1451
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Circular RNAs as Potential Biomarkers and Therapeutic Targets for Metabolic Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1134:177-191. [PMID: 30919338 DOI: 10.1007/978-3-030-12668-1_10] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Epidemiological studies provide evidence of a continuous rise in metabolic diseases throughout industrialized countries. Metabolic diseases are commonly associated with different abnormalities that hold a key role in the emergence and progression of frequent disorders including diabetes mellitus (DM), non-alcoholic fatty liver disease (NAFLD), obesity, metabolic syndrome and cardiovascular diseases. The burden of metabolic diseases is believed to arise through complex interaction between genetic and epigenetic factors, lifestyle changes and environmental exposure to triggering stimuli. The diagnosis and treatment of metabolic disorders continue to be an overwhelming challenge. Thus, the development of novel biomarkers may enhance the accuracy of the diagnosis at an early stage of the disease and allow effective intervention. Over the past decade, progress has been made in exploring the potential role of noncoding RNAs (ncRNAs) in the regulation of gene networks involved in metabolic diseases. A growing body of evidence now suggests that aberrant expression of circular RNAs (circRNAs) is relevant to the occurrence and development of metabolic diseases. Accordingly, circRNAs are proposed as predictive biomarkers and potential therapeutic targets for these diseases. As the field of circRNAs is rapidly evolving and knowledge is increasing, the present paper provides current understanding of the regulatory roles of these RNA species mainly in the pathogenesis of DM, NAFLD and obesity. Furthermore, some of the limitations to the promise of circRNAs and perspectives on their future research are discussed.
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1452
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Abstract
As a newly discovered type of RNA, circular RNAs (circRNAs) are widespread throughout the eukaryotic genome. The expression of circRNAs is regulated by both cis-elements and trans-factors, and the expression pattern of circRNAs is cell type- and disease-specific. Similar to other types of non-coding RNAs, functions of circRNAs are also versatile. CircRNAs have been reported previously to function as microRNA (miRNA) sponges, protein sponges, coding RNAs or scaffolds for protein complexes. Recently, several circRNAs have been reported to play important roles in human malignancies, including glioma. Here, we reviewed several reports related to circRNAs and glioma, as well as the potential diagnostic and therapeutic applications of circRNAs in brain cancer. In general, some circRNAs, such as circSMARCA5 and circCFH, are found to be expressed in a glioma-specific pattern, these circRNAs may be used as tumor biomarkers. In addition, some circRNAs have been found to play oncogenic roles in glioma (e.g., circNFIX and circNT5E), whereas others have been reported to function as tumor suppressors (e.g., circFBXW7 and circSHPRH). Furthermore, circRNA is a good tool for protein expression because of its higher stability compared to linear RNAs. Thus, circRNAs may also be an ideal choice for gene/protein delivery in future brain cancer therapies. There are some challenges in circRNA research in glioma and other diseases. Research related to circRNAs in glioma is comparatively new and many mysteries remain to be solved.
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Affiliation(s)
- Jinglei Liu
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou 510080, China
| | - Kun Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou 510080, China
| | - Nunu Huang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou 510080, China
| | - Nu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou 510080, China
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1453
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Networks of mRNA Processing and Alternative Splicing Regulation in Health and Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1157:1-27. [PMID: 31342435 DOI: 10.1007/978-3-030-19966-1_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
mRNA processing events introduce an intricate layer of complexity into gene expression processes, supporting a tremendous level of diversification of the genome's coding and regulatory potential, particularly in vertebrate species. The recent development of massive parallel sequencing methods and their adaptation to the identification and quantification of different RNA species and the dynamics of mRNA metabolism and processing has generated an unprecedented view over the regulatory networks that are established at this level, which contribute to sustain developmental, tissue specific or disease specific gene expression programs. In this chapter, we provide an overview of the recent evolution of transcriptome profiling methods and the surprising insights that have emerged in recent years regarding distinct mRNA processing events - from the 5' end to the 3' end of the molecule.
