1151
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Pang L, Hu J, Zhang G, Li X, Zhang X, Yu F, Lan Y, Xu J, Pang B, Han D, Xiao Y, Li X. Dysregulated long intergenic non-coding RNA modules contribute to heart failure. Oncotarget 2018; 7:59676-59690. [PMID: 28040802 PMCID: PMC5312340 DOI: 10.18632/oncotarget.10834] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/09/2016] [Indexed: 01/12/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are emerging as important regulatory molecules involved in diseases including heart failure. However, little is known about how the lincRNAs work together with protein-coding genes (PCGs) contributing to the pathogenesis of heart failure. In this study, we constructed a comprehensive transcriptome profile of lincRNAs, PCGs and miRNAs using RNA-seq and miRNA-seq data of 16 heart failure patients (HFs) and 8 non-failing individuals (NFs). Through integrating lincRNA and PCG expression profiles, we identified HF-associated lincRNA modules. We identified a heart-specific lincRNA module which was significantly enriched for differentially expressed lincRNAs and PCGs. This module was associated with heart failure rather than with other clinical traits such as sex, age, smoking and diabetes mellitus. Moreover, the module was significantly correlated with certain indicators of left ventricular function like ejection fraction and left ventricular end-diastolic diameter, implying the potential of its components as crucial biomarkers. Apart from enhancer-like function, lincRNAs in this module could act as competing endogenous RNAs (ceRNAs) to regulate genes which were associated with left-ventricular systolic function. Our work provided deep insights into the critical roles of lincRNAs in the pathology of heart failure and suggested that they could be valuable biomarkers and therapeutic targets.
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Affiliation(s)
- Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Guanxiong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Fulong Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
| | - Bo Pang
- Department of Genetics, Harbin Medical University, Harbin, Heilongjiang, China
| | - Dong Han
- National Center for Nanoscience and Technology, Haidian, Beijing, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China.,Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education, Harbin, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China
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1152
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Chen X, Zhu H, Wu X, Xie X, Huang G, Xu X, Li S, Xing C. Downregulated pseudogene CTNNAP1 promote tumor growth in human cancer by downregulating its cognate gene CTNNA1 expression. Oncotarget. 2016;7:55518-55528. [PMID: 27487124 PMCID: PMC5342433 DOI: 10.18632/oncotarget.10833] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 06/17/2016] [Indexed: 01/16/2023] Open
Abstract
Accumulating evidence indicates that deregulation of cancer-associated pseudogene is involved in the pathogenesis of cancer. In the study, we demonstrated that pseudogene CTNNAP1, for the CTNNA1 gene, was dysregulated in colorectal cancer and the degree of dysregulation was remarkably associated with tumor node metastasis (TNM) stage (P<0.05). The mechanistic experiments revealed that pseudogene CTNNAP1 played a pivotal role in the regulation of its cognate gene CTNNA1 by competition for microRNA-141. Moreover, gain-of-function approaches showed that overexpression of CTNNAP1 or CTNNA1 significantly inhibited cell proliferation and tumor growth in vitro and in vivo by inducing G0/G1 cell cycle arrest. Our findings add a new regulatory circuit via competing endogenous RNA (ceRNA) cross-talk between pseudogene CTNNAP1 and its cognate gene CTNNA1, and provide new insights into potential diagnostic biomarker for monitoring human colorectal cancer.
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1153
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Shang M, Wang X, Zhang Y, Gao Z, Wang T, Liu R. LincRNA-ROR promotes metastasis and invasion of esophageal squamous cell carcinoma by regulating miR-145/FSCN1. Onco Targets Ther 2018; 11:639-649. [PMID: 29430188 PMCID: PMC5797470 DOI: 10.2147/ott.s157638] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background and objective In an attempt to discover a new biomarker for early diagnosis and prognosis of esophageal squamous cell carcinoma (ESCC), the regulation mechanism of large intergenic non-coding RNA–regulator of reprogramming (lincRNA-ROR) as a microRNA (miRNA) sponge was studied. Patients and methods ROR expression in 91 pairs of ESCC tissue samples and matched adjacent tissues was quantified with real-time fluorescent quantitative polymerase chain reaction (qRT-PCR). The ROR–miRNA–mRNA regulatory network was built with 161 esophageal cancer (EC) tissues and 11 adjacent tumor tissues from The Cancer Genome Atlas (TCGA) database. A total of 96 cases of ESCC from TCGA database were collected for analysis on survival rates. The regulatory relationship between ROR, miR-145 and FSCN1 was verified in ESCC cells via qRT-PCR, dual luciferase reporter (DLR) assay, RNA immunoprecipitation (RIP) and Western blotting. The transwell method was used to detect cell migration and invasion. Results ROR expression in ESCC tumor tissues was significantly higher than in the adjacent tissues, p<0.001. The survival rate of ESCC patients with high ROR expression levels was lower than that of patients with low ROR expression levels (p<0.001). ROR overexpression could downregulate miR-145 by up to 50% was proven by RIP, DLR assay, and qRT-PCR. Two effective binding sites of ROR to miR-145 were verified by DLR assay. One of the sites has never been cited in the literature. The Western blotting results showed that FSCN1 was a downstream target of ROR/miR-145 (p<0.05). Transwell assays were used to show that overexpression of ROR enhanced migration and invasion behavior of ESCC and miR-145 hindered these effects. Conclusion ROR acted as a competitive endogenous RNA (ceRNA) of miR-145 in ESCC. A novel, effective miR-145 binding site of ROR was discovered. The ROR/miR-145/FSCN1 pathway was shown to take part in the metastasis of ESCC. ROR is likely an oncogene biomarker for ESCC early diagnosis and prognosis.
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Affiliation(s)
- Muhe Shang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Xianghu Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Ying Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Zhikui Gao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Tian Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, China
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1154
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Wu H, Zhou C. Long non-coding RNA UCA1 promotes lung cancer cell proliferation and migration via microRNA-193a/HMGB1 axis. Biochem Biophys Res Commun 2018; 496:738-45. [PMID: 29355524 DOI: 10.1016/j.bbrc.2018.01.097] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 01/15/2018] [Indexed: 01/27/2023]
Abstract
Lung cancer is a leading cause of death worldwide. Long non-coding RNAs have been documented aberrantly expressed and exerted crucial role in variety of cancers. Urothelial carcinoma associated 1 (UCA1) is a potential new type of biomarkers for tumor diagnosis and exerts oncogenic effect on various human cancers. However, the mechanism of oncogenic role of UCA1 in lung cancer remains unclear. In this study, we firstly confirmed the role of UCA1 in lung cancer and found that UCA1 down-regulation inhibited cell proliferation and migration in both SKMES-1 and H520 lung cancer cells. Then we demonstrated that repressed UCA1 promoted the miR-193a expression and miR-193a could bind to the predicted binding site of UCA1. We then dissected the role of miR-193a in lung cancer and proved the anti-tumor role of miR-193a. Furthermore, we found that miR-193a displayed its role in lung cancer via modulating the HMGB1 expression. In addition, we found that over-expression of HMGB1 could restore the UCA1 knockdown induced repression of cell proliferation and migration. In summary, our study demonstrated that UCA1 exerts oncogenes activity in lung cancer, acting mechanistically by upregulating HMGB1 expression through 'sponging' miR-193a.
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1155
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Li X, Zheng L, Zhang F, Hu J, Chou J, Liu Y, Xing Y, Xi T. STARD13-correlated ceRNA network inhibits EMT and metastasis of breast cancer. Oncotarget 2018; 7:23197-211. [PMID: 26985770 PMCID: PMC5029620 DOI: 10.18632/oncotarget.8099] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/28/2016] [Indexed: 12/14/2022] Open
Abstract
Competing endogenous RNAs (ceRNAs) network has been correlated with the initiation and development of cancer. Here, we identify CDH5, HOXD1, and HOXD10 as putative STARD13 ceRNAs and they display concordant patterns with STARD13 in different metastatic potential breast cancer cell lines and tissues. Notably, 3’UTRs of these genes suppress breast cancer metastasis via inhibiting epithelial-mesenchymal transition (EMT) in vitro and in vivo, which are activated through the crosstalk between STARD13 and its ceRNAs in 3’UTR- and miRNA-dependent manners. In addition, Kaplan-Meier survival analysis reveals that mRNA level of STARD13 and its ceRNAs is remarkably associated with survival of breast cancer patients. These results suggest that 3’UTRs of CDH5, HOXD1, and HOXD10 inhibit breast cancer metastasis via serving as STARD13 ceRNAs.
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Affiliation(s)
- Xiaoman Li
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Lufeng Zheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Feng Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jinhang Hu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jinjiang Chou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yu Liu
- Department of Biochemistry, School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yingying Xing
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University, Nanjing, People's Republic of China
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1156
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Ding Y, Wang ZC, Zheng Y, Hu Z, Li Y, Luo DF, Wang SY. C-Myc functions as a competing endogenous RNA in acute promyelocytic leukemia. Oncotarget 2018; 7:56422-56430. [PMID: 27486764 PMCID: PMC5302924 DOI: 10.18632/oncotarget.10896] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 07/09/2016] [Indexed: 11/25/2022] Open
Abstract
Recent reports have described a new post-transcriptional regulation that RNA transcripts can crosstalk with each other by competing for their common microRNAs. These RNA transcripts termed competing endogenous RNAs (ceRNAs) regulate the distribution of miRNAs on their targets. One corollary from ceRNA interaction is that chromosomal translocation in acute promyelocytic leukemia (APL) would perturb ceRNA regulation due to altered expression of 3'UTRs. In our study, we demonstrate that expression of PML/RARα, the APL-associated fusion oncogene is repressed by c-Myc mRNA transcript independent of protein-coding function but dependent upon microRNA. Attenuation of c-Myc transcript results in PML/RARα-degraded cellular phenotypes in APL cells, but these Myc reduction-associated cell phenotypes are sufficient to abrogate in a microRNA dependent manner. We also show that let-7 microRNA family members promote differentiation of All-Trans-Retinoic Acid (ATRA)-induced NB4 cells and their activities are affected by expression levels of both c-Myc and PML/RARα through altering miRNA targets. These results indicate that c-Myc mRNA represses PML/RARα expression via altering the distribution of let-7 miRNAs on their targets. Our findings reveal a previously unrecognized role of c-Myc as a potential ceRNA for PML/RARα in APL.
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Affiliation(s)
- Ye Ding
- Union Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China
| | - Ze-Chuan Wang
- Union Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China
| | - Yi Zheng
- Union Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China
| | - Zheng Hu
- Union Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China
| | - Yang Li
- Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, P.R. China
| | - Dong-Feng Luo
- Union Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China
| | - Shao-Yuan Wang
- Union Clinical Medical College, Fujian Medical University, Fuzhou, P.R. China.,Department of Hematology, Fujian Institute of Hematology, Fujian Provincial Key Laboratory on Hematology, Fujian Medical University Union Hospital, Fuzhou, P.R. China
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1157
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Ma Y, Zhang J, Wen L, Lin A. Membrane-lipid associated lncRNA: A new regulator in cancer signaling. Cancer Lett 2018; 419:27-29. [PMID: 29330108 DOI: 10.1016/j.canlet.2018.01.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 01/09/2023]
Abstract
Long noncoding RNAs (LncRNAs) are one of the emerging regulators which are involved in diverse biological processes. LncRNAs can participate in the regulation of gene expression via various ways in the cytoplasm and the nucleus. The function of the nuclear lncRNAs has been studied a lot. Recent studies have shown that the regulatory roles of cytoplasmic lncRNA, including membrane lipid associated lncRNA, which may open an unexplored mechanistic territory. LncRNA dysregulated expression represents a common event in pathogenesis of a variety of human genetic diseases including cancer. Lipid-associated lncRNA is capable of modulating critical cellular functions by directly interacting with phospholipids on the plasma membrane. Besides, it also could be a predictor for the poor prognosis of cancer. In this review, we sum up the roles of cytoplasmic lncRNA, especially lipid-associated lncRNA in cancer.
