151
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Zhou Z, Shen Y, Khan MR, Li A. LncReg: a reference resource for lncRNA-associated regulatory networks. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav083. [PMID: 26363021 PMCID: PMC4565966 DOI: 10.1093/database/bav083] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 08/18/2015] [Indexed: 12/13/2022]
Abstract
Long non-coding RNAs (lncRNAs) are critical in the regulation of various biological processes. In recent years, plethora of lncRNAs have been identified in mammalian genomes through different approaches, and the researchers are constantly reporting the regulatory roles of these lncRNAs, which leads to complexity of literature about particular lncRNAs. Therefore, for the convenience of the researchers, we collected regulatory relationships of the lncRNAs and built a database called ‘LncReg’. This database is developed by collecting 1081 validated lncRNA-associated regulatory entries, including 258 non-redundant lncRNAs and 571 non-redundant genes. With regulatory relationships information, LncReg can provide overall perspectives of regulatory networks of lncRNAs and comprehensive data for bioinformatics research, which is useful for understanding the functional roles of lncRNAs. Database URL: http://bioinformatics.ustc.edu.cn/lncreg/
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Affiliation(s)
- Zhong Zhou
- School of Information Science and Technology, Centers for Biomedical Engineering and
| | - Yi Shen
- School of Information Science and Technology, Centers for Biomedical Engineering and
| | - Muhammad Riaz Khan
- School of Life Science, University of Science and Technology of China, 443 Huangshan Road, Hefei 230027, China
| | - Ao Li
- School of Information Science and Technology, Centers for Biomedical Engineering and
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152
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Qi X, Zhang DH, Wu N, Xiao JH, Wang X, Ma W. ceRNA in cancer: possible functions and clinical implications. J Med Genet 2015; 52:710-8. [PMID: 26358722 DOI: 10.1136/jmedgenet-2015-103334] [Citation(s) in RCA: 912] [Impact Index Per Article: 101.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 08/21/2015] [Indexed: 01/01/2023]
Abstract
Competing endogenous RNAs (ceRNAs) are transcripts that can regulate each other at post-transcription level by competing for shared miRNAs. CeRNA networks link the function of protein-coding mRNAs with that of non-coding RNAs such as microRNA, long non-coding RNA, pseudogenic RNA and circular RNA. Given that any transcripts harbouring miRNA response element can theoretically function as ceRNAs, they may represent a widespread form of post-transcriptional regulation of gene expression in both physiology and pathology. CeRNA activity is influenced by multiple factors such as the abundance and subcellular localisation of ceRNA components, binding affinity of miRNAs to their sponges, RNA editing, RNA secondary structures and RNA-binding proteins. Aberrations in these factors may deregulate ceRNA networks and thus lead to human diseases including cancer. In this review, we introduce the mechanisms and molecular bases of ceRNA networks, discuss their roles in the pathogenesis of cancer as well as methods of predicting and validating ceRNA interplay. At last, we discuss the limitations of current ceRNA theory, propose possible directions and envision the possibilities of ceRNAs as diagnostic biomarkers or therapeutic targets.
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Affiliation(s)
- Xiaolong Qi
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Da-Hong Zhang
- Department of Clinical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jun-Hua Xiao
- Department of Gastroenterology, Shanghai East Hospital, Tongji University, School of Medicine, Shanghai, China
| | - Xiang Wang
- Department of Neurology, The Affiliated Huai'an Hospital of Xuzhou Medical College and The Second People's Hospital of Huai'an, Huai'an, China
| | - Wang Ma
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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153
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Xia T, Chen S, Jiang Z, Shao Y, Jiang X, Li P, Xiao B, Guo J. Long noncoding RNA FER1L4 suppresses cancer cell growth by acting as a competing endogenous RNA and regulating PTEN expression. Sci Rep 2015; 5:13445. [PMID: 26306906 PMCID: PMC4549704 DOI: 10.1038/srep13445] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 07/31/2015] [Indexed: 01/17/2023] Open
Abstract
Aberrantly expressed long noncoding RNAs (lncRNAs) are associated with various cancers. However, the roles of lncRNAs in the pathogenesis of most cancers are unclear. Here, we report that the lncRNA FER1L4 (fer-1-like family member 4, pseudogene) acts as a competing endogenous RNA (ceRNA) to regulate the expression of PTEN (a well-known tumor suppressor gene) by taking up miR-106a-5p in gastric cancer. We observed that FER1L4 was downregulated in gastric cancer and that its level corresponded with that of PTEN mRNA. Both FER1L4 and PTEN mRNA were targets of miR-106a-5p. Further experiments demonstrated that FER1L4 downregulation liberates miR-106a-5p and decreases the abundances of PTEN mRNA and protein. More importantly, FER1L4 downregulation accelerated cell proliferation by promoting the G0/G1 to S phase transition. We conclude that one mechanism by which lncRNAs function in in tumorigenesis is as ceRNAs for tumor suppressor mRNAs.
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Affiliation(s)
- Tian Xia
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Shengcan Chen
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Zhen Jiang
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Yongfu Shao
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Xiaoming Jiang
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Peifei Li
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Bingxiu Xiao
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China.,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, Zhejiang, 315211, China
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154
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Peng W, Si S, Zhang Q, Li C, Zhao F, Wang F, Yu J, Ma R. Long non-coding RNA MEG3 functions as a competing endogenous RNA to regulate gastric cancer progression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:79. [PMID: 26253106 PMCID: PMC4529701 DOI: 10.1186/s13046-015-0197-7] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/29/2015] [Indexed: 02/06/2023]
Abstract
Background Long noncoding RNAs (lncRNAs) have recently emerged as important regulators in governing fundamental biological processes, and many of which are likely to have functional roles in tumorigenesis. Maternally expressed gene 3 (MEG3) gene encodes a lncRNA whose expression is lost in an expanding list of primary human tumors and tumor cell lines, however its biological role and regulatory mechanism in gastric cancer (GC) development and progression are poorly defined. Methods Quantitative RT-PCR analysis was used to determine whether aberrant MEG3 expression was associated with GC patients pTNM stage and pM state. Furthermore, the effect of ectopic expression of MEG3 on cell proliferation, migration, invasion and cell apoptosis was assessed by using CCK-8, wound healing, transwell invasion assays and flow cytometric analysis, respectively, in GC cell lines HGC-27 and MGC-803. Moreover, the competing endogenous RNA (ceRNA) activity of MEG3 on miR-181a was investigated via luciferase reporter assay and immunoblot analysis. Results MEG3 is decreased in GC patients and cell lines, and its expression was associated with metastatic GC. Furthermore, ectopic expression of MEG3 in HGC-27 and MGC-803 cells inhibited cell proliferation, migration, invasion, and promoted cell apoptosis, which might be due to MEG3 sequestering oncogenic miR-181 s in GC cells. Furthermore, MEG3 could up-regulated Bcl-2 via its competing endogenous RNA (ceRNA) activity on miR-181a. Conclusions These findings suggest that lncRNA MEG3, a ceRNA of miR-181 s, could regulate gastric carcinogenesis and may serve as a potential target for antineoplastic therapies.
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Affiliation(s)
- Weizhao Peng
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Shuang Si
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Qingxia Zhang
- Department of Obstetrics and gynecology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Chaofeng Li
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Fang Zhao
- Department of Obstetrics and gynecology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Fang Wang
- Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China.
| | - Jia Yu
- Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China.
| | - Ren Ma
- Department of Obstetrics and gynecology, China-Japan Friendship Hospital, Beijing, 100029, China.
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155
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Peng W, Si S, Zhang Q, Li C, Zhao F, Wang F, Yu J, Ma R. Long non-coding RNA MEG3 functions as a competing endogenous RNA to regulate gastric cancer progression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015. [PMID: 26253106 DOI: 10.1186/s13046-015- 0197-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have recently emerged as important regulators in governing fundamental biological processes, and many of which are likely to have functional roles in tumorigenesis. Maternally expressed gene 3 (MEG3) gene encodes a lncRNA whose expression is lost in an expanding list of primary human tumors and tumor cell lines, however its biological role and regulatory mechanism in gastric cancer (GC) development and progression are poorly defined. METHODS Quantitative RT-PCR analysis was used to determine whether aberrant MEG3 expression was associated with GC patients pTNM stage and pM state. Furthermore, the effect of ectopic expression of MEG3 on cell proliferation, migration, invasion and cell apoptosis was assessed by using CCK-8, wound healing, transwell invasion assays and flow cytometric analysis, respectively, in GC cell lines HGC-27 and MGC-803. Moreover, the competing endogenous RNA (ceRNA) activity of MEG3 on miR-181a was investigated via luciferase reporter assay and immunoblot analysis. RESULTS MEG3 is decreased in GC patients and cell lines, and its expression was associated with metastatic GC. Furthermore, ectopic expression of MEG3 in HGC-27 and MGC-803 cells inhibited cell proliferation, migration, invasion, and promoted cell apoptosis, which might be due to MEG3 sequestering oncogenic miR-181 s in GC cells. Furthermore, MEG3 could up-regulated Bcl-2 via its competing endogenous RNA (ceRNA) activity on miR-181a. CONCLUSIONS These findings suggest that lncRNA MEG3, a ceRNA of miR-181 s, could regulate gastric carcinogenesis and may serve as a potential target for antineoplastic therapies.
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Affiliation(s)
- Weizhao Peng
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Shuang Si
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Qingxia Zhang
- Department of Obstetrics and gynecology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Chaofeng Li
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Fang Zhao
- Department of Obstetrics and gynecology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Fang Wang
- Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China.
| | - Jia Yu
- Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College (PUMC), Beijing, 100005, China.
| | - Ren Ma
- Department of Obstetrics and gynecology, China-Japan Friendship Hospital, Beijing, 100029, China.
