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Zou M, Huang C, Li X, He X, Chen Y, Liao W, Liao Y, Sun J, Liu Z, Zhong L, Bin J. Circular RNA expression profile and potential function of hsa_circRNA_101238 in human thoracic aortic dissection. Oncotarget 2017; 8:81825-81837. [PMID: 29137225 PMCID: PMC5669851 DOI: 10.18632/oncotarget.18998] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 06/18/2017] [Indexed: 12/29/2022] Open
Abstract
Objective To assess the circular RNAs (circRNAs) expression profile and explore the potential functions in human thoracic aortic dissection (TAD). Methods The differentially expressed circRNAs profiles of the aortic segments between human type A TAD patients (n=3) and age-matched normal donors (NA; n=3) were analyzed using the Arraystar human circRNAs microarray. Quantitative real-time PCR was used to validate the expression pattern of circRNAs, parental genes, and hsa-miR-320a; Western blotting confirmed MMP9 expression with additional samples. Bioinformatic tools including network analysis, Gene ontology, and KEGG pathway analysis were utilized. Results Among 8,173 detected circRNA genes, 156 upregulated and 106 downregulated significantly in human TAD as compared to NA (P£0.05). Quantitative real-time PCR showed an elevated expression of the upregulated hsa_circRNA_101238, hsa_circRNA_104634, hsa_circRNA_002271, hsa_circRNA_102771, hsa_circRNA_104349, COL1A1, and COL6A3 and reduced of the downregulated hsa_circRNA_102683, hsa_circRNA_005525, hsa_circRNA_103458, and FLNA. Gene ontology analysis revealed that the parental genes favored several pathological processes, such as negative regulation of cell proliferation and extracellular matrix organization. The circRNA-miRNA co-expression network predicted that 33 circRNAs might interact with at least one target miRNAs altered in TAD. KEGG pathway analysis revealed that 28 altered miRNAs were enriched on focal adhesion and vascular smooth muscle contraction. The hsa_circRNA_101238-miRNA-mRNA network indicated the highest degree of hsa-miR-320a. Quantitative real-time PCR and Western blot manifested the low expression of hsa-miR-320a and high of MMP9 in human TAD tissues, respectively. Conclusions This study revealed hundreds of differentially expressed circular RNAs in human TAD, suggesting that hsa_circRNA_101238 might inhibit the expression of hsa-miR-320a and increase that of MMP9 in TAD.
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Affiliation(s)
- Meisheng Zou
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Wards of Cadres, Guangzhou General Hospital of Guangzhou Military Region, Guangzhou, China
| | - Chixiong Huang
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xinzhong Li
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiang He
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanmei Chen
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wangjun Liao
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yulin Liao
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jie Sun
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Cardiology, Zhongshan Hospital, Sun Yat-Sen University, Zhongshan, China
| | - Ze Liu
- Wards of Cadres, Guangzhou General Hospital of Guangzhou Military Region, Guangzhou, China
| | - Lintao Zhong
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jianping Bin
- Department of Cardiology, State Key Laboratory of Organ Failure Research, Nanfang Hospital, Southern Medical University, Guangzhou, China
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2152
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Chen LL, Yang L. ALU ternative Regulation for Gene Expression. Trends Cell Biol 2017; 27:480-490. [DOI: 10.1016/j.tcb.2017.01.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/14/2016] [Accepted: 01/05/2017] [Indexed: 12/23/2022]
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2153
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Huang S, Yang B, Chen BJ, Bliim N, Ueberham U, Arendt T, Janitz M. The emerging role of circular RNAs in transcriptome regulation. Genomics 2017; 109:401-407. [PMID: 28655641 DOI: 10.1016/j.ygeno.2017.06.005] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/19/2017] [Accepted: 06/22/2017] [Indexed: 01/01/2023]
Abstract
Circular RNAs (circRNAs) are a recently discovered form of RNA that has been found to regulate mammalian transcription. CircRNAs are covalently closed, single-stranded transcripts produced from precursor mRNA. While initially circRNAs were considered to be splicing artefacts, next-generation RNA sequencing of non-polyadenylated transcriptomes has recently shown that the expression of circRNAs is widespread and over 20% of expressed genes in examined cells and tissues can produce these transcripts. Until now thousands of circRNAs have been discovered in organisms ranging from Drosophila melanogaster to Homo sapiens. Functional studies indicate that these transcripts regulate expression of protein-coding linear transcripts and thus comprise an important component of gene expression regulation. Here we provide a comprehensive overview on the biology of circRNAs, including the expression patterns and function. Moreover, we discuss current methodologies for the discovery and validation of circular transcripts. Finally, perspectives on the utilization of circRNA as molecular markers of complex diseases are presented.
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Affiliation(s)
- S Huang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - B Yang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - B J Chen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - N Bliim
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - U Ueberham
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - T Arendt
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, Leipzig, Germany
| | - M Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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2154
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Abstract
Long noncoding RNAs (lncRNAs) are emerging as potential key regulators in gene expression networks and exhibit a surprising range of shapes and sizes. Several distinct classes of lncRNAs are transcribed from different DNA elements, including promoters, enhancers, and intergenic regions in eukaryotic genomes. Additionally, others are derived from long primary transcripts with noncanonical RNA processing pathways, generating new RNA species with unexpected formats. These lncRNAs can be processed by several mechanisms, including ribonuclease P (RNase P) cleavage to generate mature 3' ends, capping by small nucleolar RNA (snoRNA)-protein (snoRNP) complexes at their ends, or the formation of circular structures. Here we review current knowledge on lncRNAs and highlight the most recent discoveries of the underlying mechanisms related to their formation.
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Affiliation(s)
- Huang Wu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
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2155
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Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L, Chen LL. Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection. Mol Cell 2017. [PMID: 28625552 DOI: 10.1016/j.molcel.2017.05.023] [Citation(s) in RCA: 476] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Circular RNAs (circRNAs) generated via back-splicing are enhanced by flanking complementary sequences. Expression levels of circRNAs vary under different conditions, suggesting participation of protein factors in their biogenesis. Using genome-wide siRNA screening that targets all human unique genes and an efficient circRNA expression reporter, we identify double-stranded RNA-binding domain containing immune factors NF90/NF110 as key regulators in circRNA biogenesis. NF90/NF110 promote circRNA production in the nucleus by associating with intronic RNA pairs juxtaposing the circRNA-forming exon(s); they also interact with mature circRNAs in the cytoplasm. Upon viral infection, circRNA expression is decreased, in part owing to the nuclear export of NF90/NF110 to the cytoplasm. Meanwhile, NF90/NF110 released from circRNP complexes bind to viral mRNAs as part of their functions in antiviral immune response. Our results therefore implicate a coordinated regulation of circRNA biogenesis and function by NF90/NF110 in viral infection.
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Affiliation(s)
- Xiang Li
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Chu-Xiao Liu
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Wei Xue
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yang Zhang
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shan Jiang
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Qing-Fei Yin
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jia Wei
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Run-Wen Yao
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Li Yang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology and Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.
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2156
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Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proc Natl Acad Sci U S A 2017; 114:E5207-E5215. [PMID: 28611215 DOI: 10.1073/pnas.1617467114] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Alternative RNA splicing plays an important role in cancer. To determine which factors involved in RNA processing are essential in prostate cancer, we performed a genome-wide CRISPR/Cas9 knockout screen to identify the genes that are required for prostate cancer growth. Functional annotation defined a set of essential spliceosome and RNA binding protein (RBP) genes, including most notably heterogeneous nuclear ribonucleoprotein L (HNRNPL). We defined the HNRNPL-bound RNA landscape by RNA immunoprecipitation coupled with next-generation sequencing and linked these RBP-RNA interactions to changes in RNA processing. HNRNPL directly regulates the alternative splicing of a set of RNAs, including those encoding the androgen receptor, the key lineage-specific prostate cancer oncogene. HNRNPL also regulates circular RNA formation via back splicing. Importantly, both HNRNPL and its RNA targets are aberrantly expressed in human prostate tumors, supporting their clinical relevance. Collectively, our data reveal HNRNPL and its RNA clients as players in prostate cancer growth and potential therapeutic targets.
