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Yoshinaga M, Takeuchi O. RNA Metabolism Governs Immune Function and Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:145-161. [PMID: 38467978 DOI: 10.1007/978-981-99-9781-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Inflammation is a complex process that protects our body from various insults such as infection, injury, and stress. Proper inflammation is beneficial to eliminate the insults and maintain organ homeostasis, however, it can become detrimental if uncontrolled. To tightly regulate inflammation, post-transcriptional mechanisms governing RNA metabolism play a crucial role in monitoring the expression of immune-related genes, such as tumor necrosis factor (TNF) and interleukin-6 (IL-6). These mechanisms involve the coordinated action of various RNA-binding proteins (RBPs), including the Regnase family, Roquin, and RNA methyltransferases, which are responsible for mRNA decay and/or translation regulation. The collaborative efforts of these RBPs are essential in preventing aberrant immune response activation and consequently safeguarding against inflammatory and autoimmune diseases. This review provides an overview of recent advancements in our understanding of post-transcriptional regulation within the immune system and explores the specific roles of individual RBPs in RNA metabolism and regulation.
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Affiliation(s)
- Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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2
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Xu L, Li W, Yang T, Hu S, Zou Q, Jiao J, Jiang N, Zhang Y. Immune-Related RNA-Binding Protein-Based Signature With Predictive and Prognostic Implications in Patients With Lung Adenocarcinoma. Front Mol Biosci 2022; 9:807622. [PMID: 35647031 PMCID: PMC9136055 DOI: 10.3389/fmolb.2022.807622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Dysregulation of RNA-binding proteins (RBPs) in cancers is associated with immune and cancer development. Here, we aimed to profile immune-related RBPs in lung adenocarcinoma (LUAD) and construct an immune-related RBP signature (IRBPS) to predict the survival and response to immunotherapy.Methods: A correlation analysis was performed to establish a co-expression network of RBPs and immune-related genes (IRGs) to characterize immune-related RBPs in the TCGA–LUAD cohort (n = 497 cases). Then, a combination of the Random survival forest (RSF) and Cox regression analysis was performed to screen the RBPs and establish IRBPS. This was followed by independent validation of IRBPS in GSE72094 (n = 398 cases), GSE31210, (n = 226 cases), and GSE26939 (n = 114 cases). Differences between the low- and high-risk groups were compared in terms of gene mutations, tumor mutation burden, tumor-infiltrating lymphocytes, and biomarkers responsive to immunotherapy.Results: DDX56, CTSL, ZC3H12D, and PSMC5 were selected and used to construct IRBPS. The high-risk scores of patients had a significantly worse prognosis in both training and testing cohorts (p < 0.0001 and p < 0.05, respectively), and they tended to be older and have an advanced TNM stage. Furthermore, IRBPS was a prognostic factor independent of age, gender, smoking history, TNM stage, and EGFR mutation status (p = 0.002). In addition, high-risk scores of IRBPS were significantly correlated with tumor-infiltrating lymphocytes (p < 0.05). They also had a high level of PD-L1 protein expression (p < 0.01), number of neoantigens (p < 0.001), and TMB (p < 0.001), implying the possible prediction of IRBPS in the immunotherapy of LUAD.Conclusion: The currently established IRBPS encompassing immune-related RBPs might serve as a promising tool to predict survival, reflect the immune microenvironment, and predict the efficacy of immunotherapy among LUAD patients.
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Affiliation(s)
- Lei Xu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Nuclear Medicine, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wanru Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ting Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Siqi Hu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qiong Zou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ju Jiao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ningyi Jiang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Nuclear Medicine, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Ningyi Jiang, ; Yong Zhang,
| | - Yong Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Nuclear Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Ningyi Jiang, ; Yong Zhang,
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3
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Chen W, Guo Z, Wu J, Lin G, Chen S, Lin Q, Yang J, Xu Y, Zeng Y. Identification of a ZC3H12D-regulated competing endogenous RNA network for prognosis of lung adenocarcinoma at single-cell level. BMC Cancer 2022; 22:115. [PMID: 35090416 PMCID: PMC8796579 DOI: 10.1186/s12885-021-08992-1] [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: 07/11/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background To identify hub genes from the competing endogenous RNA (ceRNA) network of lung adenocarcinoma (LUAD) and to explore their potential functions on prognosis of patients from a single-cell perspective. Methods We performed RNA-sequencing of LUAD to construct ceRNA regulatory network, integrating with public databases to identify the vital pathways related to patients’ prognosis and to reveal the expression level of hub genes under different conditions, the functional enrichment of co-expressed genes and their potential immune-related mechanisms. Results ZC3H12D-hsa-miR-4443-ENST00000630242 axis was found to be related with LUAD. Lower ZC3H12D expression was significantly associated with shorter overall survival (OS) of patients (HR = 2.007, P < 0.05), and its expression was higher in early-stage patients, including T1 (P < 0.05) and N0 (P < 0.05). Additionally, ZC3H12D expression was higher in immune cells displayed by single-cell RNA-sequencing data, especially in Treg cells of lung cancer and CD8 T cells, B cells and CD4 T cells of LUAD. The functional enrichment analysis showed that the co-expressed genes mainly played a role in lymphocyte activation and cytokine-cytokine receptor interaction. In addition, ZC3H12D was associated with multiple immune cells and immune molecules, including immune checkpoints CTLA4, CD96 and TIGIT. Conclusion ZC3H12D-hsa-miR-4443-ENST00000630242 ceRNA network was identified in LUAD. ZC3H12D could affect prognosis of patients by regulating mRNA, miRNA, lncRNA, immune cells and immune molecules. Therefore, it may serve as a vital predictive marker and could be regarded as a potential therapeutic target for LUAD in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08992-1.
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Zhao D, Liu X, Shan Y, Li J, Cui W, Wang J, Jiang J, Xie Q, Zhang C, Duan C. Recognition of immune-related tumor antigens and immune subtypes for mRNA vaccine development in lung adenocarcinoma. Comput Struct Biotechnol J 2022; 20:5001-5013. [PMID: 36187916 PMCID: PMC9483806 DOI: 10.1016/j.csbj.2022.08.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/03/2022] Open
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Jin Z, Zheng E, Sareli C, Kolattukudy PE, Niu J. Monocyte Chemotactic Protein-Induced Protein 1 (MCPIP-1): A Key Player of Host Defense and Immune Regulation. Front Immunol 2021; 12:727861. [PMID: 34659213 PMCID: PMC8519509 DOI: 10.3389/fimmu.2021.727861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/08/2021] [Indexed: 01/14/2023] Open
Abstract
Inflammatory response is a host-protective mechanism against tissue injury or infections, but also has the potential to cause extensive immunopathology and tissue damage, as seen in many diseases, such as cardiovascular diseases, neurodegenerative diseases, metabolic syndrome and many other infectious diseases with public health concerns, such as Coronavirus Disease 2019 (COVID-19), if failure to resolve in a timely manner. Recent studies have uncovered a superfamily of endogenous chemical molecules that tend to resolve inflammatory responses and re-establish homeostasis without causing excessive damage to healthy cells and tissues. Among these, the monocyte chemoattractant protein-induced protein (MCPIP) family consisting of four members (MCPIP-1, -2, -3, and -4) has emerged as a group of evolutionarily conserved molecules participating in the resolution of inflammation. The focus of this review highlights the biological functions of MCPIP-1 (also known as Regnase-1), the best-studied member of this family, in the resolution of inflammatory response. As outlined in this review, MCPIP-1 acts on specific signaling pathways, in particular NFκB, to blunt production of inflammatory mediators, while also acts as an endonuclease controlling the stability of mRNA and microRNA (miRNA), leading to the resolution of inflammation, clearance of virus and dead cells, and promotion of tissue regeneration via its pleiotropic effects. Evidence from transgenic and knock-out mouse models revealed an involvement of MCPIP-1 expression in immune functions and in the physiology of the cardiovascular system, indicating that MCPIP-1 is a key endogenous molecule that governs normal resolution of acute inflammation and infection. In this review, we also discuss the current evidence underlying the roles of other members of the MCPIP family in the regulation of inflammatory processes. Further understanding of the proteins from this family will provide new insights into the identification of novel targets for both host effectors and microbial factors and will lead to new therapeutic treatments for infections and other inflammatory diseases.