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1454
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Ashraf U, Benoit-Pilven C, Lacroix V, Navratil V, Naffakh N. Advances in Analyzing Virus-Induced Alterations of Host Cell Splicing. Trends Microbiol 2018; 27:268-281. [PMID: 30577974 DOI: 10.1016/j.tim.2018.11.004] [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: 07/17/2018] [Revised: 10/19/2018] [Accepted: 11/09/2018] [Indexed: 12/14/2022]
Abstract
Alteration of host cell splicing is a common feature of many viral infections which is underappreciated because of the complexity and technical difficulty of studying alternative splicing (AS) regulation. Recent advances in RNA sequencing technologies revealed that up to several hundreds of host genes can show altered mRNA splicing upon viral infection. The observed changes in AS events can be either a direct consequence of viral manipulation of the host splicing machinery or result indirectly from the virus-induced innate immune response or cellular damage. Analysis at a higher resolution with single-cell RNAseq, and at a higher scale with the integration of multiple omics data sets in a systems biology perspective, will be needed to further comprehend this complex facet of virus-host interactions.
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Affiliation(s)
- Usama Ashraf
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, F-75015 Paris, France; CNRS UMR3569, F-75015 Paris, France; Université Paris Diderot, Sorbonne Paris Cité EA302, F-75015 Paris, France
| | - Clara Benoit-Pilven
- INSERM U1028; CNRS UMR5292, Lyon Neuroscience Research Center, Genetic of Neuro-development Anomalies Team, F-69000 Lyon, France; Université Claude Bernard Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; EPI ERABLE, INRIA Grenoble Rhône-Alpes, F-38330 Montbonnot Saint-Martin, France
| | - Vincent Lacroix
- Université Claude Bernard Lyon 1, CNRS UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622 Villeurbanne, France; EPI ERABLE, INRIA Grenoble Rhône-Alpes, F-38330 Montbonnot Saint-Martin, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Université Claude Bernard Lyon 1, F-69000 Lyon, France; European Virus Bioinformatics Center, Leutragraben 1, D-07743 Jena, Germany
| | - Nadia Naffakh
- Institut Pasteur, Unité de Génétique Moléculaire des Virus à ARN, Département de Virologie, F-75015 Paris, France; CNRS UMR3569, F-75015 Paris, France; Université Paris Diderot, Sorbonne Paris Cité EA302, F-75015 Paris, France.
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1455
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Yang L, Fu J, Zhou Y. Circular RNAs and Their Emerging Roles in Immune Regulation. Front Immunol 2018; 9:2977. [PMID: 30619334 PMCID: PMC6305292 DOI: 10.3389/fimmu.2018.02977] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/04/2018] [Indexed: 01/16/2023] Open
Abstract
Circular ribonucleic acid (RNA) molecules (circRNAs) are covalently closed loop RNA molecules with no 5' end caps or 3' poly (A) tails, which are generated by back-splicing. Originally, circRNAs were considered to be byproducts of aberrant splicing. However, in recent years, development of high-throughput sequencing has led to gradual recognition of functional circRNAs, and increasing numbers of studies have elucidated their roles in cancer, neurologic diseases, and cardiovascular disorders. Nevertheless, studies of the functions of circRNAs in the immune system are relatively scarce. In this review, we detail relevant research on the biogenesis and classification of circRNAs, describe their functional mechanisms and approaches to their investigation, and summarize recent studies of circRNA function in the immune system.