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2157
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Wu AR, Wang J, Streets AM, Huang Y. Single-Cell Transcriptional Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:439-462. [PMID: 28301747 DOI: 10.1146/annurev-anchem-061516-045228] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented. In this review, we provide a broad introduction to this revolutionary technology by presenting the state-of-the-art in sample preparation methodologies, technology platforms, and computational analysis methods, while highlighting the key considerations for designing, executing, and interpreting a study using single-cell RNA sequencing.
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Affiliation(s)
- Angela R Wu
- Division of Life Science and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China;
| | - Jianbin Wang
- School of Life Sciences and Center for Life Sciences, Tsinghua University, Beijing 100084, China;
| | - Aaron M Streets
- Department of Bioengineering, University of California, Berkeley, California 94720;
| | - Yanyi Huang
- Biodynamic Optical Imaging Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Engineering, and Center for Life Sciences, Peking University, Beijing 100871, China;
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2158
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Normal and altered pre-mRNA processing in the DMD gene. Hum Genet 2017; 136:1155-1172. [DOI: 10.1007/s00439-017-1820-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022]
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2159
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Zheng Y, Li X, Huang Y, Jia L, Li W. The Circular RNA Landscape of Periodontal Ligament Stem Cells During Osteogenesis. J Periodontol 2017; 88:906-914. [PMID: 28598284 DOI: 10.1902/jop.2017.170078] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The present study aims to investigate the distinct expression pattern of circular RNAs (circRNAs) in periodontal ligament stem cells (PDLSCs) during osteogenesis. METHODS PDLSCs were isolated and cultured in osteogenic medium. Total RNA was extracted from cells at day 0 (D0), day 3 (D3), day 7 (D7), and day 14 (D14) and submitted to RNA-sequencing to detect expression profiles of circRNAs, messenger RNAs (mRNAs), and microRNAs (miRNAs). Real-time quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed to validate expression of circRNAs and miRNAs. Differential expression analysis and gene ontology analysis were performed. A circRNA-miRNA-mRNA network was constructed to reveal the potential regulatory role of circRNAs. RESULTS A total of 12,693 circRNA transcripts were detected, and circRNAs displayed stage-specific expression. Expression of four well-known circRNAs was validated by qRT-PCR. In total, 118 circRNAs were differentially expressed at D3, 128 circRNAs were differentially expressed at D7, and 139 circRNAs were differentially expressed at D14 compared with D0. Host genes of differentially expressed circRNAs were enriched in cytoplasmic or membrane-bound vesicles and extracellular matrix, indicating their potential roles in modulating biogenesis of extracellular vesicles. Moreover, mRNAs that were potentially regulated by circRNAs were enriched in bone-formation-associated processes, including extracellular matrix organization, cell differentiation, and bone morphogenetic protein signaling pathway. CONCLUSION Expression profiles of circRNAs were significantly altered during osteogenic differentiation of PDLSCs, providing a clue for future studies on the role of circRNAs in osteoblast differentiation.
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Affiliation(s)
- Yunfei Zheng
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Xiaobei Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Yiping Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Lingfei Jia
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology.,Department of Central Laboratory, Peking University School and Hospital of Stomatology
| | - Weiran Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
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2160
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Abstract
Circular RNA (circRNA) is mainly generated by the splice donor of a downstream exon joining to an upstream splice acceptor, a phenomenon known as backsplicing. It has been reported that circRNA can function as microRNA (miRNA) sponges, transcriptional regulators, or potential biomarkers. The availability of massive non-polyadenylated transcriptomes data has facilitated the genome-wide identification of thousands of circRNAs. Several circRNA detection tools or pipelines have recently been developed, and it is essential to provide useful guidelines on these pipelines for users, including a comprehensive and unbiased comparison. Here, we provide an improved and easy-to-use circRNA read simulator that can produce mimicking backsplicing reads supporting circRNAs deposited in CircBase. Moreover, we compared the performance of 11 circRNA detection tools on both simulated and real datasets. We assessed their performance regarding metrics such as precision, sensitivity, F1 score, and Area under Curve. It is concluded that no single method dominated on all of these metrics. Among all of the state-of-the-art tools, CIRI, CIRCexplorer, and KNIFE, which achieved better balanced performance between their precision and sensitivity, compared favorably to the other methods.
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Affiliation(s)
- Xiangxiang Zeng
- School of Information Science and Engineering, Xiamen University, Xiamen, China
| | - Wei Lin
- School of Information Science and Engineering, Xiamen University, Xiamen, China
| | - Maozu Guo
- School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, China
- * E-mail:
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2161
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Greene J, Baird AM, Brady L, Lim M, Gray SG, McDermott R, Finn SP. Circular RNAs: Biogenesis, Function and Role in Human Diseases. Front Mol Biosci 2017. [PMID: 28634583 PMCID: PMC5459888 DOI: 10.3389/fmolb.2017.00038] [Citation(s) in RCA: 426] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs (circRNAs) are currently classed as non-coding RNA (ncRNA) that, unlike linear RNAs, form covalently closed continuous loops and act as gene regulators in mammals. They were originally thought to represent errors in splicing and considered to be of low abundance, however, there is now an increased appreciation of their important function in gene regulation. circRNAs are differentially generated by backsplicing of exons or from lariat introns. Unlike linear RNA, the 3' and 5' ends normally present in an RNA molecule have been joined together by covalent bonds leading to circularization. Interestingly, they have been found to be abundant, evolutionally conserved and relatively stable in the cytoplasm. These features confer numerous potential functions to circRNAs, such as acting as miRNA sponges, or binding to RNA-associated proteins to form RNA-protein complexes that regulate gene transcription. It has been proposed that circRNA regulate gene expression at the transcriptional or post-transcriptional level by interacting with miRNAs and that circRNAs may have a role in regulating miRNA function in cancer initiation and progression. circRNAs appear to be more often downregulated in tumor tissue compared to normal tissue and this may be due to (i) errors in the back-splice machinery in malignant tissues, (ii) degradation of circRNAs by deregulated miRNAs in tumor tissue, or (iii) increasing cell proliferation leading to a reduction of circRNAs. circRNAs have been identified in exosomes and more recently, chromosomal translocations in cancer have been shown to generate aberrant fusion-circRNAs associated with resistance to drug treatments. In addition, though originally thought to be non-coding, there is now increasing evidence to suggest that select circRNAs can be translated into functional proteins. Although much remains to be elucidated about circRNA biology and mechanisms of gene regulation, these ncRNAs are quickly emerging as potential disease biomarkers and therapeutic targets in cancer.
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Affiliation(s)
- John Greene
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College DublinDublin, Ireland.,Department of Medical Oncology, Tallaght HospitalDublin, Ireland
| | - Anne-Marie Baird
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College DublinDublin, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's HospitalDublin, Ireland.,Department of Clinical Medicine, Trinity College DublinDublin, Ireland.,Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Queensland University of TechnologyBrisbane, QLD, Australia
| | - Lauren Brady
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College DublinDublin, Ireland
| | - Marvin Lim
- Department of Medical Oncology, St. Vincent's University HospitalDublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's HospitalDublin, Ireland.,Department of Clinical Medicine, Trinity College DublinDublin, Ireland.,HOPE Directorate, St. James's HospitalDublin, Ireland.,Labmed Directorate, St. James's HospitalDublin, Ireland
| | - Raymond McDermott
- Department of Medical Oncology, Tallaght HospitalDublin, Ireland.,Department of Medical Oncology, St. Vincent's University HospitalDublin, Ireland
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, School of Medicine, Trinity College DublinDublin, Ireland.,Thoracic Oncology Research Group, Trinity Translational Medical Institute, St. James's HospitalDublin, Ireland.,Department of Clinical Medicine, Trinity College DublinDublin, Ireland.,Department of Histopathology, St. James's HospitalDublin, Ireland
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2162
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Circular RNAs: A novel type of biomarker and genetic tools in cancer. Oncotarget 2017; 8:64551-64563. [PMID: 28969093 PMCID: PMC5610025 DOI: 10.18632/oncotarget.18350] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/23/2017] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs (circRNAs) are a novel type of universal and diverse endogenous noncoding RNAs (ncRNAs) and they form a covalently closed continuous loop without 5′ or 3′ tails unlike linear RNAs. Most circRNAs are presented with characteristics of abundance, stability, conservatism, and often exhibiting tissue/developmental-stage-specific expression. CircRNAs are generated either from exons or introns by back splicing or lariat introns. CircRNAs play important roles as miRNA sponges, gene transcription and expression regulators, RNA-binding protein (RBP) sponges and protein/peptide translators. Emerging evidence revealed the function of circRNAs in cancer and may potentially serve as a required novel biomarker and therapeutic target for cancer treatment. In this review, we discuss about the origins, characteristics and functions of circRNA and how they work as miRNA sponges, gene transcription and expression regulators, RBP sponges in cancer as well as current research methods of circRNAs, providing evidence for the significance of circRNAs in cancer diagnosis and clinical treatment.