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Affiliation(s)
- Yanxiu Ma
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Junmei Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lixia Wen
- Institute of Immunology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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1158
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Abstract
Compared to their protein-coding counterparts, almost nothing is known about the role of long noncoding RNAs (lncRNAs) in cardiac fibrosis. In the current report, Liang and Pan et al. characterized the pro-fibrotic lncRNA PFL in respect to cardiac fibrosis in mice. PFL was upregulated in the hearts of mice after myocardial infarction and in fibrotic cardiac fibroblasts. Moreover, PFL competitively sponged the cardio-protective miRNA let-7d in cardiac fibroblasts. Knockdown of platelet activating factor receptor (PTAFR) was shown to affect the pro-fibrotic collagen production mediated by PFL. PTAFR overexpression also led to collagen production and RNA abundance of PTAFR was also regulated by miRNA let-7d. Therefore, the PFL/PTAFR/let-7d-dependent gene regulatory mechanism proposed by the authors manifests the hypothesis of competing endogenous RNAs to cardiac fibrosis.
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Affiliation(s)
- Matthias S. Leisegang
- Goethe-University, Institute for Cardiovascular Physiology, Frankfurt am Main, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
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1159
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Liu Y, Huang X, Timani KA, Broxmeyer HE, He JJ. miRNA regulation of Tip110 expression and self-renewal and differentiation of human CD34+ hematopoietic cells. Oncotarget 2018; 9:4823-32. [PMID: 29435144 DOI: 10.18632/oncotarget.23572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/14/2017] [Indexed: 01/20/2023] Open
Abstract
Tip110 expression regulates hematopoiesis, but the regulatory mechanisms during hematopoiesis are not fully understood. There are a number of putative microRNA (miRNA) binding sites identified within the Tip110 3′ untranslated region (3′UTR). In this study, we determined the relationship among Tip110 miRNA, Tip110 expression and self-renewal and differentiation of human CD34+ hematopoietic cells. Using a Tip110 3UTR-based reporter gene assay, 11 miRNA showed the specific activity toward the Tip110 3′UTR and down-regulated constitutive Tip110 mRNA expression. When human cord blood CD34+ cells were differentiated, Tip110 mRNA expression showed significant decreases. Concurrently, five miRNA showed significant increases, five miRNA showed significant decreases, and one miRNA remained unchanged. To further assess the roles of miRNA in Tip110 expression and self-renewal and differentiation of human CD34+ hematopoietic cells, human cord blood CD34+ cells were transduced to express the full-length Tip110 3′UTR RNA. Expression of the Tip110 3′UTR RNA led to significant increases of Tip110 mRNA, and the number of hematopoietic stem cells and progenitor cells. Taken together, these results show important roles of Tip110 miRNA in Tip110 expression control and Tip110 regulation of hematopoiesis and offer a possibility of using Tip110 miRNA or 3′UTR as a strategy to maintain human CD34+ hematopoietic cells.
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1160
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Lu QC, Rui ZH, Guo ZL, Xie W, Shan S, Ren T. LncRNA-DANCR contributes to lung adenocarcinoma progression by sponging miR-496 to modulate mTOR expression. J Cell Mol Med 2017; 22:1527-1537. [PMID: 29266795 PMCID: PMC5824415 DOI: 10.1111/jcmm.13420] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 09/20/2017] [Indexed: 12/26/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) have emerged as new and important regulators of pathological processes including tumour development. In this study, we demonstrated that differentiation antagonizing non‐protein coding RNA (DANCR) was up‐regulated in lung adenocarcinoma (ADC) and that the knockdown of DANCR inhibited tumour cell proliferation, migration and invasion and restored cell apoptosis rescued; cotransfection with a miR‐496 inhibitor reversed these effects. Luciferase reporter assays showed that miR‐496 directly modulated DANCR; additionally, we used RNA‐binding protein immunoprecipitation (RIP) and RNA pull‐down assays to further confirm that the suppression of DANCR by miR‐496 was RISC‐dependent. Our study also indicated that mTOR was a target of miR‐496 and that DANCR could modulate the expression levels of mTOR by working as a competing endogenous RNA (ceRNA). Furthermore, the knockdown of DANCR reduced tumour volumes in vivo compared with those of the control group. In conclusion, this study showed that DANCR might be an oncogenic lncRNA that regulates mTOR expression through directly binding to miR‐496. DANCR may be regarded as a biomarker or therapeutic target for ADC.
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Affiliation(s)
- Qing-Chun Lu
- Department of Respiratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhuang-Hua Rui
- Department of Respiratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhong-Liang Guo
- Department of Respiratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wang Xie
- Department of Respiratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shan Shan
- Department of Respiratory Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
| | - Tao Ren
- Department of Respiratory Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, China
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1161
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Shuwen H, Qing Z, Yan Z, Xi Y. Competitive endogenous RNA in colorectal cancer: A systematic review. Gene 2017; 645:157-162. [PMID: 29273554 DOI: 10.1016/j.gene.2017.12.036] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/30/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
Colorectal cancer is one of the most common malignant tumours. Competitive endogenous RNA (ceRNA) networks have been hypothesized, in which various RNAs regulate each other's expression using microRNA response elements (MREs). Recent evidence has highlighted the crucial regulatory roles of ceRNA networks in colorectal cancer. In this review, we summarize the present research methods as well as the currently known ceRNA competitors and targets in colorectal cancer. In addition, we discuss the significance of ceRNA and shortcomings of current studies of colorectal cancer.
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Affiliation(s)
- Han Shuwen
- Department of Medical Oncology, Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| | - Zhou Qing
- Department of Critical Care Medicine, Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| | - Zheng Yan
- Department of Pathology, Huzhou Central Hospital, Huzhou, Zhejiang Province, China
| | - Yang Xi
- Department of Intervention and Radiotherapy, Huzhou Central Hospital, Huzhou, Zhejiang Province, China.
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1162
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Abstract
Pseudogenes are DNA sequences with high homology to the corresponding functional gene, but, because of the accumulation of various mutations, they have lost their initial functions to code for proteins. Consequently, pseudogenes have been considered until few years ago dysfunctional relatives of the corresponding ancestral genes, and then useless in the course of genome evolution. However, several studies have recently established that pseudogenes are owners of key biological functions. Indeed, some pseudogenes control the expression of functional genes by competitively binding to the miRNAs, some of them generate small interference RNAs to negatively modulate the expression of functional genes, and some of them even encode functional mutated proteins. Here, we concentrate our attention on the pseudogenes of the HMGA1 gene, that codes for the HMGA1a and HMGA1b proteins having a critical role in development and cancer progression. In this review, we analyze the family of HMGA1 pseudogenes through three aspects: classification, characterization, and their possible function and involvement in cancer.
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Affiliation(s)
- 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
| | - 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
| | - Claudio Arra
- Istituto Nazionale dei Tumori, Fondazione Pascale, 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
| | - 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
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1163
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Song YZ, Li JF. Circular RNA hsa_circ_0001564 regulates osteosarcoma proliferation and apoptosis by acting miRNA sponge. Biochem Biophys Res Commun 2017; 495:2369-2375. [PMID: 29229385 DOI: 10.1016/j.bbrc.2017.12.050] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/08/2017] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) is a novel type of non-coding RNAs generated from back splicing, which has been verified to mediate multiple tumorigenesis. However, the role of circRNA in osteosarcoma is still unclear. In the present study, we preliminarily screened the circRNAs expression profiles in osteosarcoma and investigated the potential regulation mechanism. The circRNAs expression profiles in osteosarcoma were screened using circRNA microarray analysis, and results showed that there were 1152 circRNAs up-regulated and 915 circRNAs down-regulated in tumor tissue compared to adjacent tissue. Hsa_circ_0001564, located at 5q35.3 and its associated-gene symbol is CANX, was one of the significantly overexpressed circRNAs in osteosarcoma tissue, as well as in osteosarcoma cell lines. In functional experiments, hsa_circ_001564 knockdown significantly suppressed the proliferation activity, induced cell cycle arrest in G0/G1 phase, and promoted apoptosis in HOS and MG-63 cells. Subsequently, we explored the probable mechanism of hsa_circ_001564, and fortunately, bioinformatics analysis revealed that miR-29c-3p contained the complementary binding region with hsa_circ_0001564, which was confirmed by dual-luciferase reporter assay. Moreover, rescue experiments illustrated that miR-29c-3p could reverse the oncogenesis effect of hsa_circ_001564. Our study discovers that hsa_circ_0001564 acts as miR-29c-3p sponge to mediate the tumorigenicity, which could act as a potential biomarker for the osteosarcoma and provide a novel insight for competing endogenous RNAs (ceRNAs) mechanism in osteosarcoma.
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Affiliation(s)
- Yu-Ze Song
- Department of Orthopaedics, Huaihe Hospital of Henan University, PR China
| | - Ji-Feng Li
- Department of Orthopaedics, Huaihe Hospital of Henan University, PR China.
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1164
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Guo X, Xiang C, Zhang Z, Zhang F, Xi T, Zheng L. Displacement of Bax by BMF Mediates STARD13 3'UTR-Induced Breast Cancer Cells Apoptosis in an miRNA-Depedent Manner. Mol Pharm 2017; 15:63-71. [PMID: 29179557 DOI: 10.1021/acs.molpharmaceut.7b00727] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The balance of pro- and antiapoptotic gene expression programs dominates the apoptotic progress of cancer cells. We previously demonstrated that STARD13 3'UTR suppressed breast cancer metastasis via inhibiting epithelial-mesenchymal transition (EMT). However, the roles of STARD13 3'UTR in breast cancer apoptosis remain elusive. Here, we identified that STARD13 3'UTR promoted cell apoptosis in vitro and in vivo. Mechanistically, STARD13 3'UTR acted as a ceRNA for BMF (Bcl-2 modifying factor), thus increasing BMF expression in an miRNA-dependent manner. Meanwhile, STARD13 3'UTR enhanced the interaction of BMF/Bcl-2 to release Bax (Bcl-2 associated X protein) in breast cancer cells. Finally, we verified the ceRNA relationship between STARD13 and BMF in vivo. Collectively, these findings suggest that STARD13 3'UTR could act as a ceRNA for BMF to promote apoptosis and recognize STARD13 3'UTR as a potential therapeutic target in breast cancer cells.
