501
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Liu J, Liu T, Wang X, He A. Circles reshaping the RNA world: from waste to treasure. Mol Cancer 2017; 16:58. [PMID: 28279183 PMCID: PMC5345220 DOI: 10.1186/s12943-017-0630-y] [Citation(s) in RCA: 301] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/02/2017] [Indexed: 02/08/2023] Open
Abstract
A new type of RNAs was identified from genes traditionally thought to express messenger or linear ncRNA (noncoding RNA) only. They were subsequently named as circRNAs (circular RNAs) due to the covalently closed structure. Accumulating studies were performed to explore the expression profile of circRNAs in different cell types and diseases, the outcomes totally changed our view of ncRNAs, which was thought to be junk by-products in the process of gene transcription, and enriched our poor understanding of its underlying functions. The expression profile of circRNAs is tissue-specific and alters across various stages of cell differentiation. The biological function of circRNAs is multi-faceted, involving five main features (sponge effect, post-transcriptional regulation, rolling circle translation, circRNA-derived pseudogenes and splicing interference) and varying differently from the locations, binding sites and acting modes of circRNAs. The regulating role of circRNAs is not isolated but through an enormous complicated network involving mRNAs, miRNAs and proteins. Although most of the potential functions still remain unclear, circRNAs have been proved to be ubiquitous and critical in regulating cellular processes and diseases, especially in cancers, from the laboratory to the clinic. Herein, we review circRNAs’ classification, biogenesis and metabolism, their well-studied and anticipated functions, the current understanding of the potential implications of circRNAs in tumorigenesis and cancer targeted therapy.
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Affiliation(s)
- Jing Liu
- Department of Clinical Hematology, Second Affiliated Hospital, Xi'an Jiaotong University Health Care Center, 157 West 5 Street, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Tian Liu
- Department of Clinical Hematology, Second Affiliated Hospital, Xi'an Jiaotong University Health Care Center, 157 West 5 Street, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Xiaman Wang
- Department of Clinical Hematology, Second Affiliated Hospital, Xi'an Jiaotong University Health Care Center, 157 West 5 Street, Xi'an, 710004, Shaanxi, People's Republic of China
| | - Aili He
- Department of Clinical Hematology, Second Affiliated Hospital, Xi'an Jiaotong University Health Care Center, 157 West 5 Street, Xi'an, 710004, Shaanxi, People's Republic of China.
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502
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Characterization of hsa_circ_0004277 as a New Biomarker for Acute Myeloid Leukemia via Circular RNA Profile and Bioinformatics Analysis. Int J Mol Sci 2017; 18:ijms18030597. [PMID: 28282919 PMCID: PMC5372613 DOI: 10.3390/ijms18030597] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/23/2017] [Accepted: 03/06/2017] [Indexed: 11/17/2022] Open
Abstract
Circular RNAs (circRNAs) represent a widespread class of non-coding RNAs, which drew little attention in the past. Recently, limited data showed their promising future to act as biomarkers in human cancer, but the characteristics and functions remain largely unknown in hematopoietic malignancies, especially in leukemia. In this study, with the help of circRNA microarray, we demonstrated the expression profile of circRNAs in acute myeloid leukemia (AML) patients, and identified a large number of circRNAs possibly expressed in a leukemia specific manner. We also described a circRNA signature related to AML risk-status based on the bioinformatics prediction. In particular, a downregulated circRNA, hsa_circ_0004277, was characterized and functionally evaluated in a cohort of 115 human samples, thus offering a potential diagnostic marker and treatment target in AML. Interestingly, we found chemotherapy could significantly restore the expression of hsa_circ_0004277, indicating the increasing level of hsa_circ_0004277 was associated with successful treatment. Furthermore, a detailed circRNA–miRNA–mRNA interaction network was presented for hsa_circ_0004277, allowing us to better understand its underlying mechanisms for function in AML.
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503
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Xue J, Liu Y, Luo F, Lu X, Xu H, Liu X, Lu L, Yang Q, Chen C, Fan W, Liu Q. Circ100284, via miR-217 regulation of EZH2, is involved in the arsenite-accelerated cell cycle of human keratinocytes in carcinogenesis. Biochim Biophys Acta Mol Basis Dis 2017; 1863:753-763. [DOI: 10.1016/j.bbadis.2016.12.018] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 12/21/2016] [Accepted: 12/31/2016] [Indexed: 12/12/2022]
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504
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Hsiao KY, Lin YC, Gupta SK, Chang N, Yen L, Sun HS, Tsai SJ. Noncoding Effects of Circular RNA CCDC66 Promote Colon Cancer Growth and Metastasis. Cancer Res 2017; 77:2339-2350. [PMID: 28249903 DOI: 10.1158/0008-5472.can-16-1883] [Citation(s) in RCA: 485] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 08/18/2016] [Accepted: 02/22/2017] [Indexed: 12/23/2022]
Abstract
Circular RNA (circRNA) is a class of noncoding RNA whose functions remain mostly unknown. Recent studies indicate circRNA may be involved in disease pathogenesis, but direct evidence is scarce. Here, we characterize the functional role of a novel circRNA, circCCDC66, in colorectal cancer. RNA-Seq data from matched normal and tumor colon tissue samples identified numerous circRNAs specifically elevated in cancer cells, several of which were verified by quantitative RT-PCR. CircCCDC66 expression was elevated in polyps and colon cancer and was associated with poor prognosis. Gain-of-function and loss-of-function studies in colorectal cancer cell lines demonstrated that circCCDC66 controlled multiple pathological processes, including cell proliferation, migration, invasion, and anchorage-independent growth. In-depth characterization revealed that circCCDC66 exerts its function via regulation of a subset of oncogenes, and knockdown of circCCDC66 inhibited tumor growth and cancer invasion in xenograft and orthotopic mouse models, respectively. Taken together, these findings highlight a novel oncogenic function of circRNA in cancer progression and metastasis. Cancer Res; 77(9); 2339-50. ©2017 AACR.
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Affiliation(s)
- Kuei-Yang Hsiao
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ya-Chi Lin
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sachin Kumar Gupta
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Ning Chang
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Laising Yen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - H Sunny Sun
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Shaw-Jenq Tsai
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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505
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Zhao Z, Li X, Jian D, Hao P, Rao L, Li M. Hsa_circ_0054633 in peripheral blood can be used as a diagnostic biomarker of pre-diabetes and type 2 diabetes mellitus. Acta Diabetol 2017; 54:237-245. [PMID: 27878383 PMCID: PMC5329094 DOI: 10.1007/s00592-016-0943-0] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/11/2016] [Indexed: 12/18/2022]
Abstract
AIMS The purpose of the current study was to investigate the characteristic expression of circular RNAs (circRNAs) in the peripheral blood of type 2 diabetes mellitus (T2DM) patients and their potential as diagnostic biomarkers for pre-diabetes and T2DM. METHODS CircRNAs in the peripheral blood from six healthy individuals and six T2DM patients were collected for microarray analysis, and an independent cohort study consisting of 20 normal cases, 20 pre-diabetes patients and 20 T2DM patients was conducted to verify the five chosen circRNAs. We then tested hsa_circ_0054633 in a third cohort (control group, n = 60; pre-diabetes group, n = 63; and T2DM group, n = 64) by quantitative real-time polymerase chain reaction (Q-PCR). RESULTS In total, 489 circRNAs were discovered to be differentially expressed between the two groups, and of these, 78 were upregulated and 411 were downregulated in the T2DM group. Five circRNAs were then selected as candidate biomarkers and further verified in a second cohort. Hsa_circ_0054633 was found to have the largest area under the curve (AUC). The diagnostic capacity of hsa_circ_0054633 was tested in a third cohort. After introducing the risk factors of T2DM, the hsa_circ_0054633 AUCs for the diagnosis of pre-diabetes and T2DM slightly increased from 0.751 (95% confidence interval [0.666-0.835], P < 0.001) to 0.841 ([0.773-0.910], P < 0.001) and from 0.793 ([0.716-0.871], P < 0.001) to 0.834 ([0.762-0.905], P < 0.001), respectively. CONCLUSIONS Hsa_circ_0054633 presented a certain diagnostic capability for pre-diabetes and T2DM.
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Affiliation(s)
- Zhenzhou Zhao
- Department of Cardiology, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xuejie Li
- Department of Cardiology, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Dongdong Jian
- Department of Cardiology, The First Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Peiyuan Hao
- Department of Cardiology, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Lixin Rao
- Department of Cardiology, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Muwei Li
- Department of Cardiology, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.