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2163
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Microarray Analysis of Circular RNA Expression Profile Associated with 5-Fluorouracil-Based Chemoradiation Resistance in Colorectal Cancer Cells. BIOMED RESEARCH INTERNATIONAL 2017; 2017:8421614. [PMID: 28656150 PMCID: PMC5471554 DOI: 10.1155/2017/8421614] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Revised: 03/17/2017] [Accepted: 05/08/2017] [Indexed: 12/17/2022]
Abstract
Preoperative 5-fluorouracil- (5-FU-) based chemoradiotherapy is a standard treatment for locally advanced colorectal cancer (CRC). However, the effect of 5-FU-based chemoradiotherapy on CRC is limited due to the development of chemoradiation resistance (CRR), and the molecular mechanisms underlying this resistance are yet to be investigated. Recently, circular RNAs (circRNAs), which can function as microRNA sponges, were found to be involved in the development of several cancers. In this study, we focused on clarifying the modulation of the expression profiles of circRNAs in CRR. Microarray analysis identified 71 circRNAs differentially expressed in chemoradiation-resistant CRC cells. Among them, 47 were upregulated and 24 were downregulated by more than twofold. Furthermore, expression modulation of five representative circRNAs was validated by quantitative reverse transcription PCR (qRT-PCR). Moreover, these modulated circRNAs were predicted to interact with 355 miRNAs. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the most modulated circRNAs regulate several cancers and cancer-related pathways, and the possible mechanism underlying CRR was discussed. This is the first report revealing the circRNA modulations in 5-FU chemoradiation-resistant CRC cells by microarray. The study provided a useful database for further understanding CRR and presents potential targets to overcome CRR in CRC.
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2164
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Circular RNAs roll into the regulatory network of plants. Biochem Biophys Res Commun 2017; 488:382-386. [DOI: 10.1016/j.bbrc.2017.05.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 05/09/2017] [Indexed: 12/27/2022]
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2165
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Meng S, Zhou H, Feng Z, Xu Z, Tang Y, Li P, Wu M. CircRNA: functions and properties of a novel potential biomarker for cancer. Mol Cancer 2017; 16:94. [PMID: 28535767 PMCID: PMC5440908 DOI: 10.1186/s12943-017-0663-2] [Citation(s) in RCA: 1150] [Impact Index Per Article: 143.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 05/16/2017] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs, a novel class of endogenous noncoding RNAs, are characterized by their covalently closed loop structures without a 5′ cap or a 3′ Poly A tail. Although the mechanisms of circular RNAs’ generation and function are not fully clear, recent research has shown that circular RNAs may function as potential molecular markers for disease diagnosis and treatment and play an important role in the initiation and progression of human diseases, especially in tumours. This review summarizes some information about categories, biogenesis, functions at the molecular level, properties of circular RNAs and the possibility of circular RNAs as biomarkers in cancers.
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Affiliation(s)
- Shujuan Meng
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, 410008, China
| | - Hecheng Zhou
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, 410008, China
| | - Ziyang Feng
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, 410008, China
| | - Zihao Xu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, 410008, China
| | - Ying Tang
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, Hunan, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, 410008, China
| | - Peiyao Li
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, 410008, China
| | - Minghua Wu
- The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, 410008, China.
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2166
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Wu N, Jin L, Cai J. Profiling and bioinformatics analyses reveal differential circular RNA expression in hypertensive patients. Clin Exp Hypertens 2017; 39:454-459. [PMID: 28534714 DOI: 10.1080/10641963.2016.1273944] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Na Wu
- Department of Cardiology, Beijing Chao-yang Hospital, Capital Medical University, Beijing, China
| | - Ling Jin
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jun Cai
- Hypertension Center, Fuwai Hospital, State Key Laboratory of Cardiovascular Disease, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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2167
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Abebrese EL, Ali SH, Arnold ZR, Andrews VM, Armstrong K, Burns L, Crowder HR, Day RT, Hsu DG, Jarrell K, Lee G, Luo Y, Mugayo D, Raza Z, Friend K. Identification of human short introns. PLoS One 2017; 12:e0175393. [PMID: 28520720 PMCID: PMC5435141 DOI: 10.1371/journal.pone.0175393] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/26/2017] [Indexed: 01/08/2023] Open
Abstract
Canonical pre-mRNA splicing requires snRNPs and associated splicing factors to excise conserved intronic sequences, with a minimum intron length required for efficient splicing. Non-canonical splicing-intron excision without the spliceosome-has been documented; most notably, some tRNAs and the XBP1 mRNA contain short introns that are not removed by the spliceosome. There have been some efforts to identify additional short introns, but little is known about how many short introns are processed from mRNAs. Here, we report an approach to identify RNA short introns from RNA-Seq data, discriminating against small genomic deletions. We identify hundreds of short introns conserved among multiple human cell lines. These short introns are often alternatively spliced and are found in a variety of RNAs-both mRNAs and lncRNAs. Short intron splicing efficiency is increased by secondary structure, and we detect both canonical and non-canonical short introns. In many cases, splicing of these short introns from mRNAs is predicted to alter the reading frame and change protein output. Our findings imply that standard gene prediction models which often assume a lower limit for intron size fail to predict short introns effectively. We conclude that short introns are abundant in the human transcriptome, and short intron splicing represents an added layer to mRNA regulation.
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Affiliation(s)
- Emmanuel L. Abebrese
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Syed H. Ali
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Zachary R. Arnold
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Victoria M. Andrews
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Katharine Armstrong
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Lindsay Burns
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Hannah R. Crowder
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - R. Thomas Day
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Daniel G. Hsu
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Katherine Jarrell
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Grace Lee
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Yi Luo
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Daphine Mugayo
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Zain Raza
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
| | - Kyle Friend
- Department of Chemistry and Biochemistry, Washington and Lee University, Lexington, Virginia, United States of America
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2168
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Circular RNA mediates cardiomyocyte death via miRNA-dependent upregulation of MTP18 expression. Cell Death Differ 2017; 24:1111-1120. [PMID: 28498369 DOI: 10.1038/cdd.2017.61] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 03/15/2017] [Accepted: 03/31/2017] [Indexed: 12/29/2022] Open
Abstract
Circular RNAs (circRNAs) have important roles in several cellular processes. No study has established the pathophysiological role for circRNAs in the heart. Here, we show that a circRNA (mitochondrial fission and apoptosis-related circRNA (MFACR)) regulates mitochondrial fission and apoptosis in the heart by directly targeting and downregulating miR-652-3p; this in turn blocks mitochondrial fission and cardiomyocyte cell death by suppressing MTP18 translation. MTP18 deficiency reduces mitochondrial fission and suppresses cardiomyocyte apoptosis and MI. miR-652-3p directly downregulates MTP18 and attenuates mitochondrial fission, cardiomyocyte apoptosis, and MI in vitro and in vivo. MFACR directly sequesters miR-652-3p in the cytoplasm and inhibits its activity. MFACR knockdown in cardiomyocytes and mice attenuates mitochondrial fission and MI. Our results reveal a crucial role for circRNA in regulating mitochondrial dynamics and apoptosis in the heart; as such, circRNAs may serve as a potential therapeutic avenue for cardiovascular diseases.
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2169
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Abstract
The pervasive expression of circular RNAs (circRNAs) is a recently discovered feature of gene expression in highly diverged eukaryotes. Numerous algorithms that are used to detect genome-wide circRNA expression from RNA sequencing (RNA-seq) data have been developed in the past few years, but there is little overlap in their predictions and no clear gold-standard method to assess the accuracy of these algorithms. We review sources of experimental and bioinformatic biases that complicate the accurate discovery of circRNAs and discuss statistical approaches to address these biases. We conclude with a discussion of the current experimental progress on the topic.