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Affiliation(s)
- Xinwei Guo
- School of Life Science and Technology, China Pharmaceutical University , Nanjing 210009, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University , Nanjing 210009, People's Republic of China
| | - Chenxi Xiang
- School of Life Science and Technology, China Pharmaceutical University , Nanjing 210009, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University , Nanjing 210009, People's Republic of China
| | - Zhiting Zhang
- School of Life Science and Technology, China Pharmaceutical University , Nanjing 210009, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University , Nanjing 210009, People's Republic of China
| | - Feng Zhang
- School of Life Science and Technology, China Pharmaceutical University , Nanjing 210009, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University , Nanjing 210009, People's Republic of China
| | - Tao Xi
- School of Life Science and Technology, China Pharmaceutical University , Nanjing 210009, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University , Nanjing 210009, People's Republic of China
| | - Lufeng Zheng
- School of Life Science and Technology, China Pharmaceutical University , Nanjing 210009, People's Republic of China.,Jiangsu Key Laboratory of Carcinogenesis and Intervention, China Pharmaceutical University , Nanjing 210009, People's Republic of China
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1165
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Abstract
RNA viruses have very small genomes which limits the functions they can encode. One of the strategies employed by these viruses is to mimic key factors of the host cell so they can take advantage of the interactions and activities these factors typically participate in. The viral RNA genome itself was first observed to mimic cellular tRNA over 40 years ago. Since then researchers have confirmed that distinct families of RNA viruses are accessible to a battery of cellular factors involved in tRNA-related activities. Recently, potential tRNA-like structures have been detected within the sequences of a 100 mRNAs taken from human cells, one of these being the host defense interferon-alpha mRNA; these are then additional to the examples found in bacterial and yeast mRNAs. The mimetic relationship between tRNA, cellular mRNA, and viral RNA is the central focus of two considerations described below. These are subsequently used as a preface for a final hypothesis drawing on concepts relating to mimicry from the social sciences and humanities, such as power relations and creativity. Firstly, the presence of tRNA-like structures in mRNAs indicates that the viral tRNA-like signal could be mimicking tRNA-like elements that are contextualized by the specific carrier mRNAs, rather than, or in addition to, the tRNA itself, which would significantly increase the number of potential semiotic relations mediated by the viral signals. Secondly, and in particular, mimicking a host defense mRNA could be considered a potential new viral strategy for survival. Finally, we propose that mRNA's mimicry of tRNA could be indicative of an ancestral intracellular conflict in which species of mRNAs invaded the cell, but from within. As the meaning of the mimetic signal depends on the context, in this case, the conflict that arises when the viral signal enters the cell can change the meaning of the mRNAs' internal tRNA-like signals, from their current significance to that they had in the distant past.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina “López Neyra” (Consejo Superior de Investigaciones Científicas), Granada, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina “López Neyra” (Consejo Superior de Investigaciones Científicas), Granada, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
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1166
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Fang C, Qiu S, Sun F, Li W, Wang Z, Yue B, Wu X, Yan D. Long non-coding RNA HNF1A-AS1 mediated repression of miR-34a/SIRT1/p53 feedback loop promotes the metastatic progression of colon cancer by functioning as a competing endogenous RNA. Cancer Lett 2017; 410:50-62. [DOI: 10.1016/j.canlet.2017.09.012] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/28/2017] [Accepted: 09/15/2017] [Indexed: 12/22/2022]
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1167
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Song C, Zhang J, Liu Y, Pan H, Qi HP, Cao YG, Zhao JM, Li S, Guo J, Sun HL, Li CQ. Construction and analysis of cardiac hypertrophy-associated lncRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in cardiac hypertrophy. Oncotarget 2017; 7:10827-40. [PMID: 26872060 PMCID: PMC4905442 DOI: 10.18632/oncotarget.7312] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/28/2016] [Indexed: 01/08/2023] Open
Abstract
Cardiac hypertrophy (CH) could increase cardiac after-load and lead to heart failure. Recent studies have suggested that long non-coding RNA (lncRNA) played a crucial role in the process of the cardiac hypertrophy, such as Mhrt, TERMINATOR. Some studies have further found a new interacting mechanism, competitive endogenous RNA (ceRNA), of which lncRNA could interact with micro-RNAs (miRNA) and indirectly interact with mRNAs through competing interactions. However, the mechanism of ceRNA regulated by lncRNA in the CH remained unclear. In our study, we generated a global triple network containing mRNA, miRNA and lncRNA, and extracted a CH related lncRNA-mRNA network (CHLMN) through integrating the data from starbase, miRanda database and gene expression profile. Based on the ceRNA mechanism, we analyzed the characters of CHLMN and found that 3 lncRNAs (SLC26A4-AS1, RP11-344E13.3 and MAGI1-IT1) were high related to CH. We further performed cluster module analysis and random walk with restart for the CHLMN, finally 14 lncRNAs had been discovered as the potential CH related disease genes. Our results showed that lncRNA played an important role in the CH and could shed new light to the understanding underlying mechanisms of the CH.
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Affiliation(s)
- Chao Song
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Jian Zhang
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Yan Liu
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Hao Pan
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Han-Ping Qi
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Yong-Gang Cao
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Jian-Mei Zhao
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Shang Li
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
| | - Jing Guo
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Hong-Li Sun
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, China
| | - Chun-Quan Li
- Department of Medical Informatics, Harbin Medical University-Daqing, Daqing, China
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1168
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Qu S, Liu Z, Yang X, Zhou J, Yu H, Zhang R, Li H. The emerging functions and roles of circular RNAs in cancer. Cancer Lett 2018; 414:301-9. [PMID: 29174799 DOI: 10.1016/j.canlet.2017.11.022] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/14/2017] [Accepted: 11/17/2017] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded closed RNA molecules that undergo a specific backsplicing from pre-mRNA. With the application of high-throughput sequencing and bioinformatics, circRNAs are found to be widely expressed across species. Some functionally characterized circRNAs have critical roles in gene regulation through various actions, including sponging microRNAs and proteins as well as regulating transcription and splicing. Moreover, most circRNAs are aberrantly expressed in different cancer types, and some of them have been reported to play important roles in the development and progression of cancer. Given the lack of a 5' cap structure and evidence of their ability to bind with ribosomes, circRNAs were generally considered as noncoding RNA. Notably, recent studies reported that endogenous circRNAs can be translated with a cap-independent manner, which redefines the functional roles of circRNA, further expanding the complexity of eukaryotic transcriptomes. This review aims to re-evaluate the functions and roles of circRNA from the cancer perspective. It discusses the current understanding of circRNA functions, the emerging roles of circRNA in cancer, and the challenges of future studies.
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1169
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De Martino M, Palma G, Azzariti A, Arra C, Fusco A, Esposito F. The HMGA1 Pseudogene 7 Induces miR-483 and miR-675 Upregulation by Activating Egr1 through a ceRNA Mechanism. Genes (Basel) 2017; 8:genes8110330. [PMID: 29149041 PMCID: PMC5704243 DOI: 10.3390/genes8110330] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 02/06/2023] Open
Abstract
Several studies have established that pseudogene mRNAs can work as competing endogenous RNAs and, when deregulated, play a key role in the onset of human neoplasias. Recently, we have isolated two HMGA1 pseudogenes, HMGA1P6 and HMGA1P7. These pseudogenes have a critical role in cancer progression, acting as micro RNA (miRNA) sponges for HMGA1 and other cancer-related genes. HMGA1 pseudogenes were found overexpressed in several human carcinomas, and their expression levels positively correlate with an advanced cancer stage and a poor prognosis. In order to investigate the molecular alterations following HMGA1 pseudogene 7 overexpression, we carried out miRNA sequencing analysis on HMGA1P7 overexpressing mouse embryonic fibroblasts. Intriguingly, the most upregulated miRNAs were miR-483 and miR-675 that have been described as key regulators in cancer progression. Here, we report that HMGA1P7 upregulates miR-483 and miR-675 through a competing endogenous RNA mechanism with Egr1, a transcriptional factor that positively regulates miR-483 and miR-675 expression.
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Affiliation(s)
- 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", via Pansini, 5, 80131 Naples, Italy.
| | - Giuseppe Palma
- Istituto Nazionale dei Tumori, Fondazione Pascale, via Mariano Semmola, 52, 80131 Naples, Italy.
| | - Amalia Azzariti
- IRCCS Istituto Tumori Giovanni Paolo II, Viale O. Flacco, 65, 70124 Bari, Italy.
| | - Claudio Arra
- Istituto Nazionale dei Tumori, Fondazione Pascale, via Mariano Semmola, 52, 80131 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", via Pansini, 5, 80131 Naples, Italy.
| | - 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", via Pansini, 5, 80131 Naples, Italy.
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1170
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Zheng L, Li X, Chou J, Xiang C, Guo Q, Zhang Z, Guo X, Gao L, Xing Y, Xi T. StarD13 3'-untranslated region functions as a ceRNA for TP53INP1 in prohibiting migration and invasion of breast cancer cells by regulating miR-125b activity. Eur J Cell Biol 2017; 97:23-31. [PMID: 29146309 DOI: 10.1016/j.ejcb.2017.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 09/21/2017] [Accepted: 11/08/2017] [Indexed: 11/28/2022] Open
Abstract
Competitive endogenous messenger RNA (ceRNA) affects transcription of other RNA molecules by competitively binding common microRNAs. Previous studies have shown that TP53INP1 functions as a suppressor in tumor metastasis. Our study elucidated StarD13 messenger RNA as a ceRNA in regulating migration and invasion of breast cancer cells. MicroRNA-125b was identified to induce metastasis of MCF-7 cells and bind with both StarD13 3'UTR and TP53INP1 3'UTR. Therefore, a ceRNA interaction between StarD13 and TP53INP1 mediated by competitively binding to miR-125b was indicated. Importantly, a microRNA-125b binding site at 4546-4560 nt on StarD13 was verified more vital for this ceRNA interaction. Indirectly regulation of SPARC in inducing metastasis of breast cancer cells by StarD13 via competitively binding with TP53INP1 was further confirmed. In conclusion, our findings demonstrate a ceRNA regulatory network which could give a better understanding of metastatic mechanisms of breast cancer.
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Affiliation(s)
- Lufeng Zheng
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaoman Li
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jinjiang Chou
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China
| | - Chenxi Xiang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China
| | - Qianqian Guo
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China
| | - Zhiting Zhang
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China
| | - Xinwei Guo
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China
| | - Lanlan Gao
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China
| | - Yingying Xing
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China
| | - Tao Xi
- School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention, Jiangsu Key Laboratory of Drug Discovery for Metabolic Diseases, Department of Pharmacology of Chinese Materia Medica, China Pharmaceutical University, Nanjing 210009, China.
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1171
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Qian YY, Li K, Liu QY, Liu ZS. Long non-coding RNA PTENP1 interacts with miR-193a-3p to suppress cell migration and invasion through the PTEN pathway in hepatocellular carcinoma. Oncotarget 2017; 8:107859-107869. [PMID: 29296207 PMCID: PMC5746109 DOI: 10.18632/oncotarget.22305] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/13/2017] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNA PTENP1, the pseudogene of PTEN tumor suppressor, was previously reported to be a tumour suppressor in some cancer types. However, the precise effects mediated by PTENP1 transcripts within intricate regulatory networks involving molecular interactions with PTEN and tumorigenicity in hepatocellular carcinoma (HCC) remains elusive. Here, we identify the critical biological functions of PTENP1 and discuss whether PTENP1 could directly interact with miR-193a-3p to affect the progression of HCC both in vitro and in vivo. We demonstrated that PTENP1 level in the HCC tissues was significantly lower compared with those in the adjacent normal tissues. And PTENP1 was able to repress cell invasion, metastasis, and proliferation capacity in HCC cell lines. The overexpression of PTENP1 inhibited HCC growth both in vitro and in vivo. There were a binding sequence and direct interaction between PTENP1 and miR-193a-3p. PTENP1 as an endogenous sponge interacted with miR-193a-3p, leading to regulate the downstream PTEN/Akt pathway. These results suggested that PTENP1 with its suppression effect might serve as novel biomarkers and potent therapeutic strategies in HCC.
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Affiliation(s)
- Yu-Yuan Qian
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Kun Li
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Quan-Yan Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Zhi-Su Liu
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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1172
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Zhang Y, Liang W, Zhang P, Chen J, Qian H, Zhang X, Xu W. Circular RNAs: emerging cancer biomarkers and targets. J Exp Clin Cancer Res 2017; 36:152. [PMID: 29096676 PMCID: PMC5667461 DOI: 10.1186/s13046-017-0624-z] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/19/2017] [Indexed: 12/14/2022]
Abstract
CircRNAs are a class of RNA molecules that structurally form closed loops. CircRNAs are abundant in eukaryotic transcripts and show certain levels of tissue and cell specificity. CircRNAs have been suggested to regulate gene expression at transcriptional, post-transcriptional, and translational levels. An increasing number of studies have shown that circRNAs play important roles in the development and progression of diseases including cancer. In particular, circRNAs have shown great potential in cancer diagnosis, prognosis, and therapy. In this review, we provide an overview of the biogenesis and characteristics of circRNAs, succinctly describe their functions, and comprehensively discuss about the recent advances in the roles of circRNAs in cancer with an emphasis on their clinical values.