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156
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Histone Deacetylase 10 Regulates the Cell Cycle G2/M Phase Transition via a Novel Let-7-HMGA2-Cyclin A2 Pathway. Mol Cell Biol 2015; 35:3547-65. [PMID: 26240284 DOI: 10.1128/mcb.00400-15] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/30/2015] [Indexed: 12/21/2022] Open
Abstract
Histone deacetylase (HDAC) inhibition leads to cell cycle arrest in G1 and G2, suggesting HDACs as therapeutic targets for cancer and diseases linked to abnormal cell growth and proliferation. Many HDACs are transcriptional repressors. Some may alter cell cycle progression by deacetylating histones and repressing transcription of key cell cycle regulatory genes. Here, we report that HDAC10 regulates the cell cycle via modulation of cyclin A2 expression, and cyclin A2 overexpression rescues HDAC10 knockdown-induced G2/M transition arrest. HDAC10 regulates cyclin A2 expression by deacetylating histones near the let-7 promoter, thereby repressing transcription. In HDAC10 knockdown cells, let-7f and microRNA 98 (miR-98) were upregulated and the let-7 family target, HMGA2, was downregulated. HMGA2 loss resulted in enrichment of the transcriptional repressor E4F at the cyclin A2 promoter. These findings support a role for HDACs in cell cycle regulation, reveal a novel mechanism of HDAC10 action, and extend the potential of HDACs as targets in diseases of cell cycle dysregulation.
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157
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Spira A, Halmos B, Powell CA. Update in Lung Cancer 2014. Am J Respir Crit Care Med 2015; 192:283-94. [PMID: 26230235 PMCID: PMC4584253 DOI: 10.1164/rccm.201504-0756up] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/15/2015] [Indexed: 12/14/2022] Open
Abstract
In the past 2 years, lung cancer research and clinical care have advanced significantly. Advancements in the field have improved outcomes and promise to lead to further reductions in deaths from lung cancer, the leading cause of cancer death worldwide. These advances include identification of new molecular targets for personalized targeted therapy, validation of molecular signatures of lung cancer risk in smokers, progress in lung tumor immunotherapy, and implementation of population-based lung cancer screening with chest computed tomography in the United States. In this review, we highlight recent research in these areas and challenges for the future.
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Affiliation(s)
- Avrum Spira
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - Balazs Halmos
- Department of Medicine, Columbia University Medical Center, New York, New York; and
| | - Charles A. Powell
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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158
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A cross-talk between Hepatitis B virus and host mRNAs confers viral adaptation to liver. Sci Rep 2015; 5:10572. [PMID: 26184825 PMCID: PMC4505342 DOI: 10.1038/srep10572] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 04/20/2015] [Indexed: 02/08/2023] Open
Abstract
Hepatitis B virus (HBV) chronically infects approximately 350 million people worldwide. The replication of HBV which genome is only 3.2 kb long relies heavily on host factors. Previous studies demonstrated that a highly expressed liver-specific microRNA (miRNA) miR-122 suppresses HBV expression and replication in multiple ways. In this study, we found that the miR-122 response elements in viral genome facilitate HBV expression and replication in miR-122 highly-expressed hepatocytes. Moreover, mutations in miR-122 response elements are correlated with viral loads and disease progression in HBV-infected patients. We next found that HBV mRNA with miR-122 response elements alone could lead to altered expression of multiple host genes by whole genome expression analysis. HBV mRNA-mediated miR-122 down-regulation plays a major role in HBV mRNA-induced differential gene expression. HBV mRNA could enhance viral replication via miR-122 degradation and the up-regulation of its target cyclin G1. Our study thereby reveals that under the unique condition of high abundance of miR-122 and viral mRNAs and much lower level of miR-122 target in HBV infection, HBV may have evolved to employ the miRNA-mediated virus and host mRNAs network for optimal fitness within hepatocytes.
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159
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Randhawa V, Acharya V. Integrated network analysis and logistic regression modeling identify stage-specific genes in Oral Squamous Cell Carcinoma. BMC Med Genomics 2015; 8:39. [PMID: 26179909 PMCID: PMC4502639 DOI: 10.1186/s12920-015-0114-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/06/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Oral squamous cell carcinoma (OSCC) is associated with substantial mortality and morbidity but, OSCC can be difficult to detect at its earliest stage due to its molecular complexity and clinical behavior. Therefore, identification of key gene signatures at an early stage will be highly helpful. METHODS The aim of this study was to identify key genes associated with progression of OSCC stages. Gene expression profiles were classified into cancer stage-related modules, i.e., groups of genes that are significantly related to a clinical stage. For prioritizing the candidate genes, analysis was further restricted to genes with high connectivity and a significant association with a stage. To assess predictive power of these genes, a classification model was also developed and tested by 5-fold cross validation and on an independent dataset. RESULTS The identified genes were enriched for significant processes and functional pathways, and various genes were found to be directly implicated in OSCC. Forward and stepwise, multivariate logistic regression analyses identified 13 key genes whose expression discriminated early- and late-stage OSCC with predictive accuracy (area under curve; AUC) of ~0.81 in a 5-fold cross-validation strategy. CONCLUSIONS The proposed network-driven integrative analytical approach can identify multiple genes significantly related to an OSCC stage; the classification model that is developed with these genes may help to distinguish cancer stages. The proposed genes and model hold promise for monitoring of OSCC stage progression, and our findings may facilitate cancer detection at an earlier stage, resulting in improved treatment outcomes.
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Affiliation(s)
- Vinay Randhawa
- Functional Genomics and Complex Systems Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, Himachal Pradesh, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
| | - Vishal Acharya
- Functional Genomics and Complex Systems Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Council of Scientific and Industrial Research, Palampur, Himachal Pradesh, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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160
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Yang E, Cisowski J, Nguyen N, O'Callaghan K, Xu J, Agarwal A, Kuliopulos A, Covic L. Dysregulated protease activated receptor 1 (PAR1) promotes metastatic phenotype in breast cancer through HMGA2. Oncogene 2015; 35:1529-40. [PMID: 26165842 DOI: 10.1038/onc.2015.217] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 04/11/2015] [Accepted: 04/13/2015] [Indexed: 12/24/2022]
Abstract
As the majority of patients with basal-like breast carcinoma present with invasive, metastatic disease that do not respond to available therapies, it is essential to identify new therapeutic targets that impact invasion and metastasis. Protease-activated receptor 1 (PAR1), a G-protein coupled receptor has been shown to act as an oncogene, but underlying mechanisms are not well understood. Here, we show that ectopic expression of functionally active PAR1 in MCF-7 cells induced a hormone-refractory, invasive phenotype representative of advanced basal-like breast carcinoma that readily formed metastatic lesions in lungs of mice. PAR1 was found to globally upregulate mesenchymal markers, including vimentin, a direct target of PAR1, and downregulate the epithelial markers including E-cadherin, as well as estrogen receptor. In contrast, non-signaling PAR1 mutant receptor did not lead to an invasive, hormone refractory phenotype. PAR1 expression increased spheroid formation and the level of stemness markers and self-renewal capacity in human breast cancer cells. We identified HMGA2 (high mobility group A2) as an important regulator of PAR1-mediated invasion. Inhibition of PAR1 signaling suppresses HMGA2-driven invasion in breast cancer cells. HMGA2 gene and protein are highly expressed in metastatic breast cancer cells. Overall, our results show that PAR1/HMGA2 pathway may present a novel therapeutic target.
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Affiliation(s)
- E Yang
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA.,Department of Biochemistry and Tufts Medical Center, Boston, MA, USA
| | - J Cisowski
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA
| | - N Nguyen
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA
| | - K O'Callaghan
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA
| | - J Xu
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA
| | - A Agarwal
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA
| | - A Kuliopulos
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA.,Department of Biochemistry and Tufts Medical Center, Boston, MA, USA.,Division of Hematology/Oncology, Tufts Medical Center, Boston, MA, USA.,Department of Medicine, Tufts Medical Center, Boston, MA, USA
| | - L Covic
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA.,Department of Biochemistry and Tufts Medical Center, Boston, MA, USA.,Division of Hematology/Oncology, Tufts Medical Center, Boston, MA, USA.,Department of Medicine, Tufts Medical Center, Boston, MA, USA
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161
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Oliveira-Mateos C, Guil S. LncRNAs and the Control of Oncogenic Signaling. CURRENT PATHOBIOLOGY REPORTS 2015. [DOI: 10.1007/s40139-015-0084-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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162
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Wang T, Wang G, Hao D, Liu X, Wang D, Ning N, Li X. Aberrant regulation of the LIN28A/LIN28B and let-7 loop in human malignant tumors and its effects on the hallmarks of cancer. Mol Cancer 2015; 14:125. [PMID: 26123544 PMCID: PMC4512107 DOI: 10.1186/s12943-015-0402-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Accepted: 06/24/2015] [Indexed: 12/13/2022] Open
Abstract
RNA binding proteins (RBPs) and microRNAs (miRNAs) are two of the most important post-transcriptional regulators of gene expression, and their aberrant expression contributes to the development of human malignancies. Let-7, one of the most well-known tumor suppressors, is frequently down-regulated in a variety of human cancers. The RBP LIN28A/LIN28B, a direct target of the let-7 family of miRNAs, is an inhibitor of let-7 biogenesis and is frequently up-regulated in cancers. Aberrant regulation of the LIN28A/LIN28B and let-7 loop in human malignant tumors is reportedly involved in cancer development, contributing to cellular proliferation, cell death resistance, angiogenesis, metastasis, metabolism reprogramming, tumor-associated inflammation, genome instability, acquiring immortality and evading immune destruction. In this review, we summarized the mechanisms of LIN28A/LIN28B and let-7 loop aberrant regulation in human cancer and discussed the roles and potential mechanisms of the LIN28A/LIN28B and let-7 loop in regulating the hallmarks of cancer. The crosstalk between LIN28A/LIN28B and let-7 loop and certain oncogenes (such as MYC, RAS, PI3K/AKT, NF-κB and β-catenin) in regulating hallmarks of cancer has also been discussed.
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Affiliation(s)
- Tianzhen Wang
- Department of Pathology, Harbin Medical University, Harbin, China.
| | - Guangyu Wang
- Department of Gastrointestinal Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin, China.
| | - Dapeng Hao
- Faculty of Health Sciences, University of Macau, Taipa, Macau, China.
| | - Xi Liu
- Center of Cardiovascular, Inner Mongolia People's Hospital, Hohhot, Inner Mongolia, China.
| | - Dong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
| | - Ning Ning
- Department of Gastrointestinal Surgery, International Hospital of Pecking University, Beijing, China.