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Affiliation(s)
- Zhuqing Jin
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - En Zheng
- Department of Chemistry, Zhejiang University, Hangzhou, China
| | - Candice Sareli
- Office of Human Research, Memorial Healthcare System, Hollywood, FL, United States
| | - Pappachan E Kolattukudy
- Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, United States
| | - Jianli Niu
- Office of Human Research, Memorial Healthcare System, Hollywood, FL, United States.,Burnett School of Biomedical Sciences, University of Central Florida College of Medicine, Orlando, FL, United States
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6
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Huang Z, Lan T, Wang J, Chen Z, Zhang X. Identification and validation of seven RNA binding protein genes as a prognostic signature in oral cavity squamous cell carcinoma. Bioengineered 2021; 12:7248-7262. [PMID: 34585646 PMCID: PMC8806873 DOI: 10.1080/21655979.2021.1974328] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RNA binding proteins (RBPs) play a pivotal role in various biological processes, and aberrant expression of RBPs is closely associated with tumorigenesis and progression. However, the role of RBPs in oral cavity squamous cell carcinoma (OCSCC) is yet unveiled. In this study, RNA sequences and clinical information of OCSCC samples were acquired from The Cancer Genome Atlas (TCGA) database. A total of 650 RBPs, with significantly different expression between healthy and OCSCC samples, were identified using the limma package. A prognostic model was constructed by Lasso-Cox analysis, resulting in the determination of 7 prognosis-related RBPs: ERMP1, RNASE3, ARL4D, CSRP2, ULK1, ZC3H12D, and RPS28. Based on the prognostic model, the risk scores of the OCSCC samples were calculated. The capability of the prognostic model was further evaluated using the receiver operating characteristic curve (ROC). The areas under ROC were 0.764, 0.771, and 0.809 at 1, 3 and 5-year respectively in the TCGA dataset. Internal and external validation showed satisfactory predictive capability for prognosis in OCSCC. In addition, a nomogram was created to graphically present the model. To further validate the analytical data, qRT-PCR was performed on normal and OCSCC cell lines. The mRNA expression of the 7 prognostic genes was in accordance with the analytical results. Functional analysis and gene connection networks were used to describe the biological functions and underlying interactions among the 7 prognostic genes Overall, 7 prognosis-related RBPs were identified, which could be used to predict clinical prognosis and to identify potential therapeutic targets for OCSCC.
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Affiliation(s)
- Zijing Huang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Province Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Tianjun Lan
- Department of Oral and Maxillofacial Surgery, Sun Yat-sen Memorial Hospital of Sun Yat-Sen University, Guangzhou China
| | - Junjie Wang
- Department of Stomatology, The First Affiliated Hospital of Jinan University, School of Stomatology, Jinan University, Guangzhou China
| | - Zhifeng Chen
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou China.,Department of Stomatology, Linzhi People's Hospital, Tibet China
| | - Xiaolei Zhang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Province Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, Guangdong, China
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Yan B, Guo Y, Gui Y, Jiang ZS, Zheng XL. Multifunctional RNase MCPIP1 and its Role in Cardiovascular Diseases. Curr Med Chem 2021; 28:3385-3405. [PMID: 33191882 DOI: 10.2174/0929867327999201113100918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 09/20/2020] [Accepted: 10/09/2020] [Indexed: 11/22/2022]
Abstract
Monocyte chemoattractant protein-1 induced protein 1 (MCPIP1), one of the MCPIP family members, is characterized by the presence of both C-x8-C-x5-C-x3-H (CCCH)- type zinc finger and PilT-N-terminal domains. As a potent regulator of innate immunity, MCPIP1 exerts anti-inflammatory effects through its ribonuclease (RNase) and deubiquitinating enzyme activities to degrade cytokine mRNAs and inhibit nuclear factor- kappa B (NF-κB), respectively. MCPIP1 is expressed not only in immune cells but also in many other cell types, including cardiomyocytes, vascular endothelial cells (ECs) and smooth muscle cells (SMCs). Increasing evidence indicates that MCPIP1 plays a role in the regulation of cardiac functions and is involved in the processes of vascular diseases, such as ischemia-reperfusion (I/R) and atherosclerosis. To better understand the emerging roles of MCPIP1 in the cardiovascular system, we reviewed the current literature with respect to MCPIP1 functions and discussed its association with the pathogenesis of cardiovascular diseases and the implication as a therapeutic target.
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Affiliation(s)
- Binjie Yan
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerosis of Hunan Province, Hengyang Medical College, University of South China, Hengyang City, Hunan Province 421001, China
| | - Yanan Guo
- Departments of Biochemistry & Molecular Biology and Physiology & Pharmacology, Libin Cardiovascular Institute, Cumming School of Medicine, The University of Calgary, 3330 Hospital Drive N.W., Calgary, ABT2N 4N1, Canada
| | - Yu Gui
- Departments of Biochemistry & Molecular Biology and Physiology & Pharmacology, Libin Cardiovascular Institute, Cumming School of Medicine, The University of Calgary, 3330 Hospital Drive N.W., Calgary, ABT2N 4N1, Canada
| | - Zhi-Sheng Jiang
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerosis of Hunan Province, Hengyang Medical College, University of South China, Hengyang City, Hunan Province 421001, China
| | - Xi-Long Zheng
- Departments of Biochemistry & Molecular Biology and Physiology & Pharmacology, Libin Cardiovascular Institute, Cumming School of Medicine, The University of Calgary, 3330 Hospital Drive N.W., Calgary, ABT2N 4N1, Canada
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Tomita T, Kato M, Mishima T, Matsunaga Y, Sanjo H, Ito KI, Minagawa K, Matsui T, Oikawa H, Takahashi S, Takao T, Iwai N, Mino T, Takeuchi O, Maru Y, Hiratsuka S. Extracellular mRNA transported to the nucleus exerts translation-independent function. Nat Commun 2021; 12:3655. [PMID: 34135341 PMCID: PMC8208975 DOI: 10.1038/s41467-021-23969-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
RNA in extracellular vesicles (EVs) are uptaken by cells, where they regulate fundamental cellular functions. EV-derived mRNA in recipient cells can be translated. However, it is still elusive whether “naked nonvesicular extracellular mRNA” (nex-mRNA) that are not packed in EVs can be uptaken by cells and, if so, whether they have any functions in recipient cells. Here, we show the entrance of nex-mRNA in the nucleus, where they exert a translation-independent function. Human nex-interleukin-1β (IL1β)-mRNA outside cells proved to be captured by RNA-binding zinc finger CCCH domain containing protein 12D (ZC3H12D)-expressing human natural killer (NK) cells. ZC3H12D recruited to the cell membrane binds to the 3′-untranslated region of nex-IL1β-mRNA and transports it to the nucleus. The nex-IL1β-mRNA in the NK cell nucleus upregulates antiapoptotic gene expression, migration activity, and interferon-γ production, leading to the killing of cancer cells and antimetastasis in mice. These results implicate the diverse actions of mRNA. Nonvesicular extracellular RNA (nex-RNA) that are not packed in extracellular vesicles is detected outside the cell, but it is poorly understood. Here the authors report that nex-RNA is captured by a zinc finger protein and transported to the nucleus to enhance antimetastatic characters of the cell.
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Affiliation(s)
- Takeshi Tomita
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan.,Department of Biochemistry and Molecular Biology, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan
| | - Masayoshi Kato
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan.,Department of Biochemistry and Molecular Biology, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan
| | - Taishi Mishima
- Department of Pharmacology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Yuta Matsunaga
- Department of Pharmacology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Hideki Sanjo
- Department of Molecular and Cellular Immunology, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan
| | - Ken-Ichi Ito
- Division of Breast, Endocrine and Respiratory Surgery, Department of Surgery, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan
| | - Kentaro Minagawa
- Department of Hematology/Oncology, Penn State College of Medicine, Hershey, PA, USA
| | - Toshimitsu Matsui
- Department of Hematology, Nishiwaki Municipal Hospital, Nishiwaki, Hyogo, Japan
| | - Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Noriki Iwai
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshiro Maru
- Department of Pharmacology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan.
| | - Sachie Hiratsuka
- Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan. .,Department of Biochemistry and Molecular Biology, Shinshu University, School of Medicine, Matsumoto, Nagano, Japan.