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Affiliation(s)
- Yu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Wei Liang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Peng Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Jingyan Chen
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Hui Qian
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China
| | - Xu Zhang
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China. .,Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212002, China.
| | - Wenrong Xu
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu, 212013, China.
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1173
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Gu Y, Xiao X, Yang S. LncRNA MALAT1 acts as an oncogene in multiple myeloma through sponging miR-509-5p to modulate FOXP1 expression. Oncotarget 2017; 8:101984-101993. [PMID: 29254219 PMCID: PMC5731929 DOI: 10.18632/oncotarget.21957] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/21/2017] [Indexed: 12/16/2022] Open
Abstract
Previous studies showed that Metastasis associated lung adenocarcinoma transcript 1(MALAT1) acted as an oncogene in Multiple Myeloma (MM). However, the underlying mechanism of MALAT1 in MM remains unclear. Quantitative real time-PCR(qRT-PCR) was used to determine MALAT1 expression in MM samples and cell lines. in vitro function assays were used to determine the function of MALAT1 on MM cells. Bioinformatics tools were used to predict the targets of MALAT1 and miR-509-5p, respectively. Furthermore, rescue experiments were performed to further confirm the regulation of miR-509-5p by MALAT1. In the present study, our data showed that MALAT1 expression was upregulated in MM samples and cell lines. In function assays, we confirmed that MALAT1 inhibition significantly suppressed cells proliferation, induced cells apoptosis, arrested cells in G1/S phase, and inhibited MM cells growth in vivo. Furthermore, MALAT1 was identified to function as a competitive endogenous RNA (ceRNA) for miR-509-5p to promote MM cell viability. Additionally, our results suggested that miR-509-5p targeted the 3’-UTR of FOXP1 to suppress MM cells progression. Meanwhile, our results showed that miR-509-5p inhibitors significantly abrogated the decreased expression of FOXP1 induced by MALAT1 suppression, indicating that MALAT1 could positively regulate FOXP1 expression by sponging miR-509-5p. Our findings suggested that MALAT1/miR-509-5p/FOXP1 axis was one of the key signalings in mediating MM cell growth, and further indicated that MALAT1 could act as a novel diagnostic marker and therapeutic target for the treatment of MM.
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Affiliation(s)
- Yueli Gu
- Department of Hematology, The First People's Hospital of Shangqiu, Shangqiu 476100, China
| | - Xichun Xiao
- Department of Hematology, The First People's Hospital of Shangqiu, Shangqiu 476100, China
| | - Shuo Yang
- Department of Hematology, The First People's Hospital of Shangqiu, Shangqiu 476100, China
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1174
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Teng W, Qiu C, He Z, Wang G, Xue Y, Hui X. Linc00152 suppresses apoptosis and promotes migration by sponging miR-4767 in vascular endothelial cells. Oncotarget 2017; 8:85014-85023. [PMID: 29156700 PMCID: PMC5689590 DOI: 10.18632/oncotarget.18777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/22/2017] [Indexed: 12/12/2022] Open
Abstract
Dysfunction of vascular endothelial cells (VECs), such as increased apoptosis and diminished migration, is closely connected with most cardiovascular diseases and angiogenesis-related events. LncRNAs have been involved in regulation of many pathological processes, but their roles in vascular endothelial function are hardly underreported. Here, we explore the role of a intergenic lncRNA named linc00152 in the apoptosis and migration of VECs. We found that linc00152 was downregulated in human umbilical vein VECs (HUVECs) in a dose- and time-dependent manner following treatment with oxLDL, which is a typical proinflammatory factor in the initiation and progression of vascular endothelial dysfunction. Gain- and loss-function experiments indicated that linc00152 distinctly inhibited apoptosis and improved migration in oxLDL-treated HUVECs. By sponging miR-4767, linc00152 positively regulated the expression of Bcl2L12 and EGFR proteins. Moreover, blocking miR-4767 rescued the decrease of Bcl2L12 and EGFR caused by linc00152 knockdown, as well as the changes in cell apoptosis and migration. Our findings propose a novel role of linc00152 in the improvement of vascular endothelial function and a potential target for the therapy of some cardiovascular diseases.
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Affiliation(s)
- Wei Teng
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
| | - Chunguang Qiu
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhaohui He
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
| | - Guoliang Wang
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
| | - Yongliang Xue
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
| | - Xuezhi Hui
- Department of Cardiology, The First Affiliated Hospital of Henan University, Kaifeng 475000, China
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1175
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Zhu M, Zhang M, Xing L, Li W, Jiang H, Wang L, Xu M. Transcriptomic Analysis of Long Non-Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development. Genes (Basel) 2017; 8:genes8100274. [PMID: 29039813 PMCID: PMC5664124 DOI: 10.3390/genes8100274] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/03/2017] [Accepted: 10/13/2017] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been reported to be involved in the development of maize plant. However, few focused on seed development of maize. Here, we identified 753 lncRNA candidates in maize genome from six seed samples. Similar to the mRNAs, lncRNAs showed tissue developmental stage specific and differential expression, indicating their putative role in seed development. Increasing evidence shows that crosstalk among RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in plant development. Functional roles and regulatory mechanisms of lncRNAs as competing endogenous RNAs (ceRNA) in plants, particularly in maize seed development, are unclear. We combined analyses of consistently altered 17 lncRNAs, 840 mRNAs and known miRNA to genome-wide investigate potential lncRNA-mediated ceRNA based on “ceRNA hypothesis”. The results uncovered seven novel lncRNAs as potential functional ceRNAs. Functional analyses based on their competitive coding-gene partners by Gene Ontology (GO) and KEGG biological pathway demonstrated that combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in maize seed. These findings provided a useful platform for uncovering novel mechanisms of maize seed development and may provide opportunities for the functional characterization of individual lncRNA in future studies.
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Affiliation(s)
- Ming Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei 230000, China.
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Min Zhang
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lijuan Xing
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Wenzong Li
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Haiyang Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei 230000, China.
| | - Lei Wang
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Miaoyun Xu
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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1176
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Wu H, Wu R, Chen M, Li D, Dai J, Zhang Y, Gao K, Yu J, Hu G, Guo Y, Lin C, Li X. Comprehensive analysis of differentially expressed profiles of lncRNAs and construction of miR-133b mediated ceRNA network in colorectal cancer. Oncotarget 2017; 8:21095-21105. [PMID: 28177879 PMCID: PMC5400568 DOI: 10.18632/oncotarget.15045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/09/2017] [Indexed: 01/15/2023] Open
Abstract
Background Growing evidence suggests that long non-coding RNAs (lncRNAs) play a key role in tumorigenesis. However, the mechanism remains largely unknown. Results Thousands of significantly dysregulated lncRNAs and mRNAs were identified by microarray. Furthermore, a miR-133b-meditated lncRNA-mRNA ceRNA network was revealed, a subset of which was validated in 14 paired CRC patient tumor/non-tumor samples. Gene set enrichment analysis (GSEA) results demonstrated that lncRNAs ENST00000520055 and ENST00000535511 shared KEGG pathways with miR-133b target genes. Materials and Methods We used microarrays to survey the lncRNA and mRNA expression profiles of colorectal cancer and para-cancer tissues. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed to explore the functions of the significantly dysregulated genes. An innovate method was employed that combined analyses of two microarray data sets to construct a miR-133b-mediated lncRNA-mRNA competing endogenous RNAs (ceRNA) network. Quantitative RT-PCR analysis was used to validate part of this network. GSEA was used to predict the potential functions of these lncRNAs. Conclusions This study identifies and validates a new method to investigate the miR-133b-mediated lncRNA-mRNA ceRNA network and lays the foundation for future investigation into the role of lncRNAs in colorectal cancer.
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Affiliation(s)
- Hao Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Runliu Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Miao Chen
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Daojiang Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Jing Dai
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Yi Zhang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Kai Gao
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Jun Yu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Gui Hu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Yihang Guo
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
| | - Xiaorong Li
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, P. R. China
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1177
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Abstract
Background Nuclear enriched abundant transcript 1 (NEAT1) has been demonstrated to act as a tumor inhibitor in many cancers. However, the role of NEAT1 in the development of ovarian cancer (OC) remains far from being elaborated. Hence, the aim of this study is to investigate the expression and function of NEAT1 in OC. Materials and methods The expression level of NEAT1 was determined by quantitative real-time polymerase chain reaction in OC cell lines. MTT assay, caspase-3 activity assay, and flow cytometry analysis were conducted to investigate the effects of NEAT1, miR-34a-5p, or B-cell lymphoma-2 (BCL2) on OC cell proliferation and apoptosis. Luciferase reporter assay was used to confirm the interaction of NEAT1, BCL2, and miR-34a-5p in OC cells. Results NEAT1 was significantly upregulated in OC cell lines. NEAT1 overexpression promoted proliferation by increasing the proportion of cells in S phase and suppressed apoptosis of OC cells, while knockdown of NEAT1 had the opposite effect. In addition, NEAT1 was demonstrated to directly interact with miR-34a-5p and exert its oncogenic role in OC by negatively regulating miR-34a-5p. Moreover, miR-34a-5p could directly target BCL2 and suppressed its expression. miR-34a-5p overexpression suppressed OC cell proliferation and triggered apoptosis by targeting BCL2. Furthermore, NEAT1 knockdown suppressed BCL2 expression, while anti-miR-34a-5p dramatically abated the inhibitory effect of si-NEAT1 on BCL2 expression. Conclusion NEAT1 regulated proliferation and apoptosis of OC cells by miR-34a-5p/BCL2, providing a potential therapeutic approach for the treatment of OC patients.
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Affiliation(s)
- Nan Ding
- Department of Obstetrics and Gynecology, Henan Provincial People's Hospital
| | - Haiying Wu
- Department of Obstetrics and Gynecology, Henan Provincial People's Hospital
| | - Tao Tao
- Department of Obstetrics and Gynecology, Henan Provincial People's Hospital
| | - Erxuan Peng
- Department of Obstetrics and Gynecology, Henan Provincial Tumor Hospital, Zhengzhou, China
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1178
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Lv M, Zhong Z, Huang M, Tian Q, Jiang R, Chen J. lncRNA H19 regulates epithelial-mesenchymal transition and metastasis of bladder cancer by miR-29b-3p as competing endogenous RNA. Biochim Biophys Acta Mol Cell Res 2017; 1864:1887-1899. [PMID: 28779971 DOI: 10.1016/j.bbamcr.2017.08.001] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022]
Abstract
Accumulating evidences indicate that long noncoding RNAs (lncRNAs) might play important roles in tumorigenesis and metastasis. EMT (epithelial-to-mesenchymal transition) is considered as a critical step in invasion and metastasis of various tumors including bladder cancer (BC). Recent researches have showed that lncRNA H19 is implicated in metastasis through regulating EMT and the reverse MET (mesenchymal-to-epithelial transition). However, underlying mechanisms remain largely unknown. Here, we screened lncRNA and mRNA expression profiles of BC with microarray assay. We found that H19 and DNMT3B displayed a higher co-expression in BC tissues and cells. Functionally, we demonstrated that H19 could increase proliferation, invasion and migration, regulate EMT as well as rearrange cytoskeleton of BC cells in vitro. Moreover, ectopic expression of H19 promoted tumorigenesis, angiogenesis and pulmonary metastasis in vivo, whereas knockdown of H19 has a contrary role in vivo and in vitro. Mechanistically, we proved that H19 could directly bind to miR-29b-3p (miR-29b) and derepress the expression of target DNMT3B. H19 and miR-29b-3p showed a co-localization. More importantly, up-regulating H19 antagonized miR-29b-3p-mediated proliferation, migration and EMT suppression in BC cells. Furthermore, H19 knockdown partially reversed the function of miR-29b-3p inhibitor on DNMT3B and facilitated miR-29b-3p-induced MET. Taken together, we demonstrated for the first time that H19 might function as ceRNA (competing endogenous RNA) for miR-29b-3p and relieve the suppression for DNMT3B, which led to EMT and metastasis of BC. Our findings highlight a novel mechanism of H19 in progression of BC and provide H19/miR-29b-3p/DNMT3B axis as a promising therapeutic target for BC.