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, China.
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163
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Frost L, Baez MAM, Harrilal C, Garabedian A, Fernandez-Lima F, Leng F. The Dimerization State of the Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2). PLoS One 2015; 10:e0130478. [PMID: 26114780 PMCID: PMC4482583 DOI: 10.1371/journal.pone.0130478] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/20/2015] [Indexed: 01/06/2023] Open
Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) is a chromosomal architectural transcription factor involved in cell transformation and oncogenesis. It consists of three positively charged “AT-hooks” and a negatively charged C-terminus. Sequence analyses, circular dichroism experiments, and gel-filtration studies showed that HMGA2, in the native state, does not have a defined secondary or tertiary structure. Surprisingly, using combined approaches of 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC) chemical cross-linking, analytical ultracentrifugation, fluorescence resonance energy transfer (FRET), and mass spectrometry, we discovered that HMGA2 is capable of self-associating into homodimers in aqueous buffer solution. Our results showed that electrostatic interactions between the positively charged “AT-hooks” and the negatively charged C-terminus greatly contribute to the homodimer formation.
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Affiliation(s)
- Lorraine Frost
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Maria A. M. Baez
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Christopher Harrilal
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Alyssa Garabedian
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Francisco Fernandez-Lima
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, Miami, Florida, United States of America
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, United States of America
- * E-mail:
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164
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Esposito F, De Martino M, Petti MG, Forzati F, Tornincasa M, Federico A, Arra C, Pierantoni GM, Fusco A. HMGA1 pseudogenes as candidate proto-oncogenic competitive endogenous RNAs. Oncotarget 2015; 5:8341-54. [PMID: 25268743 PMCID: PMC4226687 DOI: 10.18632/oncotarget.2202] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The High Mobility Group A (HMGA) are nuclear proteins that participate in the organization of nucleoprotein complexes involved in chromatin structure, replication and gene transcription. HMGA overexpression is a feature of human cancer and plays a causal role in cell transformation. Since non-coding RNAs and pseudogenes are now recognized to be important in physiology and disease, we investigated HMGA1 pseudogenes in cancer settings using bioinformatics analysis. Here we report the identification and characterization of two HMGA1 non-coding pseudogenes, HMGA1P6 and HMGA1P7. We show that their overexpression increases the levels of HMGA1 and other cancer-related proteins by inhibiting the suppression of their synthesis mediated by microRNAs. Consistently, embryonic fibroblasts from HMGA1P7-overexpressing transgenic mice displayed a higher growth rate and reduced susceptibility to senescence. Moreover, HMGA1P6 and HMGA1P7 were overexpressed in human anaplastic thyroid carcinomas, which are highly aggressive, but not in differentiated papillary carcinomas, which are less aggressive. Lastly, the expression of the HMGA1 pseudogenes was significantly correlated with HMGA1 protein levels thereby implicating HMGA1P overexpression in cancer progression. In conclusion, HMGA1P6 and HMGA1P7 are potential proto-oncogenic competitive endogenous RNAs.
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Affiliation(s)
- Francesco Esposito
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Marco De Martino
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Maria Grazia Petti
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Floriana Forzati
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Mara Tornincasa
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Antonella Federico
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Claudio Arra
- Istituto Nazionale dei Tumori, Fondazione Pascale, Naples, Italy
| | - Giovanna Maria Pierantoni
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
| | - Alfredo Fusco
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", Naples, Italy
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165
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Zhang Z, Zhang S, Ma P, Jing Y, Peng H, Gao WQ, Zhuang G. Lin28B promotes melanoma growth by mediating a microRNA regulatory circuit. Carcinogenesis 2015; 36:937-45. [PMID: 26071398 DOI: 10.1093/carcin/bgv085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 06/07/2015] [Indexed: 12/21/2022] Open
Abstract
It has been increasingly recognized that microRNAs (miRNAs) are often dysregulated in various human malignancies and can function as oncogenes or tumor-suppressors. However, the potential roles of miRNAs and components of the miRNA biogenesis pathway remain poorly defined in melanoma. Here, we systematically profiled miRNA expression in human melanocytes and melanoma cells, and identified a prominent function of miR-125a-5p in suppressing melanoma growth. Mechanistically, we discovered that Lin28B, a well-characterized inhibitor of let-7 miRNA biogenesis, was a direct target of miR-125a-5p in melanoma. We showed that the Lin28B was aberrantly expressed in a large proportion of melanoma patients and was functionally required for melanoma progression. We further demonstrated the involvement of let-7-dependent mechanism downstream of Lin28B, resulting in the activation of transforming growth factor-β signaling cascade. Collectively, our data implicate Lin28B as a novel oncogene in melanomagenesis by mediating a miRNA regulatory circuit.
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Affiliation(s)
- Zhenfeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200032, China and
| | - Shengzhe Zhang
- School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Pengfei Ma
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ying Jing
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Huixin Peng
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Wei-Qiang Gao
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China, School of Biomedical Engineering & Med-X Research Institute, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Guanglei Zhuang
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China,
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166
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Zheng T, Chou J, Zhang F, Liu Y, Ni H, Li X, Zheng L, Tang T, Jin L, Xi T. CXCR4 3'UTR functions as a ceRNA in promoting metastasis, proliferation and survival of MCF-7 cells by regulating miR-146a activity. Eur J Cell Biol 2015; 94:458-69. [PMID: 26095299 DOI: 10.1016/j.ejcb.2015.05.010] [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: 03/21/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 12/14/2022] Open
Abstract
CXCR4 is the most common chemokine receptor expressed on tumor cells, and it is closely correlated with cancer cell stemness. This study was carried out to explore whether CXCR4 could function as a competitive endogenous RNA to promote metastasis, proliferation and survival in MCF-7 breast cancer cells. We validated that CXCR4, together with TRAF6 and EGFR, was directly targeted by miR-146a in MCF-7 cells. Overexpression of CXCR4 3'UTR inhibited the activity of miR-146a, thus elevating the expression of CXCR4, TRAF6 and EGFR. These oncoproteins further activated NF-κB pathway and promoted the proliferation, migration, invasion and anti-apoptotic activity of MCF-7 cells. Collectively, our study provided new insights into the function of CXCR4 in breast cancer: it promotes tumor progression as both a protein-coding gene and a non-coding RNA, complicating the mechanism by which oncogenes promote tumor progression.
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Affiliation(s)
- Tianjing Zheng
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China
| | - Jinjiang Chou
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China
| | - Feng Zhang
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China
| | - Yu Liu
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China
| | - Haiwei Ni
- Medical college of Yangzhou University, #11, Huaihailu Road, Yangzhou, China
| | - Xiaoman Li
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China
| | - Lufeng Zheng
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China
| | - Tingting Tang
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China
| | - Liang Jin
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China
| | - Tao Xi
- School of Life Science and Technology, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China; Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, #24 Tongjiaxiang, Nanjing 210009, China.
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167
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Kumar MS, Armenteros-Monterroso E, East P, Chakravorty P, Matthews N, Winslow MM, Downward J. Retraction: HMGA2 functions as a competing endogenous RNA to promote lung cancer progression. Nature 2015; 523:370. [PMID: 26061768 DOI: 10.1038/nature14551] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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168
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Abstract
MicroRNAs (miRNAs) are critical regulators of gene expression. Amplification and overexpression of individual 'oncomiRs' or genetic loss of tumour suppressor miRNAs are associated with human cancer and are sufficient to drive tumorigenesis in mouse models. Furthermore, global miRNA depletion caused by genetic and epigenetic alterations in components of the miRNA biogenesis machinery is oncogenic. This, together with the recent identification of novel miRNA regulatory factors and pathways, highlights the importance of miRNA dysregulation in cancer.
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Affiliation(s)
- Shuibin Lin
- 1] Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts 02115, USA. [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Richard I Gregory
- 1] Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts 02115, USA. [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA. [3] Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA. [4] Harvard Stem Cell Institute, Boston, Massachusetts 02115, USA
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169
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Xia YY, Yin L, Jiang N, Guo WJ, Tian H, Jiang XS, Wu J, Chen M, Wu JZ, He X. Downregulating HMGA2 attenuates epithelial-mesenchymal transition-induced invasion and migration in nasopharyngeal cancer cells. Biochem Biophys Res Commun 2015; 463:357-63. [PMID: 26025649 DOI: 10.1016/j.bbrc.2015.05.068] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 05/17/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Epithelial-mesenchymal transition (EMT) is associated with invasion and metastasis of cancer cells. High-mobility group AT-hook 2 (HMGA2) has been found to play a critical role in EMT in a number of malignant tumors. However, whether HMGA2 regulates the EMT in human nasopharyngeal carcinoma (NPC) is unclear. OBJECTIVE The aim of this study was to investigate the effect and mechanism of HMGA2 in inducing invasion and migration in NPC. METHODS In NPC tissues samples, the association of HMGA2 mRNA expression with clinicopathological characteristics were estimated by real-time quantitative RT-PCR(qRT-PCR). In vitro, following the silencing of HMGA2 in CNE-1 and CNE-2 cell lines, the viability and metastatic ability were analyzed using Cell Counting Kit-8 (CCK8), colony formation assay, and transwell assay. EMT and transforming growth factor-beta (TGFβ)/Smad3 signaling pathway-related protein expression changes were evaluated using western blot. RESULTS HMGA2 was upregulated in NPC cell lines and clinical specimens (P < 0.01), and HMGA2 expression correlated significantly with metastasis (P = 0.02) and disease-free survival of NPC (hazard ratio: 3.52; 95% confidence interval: 1.34-7.79; P = 0.01). In addition, following in vitro knockdown of HMGA2, the aggressiveness of cells was markedly inhibited, Vimentin and Snail level was downregulated and E-cadherin expression was upregulated. Moreover, the expression of key proteins TGFβRII and p-Smad3 of the TGFβ/Smad3 signaling pathway was inhibited by the downregulation of HMGA2. CONCLUSION HMGA2 might maintain EMT-induced invasion and migration through the TGFβ/Smad3 signaling pathway in NPC cell lines.
