origination.
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Affiliation(s)
- Xuebing Wu
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Computational and Systems Biology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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18
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French J, Ghoussaini M, Edwards S, Meyer K, Michailidou K, Ahmed S, Khan S, Maranian M, O’Reilly M, Hillman K, Betts J, Carroll T, Bailey P, Dicks E, Beesley J, Tyrer J, Maia AT, Beck A, Knoblauch N, Chen C, Kraft P, Barnes D, González-Neira A, Alonso M, Herrero D, Tessier D, Vincent D, Bacot F, Luccarini C, Baynes C, Conroy D, Dennis J, Bolla M, Wang Q, Hopper J, Southey M, Schmidt M, Broeks A, Verhoef S, Cornelissen S, Muir K, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Fasching P, Loehberg C, Ekici A, Beckmann M, Peto J, dos Santos Silva I, Johnson N, Aitken Z, Sawyer E, Tomlinson I, Kerin M, Miller N, Marme F, Schneeweiss A, Sohn C, Burwinkel B, Guénel P, Truong T, Laurent-Puig P, Menegaux F, Bojesen S, Nordestgaard B, Nielsen S, Flyger H, Milne R, Zamora M, Arias Perez J, Benitez J, Anton-Culver H, Brenner H, Müller H, Arndt V, Stegmaier C, Meindl A, Lichtner P, Schmutzler R, Engel C, Brauch H, Hamann U, Justenhoven C, Aaltonen K, Heikkilä P, Aittomäki K, Blomqvist C, Matsuo K, Ito H, Iwata H, Sueta A, Bogdanova N, Antonenkova N, Dörk T, Lindblom A, Margolin S, Mannermaa A, Kataja V, Kosma VM, Hartikainen J, Wu A, Tseng CC, Van Den Berg D, Stram D, Lambrechts D, Peeters S, Smeets A, Floris G, Chang-Claude J, Rudolph A, Nickels S, Flesch-Janys D, Radice P, Peterlongo P, Bonanni B, Sardella D, Couch F, Wang X, Pankratz V, Lee A, Giles G, Severi G, Baglietto L, Haiman C, Henderson B, Schumacher F, Le Marchand L, Simard J, Goldberg M, Labrèche F, Dumont M, Teo S, Yip C, Ng CH, Vithana E, Kristensen V, Zheng W, Deming-Halverson S, Shrubsole M, Long J, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Grip M, Andrulis I, Knight J, Glendon G, Mulligan A, Devilee P, Seynaeve C, García-Closas M, Figueroa J, Chanock S, Lissowska J, Czene K, Klevebring D, Schoof N, Hooning M, Martens J, Collée J, Tilanus-Linthorst M, Hall P, Li J, Liu J, Humphreys K, Shu XO, Lu W, Gao YT, Cai H, Cox A, Balasubramanian S, Blot W, Signorello L, Cai Q, Pharoah P, Healey C, Shah M, Pooley K, Kang D, Yoo KY, Noh DY, Hartman M, Miao H, Sng JH, Sim X, Jakubowska A, Lubinski J, Jaworska-Bieniek K, Durda K, Sangrajrang S, Gaborieau V, McKay J, Toland A, Ambrosone C, Yannoukakos D, Godwin A, Shen CY, Hsiung CN, Wu PE, Chen ST, Swerdlow A, Ashworth A, Orr N, Schoemaker M, Ponder B, Nevanlinna H, Brown M, Chenevix-Trench G, Easton D, Dunning A. Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers. Am J Hum Genet 2013; 92:489-503. [PMID: 23540573 PMCID: PMC3617380 DOI: 10.1016/j.ajhg.2013.01.002] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Revised: 12/21/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022] Open
Abstract
Analysis of 4,405 variants in 89,050 European subjects from 41 case-control studies identified three independent association signals for estrogen-receptor-positive tumors at 11q13. The strongest signal maps to a transcriptional enhancer element in which the G allele of the best candidate causative variant rs554219 increases risk of breast cancer, reduces both binding of ELK4 transcription factor and luciferase activity in reporter assays, and may be associated with low cyclin D1 protein levels in tumors. Another candidate variant, rs78540526, lies in the same enhancer element. Risk association signal 2, rs75915166, creates a GATA3 binding site within a silencer element. Chromatin conformation studies demonstrate that these enhancer and silencer elements interact with each other and with their likely target gene, CCND1.
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MESH Headings
- Binding Sites
- Breast Neoplasms/genetics
- Case-Control Studies
- Cell Line, Tumor
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin Immunoprecipitation
- Chromosomes, Human, Pair 11/genetics
- Cyclin D1/genetics
- Cyclin D1/metabolism
- Electrophoretic Mobility Shift Assay
- Enhancer Elements, Genetic/genetics
- Female
- GATA3 Transcription Factor/antagonists & inhibitors
- GATA3 Transcription Factor/genetics
- GATA3 Transcription Factor/metabolism
- Gene Expression Regulation, Neoplastic
- Humans
- Luciferases/metabolism
- Polymorphism, Single Nucleotide/genetics
- Promoter Regions, Genetic/genetics
- RNA, Messenger/genetics
- RNA, Small Interfering/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Silencer Elements, Transcriptional/genetics
- ets-Domain Protein Elk-4/antagonists & inhibitors
- ets-Domain Protein Elk-4/genetics
- ets-Domain Protein Elk-4/metabolism
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Affiliation(s)
- Juliet D. French
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Maya Ghoussaini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Stacey L. Edwards
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kerstin B. Meyer
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Kyriaki Michailidou
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Shahana Ahmed
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Sofia Khan
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029, Finland
| | - Mel J. Maranian
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Martin O’Reilly
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Kristine M. Hillman
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joshua A. Betts
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Carroll
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Peter J. Bailey
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ed Dicks
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jonathan Beesley
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Jonathan Tyrer
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Ana-Teresa Maia
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Andrew Beck
- Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Nicholas W. Knoblauch
- Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Constance Chen
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02215, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02215, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02215, USA
| | - Daniel Barnes
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Anna González-Neira
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - M. Rosario Alonso
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Daniel Herrero
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Daniel C. Tessier
- Centre d’innovation Génome Québec et Université McGill, Montréal, QC H3A 0G1, Canada
| | - Daniel Vincent
- Centre d’innovation Génome Québec et Université McGill, Montréal, QC H3A 0G1, Canada
| | - Francois Bacot
- Centre d’innovation Génome Québec et Université McGill, Montréal, QC H3A 0G1, Canada
| | - Craig Luccarini
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Caroline Baynes
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Don Conroy
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Manjeet K. Bolla
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - John L. Hopper
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Melissa C. Southey
- Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Marjanka K. Schmidt
- Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Annegien Broeks
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Senno Verhoef
- Family Cancer Clinic, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Sten Cornelissen
- Division of Molecular Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Kenneth Muir
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | | | | | | | - Peter A. Fasching
- Department of Medicine, Division of Hematology and Oncology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Christian R. Loehberg
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich Alexander University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Matthias W. Beckmann
- University Breast Center Franconia, Department of Gynecology and Obstetrics, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Julian Peto
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Isabel dos Santos Silva
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Zoe Aitken
- Non-communicable Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Elinor J. Sawyer
- Division of Cancer Studies, NIHR Comprehensive Biomedical Research Centre, Guy’s & St. Thomas’ NHS Foundation Trust in partnership with King’s College London, London SE1 9RT, UK
| | - Ian Tomlinson
- Welcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 7BN, UK
| | - Michael J. Kerin
- Surgery, Clinical Science Institute, Galway University Hospital and National University of Ireland, Galway, Ireland
| | - Nicola Miller
- Surgery, Clinical Science Institute, Galway University Hospital and National University of Ireland, Galway, Ireland
| | - Frederik Marme
- Department of Obstetrics and Gynecology, University of Heidelberg, 69115 Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, 69120 Heidelberg, Germany
| | - Andreas Schneeweiss
- Department of Obstetrics and Gynecology, University of Heidelberg, 69115 Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, 69120 Heidelberg, Germany
| | - Christof Sohn
- Department of Obstetrics and Gynecology, University of Heidelberg, 69115 Heidelberg, Germany
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, 69115 Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Pascal Guénel
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer Team, 94807 Villejuif, France
- University Paris-Sud, UMRS 1018, 94807 Villejuif, France
| | - Thérèse Truong
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer Team, 94807 Villejuif, France
- University Paris-Sud, UMRS 1018, 94807 Villejuif, France
| | - Pierre Laurent-Puig
- Université Paris Sorbonne Cité, UMR-S775 INSERM, 75270 Paris Cedex 06, France
| | - Florence Menegaux
- INSERM (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer Team, 94807 Villejuif, France
- University Paris-Sud, UMRS 1018, 94807 Villejuif, France
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, 2730 Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, 2730 Herlev, Denmark
| | - Børge G. Nordestgaard
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, 2730 Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, 2730 Herlev, Denmark
| | - Sune F. Nielsen
- Copenhagen General Population Study, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, 2730 Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, University of Copenhagen, Copenhagen, 2730 Herlev, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, Copenhagen, 2730 Herlev, Denmark
| | - Roger L. Milne
- Genetic & Molecular Epidemiology Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - M. Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid 28046, Spain
| | | | - Javier Benitez
- Human Genotyping-CEGEN Unit, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid 28029, Spain
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California, Irvine, Irvine, CA 92697, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Heiko Müller
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | | | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, 81675 Munich, Germany
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Rita K. Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Cologne, 50931 Cologne, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christina Justenhoven
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
| | - The GENICA Network
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, 70376 Stuttgart, Germany
- University of Tübingen, 72074 Tübingen, Germany
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, 53113 Bonn, Germany
- Institute and Outpatient Clinic of Occupational Medicine, Saarland University Medical Center and Saarland University Faculty of Medicine, 66421 Homburg, Germany
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), 44789 Bochum, Germany
- Institute of Pathology, Medical Faculty of the University of Bonn, 53123 Bonn, Germany
| | - Kirsimari Aaltonen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029, Finland
- Department of Clinical Genetics, University of Helsinki and Helsinki University Central Hospital, Helsinki, 00029, Finland
| | - Päivi Heikkilä
- Department of Pathology, University of Helsinki and Helsinki University Central Hospital, Helsinki, 00029, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, University of Helsinki and Helsinki University Central Hospital, Helsinki, 00029, Finland
| | - Carl Blomqvist
- Department of Oncology, University of Helsinki and Helsinki University Central Hospital, Helsinki, 00029, Finland
| | - Keitaro Matsuo
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Hiroji Iwata
- Department of Breast Oncology, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan
| | - Aiko Sueta
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya 464-8681, Japan
| | - Natalia V. Bogdanova
- Department of Obstetrics and Gynaecology, Hannover Medical School, 30625 Hannover, Germany
- Department of Radiation Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Natalia N. Antonenkova
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, 223040 Minsk, Belarus
| | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, 30625 Hannover, Germany
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sara Margolin
- Department of Oncology-Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Arto Mannermaa
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70211 Kuopio, Finland
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, 70211 Kuopio, Finland
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, 70211 Kuopio, Finland
- Cancer Center, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Veli-Matti Kosma
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70211 Kuopio, Finland
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jaana M. Hartikainen
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, 70211 Kuopio, Finland
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, Biocenter Kuopio, Cancer Center of Eastern Finland, University of Eastern Finland, 70211 Kuopio, Finland
| | | | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Chiu-chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Daniel O. Stram
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, 3000 Leuven, Belgium
- Vesalius Research Center (VRC), VIB, 3000 Leuven, Belgium
| | - Stephanie Peeters
- Multidisciplinary Breast Center, University Hospital Leuven and KU Leuven, 3000 Leuven, Belgium
| | - Ann Smeets
- Multidisciplinary Breast Center, University Hospital Leuven and KU Leuven, 3000 Leuven, Belgium
| | - Giuseppe Floris
- Multidisciplinary Breast Center, University Hospital Leuven and KU Leuven, 3000 Leuven, Belgium
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Nickels
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Dieter Flesch-Janys
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Cancer Epidemiology/Clinical Cancer Registry and Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), 20133 Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy
| | - Paolo Peterlongo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), 20133 Milan, Italy
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, Istituto Europeo di Oncologia, 20141 Milan, Italy
| | - Domenico Sardella
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, 20139 Milan, Italy
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Vernon S. Pankratz
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Adam Lee
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Graham G. Giles
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria 3053, Australia
| | - Gianluca Severi
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria 3053, Australia
| | - Laura Baglietto
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria 3053, Australia
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Brian E. Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Fredrick Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Loic Le Marchand
- Epidemiology Program, Cancer Research Center, University of Hawaii, Honolulu, HI 96813, USA
| | - Jacques Simard
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, QC G1V 4G2, Canada
| | - Mark S. Goldberg
- Department of Medicine, McGill University, Montreal, QC H3A 1A1, Canada
- Division of Clinical Epidemiology, McGill University Health Centre, Royal Victoria Hospital, Montreal, QC H3A 1A1, Canada
| | - France Labrèche
- Département de médecine sociale et préventive, Département de santé environnementale et santé au travail, Université de Montréal, Montreal, QC H3A 3C2, Canada
| | - Martine Dumont
- Cancer Genomics Laboratory, Centre Hospitalier Universitaire de Québec and Laval University, Québec City, QC G1V 4G2, Canada
| | - Soo Hwang Teo
- Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, 47500 Selangor, Malaysia
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - Cheng Har Yip
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - Char-Hong Ng
- Breast Cancer Research Unit, University Malaya Cancer Research Institute, Faculty of Medicine, University Malaya, 50603 Kuala Lumpur, Malaysia
| | | | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0310 Oslo, Norway
- Faculty of Medicine (Faculty Division Ahus), University of Oslo, 0318 Oslo, Norway
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Sandra Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Martha Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics and Biocenter Oulu, University of Oulu, Oulu University Hospital, 90014 Oulu, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Genetics and Biocenter Oulu, University of Oulu, Oulu University Hospital, 90014 Oulu, Finland
| | - Arja Jukkola-Vuorinen
- Department of Oncology, Oulu University Hospital, University of Oulu, 90014 Oulu, Finland
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, 90014 Oulu, Finland
| | - Irene L. Andrulis
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
- Ontario Cancer Genetics Network, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Julia A. Knight
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5T 3L9, Canada
| | - Gord Glendon
- Ontario Cancer Genetics Network, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON M5G 2C4, Canada
| | - Peter Devilee
- Department of Human Genetics & Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Caroline Seynaeve
- Family Cancer Clinic, Department of Medical Oncology, Erasmus MC-Daniel den Hoed Cancer Center, 3075 EA Rotterdam, the Netherlands
- Department of Medical Oncology, Erasmus University Medical Center, 3075 EA Rotterdam, the Netherlands
| | - Montserrat García-Closas
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research and Breakthrough Breast Cancer Research Centre, London SM2 5NG, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, UK
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20892, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center & Institute of Oncology, 02-781 Warsaw, Poland
| | - Kamila Czene
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17 177, Sweden
| | - Daniel Klevebring
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17 177, Sweden
| | - Nils Schoof
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17 177, Sweden
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus University Medical Center, 3075 EA Rotterdam, the Netherlands
| | - John W.M. Martens
- Department of Medical Oncology, Erasmus University Medical Center, 3075 EA Rotterdam, the Netherlands
| | - J. Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, 3008 AE Rotterdam, the Netherlands
| | | | - Per Hall
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17 177, Sweden
| | - Jingmei Li
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Keith Humphreys
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17 177, Sweden
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Wei Lu
- Shanghai Center for Disease Control and Prevention, Shanghai 200336, China
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai 200032, China
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Angela Cox
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield S10 2RX, UK
| | - Sabapathy P. Balasubramanian
- CRUK/YCR Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield S10 2RX, UK
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
- International Epidemiology Institute, Rockville, MD 20850, USA
| | - Lisa B. Signorello
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
- International Epidemiology Institute, Rockville, MD 20850, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Paul D.P. Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Catherine S. Healey
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mitul Shah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Karen A. Pooley
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Daehee Kang
- Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Keun-Young Yoo
- Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Dong-Young Noh
- Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore
| | - Hui Miao
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117597, Singapore
| | - Jen-Hwei Sng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Xueling Sim
- Centre for Molecular Epidemiology, National University of Singapore, Singapore 117597, Singapore
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, u. Polabska 4, 70-115 Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, u. Polabska 4, 70-115 Szczecin, Poland
| | - Katarzyna Jaworska-Bieniek
- Department of Genetics and Pathology, Pomeranian Medical University, u. Polabska 4, 70-115 Szczecin, Poland
- Postgraduate School of Molecular Medicine, Warsaw Medical University, ul. Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, u. Polabska 4, 70-115 Szczecin, Poland
| | | | - Valerie Gaborieau
- International Agency for Research on Cancer, 69372 Lyon Cedex 08, France
| | - James McKay
- International Agency for Research on Cancer, 69372 Lyon Cedex 08, France
| | - Amanda E. Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research “Demokritos,” Athens 15310, Greece
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Chen-Yang Shen
- Colleague of Public Health, China Medical University, Taichong 40402, Taiwan, ROC
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Pei-Ei Wu
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Shou-Tung Chen
- Department of Surgery, Changhua Christian Hospital, Changhua City, Changhua county 500, Taiwan, ROC
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research and Breakthrough Breast Cancer Research Centre, London SM2 5NG, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, UK
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Nick Orr
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London SW3 6JB, UK
| | - Minouk J. Schoemaker
- Division of Genetics and Epidemiology, Institute of Cancer Research and Breakthrough Breast Cancer Research Centre, London SM2 5NG, UK
| | - Bruce A.J. Ponder
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki 00029, Finland
| | - Melissa A. Brown
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Georgia Chenevix-Trench
- Department of Genetics, Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Douglas F. Easton
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Alison M. Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK
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Wilkerson PM, Reis-Filho JS. the 11q13-q14 amplicon: Clinicopathological correlations and potential drivers. Genes Chromosomes Cancer 2012; 52:333-55. [DOI: 10.1002/gcc.22037] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 11/01/2012] [Indexed: 01/04/2023] Open
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Chung CC, Boland J, Yeager M, Jacobs KB, Zhang X, Deng Z, Matthews C, Berndt SI, Chanock SJ. Comprehensive resequence analysis of a 123-kb region of chromosome 11q13 associated with prostate cancer. Prostate 2012; 72:476-86. [PMID: 22468268 PMCID: PMC3325513 DOI: 10.1002/pros.21450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Genome-wide association studies of prostate cancer have identified single nucleotide polymorphism (SNP) markers in a region of chromosome 11q13.3 in men of European decent. A fine-mapping analysis with tag SNPs in the cancer genetic markers of susceptibility study identified three independent loci, marked by rs10896438, rs12793759, and rs10896449. This study further annotates common and uncommon variation across this region. METHODS A next generation resequence analysis of a 122.9-kb region of 11q13.3(68,642,755-68,765,690) was conducted in 78 unrelated individuals of European background,1 CEPH trio, and 1 YRI trio. RESULTS In total, 644 polymorphic loci were identified by our sequence analysis. Of these,166 variants—118 SNPs and 48 insertion-deletion polymorphisms (indels)—were novel,namely not present in the 1000 Genomes or International HapMap Projects. We identified 22,25, 6, and 4 variants strongly correlated (r2 ≥ 0.8) with rs10896438, rs10896449, rs12793759,and rs11228565, respectively. HapMap SNPs were in linkage disequilibrium (r2 ≥ 0.8) with 48%, 69%, 14%, and 60% of SNPs marking bins by rs10896438, rs10896449, rs12793759, and rs11228565, respectively. CONCLUSIONS Our next generation resequence analysis compliments publicly available datasets of European descent (HapMap, build 28 and 1000 Genome, Pilot 1, October 2010),underscoring the value of targeted resequence analysis prior to initiating functional studies based on public databases alone. Increasing the number of common variants enables investigators to better prioritize variants for functional studies designed to uncover the biological basis of the direct association(s) in the region.