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506
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Affiliation(s)
- Wei-Yang Lu
- a Department of Physiology and Pharmacology , The University of Western Ontario , London , Ontario , Canada.,b Robarts Research Institute, The University of Western Ontario , London , Ontario , Canada
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507
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Gnanamony M, Gondi CS. Chemoresistance in pancreatic cancer: Emerging concepts. Oncol Lett 2017; 13:2507-2513. [PMID: 28454427 DOI: 10.3892/ol.2017.5777] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 01/17/2017] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer is one of the most lethal types of cancer in the world. The incidence of pancreatic cancer increases each year with no significant decrease in mortality. Pancreatic cancer is a complex disease, and this complexity is partly attributed to late diagnosis, an aggressive phenotype, environmental factors and lack of effective treatment options. Surgical resection followed by adjuvant chemotherapy is the treatment of choice for early stage cancer, whereas gemcitabine is the standard first line therapy for patients with advanced stage disease. Treatment regimens comprising folinic acid, 5-fluorouracil, irinotecan, oxaliplatin and nab-paclitaxel have demonstrated modest effects in improving median survival rates. A number of other chemotherapeutics are currently undergoing clinical trials as components of combination therapies with gemcitabine. An increasing number of novel molecular targets and cellular pathways are being identified, which highlights the complexity of this disease. The development of chemoresistance to gemcitabine is multifactorial and there exists an interplay between pancreatic cancer cells, the tumor microenvironment and cancer stem cells. These components appear to be governed by a complex network of non-coding RNAs such as micro RNAs and long non-coding RNAs. In the present study, studies describing previous research on the understanding of the factors associated with the development of chemoresistance to gemcitabine in pancreatic cancer are reviewed. A comprehensive understanding of the multiple pathways of chemoresistance is key to develop next generation therapeutics to pancreatic cancer.
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Affiliation(s)
- Manu Gnanamony
- Department of Internal Medicine, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA
| | - Christopher S Gondi
- Department of Internal Medicine, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA.,Department of Surgery, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA.,Department of Pathology, University of Illinois College of Medicine at Peoria, Peoria, IL 61605, USA
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508
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Taborda MI, Ramírez S, Bernal G. Circular RNAs in colorectal cancer: Possible roles in regulation of cancer cells. World J Gastrointest Oncol 2017; 9:62-69. [PMID: 28255427 PMCID: PMC5314202 DOI: 10.4251/wjgo.v9.i2.62] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 11/05/2016] [Accepted: 12/14/2016] [Indexed: 02/05/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the world and the fourth principal cause of cancer deaths worldwide. Currently, there is a lack of low cost and noninvasive screening tests for CRC, becoming a serious health problem. In this context, a potential biomarker for the early detection of CRC has recently gained attention. Circular RNAs (circRNA), a re-discovered, abundant RNA specie, is a type of noncoding covalent closed RNAs formed from both exonic and intronic sequences. These circular molecules are widely expressed in cells, exceeding the abundance of the traditional linear mRNA transcript. They can regulate gene expression, acting as real sponges for miRNAs and also regulate alternative splicing or act as transcriptional factors and inclusive encoding for proteins. However, little is known about circRNA and its relationship with CRC. In this review, we focus on the biogenesis, function and role of these circRNAs in relation to CRC, including their potential as a new biomarker.
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509
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CirComPara: A Multi-Method Comparative Bioinformatics Pipeline to Detect and Study circRNAs from RNA-seq Data. Noncoding RNA 2017; 3:ncrna3010008. [PMID: 29657280 PMCID: PMC5832002 DOI: 10.3390/ncrna3010008] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 01/27/2017] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs (circRNAs) are generated by back-splicing of immature RNA forming covalently closed loops of intron/exon RNA molecules. Pervasiveness, evolutionary conservation, massive and regulated expression, and post-transcriptional regulatory roles of circRNAs in eukaryotes have been appreciated and described only recently. Moreover, being easily detectable disease markers, circRNAs undoubtedly represent a molecular class with high bearing on molecular pathobiology. CircRNAs can be detected from RNA-seq data using appropriate computational methods to identify the sequence reads spanning back-splice junctions that do not co-linearly map to the reference genome. To this end, several programs were developed and critical assessment of various strategies and tools suggested the combination of at least two methods as good practice to guarantee robust circRNA detection. Here, we present CirComPara (http://github.com/egaffo/CirComPara), an automated bioinformatics pipeline, to detect, quantify and annotate circRNAs from RNA-seq data using in parallel four different methods for back-splice identification. CirComPara also provides quantification of linear RNAs and gene expression, ultimately comparing and correlating circRNA and gene/transcript expression levels. We applied our method to RNA-seq data of monocyte and macrophage samples in relation to haploinsufficiency of the RNA-binding splicing factor Quaking (QKI). The biological relevance of the results, in terms of number, types and variations of circRNAs expressed, illustrates CirComPara potential to enlarge the knowledge of the transcriptome, adding details on the circRNAome, and facilitating further computational and experimental studies.
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510
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Sui W, Shi Z, Xue W, Ou M, Zhu Y, Chen J, Lin H, Liu F, Dai Y. Circular RNA and gene expression profiles in gastric cancer based on microarray chip technology. Oncol Rep 2017; 37:1804-1814. [DOI: 10.3892/or.2017.5415] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/09/2017] [Indexed: 12/12/2022] Open
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511
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Abstract
Circular RNAs (circRNAs), a novel type of widespread and diverse endogenous non-coding RNAs (ncRNAs), which are different from the linear RNAs, form a covalently closed continuous loop without 5' or 3' polarities. The majority of circRNAs are abundant, conserved and stable across different species, and exhibit tissue/developmental-stage-specific characteristics. They are generated primarily through a type of alternative RNA splicing called "back-splicing," in which a downstream splice donor is joined to an upstream splice acceptor through splice skipping or direct splice. Recent studies have discovered circRNAs function as microRNA sponges, binding with RNA-associated proteins to form RNA-protein complexes and then regulating gene transcription and translation into polypeptides. Emerging evidence indicates that circRNAs play important roles in the regulation of the development and progression of multiple cancers by serving as potential diagnostic and predictive biomarkers involved in tumor growth and invasion and providing new strategies for cancer diagnosis and targeted therapy. In this review, we briefly delineate the diversity and characteristics of circRNAs and discuss the highlights of the biogenesis of circRNAs and their potential functions in tumor.
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Affiliation(s)
- Li-Dan Hou
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jing Zhang
- Department of Gastroenterology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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512
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Circular RNAs in Cardiovascular Disease: An Overview. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5135781. [PMID: 28210621 PMCID: PMC5292166 DOI: 10.1155/2017/5135781] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/13/2016] [Indexed: 01/16/2023]
Abstract
Circular RNA (circRNA), a novel type of endogenous noncoding RNA (ncRNA), has become a research hotspot in recent years. CircRNAs are abundant and stably exist in creatures, and they are found with covalently closed loop structures in which they are quite different from linear RNAs. Nowadays, an increasing number of scientists have demonstrated that circRNAs may have played an essential role in the regulation of gene expression, especially acting as miRNA sponges, and have described the potential mechanisms of several circRNAs in diseases, hinting at their clinical therapeutic values. In this review, the authors summarized the current understandings of the biogenesis and properties of circRNAs and their functions and role as biomarkers in cardiovascular diseases.
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513
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Abstract
Circular RNAs (CircRNAs) were first identified as a viroid and later found to also be an endogenous RNA splicing product in eukaryotes. In recent years, a series of RNA-sequencing analyses from a diverse range of eukaryotes have shed new light on these eukaryotic circRNAs, revealing dynamic expression patterns in various developmental stages and physiological conditions. In this review, we focus on circRNAs implicated in stress response pathways and explore potential mechanisms underlying their regulation. To date, circRNAs have been shown to act as scaffolds in the assembly of protein complexes, sequester proteins from native subcellular localization, activate transcription of parental genes, inhibit RNA-protein interactions, and function as regulators of microRNA activity. Although the mechanism modulating circRNA levels during stress remains unclear, circRNAs are shown to be regulated during biogenesis, degradation, and exportation. As circRNAs do not have 5' and 3' ends, there are no entry points for exoribonucleases to initiate degradation. Such inherent stability makes this class of RNA a strong candidate to maintain homeostasis in the face of environmental challenges.
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Affiliation(s)
- Joseph W Fischer
- a McKusick-Nathans Institute of Genetic Medicine, School of Medicine , Johns Hopkins University , Baltimore , MD , USA.,b Department of Biochemistry and Molecular Biology , Bloomberg School of Public Health, Johns Hopkins University , Baltimore , MD , USA
| | - Anthony K L Leung
- a McKusick-Nathans Institute of Genetic Medicine, School of Medicine , Johns Hopkins University , Baltimore , MD , USA.,b Department of Biochemistry and Molecular Biology , Bloomberg School of Public Health, Johns Hopkins University , Baltimore , MD , USA.,c Department of Oncology , School of Medicine, Johns Hopkins University , Baltimore , MD , USA
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514
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Zhu M, Xu Y, Chen Y, Yan F. Circular BANP, an upregulated circular RNA that modulates cell proliferation in colorectal cancer. Biomed Pharmacother 2017; 88:138-144. [PMID: 28103507 DOI: 10.1016/j.biopha.2016.12.097] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are recently identified as widespread and diverse endogenous noncoding RNAs that may harbor vital functions in human and animals. However, the role of circRNAs in the process of tumorigenesis and development of colorectal cancer (CRC) remains vague. Here we characterized the circRNA expression profile from three paired CRC cancerous and adjacent normal tissues by human circRNA array, and identified 136 significantly overexpressed circRNAs and 243 downregulated circRNAs in CRC cancerous tissues (>2-fold changes). We further validated one circRNA generated from Exon 5-11 of BANP gene, termed circ-BANP. In addition, RT-PCR result showed that circ-BANP was overexpressed in 35 CRC cancerous tissues. Knockdown of circ-BANP with siRNA significantly attenuate the proliferation of CRC cells. In summary, our findings demonstrated that dysregulated circ-BANP appears to have an important role in CRC cells and could serve as a prognostic and therapeutic marker for CRC.