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Affiliation(s)
- You-You Xia
- Department of Radiation Oncology, Lianyungang First People's Hospital, Lianyungang, Jiangsu, China; The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Li Yin
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ning Jiang
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wen-Jie Guo
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hao Tian
- The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xue-Song Jiang
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Wu
- The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Meng Chen
- The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jian-Zhong Wu
- Research Center of Clinical Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xia He
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
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170
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Zhang TY, Huang B, Wu HB, Wu JH, Li LM, Li YX, Hu YL, Han M, Shen YQ, Tabata Y, Gao JQ. Synergistic effects of co-administration of suicide gene expressing mesenchymal stem cells and prodrug-encapsulated liposome on aggressive lung melanoma metastases in mice. J Control Release 2015; 209:260-71. [PMID: 25966361 DOI: 10.1016/j.jconrel.2015.05.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 04/17/2015] [Accepted: 05/08/2015] [Indexed: 11/30/2022]
Abstract
The success of conventional suicide gene therapy for cancer treatment is still limited because of lack of efficient delivery methods, as well as poor penetration into tumor tissues. Mesenchymal stem cells (MSCs) have recently emerged as potential vehicles in improving delivery issues. However, these stem cells are usually genetically modified using viral gene vectors for suicide gene overexpression to induce sufficient therapeutic efficacy. This approach may result in safety risks for clinical translation. Therefore, we designed a novel strategy that uses non-viral gene vector in modifying MSCs with suicide genes to reduce risks. In addition, these cells were co-administrated with prodrug-encapsulated liposomes for synergistic anti-tumor effects. Results demonstrate that this strategy is effective for gene and prodrug delivery, which co-target tumor tissues, to achieve a significant decrease in tumor colonization and a subsequent increase in survival in a murine melanoma lung metastasis model. Moreover, for the first time, we demonstrated the permeability of MSCs within tumor nests by using an in vitro 3D tumor spheroid model. Thus, the present study provides a new strategy to improve the delivery problem in conventional suicide gene therapy and enhance the therapeutic efficacy. Furthermore, this study also presents new findings to improve our understanding of MSCs in tumor-targeted gene delivery.
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Affiliation(s)
- Tian-Yuan Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China
| | - Bing Huang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China
| | - Hai-Bin Wu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China
| | - Jia-He Wu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China
| | - Li-Ming Li
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China
| | - Yan-Xin Li
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China
| | - Yu-Lan Hu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China
| | - Min Han
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China
| | - You-Qing Shen
- Center for Bionanoengineering and State Key Laboratory of Chemical Engineering, Zhejiang University, Hangzhou, PR China
| | - Yasuhiko Tabata
- Department of Biomaterials, Field of Tissue Engineering, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Jian-Qing Gao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, PR China.
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171
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Dai X, Jiang Y, Tan C. Let-7 Sensitizes KRAS Mutant Tumor Cells to Chemotherapy. PLoS One 2015; 10:e0126653. [PMID: 25946136 PMCID: PMC4422443 DOI: 10.1371/journal.pone.0126653] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/04/2015] [Indexed: 12/30/2022] Open
Abstract
KRAS is the most commonly mutated oncogene in human cancers and is associated with poor prognosis and drug resistance. Let-7 is a family of tumor suppressor microRNAs that are frequently suppressed in solid tumors, where KRAS mutations are highly prevalent. In this study, we investigated the potential use of let-7 as a chemosensitizer. We found that let-7b repletion selectively sensitized KRAS mutant tumor cells to the cytotoxicity of paclitaxel and gemcitabine. Transfection of let-7b mimic downregulated the expression of mutant but not wild-type KRAS. Combination of let-7b mimic with paclitaxel or gemcitabine diminished MEK/ERK and PI3K/AKT signaling concurrently, triggered the onset of apoptosis, and reverted the epithelial-mesenchymal transition in KRAS mutant tumor cells. In addition, let-7b repletion downregulated the expression of β-tubulin III and ribonucleotide reductase subunit M2, two proteins known to mediate tumor resistance to paclitaxel and gemcitabine, respectively. Let-7 may represent a new class of chemosensitizer for the treatment of KRAS mutant tumors.
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Affiliation(s)
- Xin Dai
- Department of Pharmaceutical Sciences, Mercer University, Atlanta, Georgia, United States of America
| | - Ying Jiang
- Department of Pharmaceutical Sciences, Mercer University, Atlanta, Georgia, United States of America
| | - Chalet Tan
- Department of Pharmaceutical Sciences, Mercer University, Atlanta, Georgia, United States of America
- * E-mail:
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172
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Japonicone A inhibits the growth of non-small cell lung cancer cells via mitochondria-mediated pathways. Tumour Biol 2015; 36:7473-82. [PMID: 25908173 DOI: 10.1007/s13277-015-3439-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 04/07/2015] [Indexed: 12/24/2022] Open
Abstract
Japonicone A, which is a natural product isolated from the aerial part of Inula japonica Thunb., has a wide range of clinical applications, including anti-inflammation and anti-oxidation. This study investigated the effects of japonicone A on the growth of non-small cell lung cancer (NSCLC) cell lines. The results showed that japonicone A significantly inhibited the growth of NSCLC cell lines in a dose- and time-dependent manner. This product also blocked cell cycle progression at S phase and induced mitochondrial-related apoptosis by upregulating Bax, cleaved caspase-9, cleaved caspase-3, and cleaved poly(ADP-ribose) polymerase (PARP) protein levels and by downregulating Bcl-2, cyclin D1, CDC25A, and CDK2 protein levels. In vivo, japonicone A suppressed tumor growth via the same mechanism as that observed in vitro. In conclusion, our study is the first to report that japonicone A has an inhibitory effect on the growth of NSCLC cells, indicating that japonicone A administration is a potential therapeutic approach for future NSCLC treatments.
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173
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Matouk IJ, Halle D, Gilon M, Hochberg A. The non-coding RNAs of the H19-IGF2 imprinted loci: a focus on biological roles and therapeutic potential in Lung Cancer. J Transl Med 2015; 13:113. [PMID: 25884481 PMCID: PMC4397711 DOI: 10.1186/s12967-015-0467-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/18/2015] [Indexed: 12/15/2022] Open
Abstract
Since it was first described, the imprinted cluster 11p15.5 has been reported to be deregulated in a variety of pediatric and adult cancers including that of the lung. Both protein coding and non-coding genes functioning as oncogenes or as tumor suppressor genes reside within this cluster. Oncomirs that can function as oncogenes or as tumor suppressors have also been reported. While a complete account of the role played by the 11p15.5 imprinted cluster in lung cancer is beyond the scope of this review, we will focus on the role of the non-coding RNAs processed from the H19-IGF2 loci. A special emphasis will be given to the H19/miR-675 gene locus. Their potential diagnostic and therapeutic use in lung cancer will be described.
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Affiliation(s)
- Imad J Matouk
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - David Halle
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Michal Gilon
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Abraham Hochberg
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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174
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Gao Y, Wang Y, Feng J, Feng G, Zheng M, Yang Z, Xiao Z, Lu Z, Ye L, Zhang X. A hairpin within YAP mRNA 3′UTR functions in regulation at post-transcription level. Biochem Biophys Res Commun 2015; 459:306-312. [DOI: 10.1016/j.bbrc.2015.02.106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 02/18/2015] [Indexed: 12/26/2022]
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175
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Sanchez-Mejias A, Tay Y. Competing endogenous RNA networks: tying the essential knots for cancer biology and therapeutics. J Hematol Oncol 2015; 8:30. [PMID: 25888444 PMCID: PMC4381443 DOI: 10.1186/s13045-015-0129-1] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/16/2015] [Indexed: 12/14/2022] Open
Abstract
A recently discovered dimension of post-transcriptional gene regulation involves co-regulatory crosstalk between RNA transcripts, which compete for common pools of microRNA (miRNA) molecules. These competing endogenous RNAs (ceRNAs), or natural miRNA sponges, have an active role in regulating miRNA availability within the cell and form intertwined regulatory networks. Recent reports have implicated diverse RNA species including protein-coding messenger RNAs and non-coding RNAs as ceRNAs in human development and diseases including human cancer. In this review, we discuss the most recent discoveries that implicate natural miRNA decoys in human cancer biology, as well as exciting advances in the study of ceRNA networks and dynamics. The structure and topology of intricate genome-scale ceRNA networks can be predicted computationally, and their dynamic response to fluctuations in ceRNA and miRNA levels can be studied via mathematical modeling. Additionally, the development of new methods to quantitatively determine absolute expression levels of miRNA and ceRNA molecules have expanded the capacity to accurately study the efficiency of ceRNA crosstalk in diverse biological models. These major milestones are of critical importance to identify key components of ceRNA regulatory networks that could aid the development of new approaches to cancer diagnostics and oligonucleotide-based therapeutics.