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2170
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Hsiao KY, Sun HS, Tsai SJ. Circular RNA - New member of noncoding RNA with novel functions. Exp Biol Med (Maywood) 2017; 242:1136-1141. [PMID: 28485684 DOI: 10.1177/1535370217708978] [Citation(s) in RCA: 325] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A growing body of evidence indicates that circular RNAs are not simply a side product of splicing but a new class of noncoding RNAs in higher eukaryotes. The progression for the studies of circular RNAs is accelerated by combination of several advanced technologies such as next generation sequencing, gene silencing (small interfering RNAs) and editing (CRISPR/Cas9). More and more studies showed that dysregulated expression of circular RNAs plays critical roles during the development of several human diseases. Herein, we review the current advance of circular RNAs for their biosynthesis, molecular functions, and implications in human diseases. Impact statement The accumulating evidence indicate that circular RNA (circRNA) is a novel class of noncoding RNA with diverse molecular functions. Our review summarizes the current hypotheses for the models of circRNA biosynthesis including the direct interaction between upstream and downstream introns and lariat-driven circularization. In addition, molecular functions such as a decoy of microRNA (miRNA) termed miRNA sponge, transcriptional regulator, and protein-like modulator are also discussed. Finally, we reviewed the potential roles of circRNAs in neural system, cardiovascular system as well as cancers. These should provide insightful information for studying the regulation and functions of circRNA in other model of human diseases.
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Affiliation(s)
- Kuei-Yang Hsiao
- 1 Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - H Sunny Sun
- 2 Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shaw-Jenq Tsai
- 1 Department of Physiology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
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2171
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Zhao ZJ, Shen J. Circular RNA participates in the carcinogenesis and the malignant behavior of cancer. RNA Biol 2017; 14:514-521. [PMID: 26649774 PMCID: PMC5449088 DOI: 10.1080/15476286.2015.1122162] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 11/02/2015] [Accepted: 11/16/2015] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs) are long, non-coding RNAs that result from the non-canonical splicing of linear pre-mRNAs. However, the characteristics and the critical role of circRNA in co-/post-transcriptional regulation were not well recognized until the "microRNA sponge" function of circRNA is discovered. Recent studies have mainly been devoted to the function of the circular RNA sponge for miR-7 (ciRS-7) and sex-determining region Y (SRY) by targeting microRNA-7 (miR-7) and microRNA-138 (miR-138), respectively. In this review, we illustrate the specific role of circRNAs in a wide variety of cancers and in regulating the biological behavior of cancers via miR-7 or miR-138 regulation. Furthermore, circRNA, together with its gene silencing ability, also shows its potential in RNA interference (RNAi) therapy by binding to target RNAs, which provides a novel perspective in cancer treatment. Thus, this review concerns the biogenesis, biological function, oncogenesis, progression and possible therapies for cancer involving circRNAs.
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Affiliation(s)
- Zhen-Jun Zhao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jun Shen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
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2172
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Yao T, Chen Q, Fu L, Guo J. Circular RNAs: Biogenesis, properties, roles, and their relationships with liver diseases. Hepatol Res 2017; 47:497-504. [PMID: 28185365 DOI: 10.1111/hepr.12871] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/31/2017] [Accepted: 02/08/2017] [Indexed: 02/08/2023]
Abstract
Circular RNAs (circRNAs) are a class of new-found RNA molecules that have a special covalent loop structure without a 5' cap and 3' tail. Researchers have found that circRNAs may be generated by intron-pairing-driven or lariat-driven circularization. They are cleared up by way of extracellular vesicles. They have some advantages such as stability, conservation, and tissue specificity. By serving as sponges of microRNAs, interacting with long non-coding RNAs, mRNA, or proteins, circRNAs regulate gene expression at transcriptional and post-transcriptional levels and contribute to carcinogenesis. In recent years, circRNAs have been found to be correlated with many cancers including hepatocellular carcinoma, one of the most common cancers with high mortality. This article will first introduce the biogenesis, properties, and functions of circRNAs. Then we focus on the molecular mechanisms underlying some circRNAs, including hsa_circ_0001649, hsa_circ_0005075, and cerebellar degeneration-related protein 1 antisense, on hepatocellular carcinoma metastasis.
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Affiliation(s)
- Ting Yao
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
| | - Qingqing Chen
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
| | - Liyun Fu
- Ningbo No. 2 Hospital and the Affiliated Hospital, Medical School of Ningbo University, Ningbo, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, China
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2173
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Borchardt EK, Meganck RM, Vincent HA, Ball CB, Ramos SBV, Moorman NJ, Marzluff WF, Asokan A. Inducing circular RNA formation using the CRISPR endoribonuclease Csy4. RNA (NEW YORK, N.Y.) 2017; 23:619-627. [PMID: 28223408 PMCID: PMC5393173 DOI: 10.1261/rna.056838.116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
Circular RNAs (circRNAs) are highly stable, covalently closed RNAs that are regulated in a spatiotemporal manner and whose functions are largely unknown. These molecules have the potential to be incorporated into engineered systems with broad technological implications. Here we describe a switch for inducing back-splicing of an engineered circRNA that relies on the CRISPR endoribonuclease, Csy4, as an activator of circularization. The endoribonuclease activity and 3' end-stabilizing properties of Csy4 are particularly suited for this task. Coexpression of Csy4 and the circRNA switch allows for the removal of downstream competitive splice sites and stabilization of the 5' cleavage product. This subsequently results in back-splicing of the 5' cleavage product into a circRNA that can translate a reporter protein from an internal ribosomal entry site (IRES). Our platform outlines a straightforward approach toward regulating splicing and could find potential applications in synthetic biology as well as in studying the properties of different circRNAs.
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Affiliation(s)
- Erin K Borchardt
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Gene Therapy Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Rita M Meganck
- Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Gene Therapy Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | | | - Christopher B Ball
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Silvia B V Ramos
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Nathaniel J Moorman
- Department of Microbiology and Immunology
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - William F Marzluff
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- IBGS, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Aravind Asokan
- Gene Therapy Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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2174
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Elia L, Quintavalle M. Epigenetics and Vascular Diseases: Influence of Non-coding RNAs and Their Clinical Implications. Front Cardiovasc Med 2017; 4:26. [PMID: 28497038 PMCID: PMC5406412 DOI: 10.3389/fcvm.2017.00026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 04/12/2017] [Indexed: 01/25/2023] Open
Abstract
Epigenetics refers to heritable mechanisms able to modulate gene expression that do not involve alteration of the genomic DNA sequence. Classically, mechanisms such as DNA methylation and histone modifications were part of this classification. Today, this field of study has been expanded and includes also the large class of non-coding RNAs (ncRNAs). Indeed, with the extraordinary possibilities introduced by the next-generation sequencing approaches, our knowledge of the mammalian transcriptome has greatly improved. Today, we have identifying thousands of ncRNAs, and unsurprisingly, a direct association between ncRNA dysregulation and development of cardiovascular pathologies has been identified. This class of gene modulators is further divided into short-ncRNAs and long-non-coding RNAs (lncRNAs). Among the short-ncRNA sub-group, the best-characterized players are represented by highly conserved RNAs named microRNAs (miRNAs). miRNAs principally inhibit gene expression, and their involvement in cardiovascular diseases has been largely studied. On the other hand, due to the different roles played by lncRNAs, their involvement in cardiovascular pathology development is still limited, and further studies are needed. For instance, in order to define their roles in the cellular processes associated with the development of diseases, we need to better characterize the details of their mechanisms of action; only then might we be able to develop innovative therapeutic strategies. In this review, we would like to give an overview of the current knowledge on the function of ncRNAs and their involvement in the development of vascular diseases.
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Affiliation(s)
- Leonardo Elia
- Humanitas Clinical and Research Center, Milan, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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2175
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Li LJ, Zhao W, Tao SS, Leng RX, Fan YG, Pan HF, Ye DQ. Competitive endogenous RNA network: potential implication for systemic lupus erythematosus. Expert Opin Ther Targets 2017; 21:639-648. [DOI: 10.1080/14728222.2017.1319938] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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2176
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Ottaviani L, da Costa Martins PA. Non-coding RNAs in cardiac hypertrophy. J Physiol 2017; 595:4037-4050. [PMID: 28233323 PMCID: PMC5471409 DOI: 10.1113/jp273129] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/21/2017] [Indexed: 12/23/2022] Open
Abstract
Heart failure is one of the largest contributors to disease burden and healthcare outflow in the Western world. Despite significant progress in the treatment of heart failure, disease prognosis remains very poor, with the only curative therapy still being heart transplantation. To counteract the current situation, efforts have been made to better understand the underlying molecular pathways in the progression of cardiac disease towards heart failure, and to link the disease to novel therapeutic targets such as non‐coding RNAs. The non‐coding part of the genome has gained prominence over the last couple of decades, opening a completely new research field and establishing different non‐coding RNAs species as fundamental regulators of cellular functions. Not surprisingly, their dysregulation is increasingly being linked to pathology, including to cardiac disease. Pre‐clinically, non‐coding RNAs have been shown to be of great value as therapeutic targets in pathological cardiac remodelling and also as diagnostic/prognostic biomarkers for heart failure. Therefore, it is to be expected that non‐coding RNA‐based therapeutic strategies will reach the bedside in the future and provide new and more efficient treatments for heart failure. Here, we review recent discoveries linking the function and molecular interactions of non‐coding RNAs with the pathophysiology of cardiac hypertrophy and heart failure.