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Affiliation(s)
- Mengxin Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, PR China
| | - Zhenyu Zhong
- The First Clinical College, Chongqing Medical University, Chongqing 400016, PR China
| | - Mengge Huang
- College of Clinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Qiang Tian
- Department of Cell Biology and Genetics, Southwest Medical University, Luzhou 646000, Sichuan, PR China
| | - Rong Jiang
- Laboratory of Stem Cells and Tissue Engineering, Chongqing Medical University, Chongqing, PR China
| | - Junxia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, PR China.
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1179
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Wang H, Zhao Y, Chen M, Cui J. Identification of Novel Long Non-coding and Circular RNAs in Human Papillomavirus-Mediated Cervical Cancer. Front Microbiol 2017; 8:1720. [PMID: 28970820 PMCID: PMC5609541 DOI: 10.3389/fmicb.2017.01720] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/24/2017] [Indexed: 01/04/2023] Open
Abstract
Cervical cancer is the third most common cancer worldwide and the fourth leading cause of cancer-associated mortality in women. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) may play key roles in the carcinogenesis of different cancers; however, little is known about the mechanisms of lncRNAs and circRNAs in the progression and metastasis of cervical cancer. In this study, we explored the expression profiles of lncRNAs, circRNAs, miRNAs, and mRNAs in HPV16 (human papillomavirus genotype 16) mediated cervical squamous cell carcinoma and matched adjacent non-tumor (ATN) tissues from three patients with high-throughput RNA sequencing (RNA-seq). In total, we identified 19 lncRNAs, 99 circRNAs, 28 miRNAs, and 304 mRNAs that were commonly differentially expressed (DE) in different patients. Among the non-coding RNAs, 3 lncRNAs and 44 circRNAs are novel to our knowledge. Functional enrichment analysis showed that DE lncRNAs, miRNAs, and mRNAs were enriched in pathways crucial to cancer as well as other gene ontology (GO) terms. Furthermore, the co-expression network and function prediction suggested that all 19 DE lncRNAs could play different roles in the carcinogenesis and development of cervical cancer. The competing endogenous RNA (ceRNA) network based on DE coding and non-coding RNAs showed that each miRNA targeted a number of lncRNAs and circRNAs. The link between part of the miRNAs in the network and cervical cancer has been validated in previous studies, and these miRNAs targeted the majority of the novel non-coding RNAs, thus suggesting that these novel non-coding RNAs may be involved in cervical cancer. Taken together, our study shows that DE non-coding RNAs could be further developed as diagnostic and therapeutic biomarkers of cervical cancer. The complex ceRNA network also lays the foundation for future research of the roles of coding and non-coding RNAs in cervical cancer.
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Affiliation(s)
- Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan, China
| | - Yingchao Zhao
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and TechnologyWuhan, China
| | - Mingyue Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
| | - Jie Cui
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of SciencesWuhan, China
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1180
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Wu XS, Wang F, Li HF, Hu YP, Jiang L, Zhang F, Li ML, Wang XA, Jin YP, Zhang YJ, Lu W, Wu WG, Shu YJ, Weng H, Cao Y, Bao RF, Liang HB, Wang Z, Zhang YC, Gong W, Zheng L, Sun SH, Liu YB. LncRNA-PAGBC acts as a microRNA sponge and promotes gallbladder tumorigenesis. EMBO Rep 2017; 18:1837-1853. [PMID: 28887321 DOI: 10.15252/embr.201744147] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/23/2017] [Accepted: 07/27/2017] [Indexed: 02/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play roles in the development and progression of many cancers; however, the contributions of lncRNAs to human gallbladder cancer (GBC) remain largely unknown. In this study, we identify a group of differentially expressed lncRNAs in human GBC tissues, including prognosis-associated gallbladder cancer lncRNA (lncRNA-PAGBC), which we find to be an independent prognostic marker in GBC Functional analysis indicates that lncRNA-PAGBC promotes tumour growth and metastasis of GBC cells. More importantly, as a competitive endogenous RNA (ceRNA), lncRNA-PAGBC competitively binds to the tumour suppressive microRNAs miR-133b and miR-511. This competitive role of lncRNA-PAGBC is required for its ability to promote tumour growth and metastasis and to activate the AKT/mTOR pathway. Moreover, lncRNA-PAGBC interacts with polyadenylate binding protein cytoplasmic 1 (PABPC1) and is stabilized by this interaction. This work provides novel insight on the molecular pathogenesis of GBC.
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Affiliation(s)
- Xiang-Song Wu
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fang Wang
- Department of Medical Genetics, Second Military Medical University, Shanghai, China
| | - Huai-Feng Li
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun-Ping Hu
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Jiang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Zhang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mao-Lan Li
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xu-An Wang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun-Peng Jin
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Jian Zhang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Lu
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen-Guang Wu
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Jun Shu
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Weng
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Cao
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Run-Fa Bao
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hai-Bin Liang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng Wang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Chi Zhang
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Gong
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lei Zheng
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shu-Han Sun
- Department of Medical Genetics, Second Military Medical University, Shanghai, China
| | - Ying-Bin Liu
- Department of General Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China .,Shanghai Research Center of Biliary Tract Disease, Shanghai, China.,Institute of Biliary Tract Disease, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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1181
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Tong L, Chu M, Yan B, Zhao W, Liu S, Wei W, Lou H, Zhang S, Ma S, Xu J, Wei L. MTDH promotes glioma invasion through regulating miR-130b- ceRNAs. Oncotarget 2017; 8:17738-17749. [PMID: 28107197 PMCID: PMC5392282 DOI: 10.18632/oncotarget.14717] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/21/2016] [Indexed: 02/06/2023] Open
Abstract
Cell invasion is crucial for high mortality and recurrence rate in glioma. Epithelial-mesenchymal transition (EMT) is an important step in cancer invasion. Metadherin (MTDH) contributes to EMT in several cancers, but the role and mechanism of MTDH in EMT-like process of glioma remain unknown. Here we demonstrate that MTDH was overexpressed in glioma tissues and cells and induced EMT-like change and invasion of glioma cells. Interestingly, MTDH could modulate the expression of a group of glioma-related miRNAs. In particular, MTDH upregulated miR-130b transcription via acting as a coactivator of NF-kB. MiR-130b promoted EMT-like change and invasion of glioma cells through targeting multiple EMT-related genes, including PTEN, PPP2CA and SMAD7. In addition, PTEN acted as the competing endogenous RNA (ceRNA) to affect PPP2CA and SMAD7 expression, and inhibited EMT-like change in glioma cells. Furthermore, miR-130b mediated EMT-like change induced by MTDH, and MTDH inhibited the expression levels of PTEN, PPP2CA and SMAD7. Taken together, we reveal a novel mechanism that MTDH induces EMT-like change and invasion of glioma via the regulation of miR-130b-ceRNAs, providing the first direct link between MTDH and miRNAs in cancer cells.
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Affiliation(s)
- Liping Tong
- Wu Lien-Teh institute, Department of Microbiology, Harbin Medical University, The Heilongjiang Key Laboratory of Immunity and Infection, Pathogen Biology, Harbin 150081, China
| | - Ming Chu
- Department of Neurosurgery, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China
| | - Bingqing Yan
- Wu Lien-Teh institute, Department of Microbiology, Harbin Medical University, The Heilongjiang Key Laboratory of Immunity and Infection, Pathogen Biology, Harbin 150081, China
| | - Weiyi Zhao
- Department of Neurosurgery, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China
| | - Shuang Liu
- Jiamusi University, Jiamusi 154002, China
| | - Wei Wei
- Jiamusi University, Jiamusi 154002, China
| | - Huihuang Lou
- Wu Lien-Teh institute, Department of Microbiology, Harbin Medical University, The Heilongjiang Key Laboratory of Immunity and Infection, Pathogen Biology, Harbin 150081, China
| | - Shengkun Zhang
- Department of Neurosurgery, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China
| | - Shuai Ma
- Department of Neurosurgery, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China
| | - Juan Xu
- College of Bioinformatics Science and Technology and Bio-Pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, China
| | - Lanlan Wei
- Wu Lien-Teh institute, Department of Microbiology, Harbin Medical University, The Heilongjiang Key Laboratory of Immunity and Infection, Pathogen Biology, Harbin 150081, China
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1182
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Yu S, Zhao Y, Lai F, Chu M, Hao Y, Feng Y, Zhang H, Liu J, Cheng M, Li L, Shen W, Min L. LncRNA as ceRNAs may be involved in lactation process. Oncotarget 2017; 8:98014-98028. [PMID: 29228670 PMCID: PMC5716710 DOI: 10.18632/oncotarget.20439] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/18/2017] [Indexed: 11/25/2022] Open
Abstract
The main function of the mammary gland is to secret milk for newborn growth. Milk production process is regulated by hormones, growth factors, noncoding RNAs and other factors locally. Long non-coding RNAs (lncRNAs), one type of recently discovered non-coding RNA, have been found in mammary gland and some studies suggested lncRNA may play important roles in mammary gland development. Competing endogenous RNAs (ceRNAs) are emerging to compete for miRNA binding and, in turn, regulate each other. In the current study, we sequenced mRNA, miRNA and lncRNA in goat mammary tissue at 2 points in lactation (early and mature). All data were co-expressed together from the same samples. Our data showed that the ceRNAs up-regulated during the mature lactation phase were associated with lipid, protein, carbon and amino acid synthesis and metabolism. This correlates with the function of the mature lactation phase: i.e. the continuous production of large amounts of milk, rich in proteins, lipids, amino acids and other nutrients. Alternately, the ceRNAs up-regulated during early lactation were associated with PI3K-AKT pathways and ECM-receptor interactions; these fulfil the functional role of preparing the mammary gland for full lactation. Therefore, the results suggest that ceRNAs work synergistically during different developmental stages to regulate specific functions associated with lactation control. This study suggests that ceRNAs (lncRNA-mRNA) may be involved in lactation process.