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Affiliation(s)
- Avencia Sanchez-Mejias
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
| | - Yvonne Tay
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
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176
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Ergun S, Oztuzcu S. Oncocers: ceRNA-mediated cross-talk by sponging miRNAs in oncogenic pathways. Tumour Biol 2015; 36:3129-36. [PMID: 25809705 DOI: 10.1007/s13277-015-3346-x] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/15/2015] [Indexed: 12/12/2022] Open
Abstract
Competing endogenous RNAs (ceRNAs) are RNA transcripts which can communicate with each other by decreasing targeting concentration of micro-RNA (miRNA) with the derepression of other messenger RNAs (mRNAs) having the common miRNA response elements (MREs). Oncocers are ceRNAs taking crucial roles in oncogenic pathways processed in many types of cancer, and this study analyzes oncocer-mediated cross-talk by sponging microRNAs (miRNAs) in these pathways. While doing this, breast, liver, colon, prostate, gastric, lung, endometrium, thyroid and epithelial cancers and melanoma, rhabdomyosarcoma, glioblastoma, acute promyelocytic leukemia, retinoblastoma, and neuroblastoma were analyzed with respect to ceRNA-based carcinogenesis. This study defines, firstly, oncocers in the literature and contains all oncocer-related findings found up to now. Therefore, it will help to increase our comprehension about oncocer-mediated mechanisms. Via this study, a novel perspective would be produced to make clear cancer mechanisms and suggest novel approaches to regulate ceRNA networks via miRNA competition for cancer therapeutics. Graphical Abstract Multiple RNA transcripts have common MREs for the similar miRNA in their 3'-untranslated regions (3'-UTRs). Upregulation of ceRNAs rises the abundance of specific MREs and shifts the miRNA pool distribution, as a result, leading to the increased expression of target mRNA. The depot of genomic mutations and epigenetic alterations changing gene function and expression causes cancers. Herewith, genome-based somatic base-pair mutations, DNA copy number alterations, chromosomal translocation, also transcript fusions, alternative splicing are usually seen in cancer situations. Consequently, such cases causing changed UTR expression in transcripts influence the levels of MRE or present new MREs into the cells. Alterations in MREs of ceRNAs affect the capability of a specific mRNA transcript to attach or titrate miRNAs. As a result, the disturbed ceRNA network can lead to diseases and cancers. As a new term in RNA world, oncocers-the name for ceRNAs taking crucial roles in oncogenic pathways-are processed in many types of cancer, and oncocer-mediated cross-talk are analyzed by sponging miRNAs in these pathways.
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Affiliation(s)
- Sercan Ergun
- Ulubey Vocational Higher School, Ordu University, Ordu, Turkey,
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177
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Pallante P, Sepe R, Puca F, Fusco A. High mobility group a proteins as tumor markers. Front Med (Lausanne) 2015; 2:15. [PMID: 25859543 PMCID: PMC4373383 DOI: 10.3389/fmed.2015.00015] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/07/2015] [Indexed: 01/24/2023] Open
Abstract
Almost 30 years ago, overexpression of HMGA proteins was associated with malignant phenotype of rat thyroid cells transformed with murine retroviruses. Thereafter, several studies have analyzed HMGA expression in a wide range of human neoplasias. Here, we summarize all these results that, in the large majority of the cases, confirm the association of HMGA overexpression with high malignant phenotype as outlined by chemoresistance, spreading of metastases, and a global poor survival. Even though HMGA proteins’ overexpression indicates a poor prognosis in almost all malignancies, their detection may be particularly useful in determining the prognosis of breast, lung, and colon carcinomas, suggesting for the treatment a more aggressive therapy. In particular, the expression of HMGA2 in lung carcinomas is frequently associated with the presence of metastases. Moreover, recent data revealed that often the cause for the high HMGA proteins levels detected in human malignancies is a deregulated expression of non-coding RNA. Therefore, the HMGA proteins represent tumor markers whose detection can be a valid tool for the diagnosis and prognosis of neoplastic diseases.
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Affiliation(s)
- Pierlorenzo Pallante
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale, Consiglio Nazionale delle Ricerche, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Naples , Italy
| | - Romina Sepe
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale, Consiglio Nazionale delle Ricerche, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Naples , Italy
| | - Francesca Puca
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale, Consiglio Nazionale delle Ricerche, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Naples , Italy
| | - Alfredo Fusco
- Istituto per l'Endocrinologia e l'Oncologia Sperimentale, Consiglio Nazionale delle Ricerche, Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II , Naples , Italy ; Instituto Nacional de Câncer , Rio de Janeiro , Brazil
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178
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Guil S, Esteller M. RNA-RNA interactions in gene regulation: the coding and noncoding players. Trends Biochem Sci 2015; 40:248-56. [PMID: 25818326 DOI: 10.1016/j.tibs.2015.03.001] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 12/14/2022]
Abstract
The past few years have witnessed an exciting increase in the richness and complexity of RNA-mediated regulatory circuitries, including new types of RNA-RNA interaction that underlie key steps in gene expression control in an organized and probably hierarchic system to dictate final protein output. Both small (especially miRNAs) and long coding (lc) and noncoding (nc) RNAs contain structural domains that can sense and bind other RNAs via complementary base pairing. The versatility of the interaction confers multiple roles to RNA-RNA hybrids, from control of RNA biogenesis to competition for common targets. Here, we focus on the emerging evidence around RNA networks and their impact on gene expression regulation in light of recent breakthroughs around the crosstalk between coding RNAs and ncRNAs.
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Affiliation(s)
- Sonia Guil
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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179
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180
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Nagano H, Yamagishi N, Tomida C, Yano C, Aibara K, Kohno S, Abe T, Ohno A, Hirasaka K, Okumura Y, Mills EM, Nikawa T, Teshima-Kondo S. A novel myogenic function residing in the 5' non-coding region of Insulin receptor substrate-1 (Irs-1) transcript. BMC Cell Biol 2015; 16:8. [PMID: 25887310 PMCID: PMC4373113 DOI: 10.1186/s12860-015-0054-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/16/2015] [Indexed: 11/20/2022] Open
Abstract
Background There is evidence that several messenger RNAs (mRNAs) are bifunctional RNAs, i.e. RNA transcript carrying both protein-coding capacity and activity as functional non-coding RNA via 5′ and 3′ untranslated regions (UTRs). Results In this study, we identified a novel bifunctional RNA that is transcribed from insulin receptor substrate-1 (Irs-1) gene with full-length 5′UTR sequence (FL-Irs-1 mRNA). FL-Irs-1 mRNA was highly expressed only in skeletal muscle tissue. In cultured skeletal muscle C2C12 cells, the FL-Irs-1 transcript functioned as a bifunctional mRNA. The FL-Irs-1 transcript produced IRS-1 protein during differentiation of myoblasts into myotubes; however, this transcript functioned as a regulatory RNA in proliferating myoblasts. The FL-Irs-1 5′UTR contains a partial complementary sequence to Rb mRNA, which is a critical factor for myogenic differentiation. The overexpression of the 5′UTR markedly reduced Rb mRNA expression, and this reduction was fully dependent on the complementary element and was not compensated by IRS-1 protein. Conversely, knockdown of FL-Irs-1 mRNA increased Rb mRNA expression and enhanced myoblast differentiation into myotubes. Conclusions Our findings suggest that the FL-Irs-1 transcript regulates myogenic differentiation as a regulatory RNA in myoblasts. Electronic supplementary material The online version of this article (doi:10.1186/s12860-015-0054-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hikaru Nagano
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan. .,Facalty of Nutritional Science, Sagami Women's University, Sagamihara, 252-0383, Japan.
| | - Naoko Yamagishi
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Chisato Tomida
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Chiaki Yano
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Kana Aibara
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Shohei Kohno
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Tomoki Abe
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Ayako Ohno
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Katsuya Hirasaka
- Graduate school of Fisheries Science and Environmental Studies, Nagasaki University, Nagasaki, 852-8521, Japan.
| | - Yuushi Okumura
- Facalty of Nutritional Science, Sagami Women's University, Sagamihara, 252-0383, Japan.
| | - Edward M Mills
- Division of Pharmacology/Toxicology, College of Pharmacy, University of Texas at Austin, Austin, Texas.
| | - Takeshi Nikawa
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
| | - Shigetada Teshima-Kondo
- Department of Nutritional Physiology, Institute of Health Biosciences, Tokushima University Graduate School, Tokushima, 770-8503, Japan.
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181
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Saitoh M. Epithelial-mesenchymal transition is regulated at post-transcriptional levels by transforming growth factor-β signaling during tumor progression. Cancer Sci 2015; 106:481-8. [PMID: 25664423 PMCID: PMC4452147 DOI: 10.1111/cas.12630] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/28/2015] [Accepted: 02/03/2015] [Indexed: 12/18/2022] Open
Abstract
Transforming growth factor (TGF)-β acts as a tumor suppressor during cancer initiation, but as a tumor promoter during tumor progression. It has become increasingly clear that TGF-β plays fundamental roles in multiple steps of tumor progression, including epithelial-mesenchymal transition (EMT). The EMT, first described by developmental biologists at the beginning of the 1980s, plays crucial roles in appropriate embryonic development, but also functions in adults during wound healing, organ fibrosis, and tumor progression. During EMT, epithelial cells lose their epithelial polarity and acquire mesenchymal phenotypes, endowing them with migratory and invasive properties. Many secreted polypeptides are implicated in this process, and act in a sequential or cooperative manner. TGF-β induces EMT by propagating intracellular signaling pathways and activating transcriptional factors. Here, I discuss new insights into the molecular mechanisms underlying induction of EMT by TGF-β in cooperation with Ras or growth factors, along with the signals that induce EMT through transcriptional and post-transcriptional regulation.
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Affiliation(s)
- Masao Saitoh
- Department of Biochemistry, Center for Medical Education and Sciences, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Japan
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182
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Interferon-alpha competing endogenous RNA network antagonizes microRNA-1270. Cell Mol Life Sci 2015; 72:2749-61. [PMID: 25746225 PMCID: PMC4477080 DOI: 10.1007/s00018-015-1875-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 12/18/2022]
Abstract
A new form of circuitry for gene regulation has been identified in which RNAs can crosstalk by competing for shared microRNAs (miRNAs). Such competing endogenous RNAs (ceRNAs) form a network via shared miRNA response elements (MREs) to antagonize miRNA function. We previously reported natural antisense RNA (AS) as an important modulator of interferon-α1 (IFN-α1) mRNA levels by promoting IFN-α1 mRNA stability. We show that IFN-α1 AS forms a ceRNA network with specific IFN-α AS (IFN-α7/-α8/-α10/-α14) and mRNA (IFN-α8/-α10/-α14/-α17) subtypes from the IFN-α gene (IFNA) family to antagonize miRNA-1270 (miR-1270), thereby modulating IFN-α1 mRNA levels. Bioinformatic analysis demonstrated that IFN-α1 AS harbors multiple miR-1270 MREs (MRE-1270s), whose presence was substantiated by miR-1270 overexpression and transfection of antimiR-1270. The antimiR-1270, complementary to the miR-1270 seed region, revealed that IFN-α1 AS likely shares the MRE-1270 with IFN-α1 mRNA and specific IFN-α AS and mRNA subtypes. Subsequent bioinformatic analysis for MRE-1270s showed that IFN-α1 AS and other RNA subtypes shared the 6-mer MRE-1270 site. Further MRE-mapping demonstrated that the total number of MRE-1270s in IFN-α1 AS accounted for approximately 30 % of the miR-1270 population. AntimiR-1270 transfection also caused specific de-repression of five cellular mRNAs, including that of CAPRIN1. These results suggest that IFN-α1 AS, together with specific IFN-α AS and mRNA subtypes, as well as the five cellular mRNAs, participate as competing molecules in the ceRNA network against miR-1270. This coordinated regulatory architecture suggests a vital function for the innate immune system in maintaining precise physiological type I IFN levels via post-transcriptional regulatory mechanisms.
