101
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Bejugam PR, Das A, Panda AC. Seeing Is Believing: Visualizing Circular RNAs. Noncoding RNA 2020; 6:E45. [PMID: 33187156 PMCID: PMC7712394 DOI: 10.3390/ncrna6040045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 02/07/2023] Open
Abstract
Advancement in the RNA sequencing techniques has discovered hundreds of thousands of circular RNAs (circRNAs) in humans. However, the physiological function of most of the identified circRNAs remains unexplored. Recent studies have established that spliceosomal machinery and RNA-binding proteins modulate circRNA biogenesis. Furthermore, circRNAs have been implicated in regulating crucial cellular processes by interacting with various proteins and microRNAs. However, there are several challenges in understanding the mechanism of circRNA biogenesis, transport, and their interaction with cellular factors to regulate cellular events because of their low abundance and sequence similarity with linear RNA. Addressing these challenges requires systematic studies that directly visualize the circRNAs in cells at single-molecule resolution along with the molecular regulators. In this review, we present the design, benefits, and weaknesses of RNA imaging techniques such as single-molecule RNA fluorescence in situ hybridization and BaseScope in fixed cells and fluorescent RNA aptamers in live-cell imaging of circRNAs. Furthermore, we propose the potential use of molecular beacons, multiply labeled tetravalent RNA imaging probes, and Cas-derived systems to visualize circRNAs.
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Affiliation(s)
- Pruthvi Raj Bejugam
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
| | - Aniruddha Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha 751024, India
| | - Amaresh Chandra Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India; (P.R.B.); (A.D.)
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102
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seekCRIT: Detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data. PLoS Comput Biol 2020; 16:e1008338. [PMID: 33079938 PMCID: PMC7598922 DOI: 10.1371/journal.pcbi.1008338] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/30/2020] [Accepted: 09/13/2020] [Indexed: 11/19/2022] Open
Abstract
Over the past two decades, researchers have discovered a special form of alternative splicing that produces a circular form of RNA. Although these circular RNAs (circRNAs) have garnered considerable attention in the scientific community for their biogenesis and functions, the focus of current studies has been on the tissue-specific circRNAs that exist only in one tissue but not in other tissues or on the disease-specific circRNAs that exist in certain disease conditions, such as cancer, but not under normal conditions. This approach was conducted in the relative absence of methods that analyze a group of common circRNAs that exist in both conditions, but are more abundant in one condition relative to another (differentially expressed). Studies of differentially expressed circRNAs (DECs) between two conditions would serve as a significant first step in filling this void. Here, we introduce a novel computational tool, seekCRIT (seek for differentially expressed CircRNAs In Transcriptome), that identifies the DECs between two conditions from high-throughput sequencing data. Using rat retina RNA-seq data from ischemic and normal conditions, we show that over 74% of identifiable circRNAs are expressed in both conditions and over 40 circRNAs are differentially expressed between two conditions. We also obtain a high qPCR validation rate of 90% for DECs with a FDR of < 5%. Our results demonstrate that seekCRIT is a novel and efficient approach to detect DECs using rRNA depleted RNA-seq data. seekCRIT is freely downloadable at https://github.com/UofLBioinformatics/seekCRIT. The source code is licensed under the MIT License. seekCRIT is developed and tested on Linux CentOS-7. The focus of circRNA studies has been on condition-specific circRNAs, however, there are situations in which circRNAs exist in both conditions with different abundance. Here, we introduce a new and robust analytic software, seekCRIT (seek for differentially expressed CircRNAs In Transcriptome), that identifies the differentially expressed circRNAs (DECs) between two conditions from high-throughput sequencing data. seekCRIT provides a straightforward normalized quantification of circRNAs and statistical measures by adapting a junction-count-based estimation approach. Using publicly available ribosomal RNA depleted RNA-seq data and our own rat retina RNA-seq data, we show that seekCRIT can efficiently detect circRNAs and identify DECs. We also obtain a high qPCR validation rate of 90% for DECs with a FDR of < 5%. Our results demonstrate that seekCRIT is a novel and efficient software to detect DECs using rRNA depleted RNA-seq data.
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103
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Disease-Associated Circular RNAs: From Biology to Computational Identification. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6798590. [PMID: 32908906 PMCID: PMC7450300 DOI: 10.1155/2020/6798590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA. An accumulating number of studies have shown that circRNAs are potential biomarkers for major human diseases such as cancer and Alzheimer's disease. Thus, identification and prediction of human disease-associated circRNAs are of significant importance. To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications. In this review, we briefly introduce the biology of circRNAs, including the biogenesis, characteristics, and biological functions. In addition, we outline about 30 recent bioinformatic analysis tools that are publicly available for circRNA study. Principles for applying these computational strategies and considerations will be briefly discussed. Lastly, we give a complete survey on more than 20 key computational databases that are frequently used. To our knowledge, this is the most complete and updated summary on publicly available circRNA resources. In conclusion, this review summarizes key aspects of circRNA biology and outlines key computational strategies that will facilitate the genome-wide identification and prediction of circRNAs.
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104
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Tucker D, Zheng W, Zhang DH, Dong X. Circular RNA and its potential as prostate cancer biomarkers. World J Clin Oncol 2020; 11:563-572. [PMID: 32879844 PMCID: PMC7443832 DOI: 10.5306/wjco.v11.i8.563] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 06/09/2020] [Accepted: 07/19/2020] [Indexed: 02/06/2023] Open
Abstract
Advancing knowledge of the transcriptome has revealed that circular RNAs (circRNAs) are widely expressed and evolutionarily conserved molecules that may serve relevant biological roles. More interesting is the accumulating evidence which demonstrates the implication of circRNAs in diseases, especially cancers. This revelation has helped to form the rationale for many studies exploring their utility as clinical biomarkers. CircRNAs are highly stable due to their unique structures, exhibit some tissue specificity, and are enriched in exosomes, which facilitate their detection in a range of body fluids. These properties make circRNAs ideal candidates for biomarker development in many diseases. This review will outline the discovery, biogenesis, and proposed functions of circRNAs.
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Affiliation(s)
- Dwayne Tucker
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Wei Zheng
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou 310024, Zhejiang Province, China
| | - Da-Hong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou 310024, Zhejiang Province, China
| | - Xuesen Dong
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
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105
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Circular RNAs in Hematopoiesis with a Focus on Acute Myeloid Leukemia and Myelodysplastic Syndrome. Int J Mol Sci 2020; 21:ijms21175972. [PMID: 32825172 PMCID: PMC7503587 DOI: 10.3390/ijms21175972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs (circRNAs) constitute a recently recognized group of noncoding transcripts that function as posttranscriptional regulators of gene expression at a new level. Recent developments in experimental methods together with rapidly evolving bioinformatics approaches have accelerated the exploration of circRNAs. The differentiation of hematopoietic stem cells into a broad spectrum of specialized blood lineages is a tightly regulated process that depends on a multitude of factors, including circRNAs. However, despite the growing number of circRNAs described to date, the roles of the majority of them in hematopoiesis remain unknown. Given their stability and disease-specific expression, circRNAs have been acknowledged as novel promising biomarkers and therapeutic targets. In this paper, the biogenesis, characteristics, and roles of circRNAs are reviewed with an emphasis on their currently recognized or presumed involvement in hematopoiesis, especially in acute myeloid leukemia and myelodysplastic syndrome.
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106
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Sun YM, Chen YQ. Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application. J Hematol Oncol 2020; 13:109. [PMID: 32778133 PMCID: PMC7416809 DOI: 10.1186/s13045-020-00945-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/27/2020] [Indexed: 12/20/2022] Open
Abstract
Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have apparent protein-coding roles, but they have been verified to play important roles in diverse biological processes, including disease pathogenesis. With the development of innovative technologies, an increasing number of novel ncRNAs have been uncovered; information about their prominent tissue-specific expression patterns, various interaction networks, and subcellular locations will undoubtedly enhance our understanding of their potential functions. Here, we summarized the principles and innovative methods for identifications of novel ncRNAs that have potential functional roles in cancer biology. Moreover, this review also provides alternative ncRNA databases based on high-throughput sequencing or experimental validation, and it briefly describes the current strategy for the clinical translation of cancer-associated ncRNAs to be used in diagnosis.