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Affiliation(s)
- Charles C Chung
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Tao S, Wang Z, Feng J, Hsu FC, Jin G, Kim ST, Zhang Z, Gronberg H, Zheng LS, Isaacs WB, Xu J, Sun J. A genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants. Carcinogenesis 2012; 33:598-603. [PMID: 22219177 DOI: 10.1093/carcin/bgr316] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified ∼30 single-nucleotide polymorphisms (SNPs) consistently associated with prostate cancer (PCa) risk. To test the hypothesis that other sequence variants in the genome may interact with those 32 known PCa risk-associated SNPs identified from GWAS to affect PCa risk, we performed a systematic evaluation among three existing PCa GWAS populations: CAncer of the Prostate in Sweden population, a Johns Hopkins Hospital population, and the Cancer Genetic Markers of Susceptibility population, with a total sample size of 4723 PCa cases and 4792 control subjects. Meta-analysis of the interaction term between each of those 32 SNPs and SNPs in the genome was performed in three PCa GWAS populations. The most significant interaction detected was between rs12418451 in MYEOV and rs784411 in CEP152, with a P(interaction) of 1.15 × 10(-7) in the meta-analysis. In addition, we emphasized two pairs of interactions with potential biological implication, including an interaction between rs7127900 near insulin-like growth factor-2 (IGF2)/IGF2AS and rs12628051 in TNRC6B, with a P(interaction) of 3.39 × 10(-6) and an interaction between rs7679763 near TET2 and rs290258 in SYK, with a P(interaction) of 1.49 × 10(-6). Those results show statistical evidence for novel loci interacting with known risk-associated SNPs to modify PCa risk. The interacting loci identified provide hints on the underlying molecular mechanism of the associations with PCa risk for the known risk-associated SNPs. Additional studies are warranted to further confirm the interaction effects detected in this study.
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Affiliation(s)
- Sha Tao
- Center for Genetic Epidemiology and Prevention, Van Andel Research Institute, Grand Rapids, MI, USA
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Takita J, Chen Y, Okubo J, Sanada M, Adachi M, Ohki K, Nishimura R, Hanada R, Igarashi T, Hayashi Y, Ogawa S. Aberrations of NEGR1 on 1p31 and MYEOV on 11q13 in neuroblastoma. Cancer Sci 2011; 102:1645-50. [DOI: 10.1111/j.1349-7006.2011.01995.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Brown J, Bothma H, Veale R, Willem P. Genomic imbalances in esophageal carcinoma cell lines involve Wnt pathway genes. World J Gastroenterol 2011; 17:2909-23. [PMID: 21734802 PMCID: PMC3129505 DOI: 10.3748/wjg.v17.i24.2909] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 10/30/2010] [Accepted: 11/06/2010] [Indexed: 02/06/2023] Open
Abstract
AIM: To identify molecular markers shared across South African esophageal squamous cell carcinoma (ESCC) cell lines using cytogenetics, fluorescence in situ hybridization (FISH) and single nucleotide polymorphism (SNP) array copy number analysis.
METHODS: We used conventional cytogenetics, FISH, and multicolor FISH to characterize the chromosomal rearrangements of five ESCC cell lines established in South Africa. The whole genome copy number profile was established from 250K SNP arrays, and data was analyzed with the CNAT 4.0 and GISTIC software.
RESULTS: We detected common translocation breakpoints involving chromosomes 1p11-12 and 3p11.2, the latter correlated with the deletion, or interruption of the EPHA3 gene. The most significant amplifications involved the following chromosomal regions and genes: 11q13.3 (CCND1, FGF3, FGF4, FGF19, MYEOV), 8q24.21(C-MYC, FAM84B), 11q22.1-q22.3 (BIRC2, BIRC3), 5p15.2 (CTNND2), 3q11.2-q12.2 (MINA) and 18p11.32 (TYMS, YES1). The significant deletions included 1p31.2-p31.1 (CTH, GADD45α, DIRAS3), 2q22.1 (LRP1B), 3p12.1-p14.2 (FHIT), 4q22.1-q32.1 (CASP6, SMAD1), 8p23.2-q11.1 (BNIP3L) and 18q21.1-q21.2 (SMAD4, DCC). The 3p11.2 translocation breakpoint was shared across four cell lines, supporting a role for genes involved at this site, in particular, the EPHA3 gene which has previously been reported to be deleted in ESCC.
CONCLUSION: The finding that a significant number of genes that were amplified (FGF3, FGF4, FGF19, CCND1 and C-MYC) or deleted (SFRP2 gene) are involved in the Wnt and fibroblast growth factor signaling pathways, suggests that these pathways may be activated in these cell lines.
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Chung CC, Chanock SJ. Current status of genome-wide association studies in cancer. Hum Genet 2011; 130:59-78. [DOI: 10.1007/s00439-011-1030-9] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 06/02/2011] [Indexed: 12/18/2022]
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Chung CC, Ciampa J, Yeager M, Jacobs KB, Berndt SI, Hayes RB, Gonzalez-Bosquet J, Kraft P, Wacholder S, Orr N, Yu K, Hutchinson A, Boland J, Chen Q, Feigelson HS, Thun MJ, Diver WR, Albanes D, Virtamo J, Weinstein S, Schumacher FR, Cancel-Tassin G, Cussenot O, Valeri A, Andriole GL, Crawford ED, Haiman CA, Henderson BE, Kolonel L, Le Marchand L, Siddiq A, Riboli E, Key TJ, Kaaks R, Isaacs WB, Isaacs SD, Grönberg H, Wiklund F, Xu J, Vatten LJ, Hveem K, Njolstad I, Gerhard DS, Tucker M, Hoover RN, Fraumeni JF, Hunter DJ, Thomas G, Chatterjee N, Chanock SJ. Fine mapping of a region of chromosome 11q13 reveals multiple independent loci associated with risk of prostate cancer. Hum Mol Genet 2011; 20:2869-78. [PMID: 21531787 DOI: 10.1093/hmg/ddr189] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Genome-wide association studies have identified prostate cancer susceptibility alleles on chromosome 11q13. As part of the Cancer Genetic Markers of Susceptibility (CGEMS) Initiative, the region flanking the most significant marker, rs10896449, was fine mapped in 10 272 cases and 9123 controls of European origin (10 studies) using 120 common single nucleotide polymorphisms (SNPs) selected by a two-staged tagging strategy using HapMap SNPs. Single-locus analysis identified 18 SNPs below genome-wide significance (P< 10(-8)) with rs10896449 the most significant (P= 7.94 × 10(-19)). Multi-locus models that included significant SNPs sequentially identified a second association at rs12793759 [odds ratio (OR) = 1.14, P= 4.76 × 10(-5), adjusted P= 0.004] that is independent of rs10896449 and remained significant after adjustment for multiple testing within the region. rs10896438, a proxy of previously reported rs12418451 (r(2)= 0.96), independent of both rs10896449 and rs12793759 was detected (OR = 1.07, P= 5.92 × 10(-3), adjusted P= 0.054). Our observation of a recombination hotspot that separates rs10896438 from rs10896449 and rs12793759, and low linkage disequilibrium (rs10896449-rs12793759, r(2)= 0.17; rs10896449-rs10896438, r(2)= 0.10; rs12793759-rs10896438, r(2)= 0.12) corroborate our finding of three independent signals. By analysis of tagged SNPs across ∼123 kb using next generation sequencing of 63 controls of European origin, 1000 Genome and HapMap data, we observed multiple surrogates for the three independent signals marked by rs10896449 (n= 31), rs10896438 (n= 24) and rs12793759 (n= 8). Our results indicate that a complex architecture underlying the common variants contributing to prostate cancer risk at 11q13. We estimate that at least 63 common variants should be considered in future studies designed to investigate the biological basis of the multiple association signals.