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Affiliation(s)
- Lara Ottaviani
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Paula A da Costa Martins
- Department of Cardiology, CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
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2177
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Savelyeva AV, Bariakin DN, Kuligina EV, Morozov VV, Richter VA, Semenov DV. Circular RNAs of human blood cells, plasma, and plasma subfractions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162017020133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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2178
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Rong D, Tang W, Li Z, Zhou J, Shi J, Wang H, Cao H. Novel insights into circular RNAs in clinical application of carcinomas. Onco Targets Ther 2017; 10:2183-2188. [PMID: 28458561 PMCID: PMC5403007 DOI: 10.2147/ott.s134403] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs), formed by nonsequential back-splicing of pre-messenger RNA (pre-mRNA) transcripts, have been widely concerned in recent years. With advances in high-throughput RNA sequencing (RNA-seq) technology, previous work has revealed that a large number of circRNAs, which are endogenous, abundant and stable in mammalian cells, may be involved in atherosclerotic vascular disease risk, neurological disorders, prion diseases and carcinomas. Remarkably, interaction between circRNAs and microRNA has already been observed to perform a significant role in a variety of cancers, including gastric cancer and colorectal cancer. Recent work has suggested that circRNAs may play critical roles in the initiation and development of cancers and could become potential new biomarkers for cancers. Herein, we review the current understanding of the roles of circRNAs in cancers and the potential implications of circRNAs in cancer-targeted therapy.
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Affiliation(s)
- Dawei Rong
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Weiwei Tang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Zhouxiao Li
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China.,Department of Plastic and Hand Surgery, University Hospital Munich, Munich, Germany
| | | | - Junfeng Shi
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Hanjin Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
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2179
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Conn VM, Hugouvieux V, Nayak A, Conos SA, Capovilla G, Cildir G, Jourdain A, Tergaonkar V, Schmid M, Zubieta C, Conn SJ. A circRNA from SEPALLATA3 regulates splicing of its cognate mRNA through R-loop formation. NATURE PLANTS 2017; 3:17053. [PMID: 28418376 DOI: 10.1038/nplants.2017.53] [Citation(s) in RCA: 427] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 03/20/2017] [Indexed: 05/03/2023]
Abstract
Circular RNAs (circRNAs) are a diverse and abundant class of hyper-stable, non-canonical RNAs that arise through a form of alternative splicing (AS) called back-splicing. These single-stranded, covalently-closed circRNA molecules have been identified in all eukaryotic kingdoms of life1, yet their functions have remained elusive. Here, we report that circRNAs can be used as bona fide biomarkers of functional, exon-skipped AS variants in Arabidopsis, including in the homeotic MADS-box transcription factor family. Furthermore, we demonstrate that circRNAs derived from exon 6 of the SEPALLATA3 (SEP3) gene increase abundance of the cognate exon-skipped AS variant (SEP3.3 which lacks exon 6), in turn driving floral homeotic phenotypes. Toward demonstrating the underlying mechanism, we show that the SEP3 exon 6 circRNA can bind strongly to its cognate DNA locus, forming an RNA:DNA hybrid, or R-loop, whereas the linear RNA equivalent bound significantly more weakly to DNA. R-loop formation results in transcriptional pausing, which has been shown to coincide with splicing factor recruitment and AS2-4. This report presents a novel mechanistic insight for how at least a subset of circRNAs probably contribute to increased splicing efficiency of their cognate exon-skipped messenger RNA and provides the first evidence of an organismal-level phenotype mediated by circRNA manipulation.
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Affiliation(s)
- Vanessa M Conn
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
| | - Véronique Hugouvieux
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
| | - Aditya Nayak
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
| | - Stephanie A Conos
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
| | - Giovanna Capovilla
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Gökhan Cildir
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
| | - Agnès Jourdain
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
| | - Vinay Tergaonkar
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
- Laboratory of NF-κB Signaling, Institute of Molecular and Cell Biology (IMCB), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
| | - Markus Schmid
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Chloe Zubieta
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
| | - Simon J Conn
- Laboratoire de Physiologie Cellulaire and Végétale, CNRS, CEA, INRA, Université Grenoble-Alpes, BIG, UMR 5168, Grenoble 38000, France
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
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2180
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Noto JJ, Schmidt CA, Matera AG. Engineering and expressing circular RNAs via tRNA splicing. RNA Biol 2017; 14:978-984. [PMID: 28402213 DOI: 10.1080/15476286.2017.1317911] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Circular (circ)RNAs have recently become a subject of great biologic interest. It is now clear that they represent a diverse and abundant class of RNAs with regulated expression and evolutionarily conserved functions. There are several mechanisms by which RNA circularization can occur in vivo. Here, we focus on the biogenesis of tRNA intronic circular RNAs (tricRNAs) in archaea and animals, and we detail their use as research tools for orthogonal, directed circRNA expression in vivo.
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Affiliation(s)
- John J Noto
- a Curriculum in Genetics and Molecular Biology , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Integrative Program for Biological and Genome Sciences , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - Casey A Schmidt
- a Curriculum in Genetics and Molecular Biology , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Integrative Program for Biological and Genome Sciences , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
| | - A Gregory Matera
- a Curriculum in Genetics and Molecular Biology , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,b Integrative Program for Biological and Genome Sciences , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,c Lineberger Comprehensive Cancer Center , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,d Department of Biology , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA.,e Department of Genetics , The University of North Carolina at Chapel Hill , Chapel Hill , NC , USA
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2181
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Fu L, Yao T, Chen Q, Mo X, Hu Y, Guo J. Screening differential circular RNA expression profiles reveals hsa_circ_0004018 is associated with hepatocellular carcinoma. Oncotarget 2017; 8:58405-58416. [PMID: 28938566 PMCID: PMC5601662 DOI: 10.18632/oncotarget.16881] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) have been emerged as an indispensable part of endogenous RNA network. However, the expression significance of circRNAs in hepatocellular carcinoma (HCC) is rarely revealed. The aim of this study was to determine the circRNA expression profile in HCC, and to investigate their clinical significances and relevant mechanisms for cancer progression. The global circRNA expression profile in HCC was measured by circRNA microarray. Levels of one representative circRNAs, hsa_circ_0004018, were confirmed by real-time reverse transcription-polymerase chain reaction. The expression levels of hsa_circ_0004018 in HCC were significantly lower compared with para-tumorous tissue (P<0.001). Our data further showed that lower expression of hsa_circ_0004018 was correlated with serum alpha-fetoprotein (AFP) level, tumor diameters, differentiation, Barcelona Clinic Liver Cancer stage and Tumor-node-metastasis stage. More importantly, we detected liver tissues from chronic hepatitis, cirrhosis and HCC patients; and found that hsa_circ_0004018 harbored HCC-stage-specific expression features in diverse chronic liver diseases (P<0.001). The area under receiver operating characteristic curve was up to 0.848 (95% CI=0.803–0.894, P<0.001). The sensitivity and specificity were 0.716 and 0.815, respectively. Finally, hsa_circ_0004018 might be involved in cancer-related pathways via interactions with miRNAs.