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Affiliation(s)
- Yu-Meng Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
| | - Yue-Qin Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 People’s Republic of China
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107
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Singh NN, Ottesen EW, Singh RN. A survey of transcripts generated by spinal muscular atrophy genes. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194562. [PMID: 32387331 PMCID: PMC7302838 DOI: 10.1016/j.bbagrm.2020.194562] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/01/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023]
Abstract
Human Survival Motor Neuron (SMN) genes code for SMN, an essential multifunctional protein. Complete loss of SMN is embryonic lethal, while low levels of SMN lead to spinal muscular atrophy (SMA), a major genetic disease of children and infants. Reduced levels of SMN are associated with the abnormal development of heart, lung, muscle, gastro-intestinal system and testis. The SMN loci have been shown to generate a vast repertoire of transcripts, including linear, back- and trans-spliced RNAs as well as antisense long noncoding RNAs. However, functions of the majority of these transcripts remain unknown. Here we review the nature of RNAs generated from the SMN loci and discuss their potential functions in cellular metabolism.
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Affiliation(s)
- Natalia N Singh
- Department of Biomedical Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Eric W Ottesen
- Department of Biomedical Science, Iowa State University, Ames, IA, 50011, United States of America
| | - Ravindra N Singh
- Department of Biomedical Science, Iowa State University, Ames, IA, 50011, United States of America.
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108
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circRNA Hipk3 Induces Cardiac Regeneration after Myocardial Infarction in Mice by Binding to Notch1 and miR-133a. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:636-655. [PMID: 32736292 PMCID: PMC7393325 DOI: 10.1016/j.omtn.2020.06.024] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/07/2020] [Accepted: 06/24/2020] [Indexed: 02/06/2023]
Abstract
The synergism between cardiomyogenesis and angiogenesis is essential for cardiac regeneration. Circular RNAs (circRNAs) play pivotal roles in cell growth and angiogenesis, but their functions in cardiac regeneration are not yet known. In this study, we investigated the role and underlying mechanisms of circRNA Hipk3 (circHipk3) in both cardiomyogenesis and angiogenesis during cardiac regeneration. We found that circHipk3 was overexpressed in the fetal or neonatal heart of mice. The transcription factor Gata4 bound to the circHipk3 promoter and increased circHipk3 expression. Cardiomyocyte (CM) proliferation in vitro and in vivo was inhibited by circHipk3 knockdown and increased by circHipk3 overexpression. Moreover, circHipk3 overexpression promoted coronary vessel endothelial cell proliferation, migration, and tube-forming capacity and subsequent angiogenesis. More importantly, circHipk3 overexpression attenuated cardiac dysfunction and decreased fibrotic area after myocardial infarction (MI). Mechanistically, circHipk3 promoted CM proliferation by increasing Notch1 intracellular domain (N1ICD) acetylation, thereby increasing N1ICD stability and preventing its degradation. In addition, circHipk3 acted as a sponge for microRNA (miR)-133a to promote connective tissue growth factor (CTGF) expression, which activated endothelial cells. Our findings suggested that circHipk3 might be a novel therapeutic target for preventing heart failure post-MI.
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109
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Branscome H, Paul S, Yin D, El-Hage N, Agbottah ET, Zadeh MA, Liotta LA, Kashanchi F. Use of Stem Cell Extracellular Vesicles as a "Holistic" Approach to CNS Repair. Front Cell Dev Biol 2020; 8:455. [PMID: 32587858 PMCID: PMC7298153 DOI: 10.3389/fcell.2020.00455] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 05/15/2020] [Indexed: 12/20/2022] Open
Abstract
Neurodegeneration is a hallmark of many diseases and disorders of the central nervous system (CNS). High levels of neuroinflammation are often associated with irreparable damage to CNS cells due to the dysregulation of signaling cascades that are unable to restore a homeostatic balance. Due to the inherent complexity of the CNS, development of CNS-related therapeutics has met limited success. While stem cell therapy has been evaluated in the context of CNS repair, the mechanisms responsible for their functional properties have not been clearly defined. In recent years, there has been growing interest in the use of stem cell extracellular vesicles (EVs) for the treatment of various CNS pathologies as these vesicles are believed to mediate many of the functional effects associated with their donor stem cells. The potency of stem cell EVs is believed to be largely driven by their biological cargo which includes various types of RNAs, proteins, and cytokines. In this review, we describe the characteristic properties of stem cell EVs and summarize their reported neuroprotective and immunomodulatory functions. A special emphasis is placed on the identification of specific biological cargo, including proteins and non-coding RNA molecules, that have been found to be associated with stem cell EVs. Collectively, this review highlights the potential of stem cell EVs as an alternative to traditional stem cell therapy for the repair of cellular damage associated with diverse CNS pathologies.
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Affiliation(s)
- Heather Branscome
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, United States
- American Type Culture Collection (ATCC), Manassas, VA, United States
| | - Siddhartha Paul
- American Type Culture Collection (ATCC) Cell Systems, Gaithersburg, MD, United States
| | - Dezhong Yin
- American Type Culture Collection (ATCC) Cell Systems, Gaithersburg, MD, United States
| | - Nazira El-Hage
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
| | - Emmanuel T. Agbottah
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Mohammad Asad Zadeh
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, United States
| | - Lance A. Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, United States
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, United States
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110
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Yao J, Qian K, Chen C, Liu X, Yu D, Yan X, Liu T, Li S. ZNF139/ circZNF139 promotes cell proliferation, migration and invasion via activation of PI3K/AKT pathway in bladder cancer. Aging (Albany NY) 2020; 12:9915-9934. [PMID: 32454461 PMCID: PMC7288921 DOI: 10.18632/aging.103256] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/29/2020] [Indexed: 02/07/2023]
Abstract
Existing reports identify the involved roles of ZNF139 and its one circular RNA (circRNA), circZNF139, in the progression of various tumors. However, their relevance and function role in bladder cancer (BC) remain largely unexplored. Herein, we aimed to reconnoiter the role and potential mechanism of ZNF139 and circZNF139 in the progression of BC. Firstly, bioinformatics analyses indicated ZNF139 was upregulated in BC tissues and correlated with disease-free survival of BC patients. The subcellular localization and structural analyses of ZNF139 conveyed the possibility of ZNF139 functioning as a transcription factor. Secondly, circZNF139 was validated by bioinformatics analyses and RNase R tests. ZNF139 and circZNF139 were both significantly upregulated in BC cell lines. Functionally, ZNF139/circZNF139 had facilitated effects on the proliferative, clonal, migratory, and invasive potential of BC cells. Mechanistically, GO, KEGG pathway analyses and western blot assays altogether unveiled ZNF139/circZNF139 activated PI3K/AKT pathway in BC cells, supported by the alteration of AKT at phosphorylation level and PI3K at the protein level. Collectively, this work reveals ZNF139 and circZNF139 cooperate closely with each other to promote cell proliferation, migration and invasion via activation of PI3K/AKT pathway in BC.
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Affiliation(s)
- Jie Yao
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Kaiyu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China
| | - Chen Chen
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China
| | - Xiaoping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Donghu Yu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xin Yan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tongzu Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Sheng Li
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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111
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Liu J, Zhang X, Yan M, Li H. Emerging Role of Circular RNAs in Cancer. Front Oncol 2020; 10:663. [PMID: 32670861 PMCID: PMC7326090 DOI: 10.3389/fonc.2020.00663] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs), which are generated mainly from back-splicing of exons in precursor mRNAs (pre-mRNAs), are a novel class of endogenous covalently closed RNA molecules. Their functions as microRNA sponges, protein scaffolds, and modulators of transcription and splicing, as well as occasional templates for polypeptide production, are beginning to be recognized, though the investigation of circRNAs is in its infancy. circRNAs play critical roles in diverse cellular processes. Aberrant expression of circRNAs in malignancies sustains cellular growth and proliferation, promotes cellular invasiveness, and circumvents cellular senescence and death, suggesting their potential for exploitation as clinical biomarkers and therapeutic targets. In this review, we highlight recent progress in research on circRNAs in cancer, emphasizing the molecular mechanisms and potential clinical value of circRNAs.
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Affiliation(s)
- Jing Liu
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China
| | - Xin Zhang
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China
| | - Meinan Yan
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China
| | - Hui Li
- Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China.,National Clinical Research Center for Cancer, Tianjin, China
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112
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Wu W, Ji P, Zhao F. CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes. Genome Biol 2020; 21:101. [PMID: 32345360 PMCID: PMC7187532 DOI: 10.1186/s13059-020-02018-y] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/14/2020] [Indexed: 12/19/2022] Open
Abstract
Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected from 19 normal tissues across six vertebrate species. This database contains 1,007,087 highly reliable circRNAs, of which over 81.3% have been assembled into full-length sequences. We profile their expression pattern, conservation, and functional annotation. We describe a novel multiple conservation score, co-expression, and regulatory networks for circRNA annotation and prioritization. CircAtlas can be accessed at http://circatlas.biols.ac.cn/.