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Affiliation(s)
- Shuai Yu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
| | - Yong Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
| | - Fangnong Lai
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
| | - Meiqiang Chu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
| | - Yanan Hao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
| | - Yanni Feng
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, P.R. China
| | - Jing Liu
- Core Laboratories of Qingdao Agricultural University, Qingdao, P. R. China
| | - Ming Cheng
- Qingdao Veterinary and Livestock Administration, Qingdao, P.R. China
| | - Lan Li
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
| | - Wei Shen
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
| | - Lingjiang Min
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, P. R. China
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1183
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Wang H, Huo X, Yang XR, He J, Cheng L, Wang N, Deng X, Jin H, Wang N, Wang C, Zhao F, Fang J, Yao M, Fan J, Qin W. STAT3-mediated upregulation of lncRNA HOXD-AS1 as a ceRNA facilitates liver cancer metastasis by regulating SOX4. Mol Cancer 2017; 16:136. [PMID: 28810927 PMCID: PMC5558651 DOI: 10.1186/s12943-017-0680-1] [Citation(s) in RCA: 396] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/15/2017] [Indexed: 12/17/2022] Open
Abstract
Background Several of the thousands of human long noncoding RNAs (lncRNAs) have been functionally characterized, yet their potential involvement in hepatocellular carcinoma (HCC) remains poorly understood. Methods LncRNA-HOXD-AS1 was identified by microarray and validated by real-time PCR. The clinicopathological significance of HOXD-AS1 was analyzed by Kaplan-Meier method. Chromatin immunoprecipitation was conducted to examine the mechanism of HOXD-AS1 upregulation. The role of HOXD-AS1 in HCC cells was assessed both in vitro and in vivo. ceRNA function of HOXD-AS1 was evaluated by RNA immunoprecipitation and biotin-coupled miRNA pull down assays. Results In this study, we found that HOXD-AS1 was significantly upregulated in HCC tissues. Clinical investigation demonstrated high expression level of HOXD-AS1 was associated with poor prognosis and high tumor node metastasis stage of HCC patients, and was an independent risk factor for survival. Moreover, our results revealed that STAT3 could specifically interact with the promoter of HOXD-AS1 and activate HOXD-AS1 transcription. Knockdown of HOXD-AS1 significantly inhibited migration and invasion of HCC cells in vitro and distant lung metastasis in vivo. Additionally, HOXD-AS1 was enriched in the cytoplasm, and shared miRNA response elements with SOX4. Overexpression of HOXD-AS1 competitively bound to miR-130a-3p that prevented SOX4 from miRNA-mediated degradation, thus activated the expression of EZH2 and MMP2 and facilitated HCC metastasis. Conclusions In summary, HOXD-AS1 is a prognostic marker for HCC patients and it may play a pro-metastatic role in hepatocarcinogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0680-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hui Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Xisong Huo
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Xin-Rong Yang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Jia He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Lijun Cheng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Na Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Xuan Deng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Haojie Jin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Ning Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Cun Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Fangyu Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Jingyuan Fang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Ming Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China
| | - Jia Fan
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai, 200032, China.
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, No.25/Ln2200 Xie-Tu Road, Shanghai, 200032, China.
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1184
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Wei Y, Chang Z, Wu C, Zhu Y, Li K, Xu Y. Identification of potential cancer-related pseudogenes in lung adenocarcinoma based on ceRNA hypothesis. Oncotarget 2017; 8:59036-59047. [PMID: 28938616 PMCID: PMC5601712 DOI: 10.18632/oncotarget.19933] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/26/2017] [Indexed: 01/01/2023] Open
Abstract
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes. We described the characteristics of the candidate pseudogenes and performed functional enrichment. Through analyzing neighboring genes we found these pseudogenes were surrounded by tumor genes and may involve in tumor pathway. Furthermore, the DNA methylation analysis indicated that 21 pseudogenes co-methylated with their competitive mRNAs. In the co-methylated network, we discovered 6 differentially expressed pseudogenes, which we termed potential LUAD-associated pseudogenes. We further revealed that the 3 ceRNA triples (miR-21-5p-NKAPP1-PRDM11, miR-29c-3p-MSTO2P-EZH2 and miR-29c-3p-RPLP0P2-EZH2), whose high risk groups were associated with the poor prognosis of LUAD, may be considered as potential prognostic signatures. Moreover, by integrating target information of microRNA we also provided a new perspective for the discovery of potential small molecule drugs. This work may facilitate cancer research and serve as the basis for future efforts to understand the role of pseudogenes, develop novel biomarkers and improve knowledge of tumor biology.
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Affiliation(s)
- Yunzhen Wei
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Zhiqiang Chang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Cheng Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yinling Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Kun Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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1185
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Pan RY, Liu P, Zhou HT, Sun WX, Song J, Shu J, Cui GJ, Yang ZJ, Jia EZ. Circular RNAs promote TRPM3 expression by inhibiting hsa-miR-130a-3p in coronary artery disease patients. Oncotarget 2017; 8:60280-60290. [PMID: 28947970 PMCID: PMC5601138 DOI: 10.18632/oncotarget.19941] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/25/2017] [Indexed: 12/31/2022] Open
Abstract
We investigated the differential expression of circular RNAs (circRNAs) in plasma samples from three coronary artery disease (CAD) patients to identify putative therapeutic targets. We identified 24 differentially expressed circRNAs (18 up-regulated and 6 down-regulated) and 7 differentially expressed mRNAs (6 up-regulated and 1 down-regulated) in CAD patients based on competing endogenous RNA (ceRNA) microarray analysis. MiR-221(p = 0.001), miR-155(p = 0.049), and miR-130a (p = 0.001) were downregulated in CAD patients based on qRT-PCR analysis of another independent population of 932 study subjects (648 CAD subjects and 284 controls). We constructed a hsa-miR-130a-3p-mediated circRNA-mRNA ceRNA network using the miRanda database. This included 9 circRNAs (hsa_circ_0089378, hsa_circ_0083357, hsa_circ_0082824, hsa_circ_0068942, hsa_circ_0057576, hsa_circ_0054537, hsa_circ_0051172, hsa_circ_0032970, and hsa_circ_0006323) and 1 mRNA (transient receptor potential cation channel subfamily M member 3 [TRPM3]). We have shown that 9 circRNAs promote TRPM3 expression by inhibiting hsa-miR-130a-3p in CAD patients.
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Affiliation(s)
- Ren-You Pan
- Department of Cardiovascular Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng 224000, Jiangsu Province, China
| | - Ping Liu
- Department of Cardiovascular Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng 224000, Jiangsu Province, China
| | - Hai-Tang Zhou
- Department of Cardiovascular Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng 224000, Jiangsu Province, China
| | - Wei-Xin Sun
- Department of Cardiovascular Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng 224000, Jiangsu Province, China
| | - Jun Song
- Department of Cardiovascular Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng 224000, Jiangsu Province, China
| | - Jiang Shu
- Department of Cardiovascular Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng 224000, Jiangsu Province, China
| | - Guo-Jing Cui
- Department of Cardiovascular Medicine, Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng 224000, Jiangsu Province, China
| | - Zhi-Jian Yang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
| | - En-Zhi Jia
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, Jiangsu Province, China
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1186
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Luan W, Li R, Liu L, Ni X, Shi Y, Xia Y, Wang J, Lu F, Xu B. Long non-coding RNA HOTAIR acts as a competing endogenous RNA to promote malignant melanoma progression by sponging miR-152-3p. Oncotarget 2017; 8:85401-85414. [PMID: 29156728 PMCID: PMC5689618 DOI: 10.18632/oncotarget.19910] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 07/12/2017] [Indexed: 12/16/2022] Open
Abstract
HOX transcript antisense RNA (HOTAIR) is associated with the growth and metastasis of many human tumors, but its biological roles in malignant melanoma remain unclear. In this study, we show that HOTAIR is overexpressed in melanoma tissues and cells, especially in metastatic melanoma. High HOTAIR levels correlate with poor prognosis in melanoma patients. We also determined that HOTAIR functions as a competing endogenous RNA (ceRNA) for miR-152-3p. miR-152-3p was decreased and acted as a tumor suppressor in melanoma, and c-MET was the functional target of miR-152-3p. Furthermore, HOTAIR promotes the growth and metastasis of melanoma cells by competitively binding miR-152-3p, which functionally liberates c-MET mRNA and results in the activation of the downstream PI3k/Akt/mTOR signaling pathway. We determined that HOTAIR acts as a ceRNA to promote malignant melanoma progression by sponging miR-152-3p. This finding elucidates a new mechanism for HOTAIR in melanoma development and provides a potential therapeutic target for melanoma patients.
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Affiliation(s)
- Wenkang Luan
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Rubo Li
- Department of Neurosurgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Liang Liu
- Department of Neurosurgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xin Ni
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yan Shi
- Department of Neurosurgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yun Xia
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Jinlong Wang
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Feng Lu
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Bin Xu
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
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1187
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Wang Y, Zhang Y, Yang T, Zhao W, Wang N, Li P, Zeng X, Zhang W. Long non-coding RNA MALAT1 for promoting metastasis and proliferation by acting as a ceRNA of miR-144-3p in osteosarcoma cells. Oncotarget 2017; 8:59417-59434. [PMID: 28938647 PMCID: PMC5601743 DOI: 10.18632/oncotarget.19727] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/29/2017] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in various biological processes and diseases including osteosarcoma. Long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is overly expressed in osteosarcoma. But the function and mechanism it works on in osteosarcoma proliferation and metastasis mediated by Rho associated coiled-coil containing protein kinase 1 (ROCK1) and Rho associated coiled-coil containing protein kinase 2 (ROCK2) remain unclear. In the present study, an elevated MALAT1 was found in osteosarcoma tissues and cell lines, and the elevated MALAT1 was correlated with a poor prognosis in osteosarcoma patients. The functional experiments show that a decreased MALAT1 could remarkably inhibit osteosarcoma cell metastasis and proliferation but induce cell cycle arrest, indicating that MALAT1 functioned as an oncogene in osteosarcoma. Furthermore, we confirmed that MALAT1 and ROCK1/ROCK2 which were targeted by microRNA-144-3p (miR-144-3p) shared the same miR-144-3p combining site. Furthermore, the constructed luciferase assay verified that MALAT1 was a target of miR-144-3p. Additionally, the results of a qRT-PCR demonstrated that MALAT1 and miR-144-3p repressed each other's expression in a reciprocal manner. Finally, we affirmed that an overexpression of MALAT1 inhibited ROCK1/ROCK2 expression and its mediated metastasis and proliferation by working as a competitive endogenous RNA (ceRNA) via miR-144-3p. In summary, the findings of this study based on the ceRNA theory, combining the research foundation of miR-144-3p, ROCK1 and ROCK2, taking MALAT1 as a new point of study, provided new insights into molecular level proliferation reversal and metastasis of osteosarcoma.
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Affiliation(s)
- Yong Wang
- The 4th Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, P. R. China
| | - Yueyang Zhang
- Department of Pathology, Liaoning Cancer Hospital & Institute, Shenyang, P. R. China
| | - Tao Yang
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, P. R. China
| | - Wei Zhao
- The 4th Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, P. R. China
| | - Ningning Wang
- The 2nd Department of Cardiology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, P. R. China
| | - Pengcheng Li
- The 4th Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, P. R. China
| | - Xiandong Zeng
- Department of Surgical Oncology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, P. R. China
| | - Weiguo Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, P. R. China
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1188
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Li S, Chen X, Liu X, Yu Y, Pan H, Haak R, Schmidt J, Ziebolz D, Schmalz G. Complex integrated analysis of lncRNAs-miRNAs-mRNAs in oral squamous cell carcinoma. Oral Oncol 2017; 73:1-9. [PMID: 28939059 DOI: 10.1016/j.oraloncology.2017.07.026] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/24/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES This study aims to reveal regulatory network of lncRNAs-miRNAs-mRNAs in oral squamous cell carcinoma (OSCC) through gene expression data. MATERIAL AND METHODS Differentially expressed lncRNAs, miRNAs and mRNAs (cut-off: False discovery rate (FDR)<0.05 and |fold change|>1.5) were unveiled by package edgeR of R. Cox regression analysis was performed to screen prognostic factors in OSCC related with overall survival (OS) and relapse-free survival (RFS). Protein-protein interaction (PPI) network was constructed for differentially expressed mRNAs using BioGRID, HPRD and DIP. Key hub genes were identified from top 100 differentially expressed mRNAs ranked by betweenness centrality using recursive feature elimination. LncRNA-miRNA and miRNA-mRNA regulatory network were constructed and combined into ceRNAs regulatory network. Gene ontology biological terms and Kyoto Encyclopedia of Genes and Genomes pathways were identified using Fisher's exact test. RESULTS A total of 929 differentially expressed mRNAs, 23 differentially expressed lncRNAs and 29 differentially expressed miRNAs were identified. 59 mRNAs, 6 miRNAs (hsa-mir-133a-1, hsa-mir-1-2, hsa-mir-486, hsa-mir-135b, hsa-mir-196b, hsa-mir-193b) and 6 lncRNAs (C10orf91, C2orf48, SFTA1P, FLJ41941,PART1,TTTY14) were related with OS; and 52 mRNAs, 4 miRNAs (hsa-mir-133a-1, hsa-mir-135b, hsa-mir-196b, hsa-mir-193b) and 2 lncRNAs (PART1, TTTY14) were associated with RFS. A support vector machine (SVM) classifier containing 37 key hub genes was obtained. A ceRNA regulatory network containing 417 nodes and 696 edges was constructed. ECM-receptor interaction, cytokine-cytokine receptor interaction, focal adhesion, arachidonic acid metabolism, and p53 signaling pathway were significantly enriched in the network. CONCLUSION These findings uncover the pathogenesis of OSCC and might provide potential therapeutic targets.