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Affiliation(s)
- Liyun Fu
- Department of Hepatology, Ningbo No. 2 Hospital and The Affiliated Hospital, Medical School of Ningbo University, Ningbo 315010, China
| | - Ting Yao
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Qingqing Chen
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Xiaoyan Mo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Yaoren Hu
- Department of Hepatology, Ningbo No. 2 Hospital and The Affiliated Hospital, Medical School of Ningbo University, Ningbo 315010, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
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2182
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Zhou J, Xiong Q, Chen H, Yang C, Fan Y. Identification of the Spinal Expression Profile of Non-coding RNAs Involved in Neuropathic Pain Following Spared Nerve Injury by Sequence Analysis. Front Mol Neurosci 2017; 10:91. [PMID: 28420964 PMCID: PMC5377590 DOI: 10.3389/fnmol.2017.00091] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/15/2017] [Indexed: 12/18/2022] Open
Abstract
Neuropathic pain (NP) is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. A non-coding Ribose Nucleic Acid (ncRNA) is an RNA molecule that is not translated into a protein. NcRNAs are involved in many cellular processes, and mutations or imbalances of the repertoire within the body can cause a variety of diseases. Although ncRNAs have recently been shown to play a role in NP pathogenesis, the specific effects of ncRNAs in NP remain largely unknown. In this study, sequencing analysis was performed to investigated the expression patterns of ncRNAs in the spinal cord following spared nerve injury-induced NP. A total of 134 long non-coding RNAs (lncRNAs), 12 microRNAs (miRNAs), 188 circular RNAs (circRNAs) and 1066 mRNAs were significantly regulated at 14 days after spared nerve injury (SNI) surgery. Next, quantitative real-time polymerase chain reaction (PCR) was performed to validate the expression of selected lncRNAs, miRNAs, circRNAs, and mRNAs. Bioinformatics tools and databases were employed to explore the potential ncRNA functions and relationships. Our data showed that the most significantly involved pathways in SNI pathogenesis were ribosome, PI3K-Akt signaling pathway, focal adhesion, ECM-receptor interaction, amoebiasis and protein digestion and absorption. In addition, the lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA network of NP was constructed. This is the first study to comprehensively identify regulated ncRNAs of the spinal cord and to demonstrate the involvement of different ncRNA expression patterns in the spinal cord of NP pathogenesis by sequence analysis. This information will enable further research on the pathogenesis of NP and facilitate the development of novel NP therapeutics targeting ncRNAs.
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Affiliation(s)
- Jun Zhou
- Department of Anesthesiology, The First People's Hospital of FoshanFoshan, China
| | - Qingming Xiong
- Department of Anesthesiology, The First People's Hospital of FoshanFoshan, China
| | - Hongtao Chen
- Department of Anesthesiology, Eighth People's Hospital of GuangzhouGuangzhou, China
| | - Chengxiang Yang
- Department of Anesthesiology, The First People's Hospital of FoshanFoshan, China
| | - Youling Fan
- Department of Anesthesiology, Panyu Central HospitalGuangzhou, China
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2183
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Gallego-Paez LM, Bordone MC, Leote AC, Saraiva-Agostinho N, Ascensão-Ferreira M, Barbosa-Morais NL. Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems. Hum Genet 2017; 136:1015-1042. [PMID: 28374191 PMCID: PMC5602094 DOI: 10.1007/s00439-017-1790-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/25/2017] [Indexed: 02/06/2023]
Abstract
Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.
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Affiliation(s)
- L M Gallego-Paez
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M C Bordone
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - A C Leote
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N Saraiva-Agostinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - M Ascensão-Ferreira
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - N L Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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2184
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Circular RNAs expressed in chorionic villi are probably involved in the occurrence of recurrent spontaneous abortion. Biomed Pharmacother 2017. [DOI: 10.1016/j.biopha.2017.01.172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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2185
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Errichelli L, Dini Modigliani S, Laneve P, Colantoni A, Legnini I, Capauto D, Rosa A, De Santis R, Scarfò R, Peruzzi G, Lu L, Caffarelli E, Shneider NA, Morlando M, Bozzoni I. FUS affects circular RNA expression in murine embryonic stem cell-derived motor neurons. Nat Commun 2017; 8:14741. [PMID: 28358055 PMCID: PMC5379105 DOI: 10.1038/ncomms14741] [Citation(s) in RCA: 399] [Impact Index Per Article: 49.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/26/2017] [Indexed: 12/13/2022] Open
Abstract
The RNA-binding protein FUS participates in several RNA biosynthetic processes and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia. Here we report that FUS controls back-splicing reactions leading to circular RNA (circRNA) production. We identified circRNAs expressed in in vitro-derived mouse motor neurons (MNs) and determined that the production of a considerable number of these circRNAs is regulated by FUS. Using RNAi and overexpression of wild-type and ALS-associated FUS mutants, we directly correlate the modulation of circRNA biogenesis with alteration of FUS nuclear levels and with putative toxic gain of function activities. We also demonstrate that FUS regulates circRNA biogenesis by binding the introns flanking the back-splicing junctions and that this control can be reproduced with artificial constructs. Most circRNAs are conserved in humans and specific ones are deregulated in human-induced pluripotent stem cell-derived MNs carrying the FUSP525L mutation associated with ALS. The RNA binding protein FUS functions in several RNA biosynthetic processes and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). Here the authors show that FUS controls back-splicing reactions leading to circular RNA (circRNA) production in stem cell-derived motor neurons and that ALS-associated FUS mutations affect the biogenesis of circRNAs.
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Affiliation(s)
- Lorenzo Errichelli
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy.,Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Stefano Dini Modigliani
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Pietro Laneve
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Alessio Colantoni
- Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Ivano Legnini
- Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Davide Capauto
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy.,Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Alessandro Rosa
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy.,Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Riccardo De Santis
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy.,Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Rebecca Scarfò
- Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Giovanna Peruzzi
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Lei Lu
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, 630 W 168th Street, New York, New York 10032, USA
| | - Elisa Caffarelli
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy.,Institute of Molecular Biology and Pathology, CNR, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Neil A Shneider
- Department of Neurology, Center for Motor Neuron Biology and Disease, Columbia University, 630 W 168th Street, New York, New York 10032, USA
| | - Mariangela Morlando
- Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
| | - Irene Bozzoni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy.,Deparment of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy.,Institute of Molecular Biology and Pathology, CNR, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy.,Institute Pasteur Fondazione Cenci-Bolognetti, Sapienza University of Rome, P.le A. Moro 5, Rome 00185, Italy
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2186
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Devaux Y, Creemers EE, Boon RA, Werfel S, Thum T, Engelhardt S, Dimmeler S, Squire I. Circular RNAs in heart failure. Eur J Heart Fail 2017; 19:701-709. [DOI: 10.1002/ejhf.801] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/26/2017] [Accepted: 01/31/2017] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yvan Devaux
- Cardiovascular Research Unit; Luxembourg Institute of Health; Luxembourg Luxembourg
| | - Esther E. Creemers
- Experimental Cardiology; Academic Medical Center; Amsterdam The Netherlands
| | - Reinier A. Boon
- Institute of Cardiovascular Regeneration; Goethe-University; Frankfurt Germany
- Department of Physiology; VU University Medical Center; Amsterdam The Netherlands
| | - Stanislas Werfel
- Institute of Pharmacology and Toxicology; Technical University Munich; Munich Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies; Hannover Medical School; Hannover Germany
- National Heart and Lung Institute; Imperial College London; London UK
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology; Technical University Munich; Munich Germany
- German Center for Cardiovascular Research; partner site Munich Heart Alliance; Munich Germany
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration; Goethe-University; Frankfurt Germany
| | - Iain Squire
- Department of Cardiovascular Sciences; University of Leicester; Leicester UK
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2187
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Pamudurti NR, Bartok O, Jens M, Ashwal-Fluss R, Stottmeister C, Ruhe L, Hanan M, Wyler E, Perez-Hernandez D, Ramberger E, Shenzis S, Samson M, Dittmar G, Landthaler M, Chekulaeva M, Rajewsky N, Kadener S. Translation of CircRNAs. Mol Cell 2017; 66:9-21.e7. [PMID: 28344080 PMCID: PMC5387669 DOI: 10.1016/j.molcel.2017.02.021] [Citation(s) in RCA: 1339] [Impact Index Per Article: 167.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 01/04/2017] [Accepted: 02/21/2017] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons. In addition, we found that a circRNA generated from the muscleblind locus encodes a protein, which we detected in fly head extracts by mass spectrometry. Next, by performing in vivo and in vitro translation assays, we show that UTRs of ribo-circRNAs (cUTRs) allow cap-independent translation. Moreover, we found that starvation and FOXO likely regulate the translation of a circMbl isoform. Altogether, our study provides strong evidence for translation of circRNAs, revealing the existence of an unexplored layer of gene activity.