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Affiliation(s)
- Wanying Wu
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peifeng Ji
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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113
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Zhang Y, Lin X, Geng X, Shi L, Li Q, Liu F, Fang C, Wang H. Advances in circular RNAs and their role in glioma (Review). Int J Oncol 2020; 57:67-79. [PMID: 32319596 PMCID: PMC7252450 DOI: 10.3892/ijo.2020.5049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/08/2020] [Indexed: 02/06/2023] Open
Abstract
Glioma is the most common primary tumour of the central nervous system, and is associated with a high postoperative recurrence rate and resistance to chemotherapy. High‑grade glioblastoma in particular has a very poor prognosis and poses a serious threat to human health. Related studies have confirmed that the occurrence and development of gliomas are closely associated with the abnormal expression and regulation of genes. Moreover, the number of studies on the association of the expression of non‑coding RNAs [linear RNAs, microRNAs and circular RNAs (circRNAs)] in human cells with glioma has been gradually increasing in recent years. Among those, circRNAs, previously considered to be 'splicing errors', have been shown to be highly expressed in eukaryotic cells and regulate the biological behaviour of gliomas. circRNAs are highly abundant and stable, and have become a research hotspot in the field of glioma molecular biology. The aim of the present review was to focus on the research progress regarding the association between circRNA expression and gliomas, and to provide a theoretical basis according to the currently available literature for further exploring this association. The present study may be of value for the early diagnosis, pathological grading, targeted therapy and prognostic evaluation of gliomas.
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Affiliation(s)
- Yuhao Zhang
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| | - Xiaomeng Lin
- Department of Breast Surgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Xiuchao Geng
- Hebei University of Chinese Medicine, Faculty of Integrated Traditional Chinese and Western Medicine, Shijiazhuang, Hebei 050091, P.R. China
| | - Liang Shi
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
| | - Qiang Li
- Hebei University of Chinese Medicine, Faculty of Acupuncture‑Moxibustion and Tuina, Shijiazhuang, Hebei 050200, P.R. China
| | - Fulin Liu
- Office of Academic Research, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Chuan Fang
- Department of Neurosurgery, Affiliated Hospital of Hebei University, Baoding, Hebei 071000, P.R. China
| | - Hong Wang
- Hebei University, School of Medicine, Baoding, Hebei 071000, P.R. China
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114
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Zhang Y, Guo X, Pei J, Chu M, Ding X, Wu X, Liang C, Yan P. CircRNA Expression Profile during Yak Adipocyte Differentiation and Screen Potential circRNAs for Adipocyte Differentiation. Genes (Basel) 2020; 11:E414. [PMID: 32290214 PMCID: PMC7230347 DOI: 10.3390/genes11040414] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/26/2020] [Accepted: 04/07/2020] [Indexed: 12/22/2022] Open
Abstract
The yak (Bos grunniens) is subjected to nutritional deficiency during the whole winter grazing season; deciphering the adipose metabolism and energy homeostasis under cold and nutrients stress conditions could be a novel way to understand the specific mechanism of energy metabolism. Circular RNAs (circRNAs) have elucidated that they play a key role in many biological events, but the regulatory function of adipose development remains mostly unknown. Therefore, the expression pattern of circRNAs were identified for the first time during yak adipocyte differentiation to gain insight into their potential functional involvement in bovine adipogenesis. We detected 7203 circRNA candidates, most of them contained at least two exons, and multiple circRNA isoforms could be generated from one parental gene. Analysis of differential expression circRNAs displayed that 136 circRNAs were differentially expressed at day 12 (Ad) after adipocyte differentiation, compared with the control at day 0 (Pread 0), while 7 circRNAs were detected on day 2. Sanger sequencing validated that six circRNAs had head-to-tail junction, and quantitative real-time PCR (qPCR) results revealed that the expression patterns of ten circRNAs were consistent with their expression levels from RNA-sequencing (RNA-seq) data. We further predicted the networks of circRNA-miRNA-gene based on miRNAs sponging by circRNAs, in which genes were participated in the adipocyte differentiation-related signaling pathways. After that, we constructed several adipocyte differentiation-related ceRNAs and revealed six circRNAs (novel_circ_0009127, novel_circ_0000628, novel_circ_0011513, novel_circ_0010775, novel_circ_0006981 and novel_circ_0001494) were related to adipogenesis. Furthermore, we analyzed the homology among yak, human and mouse circRNAs and found that 3536 yak circRNAs were homologous to human and mouse circRNAs. In conclusion, these findings provide a solid basis for the investigation of yak adipocyte differentiation-related circRNAs and serve as a great reference to study the energy metabolism of high-altitude animals.
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Affiliation(s)
- Yongfeng Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China;
| | - Xian Guo
- Key laboratory of yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (J.P.); (M.C.); (X.D.); (X.W.); (C.L.)
| | - Jie Pei
- Key laboratory of yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (J.P.); (M.C.); (X.D.); (X.W.); (C.L.)
| | - Min Chu
- Key laboratory of yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (J.P.); (M.C.); (X.D.); (X.W.); (C.L.)
| | - Xuezhi Ding
- Key laboratory of yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (J.P.); (M.C.); (X.D.); (X.W.); (C.L.)
| | - Xiaoyun Wu
- Key laboratory of yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (J.P.); (M.C.); (X.D.); (X.W.); (C.L.)
| | - Chunnina Liang
- Key laboratory of yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (J.P.); (M.C.); (X.D.); (X.W.); (C.L.)
| | - Ping Yan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China;
- Key laboratory of yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (X.G.); (J.P.); (M.C.); (X.D.); (X.W.); (C.L.)
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115
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CirRNAPL: A web server for the identification of circRNA based on extreme learning machine. Comput Struct Biotechnol J 2020; 18:834-842. [PMID: 32308930 PMCID: PMC7153170 DOI: 10.1016/j.csbj.2020.03.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 03/29/2020] [Accepted: 03/29/2020] [Indexed: 12/27/2022] Open
Abstract
Circular RNA (circRNA) plays an important role in the development of diseases, and it provides a novel idea for drug development. Accurate identification of circRNAs is important for a deeper understanding of their functions. In this study, we developed a new classifier, CirRNAPL, which extracts the features of nucleic acid composition and structure of the circRNA sequence and optimizes the extreme learning machine based on the particle swarm optimization algorithm. We compared CirRNAPL with existing methods, including blast, on three datasets and found CirRNAPL significantly improved the identification accuracy for the three datasets, with accuracies of 0.815, 0.802, and 0.782, respectively. Additionally, we performed sequence alignment on 564 sequences of the independent detection set of the third data set and analyzed the expression level of circRNAs. Results showed the expression level of the sequence is positively correlated with the abundance. A user-friendly CirRNAPL web server is freely available at http://server.malab.cn/CirRNAPL/.
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Key Words
- ACC, Accuracy
- CNN, Convolutional Neural Networks
- Circular RNA
- DAC, Dinucleotide-based auto-covariance
- DACC, Dinucleotide-based auto-cross-covariance
- DCC, Dinucleotide-based cross-covariance
- ELM, extreme learning machine
- Expression level
- Extreme learning machine
- GAC, Geary autocorrelation
- Identification
- MAC, Moran autocorrelation
- MCC, Matthews Correlation Coefficient
- MRMD, Maximum-Relevance-Maximum-Distance
- NMBAC, Normalized Moreau–Broto autocorrelation
- PC-PseDNC-General, General parallel correlation pseudo-dinucleotide composition
- PCGs, protein coding genes
- PSO, particle swarm optimization algorithm
- Particle swarm optimization algorithm
- PseDPC, Pseudo-distance structure status pair composition
- PseSSC, Pseudo-structure status composition
- RBF, radial basis function
- RF, random forest
- SC-PseDNC-General, General series correlation pseudo-dinucleotide composition
- SE, Sensitivity
- SP, Specifity
- SVM, support vector machine
- Triplet, Local structure-sequence triplet element
- circRNA, circular RNA
- lncRNAs, long non-coding RNAs
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116
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Zhang P, Zhang XO, Jiang T, Cai L, Huang X, Liu Q, Li D, Lu A, Liu Y, Xue W, Zhang P, Weng Z. Comprehensive identification of alternative back-splicing in human tissue transcriptomes. Nucleic Acids Res 2020; 48:1779-1789. [PMID: 31974555 PMCID: PMC7038940 DOI: 10.1093/nar/gkaa005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/14/2019] [Accepted: 01/21/2020] [Indexed: 01/16/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNAs derived from back-splicing of genes across eukaryotes. Through alternative back-splicing (ABS), a single gene produces multiple circRNAs sharing the same back-splice site. Although many ABS events have recently been discovered, to what extent ABS involves in circRNA biogenesis and how it is regulated in different human tissues still remain elusive. Here, we reported an in-depth analysis of ABS events in 90 human tissue transcriptomes. We observed that ABS occurred for about 84% circRNAs. Interestingly, alternative 5' back-splicing occurs more prevalently than alternative 3' back-splicing, and both of them are tissue-specific, especially enriched in brain tissues. In addition, the patterns of ABS events in different brain regions are similar to each other and are more complex than the patterns in non-brain tissues. Finally, the intron length and abundance of Alu elements positively correlated with ABS event complexity, and the predominant circRNAs had longer flanking introns and more Alu elements than other circRNAs in the same ABS event. Together, our results represent a resource for circRNA research-we expanded the repertoire of ABS events of circRNAs in human tissue transcriptomes and provided insights into the complexity of circRNA biogenesis, expression, and regulation.