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Shen T, Wang M, Wang X. Identification of Prognosis-related Hub RNA Binding Proteins Function through Regulating Metabolic Processes in Tongue Cancer. J Cancer 2021; 12:2230-2242. [PMID: 33758601 PMCID: PMC7974894 DOI: 10.7150/jca.52156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
RNA binding proteins (RBPs) are dysregulated and associated with the occurrence and development in various malignant tumors. However, the role of RBPs in tongue cancer are largely unclear. Here, by integrating the differential gene expression analysis and the Weighted Gene Co-expression Network Analysis (WGCNA) of TCGA-retrieved RNA-seq data, we identified a total of 171 differential co-expression RBPs. Then, in a protein-protein interaction (PPI) network containing 134 nodes (RBPs) and 315 network edges (RBP-RBP interacting networks), the top 30 hub RBPs were identified using the CytoHubba plugin of Cytoscape. Furthermore, we investigated the expression and prognostic value of these RBPs and their highly correlated networks. Among them, six RBPs (PGK1, SLC20A1, LEPR, CYP19A1, ZC3H12D, and PFKM) were shown to be the prognosis-related hub RBPs (prhRBPs). Based on these hub RBPs, we constructed a prognostic model and found that the patients in the high-risk group had dramatically poor overall survival compared to those in low-risk group. In addition, we validated the prognostic model in GSE41613, another tongue cancer patient cohort from GEO datasets. The time-dependent receiver operating characteristic (ROC) analysis of the prognostic model further confirmed the predictive capability of the risk model for tongue cancer. As suggested in functional annotation analysis, we found an intensive enrichment of these prhRBPs in metabolic pathways, including AMPK, HIF-1 signaling pathway, Glycolysis, and steroid hormone biosynthesis. Together, our study revealed the underlying role of RBP in tongue cancer biology and potentially unveiled novel targets for cancer therapy.
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Affiliation(s)
- Tao Shen
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Meiting Wang
- College of Liren, Yanshan University, Qinhuangdao, 066004, China.,Department of Neurobiology and Biophysics, School of Life Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Xiangting Wang
- Department of Geriatrics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
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10
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Zhu M, Wu Y, Wang Z, Lin M, Su B, Li C, Liang F, Chen X. miR-128-3p serves as an oncogenic microRNA in osteosarcoma cells by downregulating ZC3H12D. Oncol Lett 2020; 21:152. [PMID: 33552270 PMCID: PMC7798096 DOI: 10.3892/ol.2020.12413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Osteosarcoma is the second leading cause of cancer-associated mortality worldwide in children and adolescents. ZC3H12D has been shown to negatively regulate Toll-like receptor signaling and serves as a possible tumor suppressor gene. MicroRNAs (miRNAs/miRs) are known to play an important role in the proliferation of human osteosarcoma cells. However, whether miRNAs can affect tumor development by regulating the expression of ZC3H12D has not yet been investigated. The aim of the present study was to investigate the role of miR128-3p in regulating ZC3H12D expression, as well as its function in tumor cell proliferation, apoptosis, and metastasis. Reverse transcription-quantitative PCR, western blotting and dual luciferase reporter assays were performed to analyze the regulation of ZC3H12D expression by miR-128-3p. MTT, colony formation and flow cytometry assays were also used to analyze the effect of miR-128-3p on cell proliferation and apoptosis. A wound healing assay was performed to investigate the cell migration ability. The results demonstrated that miR-128-3p directly targeted ZC3H12D and downregulated its expression, thereby promoting cell proliferation and migration. miR-128-3p overexpression also improved resistance to cisplatin in MG-63 and 143B cell lines, supporting the hypothesis that miR-128-3p may function as an oncogene in osteosarcoma cells. The potential clinical significance of miR-128-3p as a biomarker and therapeutic target provides rationale for further investigation into the miR-128-3p-mediated molecular pathway and how it is associated with osteosarcoma development.
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Affiliation(s)
- Maoshu Zhu
- Department of Central Laboratory, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China
| | - Yulong Wu
- Department of Urinary Surgery, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China
| | - Zhaowei Wang
- Department of Gynecology, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China
| | - Minghua Lin
- Department of Pathology, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China
| | - Bin Su
- Department of Pharmacy, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China
| | - Chunyang Li
- Department of Orthopedics, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China
| | - Fulong Liang
- Department of Neurology, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China
| | - Xinjiang Chen
- Department of Orthopedics, The Fifth Hospital of Xiamen, Xiang'an, Xiamen, Fujian 361000, P.R. China
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11
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Wawro M, Wawro K, Kochan J, Solecka A, Sowinska W, Lichawska-Cieslar A, Jura J, Kasza A. ZC3H12B/MCPIP2, a new active member of the ZC3H12 family. RNA (NEW YORK, N.Y.) 2019; 25:840-856. [PMID: 30988100 PMCID: PMC6573786 DOI: 10.1261/rna.071381.119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
ZC3H12B is the most enigmatic member of the ZC3H12 protein family. The founding member of this family, Regnase-1/MCPIP1/ZC3H12A, is a well-known modulator of inflammation and is involved in the degradation of inflammatory mRNAs. In this study, for the first time, we characterized the properties of the ZC3H12B protein. We show that the biological role of ZC3H12B depends on an intact NYN/PIN RNase domain. Using RNA immunoprecipitation, experiments utilizing actinomycin D and ELISA, we show that ZC3H12B binds interleukin-6 (IL-6) mRNA in vivo, regulates its turnover, and results in reduced production of IL-6 protein upon stimulation with IL-1β. We verified that regulation of IL-6 mRNA stability occurs via interaction of ZC3H12B with the stem-loop structure present in the IL-6 3'UTR. The IL-6 transcript is not the only target of ZC3H12B. ZC3H12B also interacts with other known substrates of Regnase-1 and ZC3H12D, such as the 3'UTRs of IER3 and Regnase-1, and binds IER3 mRNA in vivo. Using immunofluorescence, we examined the localization of ZC3H12B within the cell. ZC3H12B forms small, granule-like structures in the cytoplasm that are characteristic of proteins involved in mRNA turnover. The overexpression of ZC3H12B inhibits proliferation by stalling the cell cycle in the G2 phase. This effect of ZC3H12B is also NYN/PIN dependent. The analysis of the ZC3H12B mRNA level reveals its highest expression in the human brain and the neuroblastoma cell line SH-SY5Y, although the factors regulating its expression remain elusive. Down-regulation of ZC3H12B in SH-SY5Y cells by specific shRNAs results in up-regulation of ZC3H12B-target mRNAs.
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Affiliation(s)
- Mateusz Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
| | - Karolina Wawro
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
| | - Aleksandra Solecka
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
| | - Weronika Sowinska
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
| | - Agata Lichawska-Cieslar
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
| | - Jolanta Jura
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
| | - Aneta Kasza
- Department of Cell Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow 30-387, Poland
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Wakahashi S, Kawakami F, Wakahashi K, Minagawa K, Matsuo K, Katayama Y, Yamada H, Matsui T, Sudo T. Transformed Follicular Lymphoma (TFL) Predicts Outcome in Advanced Endometrial Cancer. Cancer Epidemiol Biomarkers Prev 2018; 27:963-969. [PMID: 29784731 DOI: 10.1158/1055-9965.epi-17-0762] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 02/13/2018] [Accepted: 05/15/2018] [Indexed: 11/16/2022] Open
Abstract
Background: Transformed follicular lymphoma (TFL, ZC3H12D) was identified as a candidate tumor suppressor gene that contributes to cell-cycle arrest through regulation of Rb phosphorylation, but the clinical impact of TFL is unknown. The goal of this study was to evaluate the prognostic significance of TFL expression in advanced endometrial cancer.Methods: Tissue samples were obtained from 103 patients with Federation Internationale des Gynaecologistes et Obstetristes stage III-IV endometrial cancer. Associations between TFL expression and outcomes were evaluated using the Kaplan-Meier method and multivariate Cox proportional hazards regression models.Results: There were 24 TFL-low cases (23.3%) and the 10-year progression-free survival (PFS) and overall survival (OS) in these cases were lower than those for patients with normal TFL expression in univariate analysis (PFS, P = 0.003; OS, P = 0.106). In multivariate analysis, TFL status was a significant predictor for PFS [HR = 2.76; 95% confidence interval (CI), 1.45-5.28; P = 0.002] and OS (HR = 1.94; 95% CI, 0.91-4.11; P = 0.085), adjusted for covariates. The TFL gene maps to human chromosome 6q25.1, where estrogen receptor alpha (ERα) gene ESR1 is also located. Lack of ERα expression is a poor prognostic factor in early endometrial cancer. Among 41 ERα-low patients, 10-year PFS was significantly lower in 15 TFL-low cases (univariate analysis, P = 0.055; multivariate analysis, HR = 4.70; 95% CI, 1.68-13.20; P = 0.003).Conclusions: We identified TFL as a strong independent prognostic factor, regardless of ERα status.Impact: An investigation of the mechanism underlying tumor suppression by TFL may lead to new therapies for patients with advanced endometrial cancer. Cancer Epidemiol Biomarkers Prev; 27(8); 963-9. ©2018 AACR.