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Affiliation(s)
- Mingchen Zhu
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China; Department of Clinical Laboratory, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | - Yijun Xu
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing 211166, China.
| | - Feng Yan
- Department of Clinical Laboratory, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China.
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515
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Li L, Guo J, Chen Y, Chang C, Xu C. Comprehensive CircRNA expression profile and selection of key CircRNAs during priming phase of rat liver regeneration. BMC Genomics 2017; 18:80. [PMID: 28086788 PMCID: PMC5237265 DOI: 10.1186/s12864-016-3476-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 12/26/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Rat liver regeneration (LR) proceeds along a process of highly organized and ordered tissue growth in response to the loss or injury of liver tissue, during which many physiological processes may play important roles. The molecular mechanism of hepatocyte proliferation, energy metabolism and substance metabolism during rat LR had been elucidated. Further, the correlation of circular RNA (circRNA) abundance with proliferation has recently been clarified. However, the regulatory capacity of circRNA in rat LR remains a fascinating topic. RESULTS To investigate the regulatory mechanism of circRNA during priming phase of rat LR, high-throughput RNA sequencing technology was performed to unbiasedly profile the expression of circRNA during priming phase of rat LR. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) biological pathway analysis was conducted to predict the functions of differentially expressed circRNAs and their host linear transcripts. Co-expression networks of circRNA-miRNA were constructed based on the correlation analysis between the differentially expressed LR-related circRNAs and the condition of their miRNA binding sites. To excavate the key circRNAs in the early phase of rat LR, we comprehensively evaluated and integrated the relationship of expression level between the circRNAs and the linear transcripts as well as the distribution of miRNA binding sites in circRNA sequences. CONCLUSIONS This paper is the first to employ the comprehensive circRNA expression profile and to investigate circRNA-miRNA interactions during priming phase of rat LR. Two thousand four hundred twelve circRNAs were detected, and 159 circRNAs deriving from 116 host linear transcripts differentially expressed (p < 0.05). Six significantly changed circRNAs during priming phase of rat LR were screened as key circle molecules, and then were validated by qRT-PCR. This study will lay the foundation for revealing the functional roles of circRNAs during rat LR and help solve the remaining clinical problems.
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Affiliation(s)
- Lifei Li
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan Province, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development, Xinxiang, 453007, Henan Province, China
| | - Jianlin Guo
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan Province, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development, Xinxiang, 453007, Henan Province, China
| | - Yanhui Chen
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan Province, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development, Xinxiang, 453007, Henan Province, China
| | - Cuifang Chang
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan Province, China.,State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development, Xinxiang, 453007, Henan Province, China
| | - Cunshuan Xu
- College of Life Science, Henan Normal University, Xinxiang, 453007, Henan Province, China. .,State Key Laboratory Cultivation Base for Cell Differentiation Regulation and Henan Engineering Laboratory for Bioengineering and Drug Development, Xinxiang, 453007, Henan Province, China.
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516
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Wang K, Sun Y, Tao W, Fei X, Chang C. Androgen receptor (AR) promotes clear cell renal cell carcinoma (ccRCC) migration and invasion via altering the circHIAT1/miR-195-5p/29a-3p/29c-3p/CDC42 signals. Cancer Lett 2017; 394:1-12. [PMID: 28089832 DOI: 10.1016/j.canlet.2016.12.036] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/23/2016] [Accepted: 12/24/2016] [Indexed: 01/10/2023]
Abstract
Increasing evidence has demonstrated that the androgen receptor (AR) plays important roles to promote the metastasis of clear cell renal cell carcinoma (ccRCC). The detailed mechanisms, especially how AR functions via altering the circular RNAs (circRNAs) remain unclear. Here we identified a new circRNA (named as circHIAT1) whose expression was lower in ccRCCs than adjacent normal tissues. Targeting AR could suppress ccRCC cell progression via increasing circHIAT1 expression. ChIP assay and luciferase assay demonstrated that AR suppressed circHIAT1 expression via regulating its host gene, Hippocampus Abundant Transcript 1 (HIAT1) expression at the transcriptional level. The consequences of AR-suppressed circHIAT1 resulted in deregulating miR-195-5p/29a-3p/29c-3p expressions, which increased CDC42 expression to enhance ccRCC cell migration and invasion. Increasing this newly identified signal via circHIAT1 suppressed AR-enhanced ccRCC cell migration and invasion. Together, these results suggested that circHIAT1 functioned as a metastatic inhibitor to suppress AR-enhanced ccRCC cell migration and invasion. Targeting this newly identified AR-circHIAT1-mediated miR-195-5p/29a-3p/29c-3p/CDC42 signals may help us develop potential new therapies to better suppress ccRCC metastasis.
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Affiliation(s)
- Kefeng Wang
- Department of Urology, Shengjing Hospital, China Medical University, Shenyang, 110004, China; George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Yin Sun
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Wei Tao
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Xiang Fei
- Department of Urology, Shengjing Hospital, China Medical University, Shenyang, 110004, China.
| | - Chawnshang Chang
- George Whipple Lab for Cancer Research, Departments of Pathology, Urology, Radiation Oncology and The Wilmot Cancer Center, University of Rochester Medical Center, Rochester, NY, 14642, USA; Sex Hormone Research Center, China Medical University/Hospital, Taichung, 404, Taiwan.
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517
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CircRNA_000203 enhances the expression of fibrosis-associated genes by derepressing targets of miR-26b-5p, Col1a2 and CTGF, in cardiac fibroblasts. Sci Rep 2017; 7:40342. [PMID: 28079129 PMCID: PMC5228128 DOI: 10.1038/srep40342] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/05/2016] [Indexed: 01/11/2023] Open
Abstract
Circular RNAs (circRNAs) participate in regulating gene expression in diverse biological and pathological processes. The present study aimed to investigate the mechanism underlying the modulation of circRNA_000203 on expressions of fibrosis-associated genes in cardiac fibroblasts. CircRNA_000203 was shown upregulated in the diabetic mouse myocardium and in Ang-II-induced mouse cardiac fibroblasts. Enforced-expression of circRNA_000203 could increase expressions of Col1a2, Col3a1 and α-SMA in mouse cardiac fibroblasts. RNA pull-down and RT-qPCR assay indicated that circRNA_000203 could specifically sponge miR-26b-5p. Dual luciferase reporter assay revealed that miR-26b-5p interacted with 3′UTRs of Col1a2 and CTGF, and circ_000203 could block the interactions of miR-26b-5p and 3′UTRs of Col1a2 and CTGF. Transfection of miR-26b-5p could post-transcriptionaly inhibit expressions of Col1a2 and CTGF, accompanied with the suppressions of Col3a1 and α-SMA in cardiac fibroblasts. Additionally, over-expression of circRNA_000203 could eliminate the anti-fibrosis effect of miR-26b-5p in cardiac fibroblasts. Together, our results reveal that suppressing the function of miR-26b-5p contributes to the pro-fibrosis effect of circRNA_000203 in cardiac fibroblasts.
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518
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Abdelmohsen K, Panda AC, Munk R, Grammatikakis I, Dudekula DB, De S, Kim J, Noh JH, Kim KM, Martindale JL, Gorospe M. Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biol 2017; 14:361-369. [PMID: 28080204 DOI: 10.1080/15476286.2017.1279788] [Citation(s) in RCA: 614] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
HuR influences gene expression programs and hence cellular phenotypes by binding to hundreds of coding and noncoding linear RNAs. However, whether HuR binds to circular RNAs (circRNAs) and impacts on their function is unknown. Here, we have identified en masse circRNAs binding HuR in human cervical carcinoma HeLa cells. One of the most prominent HuR target circRNAs was hsa_circ_0031288, renamed CircPABPN1 as it arises from the PABPN1 pre-mRNA. Further analysis revealed that HuR did not influence CircPABPN1 abundance; interestingly, however, high levels of CircPABPN1 suppressed HuR binding to PABPN1 mRNA. Evaluation of PABPN1 mRNA polysomes indicated that PABPN1 translation was modulated positively by HuR and hence negatively by CircPABPN1. We propose that the extensive binding of CircPABPN1 to HuR prevents HuR binding to PABPN1 mRNA and lowers PABPN1 translation, providing the first example of competition between a circRNA and its cognate mRNA for an RBP that affects translation.