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Affiliation(s)
- Peng Zhang
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Tingting Jiang
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lingling Cai
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiao Huang
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qi Liu
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Dan Li
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Aiping Lu
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yan Liu
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Peng Zhang
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiping Weng
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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117
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The Regulatory Functions of Circular RNAs in Digestive System Cancers. Cancers (Basel) 2020; 12:cancers12030770. [PMID: 32213977 PMCID: PMC7140005 DOI: 10.3390/cancers12030770] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 02/07/2023] Open
Abstract
Circular ribonucleic acids (circRNAs), which are a type of covalently closed circular RNA, are receiving increasing attention. An increasing amount of evidence suggests that circRNAs are involved in the biogenesis and development of multiple diseases such as digestive system cancers. Dysregulated circRNAs have been found to act as oncogenes or tumour suppressors in digestive system cancers. Moreover, circRNAs are related to ageing and a wide variety of processes in tumour cells, such as cell apoptosis, invasion, migration, and proliferation. Moreover, circRNAs can perform a remarkable multitude of biological functions, such as regulating splicing or transcription, binding RNA-binding proteins to enable function, acting as microRNA (miRNA) sponges, and undergoing translated into proteins. However, in digestive system cancers, circRNAs function mainly as miRNA sponges. Herein, we summarise the latest research progress on biological functions of circRNAs in digestive system cancers. This review serves as a synopsis of potential therapeutic targets and biological markers for digestive system cancer.
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118
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Yan XM, Zhang Z, Meng Y, Li HB, Gao L, Luo D, Jiang H, Gao Y, Yuan B, Zhang JB. Genome-wide identification and analysis of circular RNAs differentially expressed in the longissimus dorsi between Kazakh cattle and Xinjiang brown cattle. PeerJ 2020; 8:e8646. [PMID: 32211228 PMCID: PMC7081781 DOI: 10.7717/peerj.8646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/27/2020] [Indexed: 12/18/2022] Open
Abstract
Xinjiang brown cattle have better meat quality than Kazakh cattle. Circular RNAs (circRNAs) are a type of RNA that can participate in the regulation of gene transcription. Whether circRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed circRNAs regulate muscle formation and differentiation are still unknown. In this study, we established two RNA-seq libraries, each of which consisted of three samples. A total of 5,177 circRNAs were identified in longissimus dorsi samples from Kazakh cattle and Xinjiang brown cattle using the Illumina platform, 46 of which were differentially expressed. Fifty-five Gene Ontology terms were significantly enriched, and 12 Kyoto Encyclopedia of Genes and Genomes pathways were identified for the differentially expressed genes. Muscle biological processes were associated with the origin genes of the differentially expressed circRNAs. In addition, we randomly selected six overexpressed circRNAs and compared their levels in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle using RT-qPCR. Furthermore, we predicted 66 interactions among 65 circRNAs and 14 miRNAs using miRanda and established a coexpression network. A few microRNAs known for their involvement in myoblast regulation, such as miR-133b and miR-664a, were identified in this network. Notably, bta_circ_03789_1 and bta_circ_05453_1 are potential miRNA sponges that may regulate insulin-like growth factor 1 receptor expression. These findings provide an important reference for prospective investigations of the role of circRNA in longissimus muscle growth and development. This study provides a theoretical basis for targeting circRNAs to improve beef quality and taste.
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Affiliation(s)
- Xiang-Min Yan
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China.,Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Ürümqi, Xinjiang, China
| | - Zhe Zhang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Yu Meng
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Hong-Bo Li
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Ürümqi, Xinjiang, China
| | - Liang Gao
- Yili Vocational and Technical College, Yili, Xinjiang, China
| | - Dan Luo
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Hao Jiang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Yan Gao
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Bao Yuan
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Jia-Bao Zhang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
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119
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Zaiou M. circRNAs Signature as Potential Diagnostic and Prognostic Biomarker for Diabetes Mellitus and Related Cardiovascular Complications. Cells 2020; 9:cells9030659. [PMID: 32182790 PMCID: PMC7140626 DOI: 10.3390/cells9030659] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/28/2020] [Accepted: 03/05/2020] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) belong to the ever-growing class of naturally occurring noncoding RNAs (ncRNAs) molecules. Unlike linear RNA, circRNAs are covalently closed transcripts mostly generated from precursor-mRNA by a non-canonical event called back-splicing. They are highly stable, evolutionarily conserved, and widely distributed in eukaryotes. Some circRNAs are believed to fulfill a variety of functions inside the cell mainly by acting as microRNAs (miRNAs) or RNA-binding proteins (RBPs) sponges. Furthermore, mounting evidence suggests that the misregulation of circRNAs is among the first alterations in various metabolic disorders including obesity, hypertension, and cardiovascular diseases. More recent research has revealed that circRNAs also play a substantial role in the pathogenesis of diabetes mellitus (DM) and related vascular complications. These findings have added a new layer of complexity to our understanding of DM and underscored the need to reexamine the molecular pathways that lead to this disorder in the context of epigenetics and circRNA regulatory mechanisms. Here, I review current knowledge about circRNAs dysregulation in diabetes and describe their potential role as innovative biomarkers to predict diabetes-related cardiovascular (CV) events. Finally, I discuss some of the actual limitations to the promise of these RNA transcripts as emerging therapeutics and provide recommendations for future research on circRNA-based medicine.
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Affiliation(s)
- Mohamed Zaiou
- School of Pharmacy, Institut Jean-Lamour, The University of Lorraine, 7 Avenue de la Foret de Haye, CEDEX BP 90170, 54500 Vandoeuvre les Nancy, France
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120
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Lei M, Zheng G, Ning Q, Zheng J, Dong D. Translation and functional roles of circular RNAs in human cancer. Mol Cancer 2020; 19:30. [PMID: 32059672 PMCID: PMC7023758 DOI: 10.1186/s12943-020-1135-7] [Citation(s) in RCA: 431] [Impact Index Per Article: 107.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/09/2020] [Indexed: 12/21/2022] Open
Abstract
Circular RNAs (circRNAs) are a new class of non-coding RNAs formed by covalently closed loops through backsplicing. Recent methodologies have enabled in-depth characterization of circRNAs for identification and potential functions. CircRNAs play important roles in various biological functions as microRNA sponges, transcriptional regulators and combining with RNA binding proteins. Recent studies indicated that some cytoplasmic circRNAs can be effectively translated into detectable peptides, which enlightened us on the importance of circRNAs in cellular physiology function. Internal Ribosome Entry site (IRES)- and N6-methyladenosines (m6A)-mediated cap-independent translation initiation have been suggested to be potential mechanism for circRNA translation. To date, several translated circRNAs have been uncovered to play pivotal roles in human cancers. In this review, we introduced the properties and functions of circRNAs, and characterized the possible mechanism of translation initiation and complexity of the translation ability of circRNAs. We summarized the emerging functions of circRNA-encoded proteins in human cancer. The works on circRNA translation will open a hidden human proteome, and enhance us to understand the importance of circRNAs in human cancer, which has been poorly explored so far.
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Affiliation(s)
- Ming Lei
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Guantao Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Qianqian Ning
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
| | - Dong Dong
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.
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121
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Li Z, Liu S, Li X, Zhao W, Li J, Xu Y. Circular RNA in Schizophrenia and Depression. Front Psychiatry 2020; 11:392. [PMID: 32457667 PMCID: PMC7221196 DOI: 10.3389/fpsyt.2020.00392] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SZ) and depression (DEP) are two common major psychiatric disorders that are associated with high risk of suicide. These disorders affect not only physical and mental health, but they also affect the social function of the individual. However, diagnoses of SZ and DEP are mainly based on symptomatic changes and the clinical experience of psychiatrists. These rather subjective measures can induce misdiagnoses and missed diagnoses. Therefore, it is necessary to further explore objective indexes for improving the early diagnoses and prognoses of SZ and DEP. Current research indicates that non-coding RNA (ncRNA) may play a role in the occurrence and development of SZ and DEP. Circular RNA (circRNA), as an important component of ncRNA, is associated with many biological functions, especially post-transcriptional regulation. Since circRNA is easily detected in peripheral blood and has a high degree of spatiotemporal tissue specificity and stability, these attributes provide us with a new idea to further explore the potential value for the diagnosis and treatment of SZ and DEP. Here, we summarize the classification, characteristics, and biological functions of circRNA and the most significant results of experimental studies, aiming to highlight the involvement of circRNA in SZ and DEP.