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Affiliation(s)
- Lan Yang
- Children's Hospital and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jinrong Fu
- Children's Hospital and Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yufeng Zhou
- Children's Hospital and Institute of Biomedical Sciences, Fudan University, Shanghai, China.,Key Laboratory of Neonatal Diseases, Ministry of Health, Shanghai, China
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1456
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Liu G, Huang K, Jie Z, Wu Y, Chen J, Chen Z, Fang X, Shen S. CircFAT1 sponges miR-375 to promote the expression of Yes-associated protein 1 in osteosarcoma cells. Mol Cancer 2018; 17:170. [PMID: 30514309 PMCID: PMC6280518 DOI: 10.1186/s12943-018-0917-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/19/2018] [Indexed: 12/16/2022] Open
Abstract
Background There is an urgent need to identify new molecular targets for treatment of osteosarcoma. Circular RNAs are a class of endogenous RNAs that are extensively found in mammalian cells and exert critical functions in the regulation of gene expression, but in osteosarcoma the underlying molecular mechanism of circular RNAs remain poorly understood. Here we assessed the tumorigenesis properties of a circular RNA, circFAT1 in osteosarcoma. Methods The effects of circFAT1/miR-375/YAP1 was evaluated on human osteosarcoma cells growth, apoptosis, migration, invasion and tumorigenesis. Signaling pathways were analyzed by western blotting, qRT-PCR, fluorescence in situ hybridization, chromogenic in situ hybridization,RNA Binding Protein Immunoprecipitation and immunofluorescence. The consequence of circFAT1 short hairpin RNA combined or not with miR-375 sponge was evaluated in mice bearing 143B xenografts on tumor growth. Results In this study, we observed significant upregulation of circFAT1 originating from exon 2 of the FAT1 gene in human osteosarcoma tissues and cell lines. Inhibition of circFAT1 effectively prevented the migration, invasion, and tumorigenesis of osteosarcoma cells in vitro and repressed osteosarcoma growth in vivo. Mechanistic studies revealed that circFAT1 contains a binding site for the microRNA-375 (miR-375) and can abundantly sponge miR-375 to upregulate the expression of Yes-associated protein 1. Moreover, inhibition of miR-375 reversed attenuation of cell proliferation, migration, and invasion, which was induced by circFAT1 knockdown, and therefore promoted tumorigenesis. Conclusions Our findings demonstrate a novel function of circFAT1 in tumorigenesis and suggest a new therapeutic target for the treatment of osteosarcoma. Electronic supplementary material The online version of this article (10.1186/s12943-018-0917-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gang Liu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China
| | - Kangmao Huang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China
| | - Zhiwei Jie
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China
| | - Yizheng Wu
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China
| | - Junxin Chen
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China
| | - Zizheng Chen
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China
| | - Xiangqian Fang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China. .,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.
| | - Shuying Shen
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, Sir Run Run Shaw Institute of Clinical Medicine of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China. .,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Sir Run Run Shaw Hospital, Medical College of Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China.
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1457
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Watanabe T, Kimura A, Kuroyanagi H. Alternative Splicing Regulator RBM20 and Cardiomyopathy. Front Mol Biosci 2018; 5:105. [PMID: 30547036 PMCID: PMC6279932 DOI: 10.3389/fmolb.2018.00105] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/09/2018] [Indexed: 12/17/2022] Open
Abstract
RBM20 is a vertebrate-specific RNA-binding protein with two zinc finger (ZnF) domains, one RNA-recognition motif (RRM)-type RNA-binding domain and an arginine/serine (RS)-rich region. RBM20 has initially been identified as one of dilated cardiomyopathy (DCM)-linked genes. RBM20 is a regulator of heart-specific alternative splicing and Rbm20ΔRRM mice lacking the RRM domain are defective in the splicing regulation. The Rbm20ΔRRM mice, however, do not exhibit a characteristic DCM-like phenotype such as dilatation of left ventricles or systolic dysfunction. Considering that most of the RBM20 mutations identified in familial DCM cases were heterozygous missense mutations in an arginine-serine-arginine-serine-proline (RSRSP) stretch whose phosphorylation is crucial for nuclear localization of RBM20, characterization of a knock-in animal model is awaited. One of the major targets for RBM20 is the TTN gene, which is comprised of the largest number of exons in mammals. Alternative splicing of the TTN gene is exceptionally complicated and RBM20 represses >160 of its consecutive exons, yet detailed mechanisms for such extraordinary regulation are to be elucidated. The TTN gene encodes the largest known protein titin, a multi-functional sarcomeric structural protein specific to striated muscles. As titin is the most important factor for passive tension of cardiomyocytes, extensive heart-specific and developmentally regulated alternative splicing of the TTN pre-mRNA by RBM20 plays a critical role in passive stiffness and diastolic function of the heart. In disease models with diastolic dysfunctions, the phenotypes were rescued by increasing titin compliance through manipulation of the Ttn pre-mRNA splicing, raising RBM20 as a potential therapeutic target.