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Affiliation(s)
- Nagarjuna Reddy Pamudurti
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Osnat Bartok
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Marvin Jens
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reut Ashwal-Fluss
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Christin Stottmeister
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Larissa Ruhe
- Non Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Mor Hanan
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Emanuel Wyler
- RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Daniel Perez-Hernandez
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Evelyn Ramberger
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Shlomo Shenzis
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Moshe Samson
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gunnar Dittmar
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Marina Chekulaeva
- Non Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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2188
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Legnini I, Di Timoteo G, Rossi F, Morlando M, Briganti F, Sthandier O, Fatica A, Santini T, Andronache A, Wade M, Laneve P, Rajewsky N, Bozzoni I. Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis. Mol Cell 2017; 66:22-37.e9. [PMID: 28344082 PMCID: PMC5387670 DOI: 10.1016/j.molcel.2017.02.017] [Citation(s) in RCA: 1593] [Impact Index Per Article: 199.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/28/2016] [Accepted: 02/16/2017] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) constitute a family of transcripts with unique structures and still largely unknown functions. Their biogenesis, which proceeds via a back-splicing reaction, is fairly well characterized, whereas their role in the modulation of physiologically relevant processes is still unclear. Here we performed expression profiling of circRNAs during in vitro differentiation of murine and human myoblasts, and we identified conserved species regulated in myogenesis and altered in Duchenne muscular dystrophy. A high-content functional genomic screen allowed the study of their functional role in muscle differentiation. One of them, circ-ZNF609, resulted in specifically controlling myoblast proliferation. Circ-ZNF609 contains an open reading frame spanning from the start codon, in common with the linear transcript, and terminating at an in-frame STOP codon, created upon circularization. Circ-ZNF609 is associated with heavy polysomes, and it is translated into a protein in a splicing-dependent and cap-independent manner, providing an example of a protein-coding circRNA in eukaryotes. CircRNAs are conserved, abundant, and regulated in myogenesis High-throughput phenotypic screening reveals functional circRNAs Circ-ZNF609 regulates myoblast proliferation Circ-ZNF609 can be translated
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Affiliation(s)
- Ivano Legnini
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Francesca Rossi
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Mariangela Morlando
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Francesca Briganti
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Olga Sthandier
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Tiziana Santini
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Adrian Andronache
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Mark Wade
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Pietro Laneve
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin and IBPM, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy; Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy; Institut Pasteur Italy, Fondazione Cenci-Bolognetti, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
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2189
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He J, Xie Q, Xu H, Li J, Li Y. Circular RNAs and cancer. Cancer Lett 2017; 396:138-144. [PMID: 28342987 DOI: 10.1016/j.canlet.2017.03.027] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are a type of non-coding RNA molecules that lack a 5'-terminal cap and 3'-terminal poly A tail. A large number of circRNAs have been identified through biological experiments, computational methods and high-throughput sequencing. CircRNA sequence composition determines if a given circRNA is exonic, intronic or retained-intronic. CircRNAs are more abundant and stable than linear mRNAs, and their expression is both step- and location-specific. CircRNAs mediate transcriptional and post-transcriptional regulation of gene and protein expression. CircRNAs regulate cancer development via multiple mechanisms, including miRNA sponges, modulating Wnt signaling pathway and epithelial-mesenchymal transition. An in-depth study of circRNA will provide a better understanding of carcinogenesis and assist in developing clinical diagnostic and therapeutic strategies.
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Affiliation(s)
- Jun He
- Department of General Surgery, Jiande Branch of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Jiande, Zhejiang 311600, China.
| | - Qichao Xie
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Hailin Xu
- Department of General Surgery, Jiande Branch of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Jiande, Zhejiang 311600, China
| | - Jiantian Li
- Department of General Surgery, Jiande Branch of the Second Affiliated Hospital, School of Medicine, Zhejiang University, Jiande, Zhejiang 311600, China
| | - Yongsheng Li
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China.
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2190
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Yang Y, Fan X, Mao M, Song X, Wu P, Zhang Y, Jin Y, Yang Y, Chen LL, Wang Y, Wong CC, Xiao X, Wang Z. Extensive translation of circular RNAs driven by N 6-methyladenosine. Cell Res 2017; 27:626-641. [PMID: 28281539 PMCID: PMC5520850 DOI: 10.1038/cr.2017.31] [Citation(s) in RCA: 1381] [Impact Index Per Article: 172.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/03/2017] [Accepted: 02/19/2017] [Indexed: 12/16/2022] Open
Abstract
Extensive pre-mRNA back-splicing generates numerous circular RNAs (circRNAs) in human transcriptome. However, the biological functions of these circRNAs remain largely unclear. Here we report that N6-methyladenosine (m6A), the most abundant base modification of RNA, promotes efficient initiation of protein translation from circRNAs in human cells. We discover that consensus m6A motifs are enriched in circRNAs and a single m6A site is sufficient to drive translation initiation. This m6A-driven translation requires initiation factor eIF4G2 and m6A reader YTHDF3, and is enhanced by methyltransferase METTL3/14, inhibited by demethylase FTO, and upregulated upon heat shock. Further analyses through polysome profiling, computational prediction and mass spectrometry reveal that m6A-driven translation of circRNAs is widespread, with hundreds of endogenous circRNAs having translation potential. Our study expands the coding landscape of human transcriptome, and suggests a role of circRNA-derived proteins in cellular responses to environmental stress.
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Affiliation(s)
- Yun Yang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University at Zijingang, Zhejiang, Hangzhou, Zhejiang 310058, China.,CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Integrative Biology and Physiology and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiaojuan Fan
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miaowei Mao
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xiaowei Song
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ping Wu
- National Center for Protein Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China
| | - Yang Zhang
- Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yongfeng Jin
- Institute of Biochemistry, College of Life Sciences, Zhejiang University at Zijingang, Zhejiang, Hangzhou, Zhejiang 310058, China
| | - Yi Yang
- Synthetic Biology and Biotechnology Laboratory, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ling-Ling Chen
- Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning 116044, China
| | - Catherine Cl Wong
- National Center for Protein Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China
| | - Xinshu Xiao
- Department of Integrative Biology and Physiology and the Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Zefeng Wang
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2191
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Gao J, Xu W, Wang J, Wang K, Li P. The Role and Molecular Mechanism of Non-Coding RNAs in Pathological Cardiac Remodeling. Int J Mol Sci 2017; 18:608. [PMID: 28287427 PMCID: PMC5372624 DOI: 10.3390/ijms18030608] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/05/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a class of RNA molecules that do not encode proteins. Studies show that ncRNAs are not only involved in cell proliferation, apoptosis, differentiation, metabolism and other physiological processes, but also involved in the pathogenesis of diseases. Cardiac remodeling is the main pathological basis of a variety of cardiovascular diseases. Many studies have shown that the occurrence and development of cardiac remodeling are closely related with the regulation of ncRNAs. Recent research of ncRNAs in heart disease has achieved rapid development. Thus, we summarize here the latest research progress and mainly the molecular mechanism of ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), in cardiac remodeling, aiming to look for new targets for heart disease treatment.
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Affiliation(s)
- Jinning Gao
- Center for Developmental Cardiology, Institute for Translational Medicine, Qingdao University, Dengzhou Road 38, Qingdao 266021, China.
| | - Wenhua Xu
- Department of Basic Medical College, Qingdao University Medical College, Ningxia Road 308, Qingdao 266071, China.
| | - Jianxun Wang
- Center for Developmental Cardiology, Institute for Translational Medicine, Qingdao University, Dengzhou Road 38, Qingdao 266021, China.
| | - Kun Wang
- Center for Developmental Cardiology, Institute for Translational Medicine, Qingdao University, Dengzhou Road 38, Qingdao 266021, China.
| | - Peifeng Li
- Center for Developmental Cardiology, Institute for Translational Medicine, Qingdao University, Dengzhou Road 38, Qingdao 266021, China.