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Affiliation(s)
- Zexuan Li
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Sha Liu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Xinrong Li
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Wentao Zhao
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Jing Li
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Yong Xu
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China.,Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China.,National Key Disciplines, Key Laboratory for Cellular Physiology of Ministry of Education, Department of Neurobiology, Shanxi Medical University, Taiyuan, China.,Department of Humanities and Social Science, Shanxi Medical University, Taiyuan, China
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122
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Lan W, Zhu M, Chen Q, Chen B, Liu J, Li M, Chen YPP. CircR2Cancer: a manually curated database of associations between circRNAs and cancers. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5979746. [PMID: 33181824 PMCID: PMC7661096 DOI: 10.1093/database/baaa085] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/07/2020] [Accepted: 09/10/2020] [Indexed: 01/16/2023]
Abstract
Accumulating evidences have shown that the deregulation of circRNA has close association with many human cancers. However, these experimental verified circRNA–cancer associations are not collected in any database. Here, we develop a manually curated database (circR2Cancer) that provides experimentally supported associations between circRNAs and cancers. The current version of the circR2Cancer contains 1439 associations between 1135 circRNAs and 82 cancers by extracting data from existing literatures and databases. In addition, circR2Cancer contains the information of cancer exacted from Disease Ontology and basic biological information of circRNAs from circBase. At the same time, circR2Cancer provides a simple and friendly interface for users to conveniently browse, search and download the data. It will be a useful and valuable resource for researchers to understanding the regulation mechanism of circRNA in cancers. Database URL http://www.biobdlab.cn:8000
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Affiliation(s)
- Wei Lan
- School of Computer, Electronic and Information, Guangxi University, No.100 Daxue East Road, Nanning, Guangxi, 530004, China.,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, No. 932 Lushan South Road, Changsha, Hunan, 410083, China
| | - Mingrui Zhu
- School of Computer, Electronic and Information, Guangxi University, No.100 Daxue East Road, Nanning, Guangxi, 530004, China
| | - Qingfeng Chen
- School of Computer, Electronic and Information, Guangxi University, No.100 Daxue East Road, Nanning, Guangxi, 530004, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, No.100 Daxue East Road, Nanning, Guangxi, 530004, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, No.100 Daxue East Road, Nanning, Guangxi, 530004, China
| | - Jin Liu
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, No. 932 Lushan South Road, Changsha, Hunan, 410083, China
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, No. 932 Lushan South Road, Changsha, Hunan, 410083, China
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Information Technology, La Trobe University Plenty Rd & Kingsbury Dr, Melbourne, Vic 3086, Australia
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123
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Ferrero G, Licheri N, Coscujuela Tarrero L, De Intinis C, Miano V, Calogero RA, Cordero F, De Bortoli M, Beccuti M. Docker4Circ: A Framework for the Reproducible Characterization of circRNAs from RNA-Seq Data. Int J Mol Sci 2019; 21:ijms21010293. [PMID: 31906249 PMCID: PMC6982331 DOI: 10.3390/ijms21010293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 12/28/2019] [Indexed: 01/09/2023] Open
Abstract
Recent improvements in cost-effectiveness of high-throughput technologies has allowed RNA sequencing of total transcriptomes suitable for evaluating the expression and regulation of circRNAs, a relatively novel class of transcript isoforms with suggested roles in transcriptional and post-transcriptional gene expression regulation, as well as their possible use as biomarkers, due to their deregulation in various human diseases. A limited number of integrated workflows exists for prediction, characterization, and differential expression analysis of circRNAs, none of them complying with computational reproducibility requirements. We developed Docker4Circ for the complete analysis of circRNAs from RNA-Seq data. Docker4Circ runs a comprehensive analysis of circRNAs in human and model organisms, including: circRNAs prediction; classification and annotation using six public databases; back-splice sequence reconstruction; internal alternative splicing of circularizing exons; alignment-free circRNAs quantification from RNA-Seq reads; and differential expression analysis. Docker4Circ makes circRNAs analysis easier and more accessible thanks to: (i) its R interface; (ii) encapsulation of computational tasks into docker images; (iii) user-friendly Java GUI Interface availability; and (iv) no need of advanced bash scripting skills for correct use. Furthermore, Docker4Circ ensures a reproducible analysis since all its tasks are embedded into a docker image following the guidelines provided by Reproducible Bioinformatics Project.
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Affiliation(s)
- Giulio Ferrero
- Department of Computer Science, University of Turin, 10149 Turin, Italy; (G.F.); (N.L.); (C.D.I.); (F.C.); (M.B.)
| | - Nicola Licheri
- Department of Computer Science, University of Turin, 10149 Turin, Italy; (G.F.); (N.L.); (C.D.I.); (F.C.); (M.B.)
| | - Lucia Coscujuela Tarrero
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy; (L.C.T.); (V.M.)
- Center for Genomic Science, Italian Institute of Technology, 20139 Milan, Italy
| | - Carlo De Intinis
- Department of Computer Science, University of Turin, 10149 Turin, Italy; (G.F.); (N.L.); (C.D.I.); (F.C.); (M.B.)
| | - Valentina Miano
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy; (L.C.T.); (V.M.)
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Raffaele Adolfo Calogero
- Department of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy;
| | - Francesca Cordero
- Department of Computer Science, University of Turin, 10149 Turin, Italy; (G.F.); (N.L.); (C.D.I.); (F.C.); (M.B.)
| | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, 10043 Turin, Italy; (L.C.T.); (V.M.)
- Correspondence:
| | - Marco Beccuti
- Department of Computer Science, University of Turin, 10149 Turin, Italy; (G.F.); (N.L.); (C.D.I.); (F.C.); (M.B.)
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124
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Zhang K, Pan X, Yang Y, Shen HB. CRIP: predicting circRNA-RBP-binding sites using a codon-based encoding and hybrid deep neural networks. RNA (NEW YORK, N.Y.) 2019; 25:1604-1615. [PMID: 31537716 PMCID: PMC6859861 DOI: 10.1261/rna.070565.119] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/21/2019] [Indexed: 05/21/2023]
Abstract
Circular RNAs (circRNAs), with their crucial roles in gene regulation and disease development, have become rising stars in the RNA world. To understand the regulatory function of circRNAs, many studies focus on the interactions between circRNAs and RNA-binding proteins (RBPs). Recently, the abundant CLIP-seq experimental data has enabled the large-scale identification and analysis of circRNA-RBP interactions, whereas, as far as we know, no computational tool based on machine learning has been proposed yet. We develop CRIP (CircRNAs Interact with Proteins) for the prediction of RBP-binding sites on circRNAs using RNA sequences alone. CRIP consists of a stacked codon-based encoding scheme and a hybrid deep learning architecture, in which a convolutional neural network (CNN) learns high-level abstract features and a recurrent neural network (RNN) learns long dependency in the sequences. We construct 37 data sets including sequence fragments of binding sites on circRNAs, and each set corresponds to an RBP. The experimental results show that the new encoding scheme is superior to the existing feature representation methods for RNA sequences, and the hybrid network outperforms conventional classifiers by a large margin, where both the CNN and RNN components contribute to the performance improvement.
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Affiliation(s)
- Kaiming Zhang
- Center for Brain-Like Computing and Machine Intelligence, Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
- Department of Medical Informatics, Erasmus Medical Center, Rotterdam 3015 CE, Netherlands
| | - Yang Yang
- Center for Brain-Like Computing and Machine Intelligence, Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, 200240, China
| | - Hong-Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai 200240, China
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125
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Wang Z, Lei X, Wu FX. Identifying Cancer-Specific circRNA-RBP Binding Sites Based on Deep Learning. Molecules 2019; 24:E4035. [PMID: 31703384 PMCID: PMC6891306 DOI: 10.3390/molecules24224035] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/25/2019] [Accepted: 11/06/2019] [Indexed: 12/17/2022] Open
Abstract
Circular RNAs (circRNAs) are extensively expressed in cells and tissues, and play crucial roles in human diseases and biological processes. Recent studies have reported that circRNAs could function as RNA binding protein (RBP) sponges, meanwhile RBPs can also be involved in back-splicing. The interaction with RBPs is also considered an important factor for investigating the function of circRNAs. Hence, it is necessary to understand the interaction mechanisms of circRNAs and RBPs, especially in human cancers. Here, we present a novel method based on deep learning to identify cancer-specific circRNA-RBP binding sites (CSCRSites), only using the nucleotide sequences as the input. In CSCRSites, an architecture with multiple convolution layers is utilized to detect the features of the raw circRNA sequence fragments, and further identify the binding sites through a fully connected layer with the softmax output. The experimental results show that CSCRSites outperform the conventional machine learning classifiers and some representative deep learning methods on the benchmark data. In addition, the features learnt by CSCRSites are converted to sequence motifs, some of which can match to human known RNA motifs involved in human diseases, especially cancer. Therefore, as a deep learning-based tool, CSCRSites could significantly contribute to the function analysis of cancer-associated circRNAs.