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Affiliation(s)
- Kotb Abdelmohsen
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Amaresh C Panda
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Rachel Munk
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Ioannis Grammatikakis
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Dawood B Dudekula
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Supriyo De
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Jiyoung Kim
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Ji Heon Noh
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Kyoung Mi Kim
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Jennifer L Martindale
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
| | - Myriam Gorospe
- a Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health , Baltimore , MD , USA
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519
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Dong Y, He D, Peng Z, Peng W, Shi W, Wang J, Li B, Zhang C, Duan C. Circular RNAs in cancer: an emerging key player. J Hematol Oncol 2017; 10:2. [PMID: 28049499 PMCID: PMC5210264 DOI: 10.1186/s13045-016-0370-2] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/06/2016] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of endogendous RNAs that form a covalently closed continuous loop and exist extensively in mammalian cells. Majority of circRNAs are conserved across species and often show tissue/developmental stage-specific expression. CircRNAs were first thought to be the result of splicing error; however, subsequent research shows that circRNAs can function as microRNA (miRNA) sponges and regulate splicing and transcription. Emerging evidence shows that circRNAs possess closely associated with human diseases, especially cancers, and may serve as better biomarkers. After miRNA and long noncoding RNA (lncRNA), circRNAs are becoming a new hotspot in the field of RNA of cancer. Here, we review biogenesis and metabolism of circRNAs, their functions, and potential roles in cancer.
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Affiliation(s)
- Yeping Dong
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China
| | - Dan He
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China
| | - Zhenzi Peng
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China
| | - Wei Peng
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China
| | - Wenwen Shi
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China
| | - Jun Wang
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China
| | - Bin Li
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China
| | - Chunfang Zhang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China
| | - Chaojun Duan
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China. .,Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China. .,Department of Thoracic Surgery, Xiangya Hospital, Central South University, Xiangya Road 87th, Changsha, 410008, Hunan, People's Republic of China.
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520
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Peripheral blood circular RNA hsa_circ_0124644 can be used as a diagnostic biomarker of coronary artery disease. Sci Rep 2017; 7:39918. [PMID: 28045102 PMCID: PMC5206672 DOI: 10.1038/srep39918] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/29/2016] [Indexed: 01/01/2023] Open
Abstract
The aim of the present study was to investigate the expression of circular RNAs (circRNAs) in the peripheral blood of coronary artery disease (CAD) patients and the potential use of circRNAs as diagnostic biomarkers of CAD. We first analysed peripheral blood circRNAs of 12 CAD patients and 12 control individuals by RNA microarray and found that 22 circRNAs were differentially expressed between these two groups: 12 were upregulated, and 10 were downregulated. Then, we selected 5 circRNAs as candidate biomarkers under stricter screening criteria and verified them in another group of subjects consisting of 30 control individuals and 30 CAD patients with different SYNTAX scores. These 5 circRNAs were all remarkably increased in the CAD group. Hsa_circ_0124644 had the largest area under the curve (AUC). We tested hsa_circ_0124644 in an independent cohort consisting of 115 control individuals and 137 CAD patients. After we included the risk factors for CAD, the AUC slightly increased from 0.769 (95% confidence interval = [0.710–0.827], P < 0.001) to 0.804 ([0.751–0.857], P < 0.001), and when combined with hsa_circ_0098964, the diagnostic value slightly increased. Taken together, our results suggest that hsa_circ_0124644 can be used as a diagnostic biomarker of CAD.
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521
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Liu D, Mewalal R, Hu R, Tuskan GA, Yang X. New technologies accelerate the exploration of non-coding RNAs in horticultural plants. HORTICULTURE RESEARCH 2017; 4:17031. [PMID: 28698797 PMCID: PMC5496985 DOI: 10.1038/hortres.2017.31] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 05/06/2023]
Abstract
Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422, USA
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522
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Circular RNA profile identifies circPVT1 as a proliferative factor and prognostic marker in gastric cancer. Cancer Lett 2016; 388:208-219. [PMID: 27986464 DOI: 10.1016/j.canlet.2016.12.006] [Citation(s) in RCA: 550] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/27/2016] [Accepted: 12/06/2016] [Indexed: 12/11/2022]
Abstract
Circular RNAs (circRNAs) comprise a novel class of widespread non-coding RNAs that may regulate gene expression in eukaryotes. However, the characterization and function of circRNAs in human cancer remain elusive. Here we identified at least 5500 distinct circRNA candidates and a series of circRNAs that are differentially expressed in gastric cancer (GC) tissues compared with matched normal tissues. We further characterized one circRNA derived from the PVT1 gene and termed it as circPVT1. The expression of circPVT1 is often upregulated in GC tissues due to the amplification of its genomic locus. circPVT1 may promote cell proliferation by acting as a sponge for members of the miR-125 family. The level of circPVT1 was observed as an independent prognostic marker for overall survival and disease-free survival of patients with GC. Our findings suggest that circPVT1 is a novel proliferative factor and prognostic marker in GC.
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523
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Dong WW, Li HM, Qing XR, Huang DH, Li HG. Identification and characterization of human testis derived circular RNAs and their existence in seminal plasma. Sci Rep 2016; 6:39080. [PMID: 27958373 PMCID: PMC5153637 DOI: 10.1038/srep39080] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs) have emerged as novel molecules of interest in gene regulation as other noncoding RNAs. Though they have been explored in some species and tissues, the expression and functions of circRNAs in human reproductive systems remain unknown. Here we revealed the expression profiles of circRNAs in human testis tissue using high-throughput sequencing. The conformation of these testis-derived circRNAs in seminal plasma was also investigated, aiming to provide a non-invasive liquid biopsy surrogate for testicular biopsy. We predicted >15,000 circRNAs in human testis, with most of them (10,792; 67%) new. In all the 5,928 circRNA forming genes, 1,017 are first reported by us to generate circRNAs. Interestingly, these genes are mostly related to spermatogenesis, sperm motility, fertilization, etc. The sequence feature, chromosome location, alternative splicing and other characteristics of the circRNAs in human testis were also explored. Moreover, we found that these testis-derived circRNAs could be stably detected in seminal plasma. Most of them were probably bound with proteins in seminal plasma and were very stable at room temperature. Our work has laid the foundations to decipher regulation mechanisms of circRNAs in spermatogenesis and to develop circRNAs as novel noninvasive biomarkers for male infertile diseases.
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Affiliation(s)
- Wei-Wei Dong
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Hui-Min Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Xing-Rong Qing
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China
| | - Dong-Hui Huang
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, 430030, P. R. China
| | - Hong-Gang Li
- Family Planning Research Institute/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, P. R. China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, 430030, P. R. China
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524
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Guo JN, Li J, Zhu CL, Feng WT, Shao JX, Wan L, Huang MD, He JD. Comprehensive profile of differentially expressed circular RNAs reveals that hsa_circ_0000069 is upregulated and promotes cell proliferation, migration, and invasion in colorectal cancer. Onco Targets Ther 2016; 9:7451-7458. [PMID: 28003761 PMCID: PMC5158168 DOI: 10.2147/ott.s123220] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Nowadays, despite great progress in cancer research, the detailed mechanisms of colorectal cancer (CRC) are still poorly understood. Circular RNAs (circRNAs), a new star of the non-coding RNA network, have been identified as critical regulators in various cancers, including CRC. Methods and results In this study, by using unsupervised hierarchical clustering analysis, a novel dysregulated circRNA, hsa_circ_0000069, was found. The expression of hsa_circ_0000069 was measured in 30 paired CRC tissues and adjacent noncancerous tissues using quantitative polymerase chain reaction. A high expression of hsa_circ_0000069 was observed in CRC tissues and correlated with patients’ age and tumor, node, metastasis (TNM) stage (P<0.05). Furthermore, by using specifically designed siRNAs in CRC cells, a functional analysis was performed which revealed that hsa_circ_0000069 knockdown could notably inhibit cell proliferation, migration, and invasion, and induce G0/G1 phase arrest of cell cycle in vitro. Conclusion This study’s findings are the first to demonstrate that hsa_circ_0000069, an important regulator in cancer progression, could be a promising target in the diagnosis and therapy in colorectal cancer.