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Affiliation(s)
- Senn Wakahashi
- Department of Obstetrics and Gynecology, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Fumi Kawakami
- Department of Diagnostic Pathology, Kobe University Hospital, Kobe, Japan
| | - Kanako Wakahashi
- Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kentaro Minagawa
- Department of Hematology/Oncology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yoshio Katayama
- Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hideto Yamada
- Department of Obstetrics and Gynecology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Toshimitsu Matsui
- Department of Hematology, Nishiwaki Municipal Hospital, Nishiwaki, Hyogo, Japan
| | - Tamotsu Sudo
- Section of Translational Research, Hyogo Cancer Center, Akashi, Japan
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MCPIP3 as a Potential Metastasis Suppressor Gene in Human Colorectal Cancer. Int J Mol Sci 2018; 19:ijms19051350. [PMID: 29751537 PMCID: PMC5983627 DOI: 10.3390/ijms19051350] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 12/18/2022] Open
Abstract
Monocyte chemotactic protein induced protein 3 (MCPIP3) belongs to the Cys–Cys–Cys–His (CCCH)-zinc finger protein family and contains a highly conserved CCCH-zinc finger domain and a Nedd4-BP1 YacP nuclease (NYN) domain. Previous studies showed that MCPIP3 inhibits the expression of proinflammatory genes, such as vascular cell adhesion molecule (VCAM)-1, in human endothelial cells, but the roles and functions of MCPIP3 in cancer cells are still unknown. In human colorectal cancer specimens, we found that the messenger RNA expression of MCPIP3 was significantly downregulated in cancer tissues compared to adjacent normal tissues (18/25; average fold change of 8.18). Two cell models were used to demonstrate the anti-migration activity of MCPIP3. First, Tet-on T-REx-293/HA-MCPIP3 cells were used to examine whether MCPIP3 can change epithelial–mesenchymal transition (EMT)-related gene expressions. Second, we used two human colorectal cancer cell lines, SW620 and HCT116, to prove the role of MCPIP3 in regulating EMT-related gene expressions. We found that overexpression of MCPIP3 inhibited cell migration according to a wound-healing assay and Transwell invasion assay and vimentin expression, and increased E-cadherin expression in these two cell lines. These results suggest that MCPIP3 might play a negative role in cell migration of human colorectal cancer cells.
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Wawro M, Kochan J, Krzanik S, Jura J, Kasza A. Intact NYN/PIN-Like Domain is Crucial for the Degradation of Inflammation-Related Transcripts by ZC3H12D. J Cell Biochem 2016; 118:487-498. [PMID: 27472830 DOI: 10.1002/jcb.25665] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 07/28/2016] [Indexed: 12/27/2022]
Abstract
ZC3H12D belongs to a recently discovered family of proteins containing four members of which the most studied and best described is the RNase ZC3H12A (MCPIP1/Regnase-1). ZC3H12A is a crucial negative regulator of inflammation. It accelerates the turnover of transcripts of a spectrum of proinflammatory cytokines, as well as its own mRNA. The biological role of ZC3H12D is less clear, although it was shown that this member of ZC3H12 family is also involved in the regulation of inflammation. Here, we show that ZC3H12A and ZC3H12D recognize a set of common target mRNAs encoding proteins that play important roles in the course of the inflammation. Similarly to ZC3H12A, ZC3H12D participates in the 3'UTR-dependent regulation of the turnover of mRNAs encoding interleukin-6 (IL-6), tumor necrosis factor (TNF), and immediate early response 3 gene (IER3). The ZC3H12A mRNA is also among the identified ZC3H12D targets. Using the combination of immunofluorescence with single molecule RNA fluorescence in situ hybridization (smRNA FISH) we have shown that ZC3H12D protein interacts with the ZC3H12A transcript. The direct binding of these two molecules in vivo was further confirmed by RNA immunoprecipitation. Simultaneously, overexpression of ZC3H12D increases the turnover rate of transcripts containing ZC3H12A 3'UTR. Using reporter gene assays we have confirmed that the Asp95 residue present in the NYN/PIN-like domain is crucial for ZC3H12D biological activity. We have also revealed that ZC3H12D recognizes the same structural elements present in the 3'UTRs of the investigated transcripts, as ZC3H12A. J. Cell. Biochem. 118: 487-498, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Mateusz Wawro
- Department of Cell Biochemistry, Jagiellonian University, Kraków, Poland
| | - Jakub Kochan
- Department of Cell Biochemistry, Jagiellonian University, Kraków, Poland
| | - Sylwia Krzanik
- Department of Cell Biochemistry, Jagiellonian University, Kraków, Poland
| | - Jolanta Jura
- Department of General Biochemistry, Jagiellonian University, Kraków, Poland
| | - Aneta Kasza
- Department of Cell Biochemistry, Jagiellonian University, Kraków, Poland
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15
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Ansari J, Shackelford RE, El-Osta H. Epigenetics in non-small cell lung cancer: from basics to therapeutics. Transl Lung Cancer Res 2016; 5:155-71. [PMID: 27186511 DOI: 10.21037/tlcr.2016.02.02] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lung cancer remains the number one cause of cancer-related deaths worldwide with 221,200 estimated new cases and 158,040 estimated deaths in 2015. Approximately 80% of cases are non-small cell lung cancer (NSCLC). The diagnosis is usually made at an advanced stage where the prognosis is poor and therapeutic options are limited. The evolution of lung cancer is a multistep process involving genetic, epigenetic, and environmental factor interactions that result in the dysregulation of key oncogenes and tumor suppressor genes, culminating in activation of cancer-related signaling pathways. The past decade has witnessed the discovery of multiple molecular aberrations that drive lung cancer growth, among which are epidermal growth factor receptor (EGFR) mutations and translocations involving the anaplastic lymphoma kinase (ALK) gene. This has translated into therapeutic agent developments that target these molecular alterations. The absence of targetable mutations in 50% of NSCLC cases and targeted therapy resistance development underscores the importance for developing alternative therapeutic strategies for treating lung cancer. Among these strategies, pharmacologic modulation of the epigenome has been used to treat lung cancer. Epigenetics approaches may circumvent the problem of tumor heterogeneity by affecting the expression of multiple tumor suppression genes (TSGs), halting tumor growth and survival. Moreover, it may be effective for tumors that are not driven by currently recognized druggable mutations. This review summarizes the molecular pathology of lung cancer epigenetic aberrations and discusses current efforts to target the epigenome with different pharmacological approaches. Our main focus will be on hypomethylating agents, histone deacetylase (HDAC) inhibitors, microRNA modulations, and the role of novel epigenetic biomarkers. Last, we will address the challenges that face this old-new strategy in treating lung cancer.
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Affiliation(s)
- Junaid Ansari
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Rodney E Shackelford
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Hazem El-Osta
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
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16
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Weiss K, Applegate C, Wang T, Batista DAS. Familial TAB2 microdeletion and congenital heart defects including unusual valve dysplasia and tetralogy of fallot. Am J Med Genet A 2015; 167A:2702-6. [PMID: 26139517 DOI: 10.1002/ajmg.a.37210] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/04/2015] [Indexed: 01/12/2023]
Abstract
Haploinsufficiency of TAB2 was recently implicated as a cause for a variety of congenital heart defects. Reported cases have genomic deletions of 2-10 Mbs including TAB2 at 6q24-25 are almost always de novo and show variable cardiac and extra cardiac phenotype. We report on an inherited, 281 kb deletion in a three generation family. This is the smallest reported deletion involving TAB2 that segregates with congenital heart defects. Three affected individuals in this family present with myxomatous cardiac valves in addition to structural heart defects commonly associated with TAB2 deletions. Findings from this family support a key role of TAB2 haploinsufficiency in congenital heart defects and expand the phenotypic spectrum of TAB2-microdeletion syndrome.