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Affiliation(s)
- Zhengfeng Wang
- School of Computer Science, Shaanxi Normal University, Xi’an 710119, China;
- College of Information Science and Engineering, Guilin University of Technology, Guilin 541004, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi’an 710119, China;
| | - Fang-Xiang Wu
- Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada;
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126
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Bioinformatic Analysis of Circular RNA-Associated ceRNA Network Associated with Hepatocellular Carcinoma. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8308694. [PMID: 31886256 PMCID: PMC6926424 DOI: 10.1155/2019/8308694] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/23/2019] [Accepted: 10/15/2019] [Indexed: 12/29/2022]
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and is associated with a high mortality rate and poor treatment efficacy. In an attempt to investigate the mechanisms involved in the pathogenesis of HCC, bioinformatic analysis and validation by qRT-PCR were performed. Three circRNA GEO datasets and one miRNA GEO dataset were selected for this purpose. Upon combined biological prediction, a total of 11 differentially expressed circRNAs, 15 differentially expressed miRNAs, and 560 target genes were screened to construct a circRNA-related ceRNA network. GO analysis and KEGG pathway analysis were performed for the 560 target genes. To further screen key genes, a protein-protein interaction network of the target genes was constructed using STRING, and the genes and modules with higher degree were identified by MCODE and CytoHubba plugins of Cytoscape. Subsequently, a module was screened out and subjected to GO enrichment analysis and KEGG pathway analysis. This module included eight genes, which were further screened using TCGA. Finally, UBE2L3 was selected as a key gene and the hsa_circ_0009910-miR-1261-UBE2L3 regulatory axis was established. The relative expression of the regulatory axis members was confirmed by qRT-PCR in 30 pairs of samples, including HCC tissues and adjacent nontumor tissues. The results suggested that hsa_circ_0009910, which was upregulated in HCC tissues, participates in the pathogenesis of HCC by acting as a sponge of miR-1261 to regulate the expression of UBE2L3. Overall, this study provides support for the possible mechanisms of progression in HCC.
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127
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Di Liddo A, de Oliveira Freitas Machado C, Fischer S, Ebersberger S, Heumüller AW, Weigand JE, Müller-McNicoll M, Zarnack K. A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress. J Mol Cell Biol 2019; 11:829-844. [PMID: 31560396 PMCID: PMC6884703 DOI: 10.1093/jmcb/mjz094] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 07/09/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
Hypoxia is associated with several diseases, including cancer. Cells that are deprived of adequate oxygen supply trigger transcriptional and post-transcriptional responses, which control cellular pathways such as angiogenesis, proliferation, and metabolic adaptation. Circular RNAs (circRNAs) are a novel class of mainly non-coding RNAs, which have been implicated in multiple cancers and attract increasing attention as potential biomarkers. Here, we characterize the circRNA signatures of three different cancer cell lines from cervical (HeLa), breast (MCF-7), and lung (A549) cancer under hypoxia. In order to reliably detect circRNAs, we integrate available tools with custom approaches for quantification and statistical analysis. Using this consolidated computational pipeline, we identify ~12000 circRNAs in the three cancer cell lines. Their molecular characteristics point to an involvement of complementary RNA sequences as well as trans-acting factors in circRNA biogenesis, such as the RNA-binding protein HNRNPC. Notably, we detect a number of circRNAs that are more abundant than their linear counterparts. In addition, 64 circRNAs significantly change in abundance upon hypoxia, in most cases in a cell type-specific manner. In summary, we present a comparative circRNA profiling in human cancer cell lines, which promises novel insights into the biogenesis and function of circRNAs under hypoxic stress.
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Affiliation(s)
- Antonella Di Liddo
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Camila de Oliveira Freitas Machado
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sandra Fischer
- Department of Biology, Technical University Darmstadt, Germany
| | | | - Andreas W Heumüller
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, Germany
| | - Michaela Müller-McNicoll
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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128
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Fang X, Wen J, Sun M, Yuan Y, Xu Q. CircRNAs and its relationship with gastric cancer. J Cancer 2019; 10:6105-6113. [PMID: 31762820 PMCID: PMC6856571 DOI: 10.7150/jca.32927] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 08/18/2019] [Indexed: 01/17/2023] Open
Abstract
Circular RNAs (circRNAs), as a type of tissue specific RNA with more stable structure than linear RNAs, was poorly understood on its correlation with gastric cancer (GC). In this review, we outline the synthesis and characteristics of circRNAs and generalize their categories and functions. Through comprehensive analysis of the reported results, we find that circRNAs not only participate in the regulation of gastric cancer (GC) cell biological behaviors, such as proliferation, invasion, migration and epithelial mesenchymal transition (EMT), but also are related to the clinicopathological features of GC such as tumor differentiation, TNM stage and metastasis, etc. According to the present screening and verification results, circRNAs are suggested to be used as biomarkers for the early diagnosis and prognosis prediction of GC, and those circRNAs involved in the genesis and development of GC have the potential as novel targets for the individualized treatment of GC.
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Affiliation(s)
- Xinxin Fang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang, China.,Department of Gastroenterology, First Affiliated Hospital, China Medical University, Shenyang City, Liaoning Province, China
| | - Jing Wen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang, China.,Department of Gastroenterology, First Affiliated Hospital, China Medical University, Shenyang City, Liaoning Province, China
| | - Mingjun Sun
- Department of Gastroenterology, First Affiliated Hospital, China Medical University, Shenyang City, Liaoning Province, China.,Key Laboratory of Gastrointestinal Cancer Etiology and Screening, Liaoning Province, Shenyang 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang, China.,Key Laboratory of Gastrointestinal Cancer Etiology and Screening, Liaoning Province, Shenyang 110001, China
| | - Qian Xu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Liaoning Provincial Education Department, Shenyang, China.,Key Laboratory of Gastrointestinal Cancer Etiology and Screening, Liaoning Province, Shenyang 110001, China
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129
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Corey S, Luo Y. Circular RNAs and neutrophils: Key factors in tackling asymptomatic moyamoya disease. Brain Circ 2019; 5:150-155. [PMID: 31620664 PMCID: PMC6785948 DOI: 10.4103/bc.bc_38_19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/01/2019] [Accepted: 09/02/2019] [Indexed: 12/23/2022] Open
Abstract
Moyamoya disease (MMD) represents a rare steno-occlusive disorder affecting the terminal ends of the internal carotid artery and promoting the development of a poor, abnormal vascular network at the brain's base. Primarily affecting East Asian countries over Western populations, MMD can be further divided into symptomatic and asymptomatic subtypes. The current knowledge of the underlying mechanisms and potential management strategies for asymptomatic cases of MMD are largely lacking and thus warrant investigation to elucidate the pathology of this rare disorder. Here, we assess research examining the expression profile of circular RNAs (circRNAs) of neutrophil transcriptome in asymptomatic MMD patients. These findings conclude that 123 differentially expressed circRNAs significantly contributed to metabolism, angiogenesis, and immune response. The hypoxia-inducing factor-1α signaling pathway was also revealed to be crucial in angiogenesis. We also evaluate current therapeutic options demonstrating the potential for MMD patients, such as EC-IC bypass and ischemic pre- and post-conditioning. These approaches combined with recent findings on the circRNA expression profile suggest a crucial role of anti-inflammatory and angiogenic-related mechanisms underlying MMD. Investigating the role of circRNAs and neutrophils in the asymptomatic MMD subtype may provide insight into its elusive pathology and direct future approaches to combat the progression of this rare disease.