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Affiliation(s)
- Takeshi Watanabe
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Psychosomatic Dentistry, Graduate School of Medical and Dental Science, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akinori Kimura
- Division of Pathology, Department of Molecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Laboratory for Integrated Research Projects on Intractable Diseases Advanced Technology Laboratories, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Laboratory for Integrated Research Projects on Intractable Diseases Advanced Technology Laboratories, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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1458
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Sun X, Jin Y, Liang Q, Tang J, Chen J, Yu Q, Li F, Li Y, Wu J, Wu S. Altered expression of circular RNAs in human placental chorionic plate-derived mesenchymal stem cells pretreated with hypoxia. J Clin Lab Anal 2018; 33:e22825. [PMID: 30485544 DOI: 10.1002/jcla.22825] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/04/2018] [Accepted: 11/04/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Hypoxic preconditioning alters the biological properties of mesenchymal stem cells (MSCs). It is not known whether this process has an effect on circular RNAs (circRNAs) in MSCs. METHODS Human placental chorionic plate-derived MSCs (hpcpMSCs) isolated from the same placentae were classed into two groups: hypoxic pretreated (hypoxia) group and normally cultured (normoxia) group. The comparative circRNA microarray analysis was used to determine circRNAs expression and verified by quantitative reverse-transcription polymerase chain reaction (qRT-PCR) in the two groups. RESULTS One hundred and two differentially expressed circRNAs in the hypoxia group were found compared to that in the normoxia group (fold change >1.5-fold and P < 0.05). The expression levels of circRNAs by qRT-PCR were consistent with those evaluated by microarray analysis. Gene ontology (GO) analysis showed that the putative function of their target genes for those differentially expressed circRNAs was primarily involved in cell development and its differentiation and regulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that transcriptional misregulation in cancer and mitogen-activated protein kinase (MAPK) signaling pathway were the most significant. MAPK signaling pathway was found to be the core regulatory pathway triggered by hypoxia. CONCLUSIONS The results indicate that the altered expression of specific circRNAs in MSCs is associated with hypoxic preconditioning. This finding provides further exploration of underlying mechanisms of the characteristic changes of MSCs with hypoxic preconditioning.
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Affiliation(s)
- Xunsha Sun
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yulin Jin
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qihua Liang
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jie Tang
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jinsong Chen
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiuxia Yu
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fatao Li
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yan Li
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jieying Wu
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Shaoqing Wu
- Guangzhou Women and Children's Medical Center, Sun Yat-sen University, Guangzhou, China.,Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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1459
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Chu Q, Bai P, Zhu X, Zhang X, Mao L, Zhu QH, Fan L, Ye CY. Characteristics of plant circular RNAs. Brief Bioinform 2018; 21:135-143. [PMID: 30445438 DOI: 10.1093/bib/bby111] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/25/2018] [Accepted: 10/12/2018] [Indexed: 11/14/2022] Open
Abstract
Circular RNA (circRNA) is a kind of covalently closed single-stranded RNA molecules that have been proved to play important roles in transcriptional regulation of genes in diverse species. With the rapid development of bioinformatics tools, a huge number (95143) of circRNAs have been identified from different plant species, providing an opportunity for uncovering the overall characteristics of plant circRNAs. Here, based on publicly available circRNAs, we comprehensively analyzed characteristics of plant circRNAs with the help of various bioinformatics tools as well as in-house scripts and workflows, including the percentage of coding genes generating circRNAs, the frequency of alternative splicing events of circRNAs, the non-canonical splicing signals of circRNAs and the networks involving circRNAs, miRNAs and mRNAs. All this information has been integrated into an upgraded online database, PlantcircBase 3.0 (http://ibi.zju.edu.cn/plantcircbase/). In this database, we provided browse, search and visualization tools as well as a web-based blast tool, BLASTcirc, for prediction of circRNAs from query sequences based on searching against plant genomes and transcriptomes.