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Affiliation(s)
- Charles C Chung
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute/NIH, 8717 Grovemont Circle, Bethesda, MD 20892, USA
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26
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Lawlor G, Doran PP, MacMathuna P, Murray DW. MYEOV (myeloma overexpressed gene) drives colon cancer cell migration and is regulated by PGE2. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2010; 29:81. [PMID: 20569498 PMCID: PMC2904283 DOI: 10.1186/1756-9966-29-81] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 06/22/2010] [Indexed: 11/10/2022]
Abstract
Introduction We have previously reported that Myeov (MYEloma OVerexpressed gene) expression is enhanced in colorectal cancer (CRC) and that it promotes CRC cell proliferation and invasion. The role of Myeov in CRC migration is unclear. ProstaglandinE2 (PGE 2) is a known factor in promoting CRC carcinogenesis. The role of PGE 2 in modulating Myeov expression has also not been defined. Aim To assess the role of Myeov expression in CRC cell migration and to evaluate the role of PGE 2 in Myeov bioactivity. Methods siRNA mediated Myeov knockdown was achieved in T84 CRC cells. Knockdown was assessed using quantitative real time PCR. The effect of knockdown on CRC cell migration was assessed using a scratch wound healing assay. Separately, T84 cells were treated with PGE 2 (0.00025 μ M, 0.1 μ M and 1 μ M) from 30 min to 3 hours and the effect on Myeov gene expression was assessed using real time PCR. Results Myeov knockdown resulted in a significant reduction in CRC cell migration, observable as early as 12 hours (P < 0.05) with a 39% reduction compared to control at 36 hours (p < 0.01). Myeov expression was enhanced after treatment with PGE 2, with the greatest effect seen at 60 mins for all 3 PGE 2 doses. This response was dose dependent with a 290%, 550% & 1,000% increase in Myeov expression for 0.00025 μ M, 0.1 μ M and 1 μ M PGE 2 respectively. Conclusion In addition to promoting CRC proliferation and invasion, our findings indicate that Myeov stimulates CRC cell migration, and its expression may be PGE 2 dependant.
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Affiliation(s)
- Garrett Lawlor
- Gastrointestinal Unit, Mater Misericordiae University Hospital, Eccles Street, Dublin 7, Ireland
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Comprehensive genetic and functional characterization of IPH-926: a novelCDH1-null tumour cell line from human lobular breast cancer. J Pathol 2009; 217:620-32. [DOI: 10.1002/path.2495] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Co-amplified genes at 8p12 and 11q13 in breast tumors cooperate with two major pathways in oncogenesis. Oncogene 2009; 28:1892-903. [PMID: 19330026 PMCID: PMC2722962 DOI: 10.1038/onc.2009.34] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Co-amplification at chromosomes 8p11-8p12 and 11q12-11q14 occurs often in breast tumors, suggesting possible cooperation between genes in these regions in oncogenesis. We used high resolution array comparative genomic hybridization (array CGH) to map the minimal amplified regions. The 8p and 11q amplicons are complex and consist of at least four amplicon cores at each site. Candidate oncogenes mapping to these regions were identified by combining copy number and RNA and protein expression analyses. These studies also suggested that CCND1 at 11q13 induced expression of ZNF703 mapping at 8p12, which was subsequently shown to be mediated via the Rb/E2F pathway. Nine candidate oncogenes from 8p12 and four from 11q13 were further evaluated for oncogenic function. None of the genes individually promoted colony formation in soft agar or collaborated with each other functionally. On the other hand, FGFR1 and DDHD2 at 8p12 cooperated functionally with MYC, while CCND1 and ZNF703 cooperated with a dominant negative form of TP53. These observations highlight the complexity and functional consequences of the genomic rearrangements that occur in these breast cancer amplicons, including transcriptional cross-talk between genes in the 8p and 11q amplicons, as well as their cooperation with major pathways of tumorigenesis.
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Gupta VK, Feber A, Xi L, Pennathur A, Wu M, Luketich JD, Godfrey TE. Association between CCND1 G/A870 polymorphism, allele-specific amplification, cyclin D1 expression, and survival in esophageal and lung carcinoma. Clin Cancer Res 2009; 14:7804-12. [PMID: 19047108 DOI: 10.1158/1078-0432.ccr-08-0744] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE Cyclin D1 is found on 11q13, which is a region frequently amplified in several tumor types. The CCND1 locus gives rise to at least two protein isoforms of D1 (D1a and D1b). A common G/A polymorphism (G/A870) is thought to influence the expression levels of D1a and D1b. D1b has been suggested to be increased in the presence of the A allele and more oncogenic than D1a. Furthermore, the A allele has been reported to correlate with increased risk of carcinoma in several tumor types, suggesting that this polymorphism and D1b are important in tumor progression. However, contradictory data about the polymorphism, D1 variant expression, and correlation with survival have been reported. We explored the relationship between gene amplification, G/A870 genotype, D1a and D1b expression, and overall survival in esophageal adenocarcinoma and non-small cell lung cancer. EXPERIMENTAL DESIGN DNA and RNA were isolated from 54 esophageal adenocarcinoma samples and 89 non-small cell lung cancer samples and were analyzed for gene amplification, genotype at the polymorphism, gene expression, and association with overall survival. RESULTS The D1 variant expression did not correlate with amplification, genotype, or overall survival in either tumor type. The total D1 expression correlated with decreased patient survival. Several other genes on 11q13 also seem to be overexpressed and correlated with decreased survival. CONCLUSIONS We report that the G/A870 polymorphism does not correlate with patient survival, or with D1a or D1b expression. However, the total D1 expression and the expression of several other genes on 11q13 seem to be associated with esophageal adenocarcinoma patient survival.