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Affiliation(s)
- Karin Weiss
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Carolyn Applegate
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tao Wang
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Denise A S Batista
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Cytogenetics and Microarray Laboratory, Kennedy Krieger Institute, Baltimore, Maryland
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17
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Huang S, Liu S, Fu JJ, Tony Wang T, Yao X, Kumar A, Liu G, Fu M. Monocyte Chemotactic Protein-induced Protein 1 and 4 Form a Complex but Act Independently in Regulation of Interleukin-6 mRNA Degradation. J Biol Chem 2015; 290:20782-20792. [PMID: 26134560 DOI: 10.1074/jbc.m114.635870] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Indexed: 01/07/2023] Open
Abstract
It was recently demonstrated that MCPIP1 is a critical factor that controls inflammation and immune homeostasis; however, the relationship between MCPIP1 and other members of this protein family is largely unknown. Here, we report that MCPIP1 interacts with MCPIP4 to form a protein complex, but acts independently in the regulation of IL-6 mRNA degradation. In an effort to identify MCPIP1-interacting proteins by co-immunoprecipitation (Co-IP) and mass-spec analysis, MCPIP4 was identified as a MCPIP1-interacting protein, which was further confirmed by Co-IP and mammalian two-hybrid assay. Immunofluorescence staining showed that MCPIP4 was co-localized with MCPIP1 in the GW-body, which features GW182 and Argonaute 2. Further studies showed that MCPIP1 and MCPIP4 act independently in regulation of IL-6 mRNA degradation. These results suggest that MCPIP1 and MCPIP4 may additively contribute to control IL-6 production in vivo.
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Affiliation(s)
- Shengping Huang
- Shock/Trauma Research Center & Department of Basic Medical Science, School of Medicine, University of Missouri Kansas City, Kansas City, Missouri 64108
| | - Shufeng Liu
- Bioscience Division, SRI International, Harrisonburg, Virginia 22802
| | - Jia J Fu
- Shock/Trauma Research Center & Department of Basic Medical Science, School of Medicine, University of Missouri Kansas City, Kansas City, Missouri 64108
| | - T Tony Wang
- Bioscience Division, SRI International, Harrisonburg, Virginia 22802
| | - Xiaolan Yao
- Division of Molecular Biology and Biochemistry, School of Biological Science, University of Missouri Kansas City, Kansas City, Missouri 64110
| | - Anil Kumar
- Division of Pharmacology and Toxicology, School of Pharmacy, University of Missouri Kansas City, Kansas City, Missouri 64108
| | - Gang Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, School of Medicine, Birmingham, Alabama 35294
| | - Mingui Fu
- Shock/Trauma Research Center & Department of Basic Medical Science, School of Medicine, University of Missouri Kansas City, Kansas City, Missouri 64108.
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18
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Zhang H, Wang WC, Chen JK, Zhou L, Wang M, Wang ZD, Yang B, Xia YM, Lei S, Fu EQ, Jiang T. ZC3H12D attenuated inflammation responses by reducing mRNA stability of proinflammatory genes. Mol Immunol 2015; 67:206-12. [PMID: 26059755 DOI: 10.1016/j.molimm.2015.05.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/07/2015] [Accepted: 05/16/2015] [Indexed: 10/23/2022]
Abstract
Infection in airspaces and lung parenchyma may cause acute lung injury and multiple organ dysfunction syndrome due to acute inflammatory response, leading to organ failure and high mortality. ZC3H12D has been shown to modulate Toll-like receptor signaling. This study aimed to investigate the change of ZC3H12D during acute lung injury and its role in inflammation processes. Mice were challenged with lipopolysaccharides (LPS) intratracheally. The expression levels of Zc3h12d, NF-κB, and cytokines were analyzed by quantitative real-time PCR (qPCR), ELISA, and Western blot. The mRNA stability was assessed by qPCR after cells were treated with actinomycin D for specified times. The 3' untranslated region (3'-UTR) of c-fos was cloned immediately downstream of the luciferase coding sequence driven by CMV promoter and luciferase activity was measured with a Luciferase Assay kit. Upon LPS treatment, ZC3H12D levels were reduced in mouse immune cells, whereas levels of NF-κB, IL-6, and TNF-α were significantly increased. Knockdown Zc3h12d in THP1 cells resulted in the upregulation of NF-κB while overexpression of Zc3h12d inhibited NF-κB expression. Ectopic Zc3h12d significantly reduced the mRNA stability of c-fos, NF-κB, TNF-α, IL-1β, and IL-6. Attachment of the c-fos 3'-UTR made luciferase expression levels sensitive to levels of ZC3H12D. The data indicated that ZC3H12D could suppress both the initial inflammation storm and chronic inflammation by targeting the mRNA of cytokines as well as NF-κB and c-fos.
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Affiliation(s)
- Hong Zhang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Wen-chen Wang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Jia-kuan Chen
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Lin Zhou
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Ming Wang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Zhen-dong Wang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Bo Yang
- Department of Thoracic Surgery, Tianjin First Center Hospital, Tianjin, China
| | - Yan-ming Xia
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Shi Lei
- The College of Biology and Pharmacy, China Three Gorges University, Yichang, Hubei 443002, China
| | - En-qing Fu
- Department of Respiratory Medicine, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China.
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19
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Ruan X, Liu H, Boardman L, Kocher JPA. Genome-wide analysis of loss of heterozygosity in breast infiltrating ductal carcinoma distant normal tissue highlights arm specific enrichment and expansion across tumor stages. PLoS One 2014; 9:e95783. [PMID: 24748104 PMCID: PMC3991715 DOI: 10.1371/journal.pone.0095783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 03/31/2014] [Indexed: 02/06/2023] Open
Abstract
Studies have shown concurrent loss of heterozygosity (LOH) in breast infiltrating ductal carcinoma (IDC) and adjacent or distant normal tissue. However, the overall extent of LOH in normal tissue and their significance to tumorigenesis remain unknown, as existing studies are largely based on selected microsatellite markers. Here we present the first autosome-wide study of LOH in IDC and distant normal tissue using informative loci deduced from SNP array-based and sequencing-based techniques. We show a consistently high LOH concurrence rate in IDC (mean = 24%) and distant normal tissue (m = 54%), suggesting for most patients (31/33) histologically normal tissue contains genomic instability that can be a potential marker of increased IDC risk. Concurrent LOH is more frequent in fragile site related genes like WWOX (9/31), NTRK2 (10/31), and FHIT (7/31) than traditional genetic markers like BRCA1 (0/23), BRCA2 (2/29) and TP53 (1/13). Analysis at arm level shows distant normal tissue has low level but non-random enrichment of LOH (topped by 8p and 16q) significantly correlated with matched IDC (Pearson r = 0.66, p = 3.5E-6) (topped by 8p, 11q, 13q, 16q, 17p, and 17q). The arm-specific LOH enrichment was independently observed in tumor samples from 548 IDC patients when stratified by tumor size based T stages. Fine LOH structure from sequencing data indicates LOH in low order tissues non-randomly overlap (∼67%) with LOH that usually has longer tract length (the length of genomic region affected by LOH) in high order tissues. The consistent observations from multiple datasets suggest progressive LOH in the development of IDC potentially through arm-specific pile up effect with discernible signature in normal tissue. Our finding also suggests that LOH detected in IDC by comparing to paired adjacent or distant normal tissue are more likely underestimated.