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183
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Li Z, Yu X, Shen J, Chan MTV, Wu WKK. MicroRNA in intervertebral disc degeneration. Cell Prolif 2015; 48:278-83. [PMID: 25736871 DOI: 10.1111/cpr.12180] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 11/22/2014] [Indexed: 12/17/2022] Open
Abstract
Aetiology of intervertebral disc degeneration (IDD) is complex, with genetic, developmental, biochemical and biomechanical factors contributing to the disease process. It is becoming obvious that epigenetic processes influence evolution of IDD as strongly as the genetic background. Deregulated phenotypes of nucleus pulposus cells, including differentiation, migration, proliferation and apoptosis, are involved in all stages of progression of human IDD. Non-coding RNAs, including microRNAs, have recently been recognized as important regulators of gene expression. Research into roles of microRNAs in IDD has been very active over the past 5 years. Our review summarizes current research enlightenment towards understanding roles of microRNAs in regulating nucleus pulposus cell functions in IDD. These exciting findings support the notion that specific modulation of microRNAs may represent an attractive approach for management of IDD.
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Affiliation(s)
- Zheng Li
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College, Beijing, 100007, China
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184
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Li P, Ruan X, Yang L, Kiesewetter K, Zhao Y, Luo H, Chen Y, Gucek M, Zhu J, Cao H. A liver-enriched long non-coding RNA, lncLSTR, regulates systemic lipid metabolism in mice. Cell Metab 2015; 21:455-67. [PMID: 25738460 PMCID: PMC4350020 DOI: 10.1016/j.cmet.2015.02.004] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 12/12/2014] [Accepted: 02/06/2015] [Indexed: 02/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) constitute a significant portion of mammalian genome, yet the physiological importance of lncRNAs is largely unknown. Here, we identify a liver-enriched lncRNA in mouse that we term liver-specific triglyceride regulator (lncLSTR). Mice with a liver-specific depletion of lncLSTR exhibit a marked reduction in plasma triglyceride levels. We show that lncLSTR depletion enhances apoC2 expression, leading to robust lipoprotein lipase activation and increased plasma triglyceride clearance. We further demonstrate that the regulation of apoC2 expression occurs through an FXR-mediated pathway. LncLSTR forms a molecular complex with TDP-43 to regulate expression of Cyp8b1, a key enzyme in the bile acid synthesis pathway, and engenders an in vivo bile pool that induces apoC2 expression through FXR. Finally, we demonstrate that lncLSTR depletion can reduce triglyceride levels in a hyperlipidemia mouse model. Taken together, these data support a model in which lncLSTR regulates a TDP-43/FXR/apoC2-dependent pathway to maintain systemic lipid homeostasis.
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Affiliation(s)
- Ping Li
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Xiangbo Ruan
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Ling Yang
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Kurtis Kiesewetter
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Yi Zhao
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China
| | - Haitao Luo
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China
| | - Yong Chen
- Proteomics Core, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Marjan Gucek
- Proteomics Core, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Haiming Cao
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, NIH, Bethesda, MD 20892, USA.
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185
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Deng L, Yang SB, Xu FF, Zhang JH. Long noncoding RNA CCAT1 promotes hepatocellular carcinoma progression by functioning as let-7 sponge. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:18. [PMID: 25884472 PMCID: PMC4339002 DOI: 10.1186/s13046-015-0136-7] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 02/12/2015] [Indexed: 12/15/2022]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have been identified as having functional roles in cancer biology and are deregulated in many cancers. The present study aimed to determine the expression, roles and functional mechanisms of a long noncoding RNA CCAT1 in the progression of hepatocellular carcinoma (HCC). METHODS CCAT1 expression levels in 66 pairs of HCC tissues and pair-matched noncancerous hepatic tissues were tested by real-time PCR. The effects of CCAT1 on HCC cells proliferation and migration were assessed using in vitro cell proliferation and migration assays. A computational screen of microRNAs (miRNAs) target sites in CCAT1 was conducted to search for specific miRNAs binding to CCAT1. The specific binding between CCAT1 and miRNAs was confirmed by RNA immunoprecipitation assay combined with luciferase reporter assay. RESULTS CCAT1 levels are markedly increased in HCC tissues compared with pair-matched noncancerous hepatic tissues. Up-regulation of CCAT1 is correlated with tumor size, microvascular invasion, AFP and poor prognosis. CCAT1 promotes the proliferation and migration of HCC cells. CCAT1 functions as a molecular sponge for let-7, antagonizes its functions, and leads to the de-repression of its endogenous targets HMGA2 and c-Myc. The effect of CCAT1 on HCC cell proliferation and migration is dependent upon its competitively binding to let-7. CONCLUSIONS These data suggest that CCAT1 plays a pivotal role in HCC progression via functioning as let-7 sponge, and implicate the potential application of CCAT1 for the prognosis and treatment of HCC.
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Affiliation(s)
- Liang Deng
- Department of Hepatobiliary Surgery, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Eastern Huangpu Road No. 183, Guangzhou, 510700, China.
| | - Shi-Bin Yang
- Department of Gastrointestinal and Pancreatic Surgery, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Eastern Huangpu Road No. 183, Guangzhou, 510700, China.
| | - Feng-Feng Xu
- Department of Hepatobiliary Surgery, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Eastern Huangpu Road No. 183, Guangzhou, 510700, China.
| | - Ji-Hong Zhang
- Department of Hepatobiliary Surgery, The Eastern Hospital of the First Affiliated Hospital, Sun Yat-sen University, Eastern Huangpu Road No. 183, Guangzhou, 510700, China.
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186
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Bai YH, Wang JP, Yang M, Zeng Y, Jiang HY. SiRNA-HMGA2 weakened AGEs-induced epithelial-to-mesenchymal transition in tubular epithelial cells. Biochem Biophys Res Commun 2015; 457:730-5. [DOI: 10.1016/j.bbrc.2015.01.063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/15/2015] [Indexed: 02/08/2023]
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187
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Kaur H, Hütt-Cabezas M, Weingart MF, Xu J, Kuwahara Y, Erdreich-Epstein A, Weissman BE, Eberhart CG, Raabe EH. The chromatin-modifying protein HMGA2 promotes atypical teratoid/rhabdoid cell tumorigenicity. J Neuropathol Exp Neurol 2015; 74:177-85. [PMID: 25575139 PMCID: PMC4695975 DOI: 10.1097/nen.0000000000000161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Atypical teratoid/rhabdoid tumor (AT/RT) is an aggressive pediatric central nervous system tumor. The poor prognosis of AT/RT warrants identification of novel therapeutic targets and strategies. High-mobility Group AT-hook 2 (HMGA2) is a developmentally important chromatin-modifying protein that positively regulates tumor growth, self-renewal, and invasion in other cancer types. High-mobility group A2 was recently identified as being upregulated in AT/RT tissue, but the role of HMGA2 in brain tumors remains unknown. We used lentiviral short-hairpin RNA to suppress HMGA2 in AT/RT cell lines and found that loss of HMGA2 led to decreased cell growth, proliferation, and colony formation and increased apoptosis. We also found that suppression of HMGA2 negatively affected in vivo orthotopic xenograft tumor growth, more than doubling median survival of mice from 58 days to 153 days. Our results indicate a role for HMGA2 in AT/RT in vitro and in vivo and demonstrate that HMGA2 is a potential therapeutic target in these lethal pediatric tumors.
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Affiliation(s)
- Harpreet Kaur
- From the Division of Neuropathology and Sidney Kimmel Comprehensive Cancer Center (HK, MH-C, MFW, CGE, EHR), Division of Pediatric Oncology (EHR), Johns Hopkins University School of Medicine, Bloomberg Children's Hospital, Baltimore, Maryland; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina (YK, BEW); and Division of Hematology, Oncology, and Blood and Bone Marrow Transplant, Children's Hospital Los Angeles (JX, AE-E); and the University of Southern California (AE-E), Los Angeles, California
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188
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Poliseno L, Pandolfi PP. PTEN ceRNA networks in human cancer. Methods 2015; 77-78:41-50. [PMID: 25644446 DOI: 10.1016/j.ymeth.2015.01.013] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 01/19/2015] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
In multiple human cancer types, a close link exists between the expression levels of Phosphatase and Tensin Homolog deleted on chromosome 10 (PTEN) and its oncosuppressive activities. Therefore, an in depth understanding of the molecular mechanisms by which PTEN expression is modulated is crucial in order to achieve a comprehensive knowledge of its biological roles. In recent years, the competition between PTEN mRNA and other RNAs for shared microRNA molecules has emerged as one such mechanism and has brought into focus the coding-independent activities of PTEN and other mRNAs. In this review article, we examine the competing endogenous RNA (ceRNA) partners of PTEN that have been identified so far. We also discuss how PTEN-centered ceRNA networks can contribute to a deeper understanding of PTEN function and tumorigenesis.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, Istituto Toscano Tumori, Pisa, Italy; Institute of Clinical Physiology, CNR, Pisa, Italy.