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Affiliation(s)
- Sydney Corey
- Department of Neurosurgery and Brain Repair, College of Medicine, University of South Florida Morsani, Tampa, FL, USA
| | - Yumin Luo
- Department of Neurosurgery and Brain Repair, College of Medicine, University of South Florida Morsani, Tampa, FL, USA.,Institute of Cerebrovascular Diseases Research and Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
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130
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Shang BQ, Li ML, Quan HY, Hou PF, Li ZW, Chu SF, Zheng JN, Bai J. Functional roles of circular RNAs during epithelial-to-mesenchymal transition. Mol Cancer 2019; 18:138. [PMID: 31526370 PMCID: PMC6745795 DOI: 10.1186/s12943-019-1071-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
Cancer has become a major health issue worldwide, contributing to a high mortality rate. Tumor metastasis is attributed to the death of most patients. Epithelial-to-mesenchymal transition (EMT) plays a vital role in inducing metastasis. During EMT, epithelial cells lose their characteristics, such as cell-to-cell adhesion and cell polarity, and cells gain motility, migratory potential, and invasive properties to become mesenchymal stem cells. Circular RNAs (circRNAs) are closely associated with tumor metastasis and patient prognosis, as revealed by increasing lines of evidence. CircRNA is a type of single-stranded RNA that forms a covalently closed continuous loop. CircRNAs are insensitive to ribonucleases and are widespread in body fluids. This work is the first review on EMT-related circRNAs. In this review, we briefly discuss the characteristics and functions of circRNAs. The correlation of circRNAs with EMT has been reported, and we discuss the ways circRNAs can regulate EMT progression through EMT transcription factors, EMT-related signaling pathways, and other mechanisms. This work summarizes current studies on EMT-related circRNAs in various cancers and provides a theoretical basis for the use of EMT-related circRNAs in targeted management and therapy.
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Affiliation(s)
- Bing-Qing Shang
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Min-Le Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Hao-Yu Quan
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Ping-Fu Hou
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Zhong-Wei Li
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Su-Fang Chu
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China
| | - Jun-Nian Zheng
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China.
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, 84 West Huaihai Road, Xuzhou, 221002, Jiangsu Province, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, Jiangsu Province, China.
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131
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Mei M, Wang Y, Li Z, Zhang M. Role of circular RNA in hematological malignancies. Oncol Lett 2019; 18:4385-4392. [PMID: 31611947 PMCID: PMC6781753 DOI: 10.3892/ol.2019.10836] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/13/2019] [Indexed: 12/18/2022] Open
Abstract
Compared with linear RNA, circular RNAs (circRNAs) form a covalently closed circular continuous loop and are highly conserved, stable and tissue-specific. In recent years, circRNAs received considerable attention in the diagnosis, classification, treatment and prognosis of hematological tumors. circRNAs function as microRNA sponges and competitive endogenous RNAs that play an essential role in the translation, regulation and interaction of proteins. The present review discussed the fundamental properties and functions of circRNAs and the latest advancements in the context of circRNAs in the clinical research of hematological malignancies, namely acute and chronic myeloid leukemia, and chronic lymphocytic leukemia. circRNAs show potential in the diagnosis and prognosis of various diseases and can be used as therapeutic targets and biomarkers for disease.
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Affiliation(s)
- Mei Mei
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yingjun Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Zhaoming Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Mingzhi Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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132
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Xia S, Feng J, Chen K, Ma Y, Gong J, Cai F, Jin Y, Gao Y, Xia L, Chang H, Wei L, Han L, He C. CSCD: a database for cancer-specific circular RNAs. Nucleic Acids Res 2019; 46:D925-D929. [PMID: 29036403 PMCID: PMC5753219 DOI: 10.1093/nar/gkx863] [Citation(s) in RCA: 277] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 09/14/2017] [Indexed: 01/05/2023] Open
Abstract
Circular RNA (circRNA) is a large group of RNA family extensively existed in cells and tissues. High-throughput sequencing provides a way to view circRNAs across different samples, especially in various diseases. However, there is still no comprehensive database for exploring the cancer-specific circRNAs. We collected 228 total RNA or polyA(-) RNA-seq samples from both cancer and normal cell lines, and identified 272 152 cancer-specific circRNAs. A total of 950 962 circRNAs were identified in normal samples only, and 170 909 circRNAs were identified in both tumor and normal samples, which could be further used as non-tumor background. We constructed a cancer-specific circRNA database (CSCD, http://gb.whu.edu.cn/CSCD). To understand the functional effects of circRNAs, we predicted the microRNA response element sites and RNA binding protein sites for each circRNA. We further predicted potential open reading frames to highlight translatable circRNAs. To understand the association between the linear splicing and the back-splicing, we also predicted the splicing events in linear transcripts of each circRNA. As the first comprehensive cancer-specific circRNA database, we believe CSCD could significantly contribute to the research for the function and regulation of cancer-associated circRNAs.
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Affiliation(s)
- Siyu Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China.,Hubei Province Key Laboratory of Allergy and Immunology, Wuhan 430071, Hubei, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, Hubei, China
| | - Jing Feng
- International School of Software, Wuhan University, Wuhan 430072, Hubei, China
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Yanbing Ma
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Jing Gong
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Fangfang Cai
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Yuxuan Jin
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Yang Gao
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Linjian Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Hong Chang
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Lei Wei
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Chunjiang He
- School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, China.,Hubei Province Key Laboratory of Allergy and Immunology, Wuhan 430071, Hubei, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan 430071, Hubei, China
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133
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Feng J, Xiang Y, Xia S, Liu H, Wang J, Ozguc FM, Lei L, Kong R, Diao L, He C, Han L. CircView: a visualization and exploration tool for circular RNAs. Brief Bioinform 2019; 19:1310-1316. [PMID: 29106456 DOI: 10.1093/bib/bbx070] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Indexed: 01/16/2023] Open
Abstract
Circular RNAs (circRNAs) are novel rising stars of noncoding RNAs, which are highly abundant and evolutionarily conserved across species. Number of publications related to circRNAs increased sharply in recent years, representing emerging focuses in the field. Therefore, tools, pipelines and databases have been developed to identify and store circRNAs. However, there is no existing tool to visualize and explore circRNAs. Therefore, we introduce CircView, a user-friendly visualization tool for circRNAs detected from existing tools. CircView enables users to visualize circRNAs and to quantify number of samples with detected circRNAs. CircView allows users to explore circRNAs detected by unique or multiple tools. Furthermore, CircView allows users to view the regulatory elements, such as microRNA response elements and RNA-binding protein binding sites. CircView is a unique tool to visualize and explore circRNAs, which helps users to better understand potential functions of circRNAs and design the functional experiments.
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Affiliation(s)
- Jing Feng
- International School of Software, Wuhan University
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School
| | - Siyu Xia
- School of Basic Medical Sciences, Wuhan University
| | - Huan Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences
| | - Jun Wang
- School of Basic Medical Sciences, Wuhan University
| | - Fatma Muge Ozguc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School
| | - Lijun Lei
- School of Basic Medical Sciences, Wuhan University
| | - Ruoshan Kong
- International School of Software, Wuhan University
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center
| | - Chunjiang He
- School of Basic Medical Sciences and Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University
| | - Leng Han
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School
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134
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Fusion of multiple heterogeneous networks for predicting circRNA-disease associations. Sci Rep 2019; 9:9605. [PMID: 31270357 PMCID: PMC6610109 DOI: 10.1038/s41598-019-45954-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs (circRNAs) are a newly identified type of non-coding RNA (ncRNA) that plays crucial roles in many cellular processes and human diseases, and are potential disease biomarkers and therapeutic targets in human diseases. However, experimentally verified circRNA-disease associations are very rare. Hence, developing an accurate and efficient method to predict the association between circRNA and disease may be beneficial to disease prevention, diagnosis, and treatment. Here, we propose a computational method named KATZCPDA, which is based on the KATZ method and the integrations among circRNAs, proteins, and diseases to predict circRNA-disease associations. KATZCPDA not only verifies existing circRNA-disease associations but also predicts unknown associations. As demonstrated by leave-one-out and 10-fold cross-validation, KATZCPDA achieves AUC values of 0.959 and 0.958, respectively. The performance of KATZCPDA was substantially higher than those of previously developed network-based methods. To further demonstrate the effectiveness of KATZCPDA, we apply KATZCPDA to predict the associated circRNAs of Colorectal cancer, glioma, breast cancer, and Tuberculosis. The results illustrated that the predicted circRNA-disease associations could rank the top 10 of the experimentally verified associations.