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2192
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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: 327] [Impact Index Per Article: 40.9] [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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2193
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Cardamone G, Paraboschi EM, Rimoldi V, Duga S, Soldà G, Asselta R. The Characterization of GSDMB Splicing and Backsplicing Profiles Identifies Novel Isoforms and a Circular RNA That Are Dysregulated in Multiple Sclerosis. Int J Mol Sci 2017; 18:ijms18030576. [PMID: 28272342 PMCID: PMC5372592 DOI: 10.3390/ijms18030576] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 02/20/2017] [Accepted: 03/01/2017] [Indexed: 01/08/2023] Open
Abstract
Abnormalities in alternative splicing (AS) are emerging as recurrent features in autoimmune diseases (AIDs). In particular, a growing body of evidence suggests the existence of a pathogenic association between a generalized defect in splicing regulatory genes and multiple sclerosis (MS). Moreover, several studies have documented an unbalance in alternatively-spliced isoforms in MS patients possibly contributing to the disease etiology. In this work, using a combination of PCR-based techniques (reverse-transcription (RT)-PCR, fluorescent-competitive, real-time, and digital RT-PCR assays), we investigated the alternatively-spliced gene encoding Gasdermin B, GSDMB, which was repeatedly associated with susceptibility to asthma and AIDs. The in-depth characterization of GSDMB AS and backsplicing profiles led us to the identification of an exonic circular RNA (ecircRNA) as well as of novel GSDMB in-frame and out-of-frame isoforms. The non-productive splicing variants were shown to be downregulated by the nonsense-mediated mRNA decay (NMD) in human cell lines, suggesting that GSDMB levels are significantly modulated by NMD. Importantly, both AS isoforms and the identified ecircRNA were significantly dysregulated in peripheral blood mononuclear cells of relapsing-remitting MS patients compared to controls, further supporting the notion that aberrant RNA metabolism is a characteristic feature of the disease.
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Affiliation(s)
- Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
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2194
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Zhang P, Zuo Z, Shang W, Wu A, Bi R, Wu J, Li S, Sun X, Jiang L. Identification of differentially expressed circular RNAs in human colorectal cancer. Tumour Biol 2017; 39:1010428317694546. [PMID: 28349836 DOI: 10.1177/1010428317694546] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Circular RNA, a class of non-coding RNA, is a new group of RNAs and is related to tumorigenesis. Circular RNAs are suggested to be ideal candidate biomarkers with potential diagnostic and therapeutic implications. However, little is known about their expression in human colorectal cancer. In our study, differentially expressed circular RNAs were detected using circular RNA array in paired tumor and adjacent non-tumorous tissues from six colorectal cancer patients. Expression levels of selected circular RNAs (hsa_circRNA_103809 and hsa_circRNA_104700) were measured by real-time polymerase chain reaction in 170 paired colorectal cancer samples for validation. Statistical analyses were conducted to investigate the association between hsa_circRNA_103809 and hsa_circRNA_104700 expression levels and respective patient clinicopathological features. Receiver operating characteristic curve was constructed to evaluate the diagnostic values. Our results indicated that there were 125 downregulated and 76 upregulated circular RNAs in colorectal cancer tissues compared with normal tissues. We also first demonstrated that the expression levels of hsa_circRNA_103809 ( p < 0.0001) and hsa_circRNA_104700 ( p = 0.0003) were significantly lower in colorectal cancer than in normal tissues. The expression level of hsa_circRNA_103809 was significantly correlated with lymph node metastasis ( p = 0.021) and tumor-node-metastasis stage ( p = 0.011), and the expression level of hsa_circRNA_104700 was significantly correlated with distal metastasis ( p = 0.036). The area under receiver operating characteristic curves of hsa_circRNA_103809 and hsa_circRNA_104700 were 0.699 ( p < 0.0001) and 0.616 ( p < 0.0001), respectively. In conclusion, these results suggest that hsa_circRNA_103809 and hsa_circRNA_104700 may be potentially involved in the development of colorectal cancer and serve as potential biomarkers for the diagnosis of colorectal cancer.
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Affiliation(s)
- Peili Zhang
- 1 Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhigui Zuo
- 2 Department of Colorectal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wenjing Shang
- 1 Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Aihua Wu
- 1 Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruichun Bi
- 1 Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianbo Wu
- 1 Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shaotang Li
- 3 Department of General Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xuecheng Sun
- 4 Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lei Jiang
- 1 Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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2195
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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: 517] [Impact Index Per Article: 64.6] [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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2196
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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: 185] [Impact Index Per Article: 23.1] [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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2197
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Zhu J, Ye J, Zhang L, Xia L, Hu H, Jiang H, Wan Z, Sheng F, Ma Y, Li W, Qian J, Luo C. Differential Expression of Circular RNAs in Glioblastoma Multiforme and Its Correlation with Prognosis. Transl Oncol 2017; 10:271-279. [PMID: 28236760 PMCID: PMC5328755 DOI: 10.1016/j.tranon.2016.12.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVE: The present study aimed to explore the expression profiles of circular RNAs (circRNAs) in glioblastoma multiforme (GBM) in an attempt to identify potential core genes in the pathogenesis of this tumor. METHODS: Differentially expressed circRNAs were screened between tumor tissues from five GBM patients and five normal brain samples using Illumina Hiseq. Bioinformatics analysis was used to analyze their potential function. CircBRAF was further detected in different WHO grades glioma tissues and normal brain tissues. Kaplan-Meier curves and multivariate Cox's analysis were used to analyze the association between circBRAF expression level and prognosis of glioma patients. RESULTS: A total of 1411 differentially expressed circRNAs were identified in GBM patients including 206 upregulated circRNAs and 1205 downregulated circRNAs. Differential expression of circRNAs was closely associated with the biological process and molecular function. The downregulated circRNAs were mainly associated with ErbB and Neurotrophin signaling pathways. Moreover, the expression level of circBRAF in normal brain tissues was significantly higher than that in glioma tissues (P < .001). CircBRAF was significantly lower in glioma patients with high pathological grade (WHO III & IV) than those with low grade (WHO I & II) (P < .001). Cox analysis revealed that high circBRAF expression was an independent biomarker for predicting good progression-free survival and overall survival in glioma patients (HR = 0.413, 95% CI 0.201-0.849; HR = 0.299, 95% CI 0.135-0.661; respectively). CONCLUSION: The present study identified a profile of dysregulated circRNAs in GBM. Bioinformatics analysis showed that dysregulated circRNAs might be associated with tumorigenesis and development of GBM. In addition, circBRAF could severe as a biomarker for predicting pathological grade and prognosis in glioma patients.
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Affiliation(s)
- Junle Zhu
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Jingliang Ye
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China; Department of Neurosurgery, No. 98 Hospital of Chinese People's Liberation Army, Huzhou 313000, China
| | - Lei Zhang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Lili Xia
- Department of Emergency, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Hongkang Hu
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Heng Jiang
- Department of spinal surgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Zhiping Wan
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Fei Sheng
- Department of Reproductive Medical Center, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Yan Ma
- Department of Reproductive Medical Center, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Wen Li
- Department of Reproductive Medical Center, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China
| | - Jun Qian
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China.
| | - Chun Luo
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai 200003, China.
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2198
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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: 7.3] [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: 12/13/2016] [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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2199
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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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2200
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Kim KM, Abdelmohsen K, Mustapic M, Kapogiannis D, Gorospe M. RNA in extracellular vesicles. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28130830 DOI: 10.1002/wrna.1413] [Citation(s) in RCA: 342] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/15/2022]
Abstract
Cells release a range of membrane-enclosed extracellular vesicles (EVs) into the environment. Among them, exosomes and microvesicles (collectively measuring 40-1000 nm in diameter) carry proteins, signaling lipids, and nucleic acids from donor cells to recipient cells, and thus have been proposed to serve as intercellular mediators of communication. EVs transport cellular materials in many physiologic processes, including differentiation, stem cell homeostasis, immune responses, and neuronal signaling. EVs are also increasingly recognized as having a direct role in pathologies such as cancer and neurodegeneration. Accordingly, EVs have been the focus of intense investigation as biomarkers of disease, prognostic indicators, and even therapeutic tools. Here, we review the classes of RNAs present in EVs, both coding RNAs (messenger RNAs) and noncoding RNAs (long noncoding RNAs, microRNAs, and circular RNAs). The rising attention to EV-resident RNAs as biomarkers stems from the fact that RNAs can be detected at extremely low quantities using a number of methods. To illustrate the interest in EV biology, we discuss EV RNAs in cancer and neurodegeneration, two major age-associated disease processes. WIREs RNA 2017, 8:e1413. doi: 10.1002/wrna.1413 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Kyoung Mi Kim
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Maja Mustapic
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Dimitrios Kapogiannis
- Laboratory of Neurosciences, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
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