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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189
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Cheng DL, Xiang YY, Ji LJ, Lu XJ. Competing endogenous RNA interplay in cancer: mechanism, methodology, and perspectives. Tumour Biol 2015; 36:479-88. [PMID: 25604144 DOI: 10.1007/s13277-015-3093-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 01/08/2015] [Indexed: 02/07/2023] Open
Abstract
Competing endogenous RNAs (ceRNAs) refer to RNA transcripts, such as mRNAs, non-coding RNAs, pseudogene transcripts, and circular RNAs, that can regulate each other by competing for the same pool of miRNAs. ceRNAs involve in the pathogenesis of several common cancers such as prostate cancer, liver cancer, breast cancer, lung cancer, gastric cancer, endometrial cancer, and so on. ceRNA activity is determined by factors such as miRNA/ceRNA abundance, ceRNAs binding affinity to miRNAs, RNA editing, and RNA-binding proteins. The alteration of any of these factors may lead to ceRNA network imbalance and thus contribute to cancer initiation and progression. There are generally three steps in ceRNA research conductions: ceRNA prediction, ceRNA validation, and ceRNA functional investigation. Deciphering ceRNA interplay in cancer provides new insight into cancer pathogenesis and opportunities for therapy exploration. In this review, we try to give readers a concise and reliable illustration on the mechanism, functions, research approaches, and perspective of ceRNA in cancer.
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Affiliation(s)
- Dong-Liang Cheng
- Department of Cardiothoracic Surgery, Shiyan Taihe Hospital, Hubei University of Medicine, Shiyan City, Hubei Province, China
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190
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Zheng W, Sai W, Yao M, Gu H, Yao Y, Qian Q, Yao D. Silencing clusterin gene transcription on effects of multidrug resistance reversing of human hepatoma HepG2/ADM cells. Tumour Biol 2015. [PMID: 25600802 DOI: 10.1007/s13277-015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abnormal clusterin (CLU) expression is associated with multidrug resistance (MDR) of hepatocellular carcinoma (HCC). In the present study, the CLU expression was analyzed in human hepatoma cells and chemoresistant counterpart HepG2/ADM cells. Compared with L02 cells, the overexpression of cellular CLU was identified in HepG2, HepG2/ADM, SMMC7721, Hep3B ,and PLC cells and relatively lower expression in Bel-7404, SNU-739, and MHCC97H cells. Specific short hairpin RNAs (shRNAs) to silence CLU gene transcription were designed, and the most effective sequences were screened. After the HepG2/ADM cells transfected with shRNA-1, the inhibition of CLU expression was 73.68 % at messenger RNA (mRNA) level by real-time quantitative RT-PCR with obvious enhancement in cell chemosensitivity, increasing apoptosis induced by doxorubicin using fluorescence kit, and Rh-123 retention qualified with flow cytometry. Knockdown CLU also significantly decreased the drug efflux pump activity through the depression of MDR1/P-glycoprotein (q = 11.739, P < 0.001). Moreover, silencing CLU led to downregulation of β-catenin (q = 13.544, P = 0.001), suggesting that downregulation of CLU might be a key point to reverse multidrug resistance of HepG2/ADM cells.
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Affiliation(s)
- Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, 20 West Temple Road, Nantong, 226001, Jiangsu Province, China
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Xia YY, Yin L, Tian H, Guo WJ, Jiang N, Jiang XS, Wu J, Chen M, Wu JZ, He X. HMGA2 is associated with epithelial-mesenchymal transition and can predict poor prognosis in nasopharyngeal carcinoma. Onco Targets Ther 2015; 8:169-76. [PMID: 25653540 PMCID: PMC4303461 DOI: 10.2147/ott.s74397] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Objective High-mobility group protein 2 (HMGA2) and epithelial–mesenchymal transition (EMT)-associated proteins play key roles in cancer progression and metastasis. However, the clinical significance of HMGA2 and its relationship with EMT markers in nasopharyngeal carcinoma (NPC) is unclear. This study aimed to assess the clinicopathological significance and prognostic value of HMGA2, E-cadherin, and vimentin in NPC. Methods Using immunohistochemistry, HMGA2, E-cadherin, and vimentin expression levels were evaluated in NPC (n=124) and non-tumoral inflammatory nasopharynx (n=20) tissues. The association of HMGA2 and EMT markers with clinicopathological characteristics and relationships between the protein levels and overall survival were analyzed. Results Compared with non-tumorous tissues, HMGA2 and vimentin levels were markedly increased in NPC tissues, whereas decreased E-cadherin levels were observed (P<0.001). Moreover, HMGA2 expression was positively correlated with vimentin levels (r=0.431, P<0.001) and negatively correlated with E-cadherin amounts (r=−0.413, P<0.001) in NPC tissues. The expression of all three proteins correlated significantly with tumor N stage, TNM stage, and 2-year metastasis. Furthermore, significant correlations were found for T stage, N stage, TNM stage, HMGA2, E-cadherin, and vimentin (all P<0.013) with poor prognosis (univariate analysis). However, multivariate analyses showed that only HMGA2 (hazard ratio [HR]: 2.683, 95% confidence interval [CI]: 1.185–6.077, P=0.018) and N stage (HR: 7.892, 95% CI: 2.731–22.807, P<0.001) were independent predictors of poor prognosis. Conclusion These results demonstrated that HMGA2, an independent prognostic factor, may promote NPC progression and metastasis, and is significantly associated with EMT proteins. Therefore, HMGA2 may be considered a potential therapeutic target in NPC.
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Affiliation(s)
- You-You Xia
- The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Li Yin
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Hao Tian
- The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Wen-Jie Guo
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Ning Jiang
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Xue-Song Jiang
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Jing Wu
- The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Meng Chen
- The Fourth Clinical Medical College of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Jian-Zhong Wu
- Research Center of Clinical Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Xia He
- Department of Radiation Oncology, The Affiliated Jiangsu Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
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192
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Zhang Y, Xie S, Xu H, Qu L. CLIP: viewing the RNA world from an RNA-protein interactome perspective. SCIENCE CHINA-LIFE SCIENCES 2015; 58:75-88. [DOI: 10.1007/s11427-014-4764-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/13/2014] [Indexed: 12/20/2022]
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193
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Arancio W, Carina V, Pizzolanti G, Tomasello L, Pitrone M, Baiamonte C, Amato MC, Giordano C. Anaplastic Thyroid Carcinoma: A ceRNA Analysis Pointed to a Crosstalk between SOX2, TP53, and microRNA Biogenesis. Int J Endocrinol 2015; 2015:439370. [PMID: 25705224 PMCID: PMC4326218 DOI: 10.1155/2015/439370] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/28/2014] [Accepted: 09/10/2014] [Indexed: 12/18/2022] Open
Abstract
It has been suggested that cancer stem cells (CSC) may play a central role in oncogenesis, especially in undifferentiated tumours. Anaplastic thyroid carcinoma (ATC) has characteristics suggestive of a tumour enriched in CSC. Previous studies suggested that the stem cell factor SOX2 has a preeminent hierarchical role in determining the characteristics of stem cells in SW1736 ATC cell line. In detail, silencing SOX2 in SW1736 is able to suppress the expression of the stem markers analysed, strongly sensitizing the line to treatment with chemotherapeutic agents. Therefore, in order to further investigate the role of SOX2 in ATC, a competing endogenous RNA (ceRNA) analysis was conducted in order to isolate new functional partners of SOX2. Among the interactors, of particular interest are genes involved in the biogenesis of miRNAs (DICER1, RNASEN, and EIF2C2), in the control cell cycle (TP53, CCND1), and in mitochondrial activity (COX8A). The data suggest that stemness, microRNA biogenesis and functions, p53 regulatory network, cyclin D1, and cell cycle control, together with mitochondrial activity, might be coregulated.
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Affiliation(s)
- Walter Arancio
- Section of Cardio-Respiratory and Endocrine-Metabolic Diseases, Biomedical Department of Internal and Specialist Medicine (Di.Bi.M.I.S.), University of Palermo, Piazza delle Cliniche 2, 90127 Palermo, Italy
- *Walter Arancio:
| | - Valeria Carina
- Section of Cardio-Respiratory and Endocrine-Metabolic Diseases, Biomedical Department of Internal and Specialist Medicine (Di.Bi.M.I.S.), University of Palermo, Piazza delle Cliniche 2, 90127 Palermo, Italy
- Istituto Ortopedico Rizzoli (IOR), Section of Biology and Genetics, Department of Pathobiology and Medical and Forensic Biotechnology (Di.Bi.Me.F.), University of Palermo, Via Divisi 83, 90100 Palermo, Italy
| | - Giuseppe Pizzolanti
- Section of Cardio-Respiratory and Endocrine-Metabolic Diseases, Biomedical Department of Internal and Specialist Medicine (Di.Bi.M.I.S.), University of Palermo, Piazza delle Cliniche 2, 90127 Palermo, Italy
| | - Laura Tomasello
- Section of Cardio-Respiratory and Endocrine-Metabolic Diseases, Biomedical Department of Internal and Specialist Medicine (Di.Bi.M.I.S.), University of Palermo, Piazza delle Cliniche 2, 90127 Palermo, Italy
| | - Maria Pitrone
- Section of Cardio-Respiratory and Endocrine-Metabolic Diseases, Biomedical Department of Internal and Specialist Medicine (Di.Bi.M.I.S.), University of Palermo, Piazza delle Cliniche 2, 90127 Palermo, Italy
| | - Concetta Baiamonte
- Section of Cardio-Respiratory and Endocrine-Metabolic Diseases, Biomedical Department of Internal and Specialist Medicine (Di.Bi.M.I.S.), University of Palermo, Piazza delle Cliniche 2, 90127 Palermo, Italy
| | - Marco Calogero Amato
- Section of Cardio-Respiratory and Endocrine-Metabolic Diseases, Biomedical Department of Internal and Specialist Medicine (Di.Bi.M.I.S.), University of Palermo, Piazza delle Cliniche 2, 90127 Palermo, Italy
| | - Carla Giordano
- Section of Cardio-Respiratory and Endocrine-Metabolic Diseases, Biomedical Department of Internal and Specialist Medicine (Di.Bi.M.I.S.), University of Palermo, Piazza delle Cliniche 2, 90127 Palermo, Italy
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Shao T, Wu A, Chen J, Chen H, Lu J, Bai J, Li Y, Xu J, Li X. Identification of module biomarkers from the dysregulated ceRNA–ceRNA interaction network in lung adenocarcinoma. MOLECULAR BIOSYSTEMS 2015; 11:3048-58. [DOI: 10.1039/c5mb00364d] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The dysregulated ceRNA–ceRNA interaction network in lung adenocarcinoma.