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Affiliation(s)
- Jia-Ni Guo
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, People's Republic of China
| | - Jin Li
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, People's Republic of China
| | - Chang-Li Zhu
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, People's Republic of China
| | - Wan-Ting Feng
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, People's Republic of China
| | - Jing-Xian Shao
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, People's Republic of China
| | - Li Wan
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, People's Republic of China
| | - Ming-de Huang
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, People's Republic of China
| | - Jing-Dong He
- Department of Medical Oncology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an City, Jiangsu Province, People's Republic of China
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525
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Xia W, Qiu M, Chen R, Wang S, Leng X, Wang J, Xu Y, Hu J, Dong G, Xu PL, Yin R. Circular RNA has_circ_0067934 is upregulated in esophageal squamous cell carcinoma and promoted proliferation. Sci Rep 2016; 6:35576. [PMID: 27752108 PMCID: PMC5067712 DOI: 10.1038/srep35576] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/16/2016] [Indexed: 12/17/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent and deadly types of cancer worldwide especially in Eastern Asia and the prognosis of ESCC remain poor. Recent evidence suggests that circular RNAs (circRNAs) play important roles in multiple diseases, including cancer. In this study, we characterized a novel circRNA termed hsa_circ_0067934 in ESCC tumor tissues and cell lines. We analyzed a cohort of 51 patients and found that hsa_circ_0067934 was significantly overexpressed in ESCC tissues compared with paired adjacent normal tissues. The high expression level of hsa_circ_0067934 was associated with poor differentiation (P = 0.025), I-II T stage (P = 0.04), and I-II TNM stage (P = 0.021). The in vitro silence of hsa_circ_0067934 by siRNA inhibited the proliferation and migration of ESCC cells and blocked cell cycle progression. Cell fraction analyses and fluorescence in situ hybridization detected that hsa_circ_0067934 was mostly located in the cytoplasm. Our findings suggest that hsa_circ_0067934 is upregulated in ESCC tumor tissue. Our data suggest that hsa_circ_0067934 represents a novel potential biomarker and therapeutic target of ESCC.
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Affiliation(s)
- Wenjia Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, 210000, China
| | - Mantang Qiu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, 210000, China
| | - Rui Chen
- The Fourth Clinical College of Nanjing Medical University, Nanjing, 210000, China.,Department of Cardiothoracic Surgery, Taixing People's Hospital, The Affiliated Taixing Hospital of Yangzhou University, Taixing 225400, China
| | - Siwei Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China.,The Fourth Clinical College of Nanjing Medical University, Nanjing, 210000, China
| | - Xuechun Leng
- Department of Thoracic Surgery, Huai'an First People's Hospital, Nanjing Medical University, Huai'an 223300, China
| | - Jie Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China.,Department of Scientific Research, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Youtao Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Jingwen Hu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China.,Department of Scientific Research, Nanjing Medical University Affiliated Cancer Hospital, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Prof Lin Xu
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Rong Yin
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
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526
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Bonizzato A, Gaffo E, te Kronnie G, Bortoluzzi S. CircRNAs in hematopoiesis and hematological malignancies. Blood Cancer J 2016; 6:e483. [PMID: 27740630 PMCID: PMC5098259 DOI: 10.1038/bcj.2016.81] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/11/2016] [Indexed: 12/12/2022] Open
Abstract
Cell states in hematopoiesis are controlled by master regulators and by complex circuits of a growing family of RNA species impacting cell phenotype maintenance and plasticity. Circular RNAs (circRNAs) are rapidly gaining the status of particularly stable transcriptome members with distinctive qualities. RNA-seq identified thousands of circRNAs with developmental stage- and tissue-specific expression corroborating earlier suggestions that circular isoforms are a natural feature of the cell expression program. CircRNAs are abundantly expressed also in the hematopoietic compartment. There are a number of studies on circRNAs in blood cells, a specific overview is however lacking. In this review we first present current insight in circRNA biogenesis discussing the relevance for hematopoiesis of the highly interleaved processes of splicing and circRNA biogenesis. Regarding molecular functions circRNAs modulate host gene expression, but also compete for binding of microRNAs, RNA-binding proteins or translation initiation and participate in regulatory circuits. We examine circRNA expression in the hematopoietic compartment and in hematologic malignancies and review the recent breakthrough study that identified pathogenic circRNAs derived from leukemia fusion genes. CircRNA high and regulated expression in blood cell types indicate that further studies are warranted to inform the position of these regulators in normal and malignant hematopoiesis.
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Affiliation(s)
- A Bonizzato
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - E Gaffo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - G te Kronnie
- Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Padova, Italy
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527
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Abstract
Circular RNAs (circRNAs) are novel endogenous non-coding RNAs characterized by the presence of a covalent bond linking the 3' and 5' ends generated by backsplicing. In this review, we summarize a number of the latest theories regarding the biogenesis, properties and functions of circRNAs. Specifically, we focus on the advancing characteristics and functions of circRNAs in the brain and neurological diseases. CircRNAs exhibit the characteristics of species conservation, abundance and tissue/developmental-stage-specific expression in the brain. We also describe the relationship between circRNAs and several neurological diseases and highlight their functions in neurological diseases.
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Affiliation(s)
- Tao-Ran Li
- a Department of Neurology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou University , Zhengzhou , PR. China.,b Department of Neurology, Beijing Tiantan Hospital , Capital Medical University , Beijing , PR. China ; China National Clinical Research Center for Neurological Diseases , Beijing , PR. China
| | - Yan-Jie Jia
- a Department of Neurology, The First Affiliated Hospital of Zhengzhou University , Zhengzhou University , Zhengzhou , PR. China
| | - Qun Wang
- b Department of Neurology, Beijing Tiantan Hospital , Capital Medical University , Beijing , PR. China ; China National Clinical Research Center for Neurological Diseases , Beijing , PR. China
| | - Xiao-Qiu Shao
- b Department of Neurology, Beijing Tiantan Hospital , Capital Medical University , Beijing , PR. China ; China National Clinical Research Center for Neurological Diseases , Beijing , PR. China
| | - Rui-Juan Lv
- b Department of Neurology, Beijing Tiantan Hospital , Capital Medical University , Beijing , PR. China ; China National Clinical Research Center for Neurological Diseases , Beijing , PR. China
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528
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Abstract
Over the past 2 decades, different types of circular RNAs have been discovered in all kingdoms of life, and apparently, those circular species are more abundant than previously thought. Apart from circRNAs in viroids and viruses, circular transcripts have been discovered in rodents more than 20 y ago and recently have been reported to be abundant in many organisms including humans. Their exact function remains still unknown, although one may expect extensive functional studies to follow the currently dominant research into identification and discovery of circRNA by sophisticated sequencing techniques and bioinformatics. Functional studies require models and as such methods for preparation of circRNA in vitro. Here, we will review current protocols for RNA circularization and discuss future prospects in the field.
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Affiliation(s)
- Sabine Müller
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
| | - Bettina Appel
- a Universität Greifswald, Institut für Biochemie , Greifswald , Germany
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529
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Abdelmohsen K, Panda AC, De S, Grammatikakis I, Kim J, Ding J, Noh JH, Kim KM, Mattison JA, de Cabo R, Gorospe M. Circular RNAs in monkey muscle: age-dependent changes. Aging (Albany NY) 2016; 7:903-10. [PMID: 26546448 PMCID: PMC4694061 DOI: 10.18632/aging.100834] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Circular RNAs (circRNAs) have been identified in numerous species, including human, mouse, nematode, and coelacanth. They are believed to function as regulators of gene expression at least in part by sponging microRNAs. Here, we describe the identification of circRNAs in monkey (Rhesus macaque) skeletal muscle. RNA sequencing analysis was employed to identify and annotate ∼12,000 circRNAs, including numerous circular intronic RNAs (ciRNAs), from skeletal muscle of monkeys of a range of ages. Reverse transcription followed by real-time quantitative (q)PCR analysis verified the presence of these circRNAs, including the existence of several highly abundant circRNAs, and the differential abundance of a subset of circRNAs as a function of age. Taken together, our study has documented systematically circRNAs expressed in skeletal muscle and has identified circRNAs differentially abundant with advancing muscle age. We propose that some of these circRNAs might influence muscle function.
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Affiliation(s)
- Kotb Abdelmohsen
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Amaresh C Panda
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Supriyo De
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Ioannis Grammatikakis
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Jiyoung Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Jun Ding
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Kyoung Mi Kim
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics, National Institute on Aging-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, USA
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530
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Kulcheski FR, Christoff AP, Margis R. Circular RNAs are miRNA sponges and can be used as a new class of biomarker. J Biotechnol 2016; 238:42-51. [PMID: 27671698 DOI: 10.1016/j.jbiotec.2016.09.011] [Citation(s) in RCA: 583] [Impact Index Per Article: 72.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/18/2016] [Accepted: 09/23/2016] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that are involved in transcriptional and posttranscriptional gene expression regulation. The development of deep sequencing of ribosomal RNA (rRNA)-depleted RNA libraries, associated with improved computational tools, has provided the identification of several new circRNAs in all sorts of organisms, from protists, plants and fungi to animals. Recently, it was discovered that endogenous circRNAs can work as microRNA (miRNA) sponges. This means that the circRNAs bind to miRNAs and consequently repress their function, providing a new model of action for this class of ncRNA, as well as indicating another mechanism that regulates miRNA activity. As miRNAs control a large set of biological processes, circRNA sponge activity will also affect these pathways. Several studies have associated miRNA sponges with human diseases, including osteoarthritis, diabetes, neurodegenerative pathologies and several types of cancer. Additionally, high stability, abundance and tissue-specific expression patterns make circRNA sponges very attractive for clinical research. Herein, we review the biogenesis, properties and function of endogenous circRNA sponges, with a special focus on those related to human cancer. A list of web tools available for the study of circRNAs is also given. Additionally, we discuss the possibility of using circRNAs as molecular markers for the diagnosis of diseases.