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Affiliation(s)
- Simin Li
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany
| | - Xiujie Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xiangqiong Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Yang Yu
- Department of Periodontology, The Stomatology Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Hongying Pan
- Department of Orthopedic surgery, Brigham and Women's Hospital, Harvard Medical School, Harvard University, Boston, USA
| | - Rainer Haak
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany
| | - Jana Schmidt
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany
| | - Dirk Ziebolz
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany.
| | - Gerhard Schmalz
- Department of Cariology, Endodontology and Periodontology, University Leipzig, Liebigstr. 12, 04103 Leipzig, Germany
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1189
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Yang T, Zhou H, Liu P, Yan L, Yao W, Chen K, Zeng J, Li H, Hu J, Xu H, Ye Z. lncRNA PVT1 and its splicing variant function as competing endogenous RNA to regulate clear cell renal cell carcinoma progression. Oncotarget 2017; 8:85353-85367. [PMID: 29156724 PMCID: PMC5689614 DOI: 10.18632/oncotarget.19743] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/19/2017] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) exert critical regulatory roles in the development and progression of several cancers. Plasmacytoma variant translocation 1 (PVT1), an lncRNA, was shown to be upregulated in clear cell renal cell carcinoma (ccRCC) in our study, while Kaplan-Meier curve and Cox regression analysis showed that high expression of PVT1 was associated with poor overall survival (OS) and disease free survival (DFS) in ccRCC patients. In vitro experiments revealed that PVT1 promoted renal cancer cell proliferation, migration, and invasion, while in vivo studies confirmed its oncogenic roles in ccRCC. Further bioinformatic analysis and RNA immunoprecipitation revealed that PVT1 could function as an oncogenic transcript partly through sponging miR-200s to regulate BMI1, ZEB1 and ZEB2 expression. Besides, a novel splicing variant of PVT1 lacking exon 4 (PVT1ΔE4) was found to have a higher expression in ccRCC and could also promote cell proliferation and invasion as the full-length transcript did. Besides, SRSF1 decreased the inclusion of exon 4 of full-length transcript and increased the relative expression of PVT1ΔE4 in ccRCC. Mechanistic investigations indicated that PVT1ΔE4 could also upregulate the expression of BMI1, ZEB1 and ZEB2 through interacting with miR-200s. Our study helps reveal new molecular events in ccRCC and provides promising diagnostic and therapeutic targets for this disease.
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Affiliation(s)
- Tao Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China.,Department of Urology, Jingzhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou 434020, PR China
| | - Hui Zhou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Peijun Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Libin Yan
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Weimin Yao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Jin Zeng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Heng Li
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Junhui Hu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
| | - Zhangqun Ye
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, PR China.,Hubei Institute of Urology, Wuhan 430030, PR China
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1190
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Huang ZW, Tian LH, Yang B, Guo RM. Long Noncoding RNA H19 Acts as a Competing Endogenous RNA to Mediate CTGF Expression by Sponging miR-455 in Cardiac Fibrosis. DNA Cell Biol 2017; 36:759-766. [PMID: 28753062 DOI: 10.1089/dna.2017.3799] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cardiac fibrosis is closely related to multiple cardiovascular system diseases, and noncoding RNAs (ncRNAs), including long noncoding RNA (lncRNA) and microRNA (miRNA), have been reported to play a vital role in fibrogenesis. The present study aims to investigate the potential regulatory mechanism of lncRNA H19 and miR-455 on fibrosis-associated protein synthesis in cardiac fibroblasts (CFs). miRNA microarray assay revealed 34 significantly dysregulated miRNAs, including 13 upregulated miRNAs and 21 downregulated miRNAs. Among these aberrantly expressed miRNAs, we paid attention to miR-455, which was significantly downregulated in diabetic mouse myocardium and Ang II-induced CFs. Loss- and gain-of-function experiments showed that miR-455 expression levels were negatively correlated with collagen I and III expression in Ang II-induced CFs. Bioinformatic prediction programs (TargetScan, miRanda, starBase) predicted that miR-455 targeted connective tissue growth factor (CTGF) and H19 with complementary binding sites at the 3'-untranslated region, which was validated by luciferase reporter assay. Functional validation assay demonstrated that H19 knockdown could enhance the antifibrotic role of miR-455 and attenuate the CTGF expression and further decrease fibrosis-associated protein synthesis (collagen I, III, and α-SMA). The present study reveals a novel function of the H19/miR-455 axis targeting CTGF in cardiac fibrosis, suggesting its potential therapeutic role in cardiac diseases.
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Affiliation(s)
- Zhi-Wen Huang
- 1 Department of Cardiovascular, Affiliated Hospital of Guangdong Medical University , Zhanjiang, Guangdong, China
| | - Li-Hong Tian
- 1 Department of Cardiovascular, Affiliated Hospital of Guangdong Medical University , Zhanjiang, Guangdong, China
| | - Bin Yang
- 2 Center of Geriatrics, Affiliated Hospital of Guangdong Medical University , Zhanjiang, Guangdong, China
| | - Run-Min Guo
- 1 Department of Cardiovascular, Affiliated Hospital of Guangdong Medical University , Zhanjiang, Guangdong, China
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1191
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Luan T, Zhang X, Wang S, Song Y, Zhou S, Lin J, An W, Yuan W, Yang Y, Cai H. Long non-coding RNA MIAT promotes breast cancer progression and functions as ceRNA to regulate DUSP7 expression by sponging miR-155-5p. Oncotarget. 2017;8:76153-76164. [PMID: 29100300 PMCID: PMC5652694 DOI: 10.18632/oncotarget.19190] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/19/2017] [Indexed: 12/02/2022] Open
Abstract
Long non-coding RNAs (lncRNA) have been reported as key regulators in the progression and metastasis of breast cancer. In this study, we found that the lncRNA myocardial infarction associated transcript (MIAT) expression was upregulated in breast cancer in The Cancer Genome Atlas (TCGA) data sets. We validated that MIAT was higher in breast cancer cell lines and advanced breast tumors than in normal controls. And MIAT overexpression associated with TNM stage and lymphnode metastasis. Knockdown MIAT inhibited breast cancer cell proliferation and promoted apoptosis. Also MIAT downregulation suppressed epithelial-mesenchymal transition (EMT) and decreased migration and invasion in MDA-MB-231 and MCF-7 breast cancer cell lines. More importantly, knockdown MIAT inhibited tumor growth in vivo. Our results suggested that MIAT acted as a competing endogenous RNA (ceRNA) to regulate the expression of dual specificity phosphatase 7 (DUSP7) by taking up miR-155-5p in breast cancer. There were positive correlation between MIAT and DUSP7 expression in breast cancer patients. We conclude that MIAT promotes breast cancer progression and functions as ceRNA to regulate DUSP7 expression by sponging miR-155-5p in breast cancer.
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1192
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Chen Z, Liu H, Yang H, Gao Y, Zhang G, Hu J. The long noncoding RNA, TINCR, functions as a competing endogenous RNA to regulate PDK1 expression by sponging miR-375 in gastric cancer. Onco Targets Ther 2017; 10:3353-3362. [PMID: 28744139 PMCID: PMC5513873 DOI: 10.2147/ott.s137726] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Accumulating evidence indicates that the long noncoding RNA, TINCR, plays a critical role in cancer progression and metastasis. However, the overall biological role and mechanisms of TINCR that were involved in human gastric cancer (GC) progression remain largely unknown. METHODS TINCR expression was measured in 56 paired tumor and adjacent nontumor tissue samples by real-time polymerase chain reaction (PCR). Insights of the mechanism of competitive endogenous RNAs (ceRNAs) were gained from bioinformatic analysis, luciferase assays. The effects of TINCR and miR-375 on GC cell apoptosis and proliferation were studied by RNA interference approaches in vitro and in vivo. The correlation of TINCR and PDK1 was identified by real-time PCR and Western blot analysis. RESULTS Our results showed that miR-375 level decreased and TINCR level increased in tumor tissues. In addition, TINCR was a target of miR-375 and inhibited its expression in GC cells. Furthermore, the low expression of TINCR increased cell apoptosis and inhibited the proliferation of GC cells, while the downregulation of miR-375 reversed the function. In particular, TINCR could negatively regulate the miR-375 expression and increased the PDK1 expression in GC cells. Finally, tumor growth suppression was retarded with miR-375 downregulated in TINCR knockdown of GC cell xenografts. CONCLUSION The long noncoding RNA TINCR functions as a competing endogenous RNA to regulate PDK1 expression by sponging miR-375 in GC. The ceRNA regulatory network of TINCR/miR-375/PDK1 allows us to better understand the pathogenesis of GC and facilitate the development of long noncoding RNA (lncRNA)-directed diagnostics in GC.
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Affiliation(s)
- Zhaoliang Chen
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Hong Liu
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Huili Yang
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Yukai Gao
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Gongwen Zhang
- Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong
| | - Jiaojiao Hu
- Department of Hematology, Zhongda Hospital, Southeast University, Nanjing, China
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1193
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Zhong Z, Huang M, Lv M, He Y, Duan C, Zhang L, Chen J. Circular RNA MYLK as a competing endogenous RNA promotes bladder cancer progression through modulating VEGFA/VEGFR2 signaling pathway. Cancer Lett 2017; 403:305-317. [PMID: 28687357 DOI: 10.1016/j.canlet.2017.06.027] [Citation(s) in RCA: 350] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/15/2017] [Accepted: 06/16/2017] [Indexed: 01/14/2023]
Abstract
Accumulating evidences indicate that circular RNAs (circRNAs) play a vital role in modulating gene expression. However, the mechanisms underlying circRNAs remain largely elusive. Here, we screened circRNA and mRNA expression profiles of bladder carcinoma (BC) using microarray analysis. We found that circRNA-MYLK and VEGFA were significantly up-regulated and co-expressed in BC. Importantly, circRNA-MYLK levels were related to the progression of stage and grade of BC. Mechanistically, we demonstrated that circRNA-MYLK could directly bind to miR-29a and relieve suppression for target VEGFA, which activated VEGFA/VEGFR2 signaling pathway. Functionally, we found that ectopically expressing circRNA-MYLK accelerated cell proliferation, migration, tube formation of HUVEC and rearranged cytoskeleton. Moreover, up-regulating circRNA-MYLK promoted epithelial-mesenchymal transition (EMT). Whereas circRNA-MYLK knockdown decreased cell proliferation, motility, and induced apoptosis. Finally, up-regulating circRNA-MYLK promoted the growth, angiogenesis and metastasis of BC xenografts. Taken together, this study demonstrated for the first time that circRNA-MYLK might function as competing endogenous RNA (ceRNA) for miR-29a, which could contribute to EMT and the development of BC through activating VEGFA/VEGFR2 and downstream Ras/ERK signaling pathway. Our data suggest that circRNA-MYLK would be a promising target for BC diagnosis and therapy.