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Affiliation(s)
- Tingting Shao
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Aiwei Wu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Juan Chen
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Hong Chen
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Jianping Lu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Jing Bai
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Yongsheng Li
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Juan Xu
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
| | - Xia Li
- College of Bioinformatics Science and Technology
- Harbin Medical University
- Harbin 150081
- China
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Hepatitis B virus regulates apoptosis and tumorigenesis through the microRNA-15a-Smad7-transforming growth factor beta pathway. J Virol 2014; 89:2739-49. [PMID: 25540364 DOI: 10.1128/jvi.02784-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Hepatitis B virus (HBV) infection causes chronic hepatitis in hundreds of millions of people worldwide, which can eventually lead to hepatocellular carcinoma (HCC). Previously, we found that HBV mRNAs can absorb microRNA-15a (miR-15a) to affect apoptosis through the Bcl-2 pathway. We asked whether HBV could inhibit apoptosis and promote tumorigenesis through different pathways. In this study, we found that the transforming growth factor β (TGF-β) pathway-inhibitory factor Smad7 is a novel target of miR-15a. We demonstrated that HBV can upregulate the level of Smad7 by downregulating miR-15a. Furthermore, we examined the level of Smad7 in liver samples from HBV-infected HCC patients and found that HBV mRNAs are positively correlated with the level of Smad7. By taking the approach of using immunoblotting and luciferase reporter assays, we revealed that HBV can abrogate TGF-β signaling via upregulating Smad7. By using annexin V staining and caspase 3/7 activity assays, we found that HBV can inhibit TGF-β-induced apoptosis of HepG2 cells. We also showed that HBV can promote tumor growth in BALB/c nude mice through upregulating the expression of Smad7. In conclusion, we demonstrated that HBV can upregulate Smad7 expression and inhibit TGF-β signaling, which makes the cells resistant to TGF-β-induced apoptosis and promotes tumorigenesis. IMPORTANCE Hepatitis B virus (HBV) infection causes chronic hepatitis, which can eventually lead to hepatocellular carcinoma (HCC). TGF-β signaling is closely linked to liver fibrosis, cirrhosis, and subsequent HCC progression and plays a unique role in the pathogenesis of HCC. At the early stage of tumor formation, TGF-β functions as a tumor suppressor that inhibits cell proliferation and induces apoptosis. Previously, we found that HBV mRNAs can sponge off miR-15a to affect apoptosis through the Bcl-2 pathway. In this study, we identified that the TGF-β-inhibitory factor Smad7 is a novel target of miR-15a. We reveal that HBV can abrogate TGF-β signaling via upregulating Smad7, inhibit TGF-β-induced apoptosis, as well as promote tumor development. Our study provides evidence to support the idea that viral RNAs can exert their functions as competing endogenous RNAs (ceRNAs) toward microRNA and participate in important cellular processes.
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197
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Yip DKS, Pang IK, Yip KY. Systematic exploration of autonomous modules in noisy microRNA-target networks for testing the generality of the ceRNA hypothesis. BMC Genomics 2014; 15:1178. [PMID: 25539629 PMCID: PMC4367885 DOI: 10.1186/1471-2164-15-1178] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/11/2014] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND In the competing endogenous RNA (ceRNA) hypothesis, different transcripts communicate through a competition for their common targeting microRNAs (miRNAs). Individual examples have clearly shown the functional importance of ceRNA in gene regulation and cancer biology. It remains unclear to what extent gene expression levels are regulated by ceRNA in general. One major hurdle to studying this problem is the intertwined connections in miRNA-target networks, which makes it difficult to isolate the effects of individual miRNAs. RESULTS Here we propose computational methods for decomposing a complex miRNA-target network into largely autonomous modules called microRNA-target biclusters (MTBs). Each MTB contains a relatively small number of densely connected miRNAs and mRNAs with few connections to other miRNAs and mRNAs. Each MTB can thus be individually analyzed with minimal crosstalk with other MTBs. Our approach differs from previous methods for finding modules in miRNA-target networks by not making any pre-assumptions about expression patterns, thereby providing objective information for testing the ceRNA hypothesis. We show that the expression levels of miRNAs and mRNAs in an MTB are significantly more anti-correlated than random miRNA-mRNA pairs and other validated and predicted miRNA-target pairs, demonstrating the biological relevance of MTBs. We further show that there is widespread correlation of expression between mRNAs in same MTBs under a wide variety of parameter settings, and the correlation remains even when co-regulatory effects are controlled for, which suggests potential widespread expression buffering between these mRNAs, which is consistent with the ceRNA hypothesis. Lastly, we also propose a potential use of MTBs in functional annotation of miRNAs. CONCLUSIONS MTBs can be used to help identify autonomous miRNA-target modules for testing the generality of the ceRNA hypothesis experimentally. The identified modules can also be used to test other properties of miRNA-target networks in general.
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Affiliation(s)
- Danny Kit-Sang Yip
- />Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Iris K Pang
- />School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- />Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- />Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- />CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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198
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Tan EJ, Kahata K, Idås O, Thuault S, Heldin CH, Moustakas A. The high mobility group A2 protein epigenetically silences the Cdh1 gene during epithelial-to-mesenchymal transition. Nucleic Acids Res 2014; 43:162-78. [PMID: 25492890 PMCID: PMC4288184 DOI: 10.1093/nar/gku1293] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The loss of the tumour suppressor E-cadherin (Cdh1) is a key event during tumourigenesis and epithelial-mesenchymal transition (EMT). Transforming growth factor-β (TGFβ) triggers EMT by inducing the expression of non-histone chromatin protein High Mobility Group A2 (HMGA2). We have previously shown that HMGA2, together with Smads, regulate a network of EMT-transcription factors (EMT-TFs) like Snail1, Snail2, ZEB1, ZEB2 and Twist1, most of which are well-known repressors of the Cdh1 gene. In this study, we show that the Cdh1 promoter is hypermethylated and epigenetically silenced in our constitutive EMT cell model, whereby HMGA2 is ectopically expressed in mammary epithelial NMuMG cells and these cells are highly motile and invasive. Furthermore, HMGA2 remodels the chromatin to favour binding of de novo DNA methyltransferase 3A (DNMT3A) to the Cdh1 promoter. E-cadherin expression could be restored after treatment with the DNA de-methylating agent 5-aza-2'-deoxycytidine. Here, we describe a new epigenetic role for HMGA2, which follows the actions that HMGA2 initiates via the EMT-TFs, thus achieving sustained silencing of E-cadherin expression and promoting tumour cell invasion.
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Affiliation(s)
- E-Jean Tan
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Kaoru Kahata
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Oskar Idås
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Sylvie Thuault
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Carl-Henrik Heldin
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden
| | - Aristidis Moustakas
- Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala SE-75124, Sweden Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala SE-75123, Sweden
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Kang R, Chen R, Zhang Q, Hou W, Wu S, Cao L, Huang J, Yu Y, Fan XG, Yan Z, Sun X, Wang H, Wang Q, Tsung A, Billiar TR, Zeh HJ, Lotze MT, Tang D. HMGB1 in health and disease. Mol Aspects Med 2014; 40:1-116. [PMID: 25010388 PMCID: PMC4254084 DOI: 10.1016/j.mam.2014.05.001] [Citation(s) in RCA: 683] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/05/2014] [Indexed: 12/22/2022]
Abstract
Complex genetic and physiological variations as well as environmental factors that drive emergence of chromosomal instability, development of unscheduled cell death, skewed differentiation, and altered metabolism are central to the pathogenesis of human diseases and disorders. Understanding the molecular bases for these processes is important for the development of new diagnostic biomarkers, and for identifying new therapeutic targets. In 1973, a group of non-histone nuclear proteins with high electrophoretic mobility was discovered and termed high-mobility group (HMG) proteins. The HMG proteins include three superfamilies termed HMGB, HMGN, and HMGA. High-mobility group box 1 (HMGB1), the most abundant and well-studied HMG protein, senses and coordinates the cellular stress response and plays a critical role not only inside of the cell as a DNA chaperone, chromosome guardian, autophagy sustainer, and protector from apoptotic cell death, but also outside the cell as the prototypic damage associated molecular pattern molecule (DAMP). This DAMP, in conjunction with other factors, thus has cytokine, chemokine, and growth factor activity, orchestrating the inflammatory and immune response. All of these characteristics make HMGB1 a critical molecular target in multiple human diseases including infectious diseases, ischemia, immune disorders, neurodegenerative diseases, metabolic disorders, and cancer. Indeed, a number of emergent strategies have been used to inhibit HMGB1 expression, release, and activity in vitro and in vivo. These include antibodies, peptide inhibitors, RNAi, anti-coagulants, endogenous hormones, various chemical compounds, HMGB1-receptor and signaling pathway inhibition, artificial DNAs, physical strategies including vagus nerve stimulation and other surgical approaches. Future work further investigating the details of HMGB1 localization, structure, post-translational modification, and identification of additional partners will undoubtedly uncover additional secrets regarding HMGB1's multiple functions.
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Affiliation(s)
- Rui Kang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
| | - Ruochan Chen
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Qiuhong Zhang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Wen Hou
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Sha Wu
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Lizhi Cao
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jin Huang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yan Yu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xue-Gong Fan
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhengwen Yan
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA; Department of Neurology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, China
| | - Xiaofang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Experimental Department of Institute of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510510, China
| | - Haichao Wang
- Laboratory of Emergency Medicine, The Feinstein Institute for Medical Research, Manhasset, NY 11030, USA
| | - Qingde Wang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Allan Tsung
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Timothy R Billiar
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Herbert J Zeh
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Daolin Tang
- Department of Surgery, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
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Xiao-Jie L, Ai-Mei G, Li-Juan J, Jiang X. Pseudogene in cancer: real functions and promising signature. J Med Genet 2014; 52:17-24. [DOI: 10.1136/jmedgenet-2014-102785] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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