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Affiliation(s)
- Xiaoyang Ruan
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Hongfang Liu
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Lisa Boardman
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jean-Pierre A. Kocher
- Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- * E-mail:
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20
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Minagawa K, Wakahashi K, Kawano H, Nishikawa S, Fukui C, Kawano Y, Asada N, Sato M, Sada A, Katayama Y, Matsui T. Posttranscriptional modulation of cytokine production in T cells for the regulation of excessive inflammation by TFL. THE JOURNAL OF IMMUNOLOGY 2014; 192:1512-24. [PMID: 24415781 DOI: 10.4049/jimmunol.1301619] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Posttranscriptional machinery regulates inflammation and is associated with autoimmunity as well as tumorigenesis in collaboration with transcription factors. We previously identified the tumor suppressor gene transformed follicular lymphoma (TFL) on 6q25 in a patient with follicular lymphoma, which transformed into diffuse large B cell lymphoma. TFL families have a common RNase domain that governs macrophage-mediated inflammation. In human peripheral blood, TFL is dominantly expressed at the glycine- and tryptophan-rich cytoplasmic processing bodies of T lymphocytes, and it is persistently upregulated in activated T cells. To address its physiological role, we established TFL(-/-) mice in which TFL(-/-) lymphocytes proliferated more rapidly than TFL(+/+) upon stimulation with inappropriate cytokine secretion, including IL-2, IL-6, and IL-10. Moreover, TFL inhibited the synthesis of cytokines such as IL-2, IL-6, IL-10, TNF-α, and IL-17a by 3' untranslated region RNA degradation. Experimental autoimmune encephalitis induced in TFL(-/-) mice demonstrated persistent severe paralysis. CNS-infiltrated CD4(+) T cells in TFL(-/-) mice contained a higher proportion of Th17 cells than did those in TFL(+/+) mice during the resolution phase, and IL-17a mRNA levels were markedly increased in TFL(-/-) cells. These results suggest that TFL may play an important role in attenuating local inflammation by suppressing the infiltration of Th17 cells in the CNS during the resolution phase of experimental autoimmune encephalitis. TFL is a novel gradual and persistent posttranscriptional regulator, and the TFL-driven attenuation of excessive inflammation could contribute to recovery from T cell-mediated autoimmune diseases.
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Affiliation(s)
- Kentaro Minagawa
- Division of Hematology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
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21
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Lin RJ, Chien HL, Lin SY, Chang BL, Yu HP, Tang WC, Lin YL. MCPIP1 ribonuclease exhibits broad-spectrum antiviral effects through viral RNA binding and degradation. Nucleic Acids Res 2013; 41:3314-26. [PMID: 23355615 PMCID: PMC3597685 DOI: 10.1093/nar/gkt019] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 12/21/2012] [Accepted: 12/21/2012] [Indexed: 12/31/2022] Open
Abstract
Monocyte chemoattractant protein 1-induced protein 1 (MCPIP1), belonging to the MCPIP family with highly conserved CCCH-type zinc finger and Nedd4-BP1, YacP Nuclease domains, has been implicated in negative regulation of the cellular inflammatory responses. In this report, we demonstrate for the first time that this RNA-binding nuclease also targets viral RNA and possesses potent antiviral activities. Overexpression of the human MCPIP1, but not MCPIP2, MCPIP3 or MCPIP4, inhibited Japanese encephalitis virus (JEV) and dengue virus (DEN) replication. The functional analysis of MCPIP1 revealed that the activities of RNase, RNA binding and oligomerization, but not deubiqutinase, are required for its antiviral potential. Furthermore, infection of other positive-sense RNA viruses, such as sindbis virus and encephalomyocarditis virus, and negative-sense RNA virus, such as influenza virus, as well as DNA virus, such as adenovirus, can also be blocked by MCPIP1. Moreover, the endogenous MCPIP1 gene expression was induced by JEV and DEN infection, and knockdown of MCPIP1 expression enhanced the replication of JEV and DEN in human cells. Thus, MCPIP1 can act as a host innate defense via RNase activity for targeting and degrading viral RNA.
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Affiliation(s)
- Ren-Jye Lin
- Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan, Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Hsu-Ling Chien
- Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan, Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Shyr-Yi Lin
- Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan, Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Bi-Lan Chang
- Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan, Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Han-Pang Yu
- Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan, Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Wei-Chun Tang
- Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan, Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Yi-Ling Lin
- Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan, Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, Genomics Research Center, Academia Sinica, Taipei 115, Taiwan and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
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22
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Fan J, Dy JG, Chang CC, Zhou X. Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays. CHINESE JOURNAL OF CANCER 2013; 32:170-85. [PMID: 23327800 PMCID: PMC3845573 DOI: 10.5732/cjc.012.10113] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Myelodysplastic syndromes have increased in frequency and incidence in the American population, but patient prognosis has not significantly improved over the last decade. Such improvements could be realized if biomarkers for accurate diagnosis and prognostic stratification were successfully identified. In this study, we propose a method that associates two state-of-the-art array technologies—single nucleotide polymorphism (SNP) array and gene expression array—with gene motifs considered transcription factor-binding sites (TFBS). We are particularly interested in SNP-containing motifs introduced by genetic variation and mutation as TFBS. The potential regulation of SNP-containing motifs affects only when certain mutations occur. These motifs can be identified from a group of co-expressed genes with copy number variation. Then, we used a sliding window to identify motif candidates near SNPs on gene sequences. The candidates were filtered by coarse thresholding and fine statistical testing. Using the regression-based LARS-EN algorithm and a level-wise sequence combination procedure, we identified 28 SNP-containing motifs as candidate TFBS. We confirmed 21 of the 28 motifs with ChIP-chip fragments in the TRANSFAC database. Another six motifs were validated by TRANSFAC via searching binding fragments on co-regulated genes. The identified motifs and their location genes can be considered potential biomarkers for myelodysplastic syndromes. Thus, our proposed method, a novel strategy for associating two data categories, is capable of integrating information from different sources to identify reliable candidate regulatory SNP-containing motifs introduced by genetic variation and mutation.
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Affiliation(s)
- Jing Fan
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115, USA.
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23
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Huang S, Qi D, Liang J, Miao R, Minagawa K, Quinn T, Matsui T, Fan D, Liu J, Fu M. The putative tumor suppressor Zc3h12d modulates toll-like receptor signaling in macrophages. Cell Signal 2011; 24:569-576. [PMID: 22036805 DOI: 10.1016/j.cellsig.2011.10.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 09/27/2011] [Accepted: 10/11/2011] [Indexed: 01/17/2023]
Abstract
Toll-like receptors (TLR) are pivotal in macrophage activation. The molecular mechanisms controlling TLR signaling and macrophage activation are not completely understood. Zc3h12d is originally identified as a possible tumor suppressor gene. However, its function remains unknown. We here report that Zc3h12d negatively regulates TLR signaling and macrophage activation. Zc3h12d was enriched in spleen, lung and lymph node. In macrophages, the expression of Zc3h12d was remarkably induced by TLR ligands through JNK and NF-κB signal pathways. On the other hand, overexpression of Zc3h12d significantly inhibited TLR2 and TLR4 activation-induced JNK, ERK and NF-κB signaling as well as macrophage inflammation. Similar to Zc3h12a/MCPIP1, Zc3h12d also decreased the global cellular protein ubiquitination. These findings suggest that Zc3h12d is a novel negative feedback regulator of TLR signaling and macrophage activation and thus may play a role in host immunity and inflammatory diseases.
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Affiliation(s)
- Shengping Huang
- Shock/Trauma Research Center & Department of Basic Medical Science, School of Medicine, University of Missouri Kansas City, MO 64108, United States
| | - Dongfei Qi
- Shock/Trauma Research Center & Department of Basic Medical Science, School of Medicine, University of Missouri Kansas City, MO 64108, United States
| | - Jian Liang
- Burnett School of Biological Science, College of Medicine, University of Central Florida, Orlando, FL 32816, United States
| | - Ruidong Miao
- Shock/Trauma Research Center & Department of Basic Medical Science, School of Medicine, University of Missouri Kansas City, MO 64108, United States
| | | | - Tim Quinn
- Shock/Trauma Research Center & Department of Basic Medical Science, School of Medicine, University of Missouri Kansas City, MO 64108, United States
| | | | - Daping Fan
- Department of Cell Biology and Anatomy, University of South Carolina, Columbia, SC 29209, United States
| | - Jianguo Liu
- Department of Internal Medicine, Saint Louis University School of Medicine, St. Louis, MO 63104, United States
| | - Mingui Fu
- Shock/Trauma Research Center & Department of Basic Medical Science, School of Medicine, University of Missouri Kansas City, MO 64108, United States.