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Affiliation(s)
- Zhenyu Zhong
- The First Clinical College, Chongqing Medical University, Chongqing, 400016, PR China
| | - Mengge Huang
- College of Clinical Medicine, Southwest Medical University, Luzhou, 646000, PR China
| | - Mengxin Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yunfeng He
- Department of Urology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, Chongqing 400016, PR China
| | - Changzhu Duan
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luyu Zhang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, Chongqing 400016, PR China
| | - Junxia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing, 400016, PR China.
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1194
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Wang G, Cui T, Sun L, Peng N, Yang C. Long noncoding RNA LeXis promotes osteosarcoma growth through upregulation of CTNNB1 expression. Am J Cancer Res 2017; 7:1577-1587. [PMID: 28744406 PMCID: PMC5523037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 06/27/2017] [Indexed: 06/07/2023] Open
Abstract
Osteosarcoma (OS) is the most common primary bone cancer in adolescents and children. Long noncoding RNAs (lncRNAs) contain > 200 nucleotides and do not have protein-coding ability. Liver-expressed LXR-induced sequence (LeXis) is a newly identified functional lncRNA. However, its expression pattern, biological function, and molecular mechanism in OS progression are unclear. The present study is the first to show that LeXis expression was upregulated in OS tissues. Increased LeXis expression was significantly correlated with high tumor stage, large tumor size, and poor prognosis. Our findings highlight the oncogenic activity of lncRNA LeXis in OS growth. Results of functional assays showed that LeXis promoted OS growth both in vitro and in vivo. Mechanistic investigation showed that LeXis directly interacted with miR-199a and suppressed its expression. Moreover, LeXis increased CTNNB1 expression by functioning as a ceRNA of CTNNB1 against miR-199a. These findings may have important implications for developing novel therapeutic strategies for OS.
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Affiliation(s)
- Guijiang Wang
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
| | - Tao Cui
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
| | - Lishan Sun
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
| | - Ningning Peng
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
| | - Cheng Yang
- No.4 Department of Orthopedics, Cangzhou Central HospitalCangzhou, Hebei Province, China
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1195
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Hu Y, Ma Z, He Y, Liu W, Su Y, Tang Z. PART-1 functions as a competitive endogenous RNA for promoting tumor progression by sponging miR-143 in colorectal cancer. Biochem Biophys Res Commun 2017; 490:317-323. [PMID: 28619512 DOI: 10.1016/j.bbrc.2017.06.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/11/2017] [Indexed: 01/22/2023]
Abstract
LncRNAs were altered in several cancers and played a crucial role in various biological activities and progressions of different diseases, including proliferation, chemical resistance, and metastasis. In the present study, we revealed that prostrate androgen-regulated transcript-1 (PART-1) was highly expressed in colorectal cancer cells and tissues, and knockdown of PART-1 suppressed cell proliferation and metastasis, both in vitro and in vivo. In addition, PART-1 functioned as a ceRNA of DNMT3A, by sponging miR-143. Finally,PART-1 induced tumor progression by regulating DNMT3A.
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Affiliation(s)
- Yongbo Hu
- Department of General Surgery, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao, Hubei, China
| | - Zhen Ma
- Department of General Surgery, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao, Hubei, China
| | - Yiming He
- Department of General Surgery, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao, Hubei, China
| | - Wei Liu
- Department of General Surgery, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao, Hubei, China
| | - Yu Su
- Department of General Surgery, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao, Hubei, China
| | - Zongbin Tang
- Department of General Surgery, Xiantao First People's Hospital Affiliated to Yangtze University, Xiantao, Hubei, China.
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1196
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Li LJ, Zhao W, Tao SS, Li J, Xu SZ, Wang JB, Leng RX, Fan YG, Pan HF, Ye DQ. Comprehensive long non-coding RNA expression profiling reveals their potential roles in systemic lupus erythematosus. Cell Immunol 2017. [PMID: 28622785 DOI: 10.1016/j.cellimm.2017.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs can regulate gene transcription, modulate protein function, and act as competing endogenous RNA. Yet, their roles in systemic lupus erythematosus remain to be elucidated. We determined the expression profiles of lncRNAs in T cells of SLE patients and healthy controls using microarrays. Up to 1935 lncRNAs and 1977 mRNAs were differentially expressed. QRT-PCR showed downregulated uc001ykl.1 and ENST00000448942 in SLE patients. Expression of uc001ykl.1 correlated with erythrocyte sedimentation rate (ESR) and C-reactive protein, whereas ENST00000448942 level correlated with ESR and anti-Sm antibodies. Short time-series expression miner analysis revealed some lncRNAs whose expressions might correlate with disease activity of SLE patients. Coding-non-coding gene coexpression analyses showed differential lncRNAs might operate via modulating expressions of their correlated, relevant mRNAs in SLE. Differential lncRNAs might also function through their ceRNAs. Our study established that the aberrant expression profiles of lncRNAs may play a role in SLE and thus warrant further investigation.
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Affiliation(s)
- Lian-Ju Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Wei Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Sha-Sha Tao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Jun Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Shu-Zhen Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Jie-Bing Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Rui-Xue Leng
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Yin-Guang Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China
| | - Dong-Qing Ye
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Disease, Hefei, Anhui, China.
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1197
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Zhou B, Yu J. A novel identified circular RNA, circRNA_010567, promotes myocardial fibrosis via suppressing miR-141 by targeting TGF-β1. Biochem Biophys Res Commun 2017; 487:769-75. [DOI: 10.1016/j.bbrc.2017.04.044] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 12/14/2022]
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1198
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Chiu HS, Martínez MR, Bansal M, Subramanian A, Golub TR, Yang X, Sumazin P, Califano A. High-throughput validation of ceRNA regulatory networks. BMC Genomics 2017; 18:418. [PMID: 28558729 PMCID: PMC5450082 DOI: 10.1186/s12864-017-3790-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/12/2017] [Indexed: 11/10/2022] Open
Abstract
Background MicroRNAs (miRNAs) play multiple roles in tumor biology. Interestingly, reports from multiple groups suggest that miRNA targets may be coupled through competitive stoichiometric sequestration. Specifically, computational models predicted and experimental assays confirmed that miRNA activity is dependent on miRNA target abundance, and consequently, changes in the abundance of some miRNA targets lead to changes to the regulation and abundance of their other targets. The resulting indirect regulatory influence between miRNA targets resembles competition and has been dubbed competitive endogenous RNA (ceRNA). Recent studies have questioned the physiological relevance of ceRNA interactions, our ability to accurately predict these interactions, and the number of genes that are impacted by ceRNA interactions in specific cellular contexts. Results To address these concerns, we reverse engineered ceRNA networks (ceRNETs) in breast and prostate adenocarcinomas using context-specific TCGA profiles, and tested whether ceRNA interactions can predict the effects of RNAi-mediated gene silencing perturbations in PC3 and MCF7 cells._ENREF_22 Our results, based on tests of thousands of inferred ceRNA interactions that are predicted to alter hundreds of cancer genes in each of the two tumor contexts, confirmed statistically significant effects for half of the predicted targets. Conclusions Our results suggest that the expression of a significant fraction of cancer genes may be regulated by ceRNA interactions in each of the two tumor contexts. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3790-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hua-Sheng Chiu
- Texas Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Mukesh Bansal
- Columbia Department of Systems Biology, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | | | - Todd R Golub
- Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA.,Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, 20815-6789, USA
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Pavel Sumazin
- Texas Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
| | - Andrea Califano
- Columbia Department of Systems Biology, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA. .,Department of Biomedical Informatics, and Department of Biochemistry and Molecular Biophysics, and Institute for Cancer Genetics, Columbia University, New York, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA.
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1199
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Wang Y, Yang T, Zhang Z, Lu M, Zhao W, Zeng X, Zhang W. Long non-coding RNA TUG1 promotes migration and invasion by acting as a ceRNA of miR-335-5p in osteosarcoma cells. Cancer Sci 2017; 108:859-867. [PMID: 28205334 PMCID: PMC5448616 DOI: 10.1111/cas.13201] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/07/2017] [Accepted: 02/11/2017] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNA (lncRNA) have been the focus of increasing attention due to the role they play in many diseases, including osteosarcoma. The function of taurine upregulated gene 1 (TUG1) and its mechanism in osteosarcoma remain unclear. In our research, we found that TUG1 was elevated and correlated with a poor prognosis in osteosarcoma patients. In addition, the following functional experiment showed that decreased TUG1 could remarkably inhibit osteosarcoma cell migration and invasion, indicating that TUG1 functioned as an oncogene in osteosarcoma. Moreover, we revealed that TUG1 and Rho-associated coiled-coil-containing protein kinase 1 (ROCK1), a metastasis-related gene targeted by microRNA-335-5p (miR-335-5p), had the same miR-335-5p combining site. The subsequent luciferase assay verified TUG1 was a target of miR-335-5p. Furthermore, the results of a real-time quantitative PCR showed that TUG1 and miR-335-5p could affect each other's expression. respectively. Finally, we affirmed that TUG1 affected ROCK1 expression and ROCK1-mediated migration/invasion by working as a competitive endogenous RNA (ceRNA) via miR-335-5p. In summary, the findings of this study, based on ceRNA theory, combining the research foundation of miR-335-5p and ROCK1, and taking TUG1 as a new study point, provide new insight into molecular-level reversing migration and invasion of osteosarcoma.
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Affiliation(s)
- Yong Wang
- The 4th Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China.,Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Tao Yang
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Zhen Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Ming Lu
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Wei Zhao
- The 4th Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Xiandong Zeng
- Department of Surgery Oncology, Central Hospital Affiliated to Shenyang Medical College, Shenyang, China
| | - Weiguo Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, China
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1200
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Zhang J, Le TD, Liu L, Li J. Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. BMC Bioinformatics 2017; 18:243. [PMID: 28482794 PMCID: PMC5423010 DOI: 10.1186/s12859-017-1672-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
Background Recent studies have shown that the crosstalk between microRNA (miRNA) sponges plays an important role in human cancers. However, the co-regulation roles of miRNA sponges in protein-protein interactions (PPIs) are still unknown. Results In this study, we propose a multi-step method called miRSCoPPI to infer miRNA sponge co-regulation of PPIs. We focus on investigating breast cancer (BRCA) related miRNA sponge co-regulation, by integrating heterogeneous data, including miRNA, long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression data, experimentally validated miRNA-target interactions, PPIs and lncRNA-target interactions, and the list of breast cancer genes. We find that the inferred BRCA-related miRSCoPPI network is highly connected and scale free. The top 10% hub genes in the BRCA-related miRSCoPPI network have potential biological implications in breast cancer. By utilizing a graph clustering method, we discover 17 BRCA-related miRSCoPPI modules. Through pathway enrichment analysis of the modules, we find that several modules are significantly enriched in pathways associated with breast cancer. Moreover, 10 modules have good performance in classifying breast tumor and normal samples, and can act as module signatures for prognostication. By using putative computationally predicted miRNA-target interactions, we have consistent results with those obtained using experimentally validated miRNA-target interactions, indicating that miRSCoPPI is robust in inferring miRNA sponge co-regulation of PPIs in human breast cancer. Conclusions Taken together, the results demonstrate that miRSCoPPI is a promising tool for inferring BRCA-related miRNA sponge co-regulation of PPIs and it can help with the understanding of the co-regulation roles of miRNA sponges on the PPIs. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1672-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan, 671003, People's Republic of China.
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.,Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5000, Australia
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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