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Affiliation(s)
- Vanita K Gupta
- Department of Pathology, Mount Sinai School of Medicine, New York, New York 10029, USA
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30
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Song H, Koessler T, Ahmed S, Ramus SJ, Kjaer SK, Dicioccio RA, Wozniak E, Hogdall E, Whittemore AS, McGuire V, Ponder BAJ, Turnbull C, Hines S, Rahman N, Eeles RA, Easton DF, Gayther SA, Dunning AM, Pharoah PDP. Association study of prostate cancer susceptibility variants with risks of invasive ovarian, breast, and colorectal cancer. Cancer Res 2008; 68:8837-42. [PMID: 18974127 PMCID: PMC2666188 DOI: 10.1158/0008-5472.can-08-2363] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Several prostate cancer susceptibility loci have recently been identified by genome-wide association studies. These loci are candidates for susceptibility to other epithelial cancers. The aim of this study was to test these tag single nucleotide polymorphisms (SNP) for association with invasive ovarian, colorectal, and breast cancer. Twelve prostate cancer-associated tag SNPs were genotyped in ovarian (2,087 cases/3,491 controls), colorectal (2,148 cases/2,265 controls) and breast (first set, 4,339 cases/4,552 controls; second set, 3,800 cases/3,995 controls) case-control studies. The primary test of association was a comparison of genotype frequencies between cases and controls, and a test for trend stratified by study where appropriate. Genotype-specific odds ratios (OR) were estimated by logistic regression. SNP rs2660753 (chromosome 3p12) showed evidence of association with ovarian cancer [per minor allele OR, 1.19; 95% confidence interval (95% CI), 1.04-1.37; P(trend) = 0.012]. This association was stronger for the serous histologic subtype (OR, 1.29; 95% CI, 1.09-1.53; P = 0.003). SNP rs7931342 (chromosome 11q13) showed some evidence of association with breast cancer (per minor allele OR, 0.95; 95% CI, 0.91-0.99; P(trend) = 0.028). This association was somewhat stronger for estrogen receptor-positive tumors (OR, 0.92; 95% CI, 0.87-0.98; P = 0.011). None of these tag SNPs were associated with risk of colorectal cancer. In conclusion, loci associated with risk of prostate cancer may also be associated with ovarian and breast cancer susceptibility. However, the effects are modest and warrant replication in larger studies.
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Affiliation(s)
- Honglin Song
- CR-UK Department of Oncology, Strangeways Research Laboratory, University of Cambridge, Cambridge, United Kingdom.
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Gibcus JH, Menkema L, Mastik MF, Hermsen MA, de Bock GH, van Velthuysen MLF, Takes RP, Kok K, Alvarez Marcos CA, van der Laan BFAM, van den Brekel MWM, Langendijk JA, Kluin PM, van der Wal JE, Schuuring E. Amplicon mapping and expression profiling identify the Fas-associated death domain gene as a new driver in the 11q13.3 amplicon in laryngeal/pharyngeal cancer. Clin Cancer Res 2008; 13:6257-66. [PMID: 17975136 DOI: 10.1158/1078-0432.ccr-07-1247] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PURPOSE Amplification of the 11q13 region is a frequent event in human cancer. The highest incidence (36%) is found in head and neck squamous cell carcinomas. Recently, we reported that the amplicon size in 30 laryngeal and pharyngeal carcinomas with 11q13 amplification is determined by unique genomic structures, resulting in the amplification of a set of genes rather than a single gene. EXPERIMENTAL DESIGN To investigate which gene(s) drive the 11q13 amplicon, we determined the smallest region of overlap with amplification and the expression levels of all genes within this amplicon. RESULTS Using array-based comparative genomic hybridization analysis, we detected a region of approximately 1.7 Mb containing 13 amplified genes in more than 25 of the 29 carcinomas. Quantitative reverse transcription-PCR revealed that overexpression of 8 potential driver genes including, cyclin D1, cortactin, and Fas-associated death domain (FADD), correlated significantly with DNA amplification. FADD protein levels correlated well with DNA amplification, implicating that FADD is also a candidate driver gene in the 11q13 amplicon. Analysis of 167 laryngeal carcinomas showed that increased expression of FADD (P = 0.007) and Ser(194) phosphorylated FADD (P = 0.011) were associated with a worse disease-specific survival. FADD was recently reported to be involved in cell cycle regulation, and cancer cells expressing high levels of the Ser(194) phosphorylated isoform of FADD proved to be more sensitive to Taxol-induced cell cycle arrest. CONCLUSION Because of the frequent amplification of the 11q13 region and concomitant overexpression of FADD in head and neck squamous cell carcinomas, we hypothesize that FADD is a marker to select patients that might benefit from Taxol-based chemoradiotherapy.
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Affiliation(s)
- Johan H Gibcus
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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Lambros MBK, Natrajan R, Reis-Filho JS. Chromogenic and fluorescent in situ hybridization in breast cancer. Hum Pathol 2007; 38:1105-22. [PMID: 17640550 DOI: 10.1016/j.humpath.2007.04.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 04/21/2007] [Accepted: 04/23/2007] [Indexed: 11/29/2022]
Abstract
Fluorescent (FISH) and chromogenic (CISH) in situ hybridization have recently become part of the diagnostic armamentarium of breast pathologists. HER2 gene testing by FISH and/or CISH has become an integral part of the diagnostic workup for patients with breast cancer. In this era of high throughput technologies, these techniques have proven instrumental for the validation of results from microarray-based comparative genomic hybridization and for the identification of novel oncogenes and tumor suppressor genes. Furthermore, FISH and CISH applied to tissue microarrays have expedited the characterization of genomic changes associated with specific breast cancer molecular subtypes and the identification of novel prognostic and predictive markers. In this review, we provide in this review a critical assessment of CISH and FISH and the impact of the analysis of amplification of specific oncogenes (eg, HER2, EGFR, MYC, CCND1, and FGFR1) and deletion of tumor suppressor genes (eg, BRCA1 and BRCA2) on our understanding of breast cancer.
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Affiliation(s)
- Maryou B K Lambros
- Molecular Pathology Laboratory, The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, SW3 6JB London, UK
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Paterson AL, Pole JCM, Blood KA, Garcia MJ, Cooke SL, Teschendorff AE, Wang Y, Chin SF, Ylstra B, Caldas C, Edwards PAW. Co-amplification of 8p12 and 11q13 in breast cancers is not the result of a single genomic event. Genes Chromosomes Cancer 2007; 46:427-39. [PMID: 17285574 DOI: 10.1002/gcc.20424] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Epithelial cancers frequently have multiple amplifications, and particular amplicons tend to occur together. These co-amplifications have been suggested to result from amplification of pre-existing junctions between two chromosomes, that is, translocation junctions. We investigated this hypothesis for two amplifications frequent in breast cancer, at 8p12 and 11q13, which had been reported to be associated in Southern blot studies. We confirmed that both genomic amplification and expression of genes was correlated between the frequently-amplified regions of 8p and 11q, in array CGH and microarray expression data, supporting the importance of co-amplification. We examined by FISH the physical structure of co-amplifications that we had identified by array CGH, in five breast cancer cell lines (HCC1500, MDA-MB-134, MDA-MB-175, SUM44, and ZR-75-1), four breast tumors, and a pancreatic cancer cell line (SUIT2). We found a variety of arrangements: amplification of translocation junctions; entirely independent amplification of the two regions on separate chromosomes; and separate amplification of 8p and 11q sequences in distinct sites on the same rearranged chromosome. In this last arrangement, interphase nuclei often showed intermingling of FISH signals from 8p12 and 11q13, giving a false impression that the sequences were interdigitated. We conclude that co-amplification of the main 8p and 11q amplicons in breast tumors is not usually the result of a preceding translocation event but most likely reflects selection of clones that have amplified both loci. This article contains supplementary material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.