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24
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Notaridou M, Quaye L, Dafou D, Jones C, Song H, Høgdall E, Kjaer SK, Christensen L, Høgdall C, Blaakaer J, McGuire V, Wu AH, Van Den Berg DJ, Pike MC, Gentry-Maharaj A, Wozniak E, Sher T, Jacobs IJ, Tyrer J, Schildkraut JM, Moorman PG, Iversen ES, Jakubowska A, Mędrek K, Lubiński J, Ness RB, Moysich KB, Lurie G, Wilkens LR, Carney ME, Wang-Gohrke S, Doherty JA, Rossing MA, Beckmann MW, Thiel FC, Ekici AB, Chen X, Beesley J, Gronwald J, Fasching PA, Chang-Claude J, Goodman MT, Chenevix-Trench G, Berchuck A, Pearce CL, Whittemore AS, Menon U, Pharoah PD, Gayther SA, Ramus SJ. Common alleles in candidate susceptibility genes associated with risk and development of epithelial ovarian cancer. Int J Cancer 2011; 128:2063-74. [PMID: 20635389 PMCID: PMC3098608 DOI: 10.1002/ijc.25554] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 05/26/2010] [Accepted: 06/24/2010] [Indexed: 12/26/2022]
Abstract
Common germline genetic variation in the population is associated with susceptibility to epithelial ovarian cancer. Microcell-mediated chromosome transfer and expression microarray analysis identified nine genes associated with functional suppression of tumorogenicity in ovarian cancer cell lines; AIFM2, AKTIP, AXIN2, CASP5, FILIP1L, RBBP8, RGC32, RUVBL1 and STAG3. Sixty-three tagging single nucleotide polymorphisms (tSNPs) in these genes were genotyped in 1,799 invasive ovarian cancer cases and 3,045 controls to look for associations with disease risk. Two SNPs in RUVBL1, rs13063604 and rs7650365, were associated with increased risk of serous ovarian cancer [HetOR = 1.42 (1.15-1.74) and the HomOR = 1.63 (1.10-1.42), p-trend = 0.0002] and [HetOR = 0.97 (0.80-1.17), HomOR = 0.74 (0.58-0.93), p-trend = 0.009], respectively. We genotyped rs13063604 and rs7650365 in an additional 4,590 cases and 6,031 controls from ten sites from the United States, Europe and Australia; however, neither SNP was significant in Stage 2. We also evaluated the potential role of tSNPs in these nine genes in ovarian cancer development by testing for allele-specific loss of heterozygosity (LOH) in 286 primary ovarian tumours. We found frequent LOH for tSNPs in AXIN2, AKTIP and RGC32 (64, 46 and 34%, respectively) and one SNP, rs1637001, in STAG3 showed significant allele-specific LOH with loss of the common allele in 94% of informative tumours (p = 0.015). Array comparative genomic hybridisation indicated that this nonrandom allelic imbalance was due to amplification of the rare allele. In conclusion, we show evidence for the involvement of a common allele of STAG3 in the development of epithelial ovarian cancer.
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Affiliation(s)
- Maria Notaridou
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Lydia Quaye
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Dimitra Dafou
- Department of Medical and Molecular Genetics, King’s College London School of Medicine, Guy’s Hospital, London, United Kingdom
| | - Chris Jones
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Honglin Song
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Estrid Høgdall
- Department of Viruses, Hormones and Cancer, Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Susanne K. Kjaer
- Department of Viruses, Hormones and Cancer, Institute of Cancer Epidemiology, Danish Cancer Society, Copenhagen, Denmark
| | - Lise Christensen
- Department of Pathology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus Høgdall
- The Gynaecologic Clinic, The Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Denmark
| | - Jan Blaakaer
- Department of Gynaecology and Obstetrics, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Valerie McGuire
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA
| | - Anna H. Wu
- University of Southern California, Keck School of Medicine, Department of Preventive Medicine, Los Angeles, CA
| | - David J. Van Den Berg
- University of Southern California, Keck School of Medicine, Department of Preventive Medicine, Los Angeles, CA
| | - Malcolm C. Pike
- University of Southern California, Keck School of Medicine, Department of Preventive Medicine, Los Angeles, CA
| | - Aleksandra Gentry-Maharaj
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Eva Wozniak
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Tanya Sher
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Ian J. Jacobs
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Jonathan Tyrer
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | | | - Patricia G. Moorman
- Department of Community and Family Medicine, Duke University Medical Center, Durham, NC
| | - Edwin S. Iversen
- Department of Statistical Science, Duke University, Medical Center, Durham, NC
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Krzysztof Mędrek
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | | | - Kirsten B. Moysich
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY
| | - Galina Lurie
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | - Lynne R. Wilkens
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | - Michael E. Carney
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Jennifer A. Doherty
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mary Anne Rossing
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Falk C. Thiel
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Xiaoqing Chen
- Genetics and Population Health, The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Jonathan Beesley
- Genetics and Population Health, The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | | | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
- Division of Hematology and Oncology, University of California at Los Angeles, David Geffen School of Medicine, Los Angeles, CA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Marc T. Goodman
- Cancer Research Center of Hawaii, University of Hawaii, Honolulu, HI
| | - Georgia Chenevix-Trench
- Genetics and Population Health, The Queensland Institute of Medical Research, Post Office Royal Brisbane Hospital, Australia
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology/Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC, 27710
| | - C. Leigh Pearce
- University of Southern California, Keck School of Medicine, Department of Preventive Medicine, Los Angeles, CA
| | - Alice S. Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA
| | - Usha Menon
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Paul D.P. Pharoah
- CR-UK Department of Oncology, University of Cambridge, Strangeways Research Laboratory, Cambridge, United Kingdom
| | - Simon A. Gayther
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
| | - Susan J. Ramus
- Gynaecological Oncology Unit, UCL EGA Institute for Women’s Health, University College London, United Kingdom
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25
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Abstract
Lung cancer in never smokers (LCINS) has lately been recognized as a unique disease based on rapidly gained knowledge from genomic changes to treatment responses. The focus of this article is on current knowledge and challenges with regard to LCINS expanded from recent reviews highlighting five areas: (1) distribution of LCINS by temporal trends, geographic regions, and populations; (2) three well-recognized environmental risk factors; (3) other plausible environmental risk factors; (4) prior chronic lung diseases and infectious diseases as risk factors; and (5) lifestyles as risk or protective factors. This article will also bring attention to recently published literature in two pioneering areas: (1) histological characteristics, clinical features with emerging new effective therapies, and social and psychological stigma; and (2) searching for susceptibility genes using integrated genomic approaches.
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Affiliation(s)
- Ping Yang
- Department of Health Sciences Research, College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.
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26
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Barresi V, Romano A, Musso N, Capizzi C, Consoli C, Martelli MP, Palumbo G, Di Raimondo F, Condorelli DF. Broad copy neutral-loss of heterozygosity regions and rare recurring copy number abnormalities in normal karyotype-acute myeloid leukemia genomes. Genes Chromosomes Cancer 2011; 49:1014-23. [PMID: 20725993 DOI: 10.1002/gcc.20810] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We analyzed, by the latest high-resolution SNP arrays, 19 Normal Karyotype (NK)-AML patients at diagnosis (Dx) and remission (R) phases, to determine the number of tumor-associated copy number abnormalities (CNAs) and copy neutral-loss of heterozygosity (CN-LOH) regions per patient and to identify possible recurring genomic abnormalities. The number of tumor-associated CNAs was determined after comparison of matched Dx/R samples using stringent conditions able to reduce the number of false positive CNAs. With the exception of a single outlier case, a low number of CNAs per patient was detected (median value of 1 somatic loss or gain per patient). However, a high prevalence of CNAs (60-70% of the patients showed at least one tumor-associated gain or loss) and few recurring CNAs were observed, thus providing new hints towards identification of cooperating mutations. An extensive search of all tumor-associated CN-LOH regions >1 Mb revealed only three broad regions (terminal 12Mb of 22q, terminal 27Mb of 1p and the whole chromosome 21) in three patients out of 19 (16%). CN-LOH of the whole chromosome 21 was responsible for homozygosity of a missense mutation (R80C) of RUNX1/AML1. Our study suggests that a relative submicroscopic copy number stability NK-AML genomes is associated with low recurrence of specific CNAs and CN-LOH in NK-AML patient population. Sequencing of candidate genes in the identified CNAs and CN-LOH regions should be considered a priority in the search of novel driver mutations of AML.