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Affiliation(s)
- Qinjie Chu
- Institute of Crop Science, Zhejiang University, Hangzhou, China.,Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Panpan Bai
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Xintian Zhu
- Institute of Crop Science, Zhejiang University, Hangzhou, China.,Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Xingchen Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Lingfeng Mao
- Institute of Crop Science, Zhejiang University, Hangzhou, China.,Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | | | - Longjiang Fan
- Institute of Crop Science, Zhejiang University, Hangzhou, China.,Institute of Bioinformatics, Zhejiang University, Hangzhou, China
| | - Chu-Yu Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, China
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1460
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Wang S, Li Q, Wang Y, Li X, Wang R, Kang Y, Xue X, Meng R, Wei Q, Feng X. Upregulation of circ-UBAP2 predicts poor prognosis and promotes triple-negative breast cancer progression through the miR-661/MTA1 pathway. Biochem Biophys Res Commun 2018; 505:996-1002. [PMID: 30314706 DOI: 10.1016/j.bbrc.2018.10.026] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023]
Abstract
Recently, a large number of studies have shown that circular RNA (circRNA) is involved in the development and progression of human cancer. However, its role in triple-negative breast cancer (TNBC) remains largely unknown. In this study, a novel circRNA, circ-UBAP2 (hsa_circ_0001846), was shown to be markedly upregulated in TNBC. Moreover, high circ-UBAP2 expression was closely associated with larger tumour size (p = 0.003), advanced TNM stage (p = 0.005), lymph node metastasis (p = 0.002), and unfavourable prognosis (p = 0.0256). Functionally, lentivirus-mediated stable knockdown of circ-UBAP2 dramatically weakened the ability of TNBC cells to proliferate and migrate and induced apoptosis in vitro and in vivo. Regarding the mechanism, we found that circ-UBAP2 was mainly observed in the cytoplasm and was capable of sponging miRNA-661 to increase the expression of the oncogene MTA1. Additionally, silencing of miRNA-661 or overexpression of MTA1 could partially rescue the attenuated malignant phenotype caused by circ-UBAP2 knockdown. Taken together, our data reveal that circ-UBAP2 plays a vital regulatory role in TNBC via the miR-661/MTA1 axis and may serve as a promising therapeutic target for TNBC patients.
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Affiliation(s)
- Shengting Wang
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China
| | - Qian Li
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China
| | - Yufang Wang
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China
| | - Xiaoming Li
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China
| | - Rui Wang
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China
| | - Yuhua Kang
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China
| | - Xukai Xue
- Department of Spine Surgery, Honghui Hospital, Xi'an Jiaotong University, 710054, China
| | - Rui Meng
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China
| | - Qi Wei
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China
| | - Xinghua Feng
- Department of Clinical Medicine, Peihua University, Xi'an, 710125, China.
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1461
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Greco S, Cardinali B, Falcone G, Martelli F. Circular RNAs in Muscle Function and Disease. Int J Mol Sci 2018; 19:ijms19113454. [PMID: 30400273 PMCID: PMC6274904 DOI: 10.3390/ijms19113454] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of RNA produced during pre-mRNA splicing that are emerging as new members of the gene regulatory network. In addition to being spliced in a linear fashion, exons of pre-mRNAs can be circularized by use of the 3' acceptor splice site of upstream exons, leading to the formation of circular RNA species. In this way, genetic information can be re-organized, increasing gene expression potential. Expression of circRNAs is developmentally regulated, tissue and cell-type specific, and shared across eukaryotes. The importance of circRNAs in gene regulation is now beginning to be recognized and some putative functions have been assigned to them, such as the sequestration of microRNAs or proteins, the modulation of transcription, the interference with splicing, and translation of small proteins. In accordance with an important role in normal cell biology, circRNA deregulation has been reported to be associated with diseases. Recent evidence demonstrated that circRNAs are highly expressed in striated muscle tissue, both skeletal and cardiac, that is also one of the body tissue showing the highest levels of alternative splicing. Moreover, initial studies revealed altered circRNA expression in diseases involving striated muscle, suggesting important functions of these molecules in the pathogenetic mechanisms of both heart and skeletal muscle diseases. The recent findings in this field will be described and discussed.