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Affiliation(s)
- Anna L Paterson
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Cambridge, UK
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Leyden J, Murray D, Moss A, Arumuguma M, Doyle E, McEntee G, O'Keane C, Doran P, MacMathuna P. Net1 and Myeov: computationally identified mediators of gastric cancer. Br J Cancer 2006; 94:1204-12. [PMID: 16552434 PMCID: PMC2361249 DOI: 10.1038/sj.bjc.6603054] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gastric adenocarcinoma (GA) is a significant cause of mortality worldwide. The molecular mechanisms of GA remain poorly characterised. Our aim was to characterise the functional activity of the computationally identified genes, NET 1 and MYEOV in GA. Digital Differential Display was used to identify genes altered expression in GA-derived EST libraries. mRNA levels of a subset of genes were quantitated by qPCR in a panel of cell lines and tumour tissue. The effect of pro- and anti-inflammatory stimuli on gene expression was investigated. Cell proliferation and invasion were measured using in an in-vitro GA model following inhibition of expression using siRNA. In all, 23 genes not previously reported in association with GA were identified. Two genes, Net1 and Myeov, were selected for further analysis and increased expression was detected in GA tissue compared to paired normal tissue using quantitative PCR. siRNA-mediated downregulation of Net1 and Myeov resulted in decreased proliferation and invasion of gastric cancer cells in vitro. These functional studies highlight a putative role for NET1 and Myeov in the development and progression of gastric cancer. These genes may provide important targets for intervention in GA, evidenced by their role in promoting invasion and proliferation, key phenotypic hallmarks of cancer cells.
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Affiliation(s)
- J Leyden
- Gastrointestinal Unit, Mater Misericordiae University Hospital, University College Dublin, Ireland
| | - D Murray
- Genome Resource Unit, Department of Medicine and Therapeutics, Mater Misericordiae University Hospital, University College Dublin, Dublin 7, Ireland
| | - A Moss
- Gastrointestinal Unit, Mater Misericordiae University Hospital, University College Dublin, Ireland
| | - M Arumuguma
- Department of Surgery, Mater Misericordiae University Hospital, University College Dublin, Ireland
| | - E Doyle
- Department of Pathology, Mater Misericordiae University Hospital, University College Dublin, Ireland
| | - G McEntee
- Department of Surgery, Mater Misericordiae University Hospital, University College Dublin, Ireland
| | - C O'Keane
- Department of Pathology, Mater Misericordiae University Hospital, University College Dublin, Ireland
| | - P Doran
- Genome Resource Unit, Department of Medicine and Therapeutics, Mater Misericordiae University Hospital, University College Dublin, Dublin 7, Ireland
- Genome Resource Unit, Department of Medicine and Therapeutics, Mater Misericordiae University Hospital, University College Dublin, Dublin 7, Ireland. E-mail:
| | - P MacMathuna
- Gastrointestinal Unit, Mater Misericordiae University Hospital, University College Dublin, Ireland
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Reis-Filho JS, Savage K, Lambros MBK, James M, Steele D, Jones RL, Dowsett M. Cyclin D1 protein overexpression and CCND1 amplification in breast carcinomas: an immunohistochemical and chromogenic in situ hybridisation analysis. Mod Pathol 2006; 19:999-1009. [PMID: 16648863 DOI: 10.1038/modpathol.3800621] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Conflicting results on the prevalence of cyclin D1 ovexpression and its correlation with CCND1 amplification and outcome of breast cancer patients have been reported. Owing to limited sensitivity and specificity of most antibodies against cyclin D1, evaluation of cyclin D1 immunoexpression is reported to be problematic. The aims of this study were to assess the prevalence of cyclin D1 expression in breast carcinomas using the SP4 rabbit monoclonal antibody; to correlate cyclin D1 expression with amplification, assessed using chromogenic in situ hybridisation (CISH); and to analyse the relationship between CCND1 amplification and overexpression with clinicopathological parameters and outcome in a tissue microarray containing replicate tumour samples from 245 breast cancer patients. Immunohistochemistry for cyclin D1 was performed using the SP4 and the results were scored according to the Allred scoring system. CISH was carried out using the Zymed CCND1 SpotLight probe. CISH signals were counted in 60 morphologically unequivocal neoplastic cells. Amplification was defined as >5 signals per nucleus in more than 50% of cancer cells, or when large gene copy clusters were seen. Strong cyclin D1 expression and CCND1 amplification were found in 67.4 and 14.5% of the cases, respectively. A strong correlation between cyclin D1 overexpression and CCND1 amplification was demonstrated (P<0.0001). Cyclin D1 expression showed a positive correlation with hormone receptor expression (both ER and PgR, P<0.0001). An inverse correlation was observed between an immunohistochemical panel of 'basal-like' markers and both cyclin D1 overexpression (P<0.0001) and CCND1 amplification (P<0.0001). On univariate analysis cyclin D1 expression showed a correlation with longer overall survival (OS). Neither cyclin D1 nor CCND1 were independent prognostic factors for disease-free survival or OS. The results of this study confirm the association between cyclin D1 overexpression and positivity for hormone receptors and the lack of CCND1 amplification in basal-like breast carcinomas.
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Affiliation(s)
- Jorge S Reis-Filho
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK.
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36
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Moss AC, Lawlor G, Murray D, Tighe D, Madden SF, Mulligan AM, Keane CO, Brady HR, Doran PP, MacMathuna P. ETV4 and Myeov knockdown impairs colon cancer cell line proliferation and invasion. Biochem Biophys Res Commun 2006; 345:216-21. [PMID: 16678123 DOI: 10.1016/j.bbrc.2006.04.094] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2006] [Accepted: 04/19/2006] [Indexed: 11/20/2022]
Abstract
We have identified novel colorectal cancer-associated genes using NCBI's UNIGENE cDNA libraries. Colon cancer libraries were examined using Digital Differential Display and disease-associated genes were selected. Among these were ETV4 and MYEOV, novel colorectal cancer-associated genes. Samples of matched normal and neoplastic colon were obtained from human subjects and gene expression was quantified using real-time PCR. ETV4 gene expression was significantly increased in colonic neoplasia in comparison to matched normal colonic tissue (p<0.05). Myeov expression was also increased in colon neoplasia in comparison to matched normal tissue. The effect of siRNA-mediated knockdown of ETV4 and Myeov on cell proliferation and invasion was assessed. ETV4 knockdown resulted in a 90% decrease in cell proliferation (p<0.05) and a 67% decrease in cell invasion. Myeov knockdown resulted in a 48% decrease in cell proliferation (p<0.05) and a 36% decrease in cell invasion. These data suggest that ETV4 and Myeov may provide novel targets for therapeutic intervention.