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Affiliation(s)
- Vincenza Barresi
- Laboratorio sui Sistemi Complessi, Scuola Superiore di Catania, Università di Catania, Italy
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27
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Minagawa K, Matsui T. p58TFL Does Not Localize to Messenger RNA Processing Bodies - Response. Mol Cancer Res 2010. [DOI: 10.1158/1541-7786.mcr-09-0410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kentaro Minagawa
- Hematology/Oncology, Department of Medicine, Kobe University, Graduate School of Medicine, Kobe, Japan
| | - Toshimitsu Matsui
- Hematology/Oncology, Department of Medicine, Kobe University, Graduate School of Medicine, Kobe, Japan
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28
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Minagawa K, Katayama Y, Nishikawa S, Yamamoto K, Sada A, Okamura A, Shimoyama M, Matsui T. Inhibition of G1 to S Phase Progression by a Novel Zinc Finger Protein P58TFL at P-bodies. Mol Cancer Res 2009; 7:880-9. [DOI: 10.1158/1541-7786.mcr-08-0511] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Wei YC, Zhou FL, He DL, Bai JR, Hui LY, Wang XY, Nan KJ. The level of oxidative stress and the expression of genes involved in DNA-damage signaling pathways in depressive patients with colorectal carcinoma. J Psychosom Res 2009; 66:259-66. [PMID: 19232240 DOI: 10.1016/j.jpsychores.2008.09.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2008] [Revised: 07/22/2008] [Accepted: 09/02/2008] [Indexed: 12/28/2022]
Abstract
OBJECTIVES This study investigated the connection among the oxidative stress, depression and expression of specific genes involved in DNA-damage signaling pathways in patients with colorectal carcinoma (CRC). METHODS A unique Dukes'C subset of patients with newly diagnosed colorectal adenocarcinoma were assessed using the Hamilton Depression Rating Scale (HAMD), Zung Self-rating Depression Scale (SDS), Zung Self-rating Anxiety Scale (SAS), Symptom Checklist 90 (SCL-90) and other multiple-item questionnaires. Oxidative-stress-related parameters in sera and the expression of genes were monitored during a pretreatment period. RESULTS Eighty-two eligibility cases were divided into 2 groups based on an HAMD score cutoff of 20: the mean score was 28.29 in Group A (depression, n=52) and 16.50 in Group B (nondepression, n=30). The serum total antioxidant capacity, catalase, and superoxide dismutase concentrations were lower in Group A, whereas those of nitric oxide and malondialdehyde were higher in Group A. Importantly, the 8-hydroxy-deoxyguanosine level was higher in Group A than in Group B (P<.05). Microarray analysis revealed that the expressions of p34, PA26, and ABL were higher in Group A, whereas those of HRAD51, CR6, and XRCC3 were higher in Group B. CONCLUSION Oxidative stress is capable of causing neuronal toxicity via lipid peroxidation, DNA damage, and abnormalities of gene expression, and therefore is a possible pathogenic mechanism underlying depression in patients with CRC.
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Affiliation(s)
- Yong-chang Wei
- Department of Clinical Oncology, First Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China.
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30
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Abstract
Lung cancer has become a global public health burden, further substantiating the need for early diagnosis and more effective targeted therapies. The key to accomplishing both these goals is a better understanding of the genes and pathways disrupted during the initiation and progression of this disease. Gene promoter hypermethylation is an epigenetic modification of DNA at promoter CpG islands that together with changes in histone structure culminates in loss of transcription. The fact that gene promoter hypermethylation is a major mechanism for silencing genes in lung cancer has stimulated the development of screening approaches to identify additional genes and pathways that are disrupted within the epigenome. Some of these approaches include restriction landmark scanning, methylation CpG island amplification coupled with representational difference analysis, and transcriptome-wide screening. Genes identified by these approaches, their function, and prevalence in lung cancer are described. Recently, we used global screening approaches to interrogate 43 genes in and around the candidate lung cancer susceptibility locus, 6q23-25. Five genes, TCF21, SYNE1, AKAP12, IL20RA, and ACAT2, were methylated at 14 to 81% prevalence, but methylation was not associated with age at diagnosis or stage of lung cancer. These candidate tumor suppressor genes likely play key roles in contributing to sporadic lung cancer. The realization that methylation is a dominant mechanism in lung cancer etiology and its reversibility by pharmacologic agents has led to the initiation of translational studies to develop biomarkers in sputum for early detection and the testing of demethylating and histone deacetylation inhibitors for treatment of lung cancer.
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31
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Liang J, Song W, Tromp G, Kolattukudy PE, Fu M. Genome-wide survey and expression profiling of CCCH-zinc finger family reveals a functional module in macrophage activation. PLoS One 2008; 3:e2880. [PMID: 18682727 PMCID: PMC2478707 DOI: 10.1371/journal.pone.0002880] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Accepted: 07/11/2008] [Indexed: 01/24/2023] Open
Abstract
Previously, we have identified a novel CCCH zinc finger protein family as negative regulators of macrophage activation. To gain an overall insight into the entire CCCH zinc finger gene family and to evaluate their potential role in macrophage activation, here we performed a genome-wide survey of CCCH zinc finger genes in mouse and human. Totally 58 CCCH zinc finger genes in mouse and 55 in human were identified and most of them have not been reported previously. Phylogenetic analysis revealed that the mouse CCCH family was divided into 6 groups. Meanwhile, we employed quantitative real-time PCR to profile their tissue expression patterns in adult mice. Clustering analysis showed that most of CCCH genes were broadly expressed in all of tissues examined with various levels. Interestingly, several CCCH genes Mbnl3, Zfp36l2, Zfp36, Zc3h12a, Zc3h12d, Zc3h7a and Leng9 were enriched in macrophage-related organs such as thymus, spleen, lung, intestine and adipose. Consistently, a comprehensive assessment of changes in expression of the 58 members of the mouse CCCH family during macrophage activation also revealed that these CCCH zinc finger genes were associated with the activation of bone marrow-derived macrophages by lipopolysaccharide. Taken together, this study not only identified a functional module of CCCH zinc finger genes in the regulation of macrophage activation but also provided the framework for future studies to dissect the function of this emerging gene family.
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Affiliation(s)
- Jian Liang
- Biomolecular Science Center, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Wenjun Song
- Biomolecular Science Center, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Gail Tromp
- Biomolecular Science Center, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Pappachan E. Kolattukudy
- Biomolecular Science Center, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Mingui Fu
- Biomolecular Science Center, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
- * E-mail:
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32
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Abstract
Lung cancer is the leading cause of cancer-related death and thus a major health problem. The efficiency of current treatment modalities for lung cancer depends strongly on the time of diagnosis, with better chances of survival if a tumor has been detected at an early stage. Thus, there is an urgent need for rapid and efficient early detection methods. Biomarkers represent a possible alternative to current, rather expensive, screening tools such as spiral computer tomography (CT), or may allow the identification of high risk groups for whom screening would be cost efficient. Although most lung cancers are the consequence of smoking, a substantial fraction of molecular-epidemiological studies point to high-prevalence, low-penetrance genetic polymorphisms as modifiers of environmental lung cancer risk. In the past the genomics field has also made significant advances in identifying genetic lesions that can now be harvested with the goal of identifying novel biomarkers for lung cancer. Furthermore, the importance of epigenetic changes that occur during lung cancer development has been reported, but has been underestimated in the past. Novel high-throughput, quantitative assays for the detection of DNA methylation or histone tail modifications are now applied, to search for alterations in the lung cancer genome and will identify novel cancer-related genes that may become attractive targets for treatment, provide new insight into the biology of lung cancers, and could also become useful biomarkers for the early detection of lung cancer in sputum, or may be used as prognostic markers. Thus, an integrative approach in lung cancer research combining epidemiological, genetic and epigenetic information becomes an important concept for the future.
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Affiliation(s)
- Angela Risch
- German Cancer Research Center, Division of Epigenomics and Cancer Risk Factors, Heidelberg, Germany
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33
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Tessema M, Willink R, Do K, Yu YY, Yu W, Machida EO, Brock M, Van Neste L, Stidley CA, Baylin SB, Belinsky SA. Promoter Methylation of Genes in and around the Candidate Lung Cancer Susceptibility Locus6q23-25. Cancer Res 2008; 68:1707-14. [DOI: 10.1158/0008-5472.can-07-6325] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Minagawa K, Yamamoto K, Nishikawa S, Ito M, Sada A, Yakushijin K, Okamura A, Shimoyama M, Katayama Y, Matsui T. Deregulation of a possible tumour suppressor gene, ZC3H12D, by translocation of IGK@ in transformed follicular lymphoma with t(2;6)(p12;q25). Br J Haematol 2007; 139:161-3. [PMID: 17854321 DOI: 10.1111/j.1365-2141.2007.06752.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Kentaro Minagawa
- Haematology/Oncology, Department of Medicine, Kobe University Graduate School of Medicine, Kobe, Japan
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