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Affiliation(s)
- Franceli Rodrigues Kulcheski
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil
| | | | - Rogerio Margis
- Programa de Pós-graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, UFRGS, Brazil.
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531
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Takenaka K, Chen BJ, Modesitt SC, Byrne FL, Hoehn KL, Janitz M. The emerging role of long non-coding RNAs in endometrial cancer. Cancer Genet 2016; 209:445-455. [PMID: 27810073 DOI: 10.1016/j.cancergen.2016.09.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/19/2016] [Accepted: 09/08/2016] [Indexed: 12/22/2022]
Abstract
The human genome is pervasively transcribed and approximately 98% of the genome is non-coding. Long non-coding RNAs (lncRNAs) are a heterogeneous group of RNA transcripts that are >200 nucleotides in length with minimal to no protein-coding potential. Similar to proteins, lncRNAs have important biological functions in both normal cells and disease states including many types of cancer. This review summarizes recent advances in our understanding of lncRNAs in cancer biology and highlights the potential for lncRNA as diagnostic biomarkers and therapeutics. Herein we focus on the poorly understood role of lncRNAs in endometrial cancer, the most common gynecologic malignancy in the developed world.
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Affiliation(s)
- Konii Takenaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Bei Jun Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Susan C Modesitt
- Division of Gynecologic Oncology, Obstetrics and Gynecology Department, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Frances L Byrne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Kyle L Hoehn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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532
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The circular RNA ciRS-7 (Cdr1as) acts as a risk factor of hepatic microvascular invasion in hepatocellular carcinoma. J Cancer Res Clin Oncol 2016; 143:17-27. [PMID: 27614453 DOI: 10.1007/s00432-016-2256-7] [Citation(s) in RCA: 247] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 02/05/2023]
Abstract
PURPOSE Circular RNAs (circRNA) represent a novel class of widespread and diverse endogenous RNAs that regulate gene expression in mammals. microRNA-7 (miR-7) is a well-demonstrated suppressor of hepatocellular carcinoma (HCC). Recent studies have showed that one such circRNA, ciRS-7 (also termed as Cdr1as) was the inhibitor and sponge of miR-7 in the embryonic zebrafish midbrain and islet cells. However, the relationships among ciRS-7, miR-7 and clinical features of HCC remain to be clarified. METHODS Expression levels of ciRS-7, miR-7 and three miR-7-targeted mRNAs in 108 pairs of HCC and their matched non-tumor tissues were examined by quantitative reverse transcription polymerase chain reaction (qRT-PCR). The protein production of these three miR-7-targeted mRNAs was further verified by Western blot. The relationship between ciRS-7 level and clinicopathological features as well as the recurrence of HCC patients was analyzed. The univariate and multivariate logistic regression analyses were used to detect the risk factors of hepatic microvascular invasion (MVI). The correlation among ciRS-7, miR-7 and miR-7-targeted mRNAs was evaluated using Spearman's correlation test. RESULTS There was no significant difference of ciRS-7 expression levels between the HCC tissues and the matched non-tumor tissues (0.67 ± 1.49 vs. 0.44 ± 0.45, p = 0.13), and the ciRS-7 levels in more than half of HCC tissues (65 out of 108, 60.2 %) were down-regulated when compared with their matched non-tumor tissues. However, the expression of ciRS-7 was significantly correlated with the following three clinicopathological characteristics of HCC patients: age <40 years (p = 0.02), serum AFP ≥400 ng/µl (p < 0.01) and hepatic MVI (p = 0.03). Meanwhile, up-regulated ciRS-7 expression was not only an independent risk factor of hepatic MVI but also had a capable predictive ability for MVI (AUC = 0.68, p = 0.001) at the cut-off value of 0.135. Furthermore, the expression of ciRS-7 in HCC tissues with concurrent MVI was inversely correlated with that of miR-7 (r = -0.39, p = 0.007) and positively related with that of two miR-7-targeted genes [PIK3CD (r = 0.55, p < 0.001) and p70S6K (r = 0.34, p = 0.021)]. In addition, the median recurrent time of patients from higher ciRS-7 level group was shorter than that of lower ciRS-7 group (18 vs. 25 months), but no significant difference was observed (p = 0.38). CONCLUSIONS The expression levels of ciRS-7 were comparable between HCC and matched non-tumor tissues. However, the highly ciRS-7 expression in HCC tissues was significantly correlated with hepatic MVI, AFP level and younger age and thus partly related with the deterioration of HCC. Especially, ciRS-7 was one of the independent factors of hepatic MVI. These data suggested that ciRS-7 may be a promising biomarker of hepatic MVI and a novel therapy target for restraining MVI.
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533
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Panda AC, Grammatikakis I, Munk R, Gorospe M, Abdelmohsen K. Emerging roles and context of circular RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27612318 DOI: 10.1002/wrna.1386] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 12/30/2022]
Abstract
Circular RNAs (circRNAs) represent a large class of noncoding RNAs (ncRNAs) that have recently emerged as regulators of gene expression. They have been shown to suppress microRNAs, thereby increasing the translation and stability of the targets of such microRNAs. In this review, we discuss the emerging functions of circRNAs, including RNA transcription, splicing, turnover, and translation. We also discuss other possible facets of circRNAs that can influence their function depending on the cell context, such as circRNA abundance, subcellular localization, interacting partners (RNA, DNA, and proteins), dynamic changes in interactions following stimulation, and potential circRNA translation. The ensuing changes in gene expression patterns elicited by circRNAs are proposed to drive key cellular processes, such as cell proliferation, differentiation, and survival, that govern health and disease. WIREs RNA 2017, 8:e1386. doi: 10.1002/wrna.1386 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Amaresh C Panda
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Ioannis Grammatikakis
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
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534
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Abstract
Circular RNA from backspliced exons (or exonic circular RNA, circRNA) is a type of covalently closed non-colinear RNA that was recently rediscovered in eukaryotes. Although circRNAs are often expressed at low levels, emerging evidence indicates that many circRNAs are linked to physiological development and various diseases. Notably, circRNAs have been shown to serve as oncogenic stimuli or tumor suppressors in cancer. circRNAs may regulate gene expression through different mechanisms. In addition, circRNAs have been shown to be useful as biomarkers of diseases due to their stability, specific expression and relation to diseases both in cells and in extracellular fluid. This review summarizes current knowledge of human circRNAs and discusses the emerging role and clinical implication of these multifarious transcripts.
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Affiliation(s)
- Dongbin Lyu
- a Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai , China.,b Department of Oncology , Shanghai Medical College, Fudan University , Shanghai , China
| | - Shenglin Huang
- a Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai , China.,b Department of Oncology , Shanghai Medical College, Fudan University , Shanghai , China
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535
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Floris G, Zhang L, Follesa P, Sun T. Regulatory Role of Circular RNAs and Neurological Disorders. Mol Neurobiol 2016; 54:5156-5165. [PMID: 27558238 DOI: 10.1007/s12035-016-0055-4] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/11/2016] [Indexed: 01/22/2023]
Abstract
Circular RNAs (circRNAs) are a class of long noncoding RNAs that are characterized by the presence of covalently linked ends and have been found in all life kingdoms. Exciting studies in regulatory roles of circRNAs are emerging. Here, we summarize classification, characteristics, biogenesis, and regulatory functions of circRNAs. CircRNAs are found to be preferentially expressed along neural genes and in neural tissues. We thus highlight the association of circRNA dysregulation with neurodegenerative diseases such as Alzheimer's disease. Investigation of regulatory role of circRNAs will shed novel light in gene expression mechanisms during development and under disease conditions and may identify circRNAs as new biomarkers for aging and neurodegenerative disorders.
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Affiliation(s)
| | | | - Paolo Follesa
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Tao Sun
- Department of Cell and Developmental Biology, Cornell University Weill Medical College, 1300 York Avenue, Box 60, New York, NY, 10065, USA.
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536
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Qu S, Zhong Y, Shang R, Zhang X, Song W, Kjems J, Li H. The emerging landscape of circular RNA in life processes. RNA Biol 2016; 14:992-999. [PMID: 27617908 PMCID: PMC5680710 DOI: 10.1080/15476286.2016.1220473] [Citation(s) in RCA: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNA that assumes a covalently closed continuous conformation. CircRNAs were previously thought to be the byproducts of splicing errors caused by low abundance and the technological limitations. With the recent development of high-throughput sequencing technology, numerous circRNAs have been discovered in many species. Recent studies have revealed that circRNAs are stable and widely expressed, and often exhibit cell type-specific or tissue-specific expression. Most circRNAs can be generated from exons, introns, or both. Remarkably, emerging evidence indicates that some circRNAs can serve as microRNA (miRNA) sponges, regulate transcription or splicing, and can interact with RNA binding proteins (RBPs). Moreover, circRNAs have been reported to play essential roles in myriad life processes, such as aging, insulin secretion, tissue development, atherosclerotic vascular disease risk, cardiac hypertrophy and cancer. Although circRNAs are ancient molecules, they represent a newly appreciated form of noncoding RNA and as such have great potential implications in clinical and research fields. Here, we review the current understanding of circRNA classification, function and significance in physiological and pathological processes. We believe that future research will increase our understanding of the regulation and function of these novel molecules.