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Affiliation(s)
- Alan C Moss
- Conway Institute of Biomolecular and Biomedical Research, UCD, Ireland.
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37
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Thorns C, Bastian B, Pinkel D, Roydasgupta R, Fridlyand J, Merz H, Krokowski M, Bernd HW, Feller AC. Chromosomal aberrations in angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma unspecified: A matrix-based CGH approach. Genes Chromosomes Cancer 2006; 46:37-44. [PMID: 17044049 DOI: 10.1002/gcc.20386] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Angioimmunoblastic T-cell lymphoma (AILT) is a histopathologically well-defined entity. However, despite a number of cytogenetic studies, the genetic basis of this lymphoma entity is not clear. Moreover, there is an overlap to some cases of peripheral T-cell lymphoma unspecified (PTCL-u) in respect to morphological and genetic features. We used array-based comparative genomic hybridization (CGH) to study genetic imbalances in 39 AILT and 20 PTCL-u. Array-based CGH revealed complex genetic imbalances in both AILT and PTCL-u. Chromosomal imbalances were more frequent in PTCL-u than in AILT and gains exceeded the losses. The most recurrent changes in AILT were gains of 22q, 19, and 11p11-q14 (11q13) and losses of 13q. The most frequent changes in PTCL-u were gains of 17 (17q11-q25), 8 (involving the MYC locus at 8q24), and 22q and losses of 13q and 9 (9p21-q33). Interestingly, gains of 4q (4q28-q31 and 4q34-qtel), 8q24, and 17 were significantly more frequent in PTCL-u than in AILT. The regions 6q (6q16-q22) and 11p11 were predominantly lost in PTCL-u. Moreover, we could identify a recurrent gain of 11q13 in both AILT and PTCL-u, which has previously not been described in AILT. Trisomies 3 and 5, which have been described as typical aberrations in AILT, were identified only in a small number of cases. In conclusion, CGH revealed common genetic events in peripheral T-cell lymphomas as well as peculiar differences between AILT and PTCL-u.
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Affiliation(s)
- Christoph Thorns
- Department of Pathology, German Consultation and Reference Center for Lymphomas, University Clinic Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.
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38
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de Almeida RA, Heuser T, Blaschke R, Bartram CR, Janssen JWG. Control of MYEOV protein synthesis by upstream open reading frames. J Biol Chem 2005; 281:695-704. [PMID: 16275643 DOI: 10.1074/jbc.m511467200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The myeov gene has been isolated by the tumorigenicity assay and is localized at chromosome 11q13, a frequent site for chromosomal rearrangements in various carcinomas and B-cell neoplasms. In addition, myeov is coamplified with cyclin D1 and overexpressed in carcinomas of various organs. The mechanisms of myeov regulation remain enigmatic. The 5'-untranslated region (5'-UTR) of the myeov gene is long, encompasses several upstream AUGs, and is predicted to fold in a strong secondary structure, suggesting that its translation might be regulated by an internal ribosomal entry site. Here we show that initial experiments using monocistronic and dicistronic reporter constructs supported this assumption. However, the application of in vitro transcription/translation assays, Northern blot analysis, and promoterless dicistronic constructs revealed promoter activity of the myeov 5'-UTR. DNA transfection of dicistronic DNA constructs, normal and mutated forms of myeov cDNA fragments cloned in a eukaryotic expression vector, and direct RNA transfection analysis revealed that upstream AUG triplets in the 5'-UTR of the myeov transcript abrogate translation. Alternative splicing mechanisms in specific cell types and/or developmental stage may evade this translation control. Control experiments suggest that the 5'-UTR from encephalomyocarditis virus, when inserted at the midpoint of a dicistronic vector, is also able to function as a cryptic promoter.
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MESH Headings
- 5' Untranslated Regions
- Base Sequence
- Blotting, Northern
- Cell Line
- Chromosomes, Human, Pair 11
- Cyclin D1/metabolism
- DNA/metabolism
- DNA, Complementary/metabolism
- Encephalomyocarditis virus/genetics
- Gene Expression Regulation, Neoplastic
- Genes, Reporter
- Genetic Vectors
- Humans
- Immunoblotting
- Luciferases/metabolism
- Models, Genetic
- Molecular Sequence Data
- Mutation
- Oncogene Proteins/biosynthesis
- Oncogene Proteins/genetics
- Open Reading Frames
- Promoter Regions, Genetic
- Protein Biosynthesis
- Protein Structure, Secondary
- Proto-Oncogene Proteins
- RNA/metabolism
- Transcription, Genetic
- Transfection
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39
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Rodriguez C, Hughes-Davies L, Vallès H, Orsetti B, Cuny M, Ursule L, Kouzarides T, Theillet C. Amplification of the BRCA2 Pathway Gene EMSY in Sporadic Breast Cancer Is Related to Negative Outcome. Clin Cancer Res 2004; 10:5785-91. [PMID: 15355907 DOI: 10.1158/1078-0432.ccr-03-0410] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA amplification at band q13 of chromosome 11 is common in breast cancer, and CCND1 and EMS1 remain the strongest candidate genes. However, amplification patterns are consistent with the existence of four cores of amplification, suggesting the involvement of additional genes. Here we present evidence strongly suggesting the involvement of the recently characterized EMSY gene in the formation of the telomeric amplicon. EMSY maps at 11q13.5, 100 kb centromeric to the GARP gene, which has been mapped within the core of the distal amplicon. The EMSY protein was shown to interact with BRCA2 and has a role in chromatin remodeling. This makes EMSY a strong candidate oncogene for the 11q13.5 amplicon. DNA amplification was studied in a total of 940 primary breast tumors and 39 breast cancer cell lines. Amplification profiles were consistent with the EMSY-GARP locus being amplified independently of CCND1 and/or EMS1. EMSY RNA expression levels were studied along with those of five other genes located at 11q13.5 by real-time quantitative PCR in the 39 cell lines and a subset of 65 tumors. EMSY overexpression correlated strongly with DNA amplification in both primary tumors and cell lines. In a subset of 296 patients, EMSY amplification was found by both uni- and multivariate analyses to correlate with shortened disease-free survival. These data indicate that EMSY is a strong candidate oncogene for the 11q13.5 amplicon.
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MESH Headings
- BRCA2 Protein/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/metabolism
- Carcinoma, Lobular/pathology
- Centromere/genetics
- Chromosomes, Human, Pair 11/genetics
- Cohort Studies
- Female
- Gene Amplification
- Humans
- Neoplasm Invasiveness/genetics
- Neoplasm Invasiveness/pathology
- Neoplasm Proteins
- Nuclear Proteins
- Prognosis
- Repressor Proteins/genetics
- Retrospective Studies
- Signal Transduction
- Tumor Cells, Cultured
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Affiliation(s)
- Carmen Rodriguez
- Génotype et Phénotypes Tumoraux E 229 INSERM, Centre Val d'Aurelle, Montpellier, France
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