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Affiliation(s)
- Simona Greco
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, 00015 Rome, Italy.
| | - Germana Falcone
- Institute of Cell Biology and Neurobiology, National Research Council, Monterotondo, 00015 Rome, Italy.
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS-Policlinico San Donato, San Donato Milanese, 20097 Milan, Italy.
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1462
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Tang W, Fu K, Sun H, Rong D, Wang H, Cao H. CircRNA microarray profiling identifies a novel circulating biomarker for detection of gastric cancer. Mol Cancer 2018; 17:137. [PMID: 30236115 PMCID: PMC6147053 DOI: 10.1186/s12943-018-0888-8] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/12/2018] [Indexed: 12/17/2022] Open
Abstract
CircRNA expression profiles for gastric cancer (GC) were screened using plasma samples from 10 GC patients with different TNM stages and 5 healthy individuals as controls. Results showed lower expression of circ-KIAA1244 in GC tissues, plasmas, and cells compare to normal controls. Further clinical data analysis demonstrated that a decreased expression of circ-KIAA1244 in plasmas was negatively correlated with TNM stage and lymphatic metastasis, and a shorter overall survival time of GC patients. Moreover, we found that circ-KIAA1244 could be detected in GC plasma exosomes and showed no obvious significance compared to the expression level in the corresponding plasmas. This study revealed a GC-tissues-derived circ-KIAA1244 could serve a novel circulating biomarker for detection of GC.
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Affiliation(s)
- Weiwei Tang
- Department of general surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Kai Fu
- Department of general surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Handong Sun
- Department of general surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dawei Rong
- Department of general surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hanjin Wang
- Department of general surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
| | - Hongyong Cao
- Department of general surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
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1463
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Affiliation(s)
- Asfar S Azmi
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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1464
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Dong R, Ma XK, Li GW, Yang L. CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:226-233. [PMID: 30172046 PMCID: PMC6203687 DOI: 10.1016/j.gpb.2018.08.001] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Revised: 07/17/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) from back-splicing of exon(s) have been recently identified to be broadly expressed in eukaryotes, in tissue- and species-specific manners. Although functions of most circRNAs remain elusive, some circRNAs are shown to be functional in gene expression regulation and potentially relate to diseases. Due to their stability, circRNAs can also be used as biomarkers for diagnosis. Profiling circRNAs by integrating their expression among different samples thus provides molecular basis for further functional study of circRNAs and their potential application in clinic. Here, we report CIRCpedia v2, an updated database for comprehensive circRNA annotation from over 180 RNA-seq datasets across six different species. This atlas allows users to search, browse, and download circRNAs with expression features in various cell types/tissues, including disease samples. In addition, the updated database incorporates conservation analysis of circRNAs between humans and mice. Finally, the web interface also contains computational tools to compare circRNA expression among samples. CIRCpedia v2 is accessible at http://www.picb.ac.cn/rnomics/circpedia.
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Affiliation(s)
- Rui Dong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xu-Kai Ma
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Wei Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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1465
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Jiao J, Gao T, Shi H, Sheng A, Xiang Y, Shu Y, Li G. A method to directly assay circRNA in real samples. Chem Commun (Camb) 2018; 54:13451-13454. [DOI: 10.1039/c8cc08319c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
‘MicroRNA sponge’ and duplex-specific nuclease (DSN)-assisted signal amplification were employed to propose a method for direct assay of circular RNA (circRNA) in real samples, which is rapid, sensitive, and easy to operate.
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Affiliation(s)
- Jin Jiao
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences
- Department of Biochemistry
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Tao Gao
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences
- Department of Biochemistry
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Hai Shi
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences
- Department of Biochemistry
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Anzhi Sheng
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai
- P. R. China
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences
- Department of Biochemistry
- Nanjing University
- Nanjing 210093
- P. R. China
| | - Yongqian Shu
- Department of Oncology
- The First Affiliated Hospital of Nanjing Medical University
- Nanjing 210029
- P. R. China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences
- Department of Biochemistry
- Nanjing University
- Nanjing 210093
- P. R. China
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