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Affiliation(s)
- Shibin Qu
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Yue Zhong
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China.,b Department of General Surgery , The Second People's Hospital of Shaanxi Province , Xi'an , China
| | - Runze Shang
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Xuan Zhang
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Wenjie Song
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
| | - Jørgen Kjems
- c Department of Molecular Biology and Genetics (MBG) and Interdisciplinary Nanoscience Center (iNANO) , Aarhus University , Aarhus , Denmark
| | - Haimin Li
- a Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University , Xi'an , China
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537
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Zhang M, Du X. Noncoding RNAs in gastric cancer: Research progress and prospects. World J Gastroenterol 2016; 22:6610-6618. [PMID: 27547004 PMCID: PMC4970485 DOI: 10.3748/wjg.v22.i29.6610] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/26/2016] [Accepted: 06/15/2016] [Indexed: 02/06/2023] Open
Abstract
Noncoding RNAs (ncRNAs) have attracted much attention in cancer research field. They are involved in cellular development, proliferation, differentiation and apoptosis. The dysregulation of ncRNAs has been reported in tumor initiation, progression, invasion and metastasis in various cancers, including gastric cancer (GC). In the past few years, an accumulating body of evidence has deepened our understanding of ncRNAs, and several emerging ncRNAs have been identified, such as PIWI-interacting RNAs (piRNAs) and circular RNAs (circRNAs). The competing endogenous RNA (ceRNA) networks include mRNAs, microRNAs, long ncRNAs (lncRNAs) and circRNAs, which play critical roles in the tumorigenesis of GC. This review summarizes the recent hotspots of ncRNAs involved in GC pathobiology and their potential applications in GC. Finally, we briefly discuss the advances in the ceRNA network in GC.
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538
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Zhong Z, Lv M, Chen J. Screening differential circular RNA expression profiles reveals the regulatory role of circTCF25-miR-103a-3p/miR-107-CDK6 pathway in bladder carcinoma. Sci Rep 2016; 6:30919. [PMID: 27484176 PMCID: PMC4971518 DOI: 10.1038/srep30919] [Citation(s) in RCA: 333] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 07/11/2016] [Indexed: 12/19/2022] Open
Abstract
Circular RNAs (circRNAs), a kind of non-coding RNAs, have shown large capabilities in gene regulation. However, the mechanisms underlying circRNAs remain largely unknown so far. Recent studies demonstrated that circRNAs play miRNA sponge effects and regulate gene expression by microRNA response elements. Here, we screened circRNA expression profiles of bladder carcinoma using microarray assay. A total of 469 dysregulated circular transcripts are found in bladder cancer compared with normal tissues, among which 285 were up-regulated and 184 were down-regulated. Six circRNAs were identified to have significant differences by qRT-PCR. We speculated that circRNAs might involve in cancer-related pathways via interactions with miRNA by multiple bioinformatical approaches. Therefore, we further predicted that circTCF25 could sequester miR-103a-3p/miR-107, which potentially lead to the up-regulation of thirteen targets related to cell proliferation, migration and invasion. Subsequently, we demonstrated that over-expression of circTCF25 could down-regulate miR-103a-3p and miR-107, increase CDK6 expression, and promote proliferation and migration in vitro and vivo. This is the first study to exploit circRNA profiling and circRNA/miRNA interactions in bladder cancer. Our work laid the foundation to investigate the functions of circRNAs in cancers. The data also suggest that circTCF25 might be a new promising marker for bladder cancer.
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Affiliation(s)
- Zhenyu Zhong
- The First Clinical College, Chongqing Medical University, Chongqing 400016, China
| | - Mengxin Lv
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Junxia Chen
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
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539
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Li LJ, Huang Q, Pan HF, Ye DQ. Circular RNAs and systemic lupus erythematosus. Exp Cell Res 2016; 346:248-54. [DOI: 10.1016/j.yexcr.2016.07.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/20/2016] [Indexed: 01/01/2023]
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540
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Su H, Lin F, Deng X, Shen L, Fang Y, Fei Z, Zhao L, Zhang X, Pan H, Xie D, Jin X, Xie C. Profiling and bioinformatics analyses reveal differential circular RNA expression in radioresistant esophageal cancer cells. J Transl Med 2016; 14:225. [PMID: 27465405 PMCID: PMC4964270 DOI: 10.1186/s12967-016-0977-7] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/13/2016] [Indexed: 12/20/2022] Open
Abstract
Background Acquired radioresistance during radiotherapy is considered as the most important reason for local tumor recurrence or treatment failure. Circular RNAs (circRNAs) have recently been identified as microRNA sponges and involve in various biological processes. The purpose of this study is to investigate the role of circRNAs in the radioresistance of esophageal cancer. Methods Total RNA was isolated from human parental cell line KYSE-150 and self-established radioresistant esophageal cancer cell line KYSE-150R, and hybridized to Arraystar Human circRNA Array. Quantitative real-time PCR was used to confirm the circRNA expression profiles obtained from the microarray data. Bioinformatic tools including gene ontology (GO) analysis, KEGG pathway analysis and network analysis were done for further assessment. Results Among the detected candidate 3752 circRNA genes, significant upregulation of 57 circRNAs and downregulation of 17 circRNAs in human radioresistant esophageal cancer cell line KYSE-150R were observed compared with the parental cell line KYSE-150 (fold change ≥2.0 and P < 0.05). There were 9 out of these candidate circRNAs were validated by real-time PCR. GO analysis revealed that numerous target genes, including most microRNAs were involved in the biological processes. There were more than 400 target genes enrichment on Wnt signaling pathway. CircRNA_001059 and circRNA_000167 were the two largest nodes in circRNA/microRNA co-expression network. Conclusions Our study revealed a comprehensive expression and functional profile of differentially expressed circRNAs in radioresistant esophageal cancer cells, indicating possible involvement of these dysregulated circRNAs in the development of radiation resistance. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0977-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Huafang Su
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Fuqiang Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xia Deng
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Lanxiao Shen
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Ya Fang
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Zhenghua Fei
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Lihao Zhao
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Xuebang Zhang
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Huanle Pan
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China
| | - Deyao Xie
- Department of Thoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xiance Jin
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China.
| | - Congying Xie
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, No. 2 Fuxue Lane, Wenzhou, 325000, China.
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541
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Zhang C, Wu H, Wang Y, Zhu S, Liu J, Fang X, Chen H. Circular RNA of cattle casein genes are highly expressed in bovine mammary gland. J Dairy Sci 2016; 99:4750-4760. [DOI: 10.3168/jds.2015-10381] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 02/20/2016] [Indexed: 12/11/2022]
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542
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Wang F, Nazarali AJ, Ji S. Circular RNAs as potential biomarkers for cancer diagnosis and therapy. Am J Cancer Res 2016; 6:1167-1176. [PMID: 27429839 PMCID: PMC4937728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 05/10/2016] [Indexed: 06/06/2023] Open
Abstract
Circular RNAs (circRNAs) are a naturally occurring type of universal and diverse endogenous noncoding RNAs which unlike linear RNAs, have covalently linked ends. They are usually stable, abundant, conserved RNA molecules and often exhibit tissue/developmental-stage specific expression. Functional circRNAs have been identified to act as microRNA sponges and RNA-binding protein (RBP) sequestering agents as well as transcriptional regulators. These multiple functional roles elicit a great potential for circRNAs in biological applications. Emerging evidence shows that circRNAs play important roles in several diseases, particularly in cancer where they act through regulating protein expression of the pivotal genes that are critical for carcinogenesis. The presence of abundant circRNAs in saliva, exosomes and clinical standard blood samples will make them potential diagnostic or predictive biomarkers for diseases, particularly for cancer development, progression and prognosis. Here, we review the current literature and provide evidence for the impact of circRNAs in cancers and their potential significance in cancer prognosis and clinical treatment.
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Affiliation(s)
- Fengling Wang
- Department of Biochemistry and Molecular Biology, Medical School, Henan UniversityChina
| | - Adil J Nazarali
- College of Pharmacy and Nutrition and Neuroscience Research Cluster, University of SaskatchewanCanada
| | - Shaoping Ji
- Department of Biochemistry and Molecular Biology, Medical School, Henan UniversityChina
- College of Pharmacy and Nutrition and Neuroscience Research Cluster, University of SaskatchewanCanada
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543
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Li J, Tian H, Yang J, Gong Z. Long Noncoding RNAs Regulate Cell Growth, Proliferation, and Apoptosis. DNA Cell Biol 2016; 35:459-70. [PMID: 27213978 DOI: 10.1089/dna.2015.3187] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The revolutionary findings in nonprotein-coding part of human genome analysis have revealed a large number of RNA transcripts longer than 200 nucleotides that lack coding protein function, termed long noncoding RNAs (lncRNAs). Recently, accumulating shreds of evidence suggest that lncRNAs are widely distributed in human genome and deeply involved in cellular activities such as cell growth, proliferation, and apoptosis. Generally, lncRNAs regulate cell behaviors by targeting cell cycle-associated cyclins, cyclin-dependent kinases (CDKs), and/or CDK inhibitors. Specifically, lncRNAs serve as scaffolds or guides for chromatin-modifying complexes and act as signals in response to DNA damage. In addition, lncRNAs function as protein decoys and microRNA decoys, as well as interveners in cell division by modulating oncogenes and/or tumor suppressors. In this review, we mainly focus on the current understanding of the molecular mechanisms, how lncRNAs influence cellular processes and cancer progression. Finally, we also prospect the limitations of lncRNAs in cell behaviors and the novel roles of lncRNAs in epigenetic regulations.
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Affiliation(s)
- Jingqiu Li
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
| | - Haihua Tian
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China .,3 Department of Laboratory Medicine, Ningbo Kangning Hospital , Ningbo, China
| | - Jie Yang
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
| | - Zhaohui Gong
- 1 Department of Biochemistry and Molecular Biology, Ningbo University School of Medicine , Ningbo, China .,2 Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine , Ningbo, China
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544
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Shao Y, Chen Y. Roles of Circular RNAs in Neurologic Disease. Front Mol Neurosci 2016; 9:25. [PMID: 27147959 PMCID: PMC4829598 DOI: 10.3389/fnmol.2016.00025] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 03/27/2016] [Indexed: 11/30/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel type of endogenous noncoding RNA receiving increasing attention. They have been shown to act as a natural microRNA sponges that repress the activity of corresponding miRNAs by binding with them, thus regulating target genes. Numerous studies have shown that miRNAs are involved in the pathogenesis of neurological diseases. Therefore, circRNAs may act as important regulatory factors in the occurrence and development processes of neurological disease.
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Affiliation(s)
- Yiye Shao
- Department of Neurology, Jinshan Hospital, Fudan UniversityShanghai, China; Department of Neurology, Shanghai Medical College, Fudan UniversityShanghai, China
| | - Yinghui Chen
- Department of Neurology, Jinshan Hospital, Fudan UniversityShanghai, China; Department of Neurology, Shanghai Medical College, Fudan UniversityShanghai, China
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545
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Chen L, Huang C, Wang X, Shan G. Circular RNAs in Eukaryotic Cells. Curr Genomics 2016; 16:312-8. [PMID: 27047251 PMCID: PMC4763969 DOI: 10.2174/1389202916666150707161554] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 04/20/2015] [Accepted: 04/25/2015] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs (circRNAs) are now recognized as large species of transcripts in eukaryotic cells. From model organisms such as C. elegans, Drosophila, mice to human beings, thousands of circRNAs formed from back-splicing of exons have been identified. The known complexity of transcriptome has been greatly expanded upon the discovery of these RNAs. Studies about the biogenesis and physiological functions have yielded substantial knowledge for the circRNAs, and they are now more likely to be viewed as regulatory elements coded by the genome rather than unavoidable noise of gene expression. Certain human diseases may also relate to circRNAs. These circRNAs show diversifications in features such as sequence composition and cellular localization, and thus we propose that they may be divided into subtypes such as cytoplasmic circRNAs, nuclear circRNAs, and exon-intron circRNAs (EIciRNAs). Here we summarize and discuss knowns and unknowns for these RNAs, and we need to keep in mind that the whole field is still at the beginning of exciting explorations.
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Affiliation(s)
- Liang Chen
- School of Life Sciences & CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, Anhui Province 230027, P.R. China
| | - Chuan Huang
- School of Life Sciences & CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, Anhui Province 230027, P.R. China
| | - Xiaolin Wang
- School of Life Sciences & CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, Anhui Province 230027, P.R. China
| | - Ge Shan
- School of Life Sciences & CAS Key Laboratory of Brain Function and Disease, University of Science and Technology of China, Hefei, Anhui Province 230027, P.R. China
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546
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Abstract
The competitive endogenous RNA (ceRNA) hypothesis proposes that transcripts with shared microRNA (miRNA) binding sites compete for post-transcriptional control. This hypothesis has gained substantial attention as a unifying function for long non-coding RNAs, pseudogene transcripts and circular RNAs, as well as an alternative function for messenger RNAs. Empirical evidence supporting the hypothesis is accumulating but not without attracting scepticism. Recent studies that model transcriptome-wide binding-site abundance suggest that physiological changes in expression of most individual transcripts will not compromise miRNA activity. In this Review, we critically evaluate the evidence for and against the ceRNA hypothesis to assess the impact of endogenous miRNA-sponge interactions.
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Affiliation(s)
- Daniel W Thomson
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Kensington NSW 2052, Australia
| | - Marcel E Dinger
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst NSW 2010, Australia.,St Vincent's Clinical School, UNSW Australia, Kensington NSW 2052, Australia
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547
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Wang Y, Hou J, He D, Sun M, Zhang P, Yu Y, Chen Y. The Emerging Function and Mechanism of ceRNAs in Cancer. Trends Genet 2016; 32:211-224. [PMID: 26922301 PMCID: PMC4805481 DOI: 10.1016/j.tig.2016.02.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/19/2016] [Accepted: 02/02/2016] [Indexed: 01/17/2023]
Abstract
Complex diseases, such as cancer, are often associated with aberrant gene expression at both the transcriptional and post-transcriptional level. Over the past several years, competing endogenous RNAs (ceRNAs) have emerged as an important class of post-transcriptional regulators that alter gene expression through a miRNA-mediated mechanism. Recent studies in both solid tumors and hematopoietic malignancies showed that ceRNAs have significant roles in cancer pathogenesis by altering the expression of key tumorigenic or tumor-suppressive genes. Characterizing the identity, function, and mechanism of the ceRNAs will not only further our fundamental understanding of RNA-mediated cancer pathogenesis, but may also shed light on the development of new RNA-based therapeutic strategies for treating cancer.
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Affiliation(s)
- Yunfei Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jiakai Hou
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dandan He
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yonghao Yu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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548
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Guarnerio J, Bezzi M, Jeong J, Paffenholz S, Berry K, Naldini M, Lo-Coco F, Tay Y, Beck A, Pandolfi P. Oncogenic Role of Fusion-circRNAs Derived from Cancer-Associated Chromosomal Translocations. Cell 2016; 165:289-302. [DOI: 10.1016/j.cell.2016.03.020] [Citation(s) in RCA: 329] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/18/2015] [Accepted: 03/10/2016] [Indexed: 02/07/2023]
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549
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Vidal AF, Sandoval GTV, Magalhães L, Santos SEB, Ribeiro-dos-Santos Â. Circular RNAs as a new field in gene regulation and their implications in translational research. Epigenomics 2016; 8:551-62. [PMID: 27035397 DOI: 10.2217/epi.16.3] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs are a class of long noncoding RNA that were recently rediscovered as diverse, highly abundant, conserved and naturally occurring RNAs in eukaryotes. They are characterized by their 5' and 3' covalently joined ends. Some studies have attributed functions for circular RNAs, such as miRNAs sponges and transcriptional regulators, indicating that they may be largely biomarkers of both physiological and pathological processes. Circular RNAs have the potential to play important roles in transcription and post-transcription, giving rise to a whole complexity level to gene expression regulation. In this review, we discuss the biogenesis of circular RNAs, their properties and functions as well as different methods for their identification and their role in some diseases.
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Affiliation(s)
- Amanda F Vidal
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Gloria T V Sandoval
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Leandro Magalhães
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Sidney E B Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém, Pará, Brazil.,Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, Pará, Brazil
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550
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Chen Y, Li C, Tan C, Liu X. Circular RNAs: a new frontier in the study of human diseases. J Med Genet 2016; 53:359-65. [PMID: 26945092 DOI: 10.1136/jmedgenet-2016-103758] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/08/2016] [Indexed: 02/05/2023]
Abstract
Circular RNAs (circRNAs) are recently discovered new endogenous non-coding RNAs and an area of much research activity. In addition to their potential as major gene regulators, reports are linking heterogeneous circRNA groups with many different human disorders, especially cancer. In this review, we focus on the rapidly advancing field of circRNAs that play a part in human diseases. We list tools (eg, public databases) that scan genome spans of interest to identify known circRNAs; describe the relationship between dysregulated circRNAs and human disease, highlighting their specific roles; and consider the possible use of current and potential circRNA research applications in treating human diseases. Specifically, we review the role of circRNAs as biomarkers, drug targets and therapeutic agents.
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Affiliation(s)
- Yonghua Chen
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng Li
- Rehabilitation Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chunlu Tan
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xubao Liu
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, Chengdu, China
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