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135
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Huang J, Zhao J, Zheng Q, Wang S, Wei X, Li F, Shang J, Lei C, Ma Y. Characterization of Circular RNAs in Chinese Buffalo ( Bubalus bubalis) Adipose Tissue: A Focus on Circular RNAs Involved in Fat Deposition. Animals (Basel) 2019; 9:E403. [PMID: 31266200 PMCID: PMC6680660 DOI: 10.3390/ani9070403] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/21/2019] [Accepted: 06/23/2019] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) have been identified as a novel type of regulators involved in multiple biological processes. However, circRNAs with a potential function in fat deposition in buffalo are poorly understood. In this study, six RNA libraries of adipose tissue were constructed for three young and three adult Chinese buffaloes with paired-ends RNA sequencing using the Illumina HiSeq 3000 platform. A total of 5141 circRNAs were computationally identified. Among them, 252 circRNAs were differentially expressed (DE) between the young and adult buffaloes. Of these, 54 were upregulated and 198 were downregulated in the adult group. Eight DE circRNAs were further identified by quantitative real-time-PCR (qRT-PCR) and Sanger sequencing. Co-expression analysis revealed that 34 circRNAs demonstrated a strong correlation with fat deposition-associated genes (|r| > 0.980). Among these, expressional correlation between two circRNAs (19:45387150|45389986 and 21:6969877|69753491) and PR/SET domain 16 was further verified using qRT-PCR, and a strong correlation was revealed (1 > |r| > 0.8). These results strongly suggest that circRNAs 19:45387150|45389986 and 21:6969877|69753491 are potential regulators of buffalo fat deposition. In summary, this study characterized the circRNA profiles of adipose tissues at different stages for the first time and revealed two circRNAs strongly correlated with fat deposition-associated genes, which provided new candidate regulators for fat deposition in buffalo.
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Affiliation(s)
- Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan 464000, China
| | - Jinhui Zhao
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Qiuzhi Zheng
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Shuzhe Wang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Xuefeng Wei
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Fen Li
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Jianghua Shang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China.
- Institute for Conservation and Utilization of Agro-Bioresources in Dabie Mountains, Xinyang, Henan 464000, China.
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136
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Su M, Xiao Y, Ma J, Tang Y, Tian B, Zhang Y, Li X, Wu Z, Yang D, Zhou Y, Wang H, Liao Q, Wang W. Circular RNAs in Cancer: emerging functions in hallmarks, stemness, resistance and roles as potential biomarkers. Mol Cancer 2019; 18:90. [PMID: 30999909 PMCID: PMC6471953 DOI: 10.1186/s12943-019-1002-6] [Citation(s) in RCA: 276] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of RNA molecules with closed loops and high stability. CircRNAs are abundantly expressed in eukaryotic organisms and exhibit both location- and step-specificity. In recent years, circRNAs are attracting considerable research attention attributed to their possible contributions to gene regulation through a variety of actions, including sponging microRNAs, interacting with RNA-binding proteins, regulating transcription and splicing, and protein translation. Growing evidence has revealed that circRNAs play critical roles in the development and progression of diseases, especially in cancers. Without doubt, expanding our understanding of circRNAs will enrich knowledge of cancer and provide new opportunities for cancer therapy. In this review, we provide an overview of the characteristics, functions and functional mechanisms of circRNAs. In particular, we summarize current knowledge regarding the functions of circRNAs in the hallmarks, stemness, resistance of cancer, as well as the possibility of circRNAs as biomarkers in cancer.
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Affiliation(s)
- Min Su
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China.,Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Yuhang Xiao
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Department of Pharmacy, Xiangya Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410001, People's Republic of China
| | - Junliang Ma
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Yanyan Tang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Bo Tian
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Yuqin Zhang
- Department of Pharmacy, Xiangya Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410001, People's Republic of China
| | - Xu Li
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Zhining Wu
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Desong Yang
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Yong Zhou
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China
| | - Hui Wang
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianjin Liao
- Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China. .,Department of the Central Laboratory, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China.
| | - Wenxiang Wang
- Department of the 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410013, People's Republic of China. .,Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.
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137
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Feng J, Chen K, Dong X, Xu X, Jin Y, Zhang X, Chen W, Han Y, Shao L, Gao Y, He C. Genome-wide identification of cancer-specific alternative splicing in circRNA. Mol Cancer 2019; 18:35. [PMID: 30849979 PMCID: PMC6408762 DOI: 10.1186/s12943-019-0996-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 03/04/2019] [Indexed: 01/05/2023] Open
Abstract
Circular RNA (circRNA) is a group of RNA families generated by RNA circularization, which was discovered ubiquitously across different cancers. However, the internal structure of circRNA is difficult to determine due to alternative splicing that occurs in its exons and introns. Furthermore, cancer-specific alternative splicing of circRNA is less likely to be identified. Here, we proposed a de novo algorithm, CircSplice, that could identify internal alternative splicing in circRNA and compare differential circRNA splicing events between different conditions (http://gb.whu.edu.cn/CircSplice or https://github.com/GeneFeng/CircSplice). By applying CircSplice in clear cell renal cell carcinoma and bladder cancer, we detected 4498 and 2977 circRNA alternative splicing (circ-AS) events in the two datasets respectively and confirmed the expression of circ-AS events by RT-PCR. We further inspected the distributions and patterns of circ-AS in cancer and adjacent normal tissues. To further understand the potential functions of cancer-specific circ-AS, we classified those events into tumor suppressors and oncogenes and performed pathway enrichment analysis. This study is the first comprehensive view of cancer-specific circRNA alternative splicing, which could contribute significantly to regulation and functional research of circRNAs in cancers.
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Affiliation(s)
- Jing Feng
- School of Computer Science, Wuhan University, Wuhan, 430072, Hubei, China.
| | - Ke Chen
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xin Dong
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China.,Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, 430071, Hubei, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei, China
| | - Xiaolong Xu
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yuxuan Jin
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Xinyang Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Wenbo Chen
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yujing Han
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Lin Shao
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Yang Gao
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Chunjiang He
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei, China. .,Hubei Province Key Laboratory of Allergy and Immunology, Wuhan, 430071, Hubei, China. .,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, Hubei, China.
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138
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Harries LW. RNA Biology Provides New Therapeutic Targets for Human Disease. Front Genet 2019; 10:205. [PMID: 30906315 PMCID: PMC6418379 DOI: 10.3389/fgene.2019.00205] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 02/26/2019] [Indexed: 12/11/2022] Open
Abstract
RNA is the messenger molecule that conveys information from the genome and allows the production of biomolecules required for life in a responsive and regulated way. Most genes are able to produce multiple mRNA products in response to different internal or external environmental signals, in different tissues and organs, and at specific times in development or later life. This fine tuning of gene expression is dependent on the coordinated effects of a large and intricate set of regulatory machinery, which together orchestrate the genomic output at each locus and ensure that each gene is expressed at the right amount, at the right time and in the correct location. This complexity of control, and the requirement for both sequence elements and the entities that bind them, results in multiple points at which errors may occur. Errors of RNA biology are common and found in association with both rare, single gene disorders, but also more common, chronic diseases. Fortunately, complexity also brings opportunity. The existence of many regulatory steps also offers multiple levels of potential therapeutic intervention which can be exploited. In this review, I will outline the specific points at which coding RNAs may be regulated, indicate potential means of intervention at each stage, and outline with examples some of the progress that has been made in this area. Finally, I will outline some of the remaining challenges with the delivery of RNA-based therapeutics but indicate why there are reasons for optimism.
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Affiliation(s)
- Lorna W. Harries
- RNA-Mediated Mechanisms of Disease, College of Medicine and Health, The Institute of Biomedical and Clinical Science, Medical School, University of Exeter, Exeter, United Kingdom
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139
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Sekar S, Liang WS. Circular RNA expression and function in the brain. Noncoding RNA Res 2019; 4:23-29. [PMID: 30891534 PMCID: PMC6404376 DOI: 10.1016/j.ncrna.2019.01.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/26/2018] [Accepted: 01/04/2019] [Indexed: 01/16/2023] Open
Abstract
Within the last decade, active research on circular RNAs (circRNAs) has dramatically improved our understanding of the expression and function of these non-coding RNAs. While several mechanisms for circRNA function have been proposed, including sequestration of microRNAs and regulation of cellular proteins, studies provide evidence that circRNAs can regulate transcription and may also serve as biomarkers. Due to the heterogeneous nature of the brain, and the dynamic transcriptional mechanisms that support neurobiological pathways, the influence of circRNAs is potentially extensive. Understanding how circRNAs contribute to key neurological pathways will fill gaps in our understanding of brain function and provide valuable insight into novel therapeutic approaches to treat neurological diseases. Here, we review recent research on circRNA expression in the brain, describe the proposed functions of circRNAs, and evaluate the role of circRNAs in neurological diseases.
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140
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Characterization of tissue-specific biomarkers with the expression of circRNAs in forensically relevant body fluids. Int J Legal Med 2019; 133:1321-1331. [PMID: 30810820 DOI: 10.1007/s00414-019-02027-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/14/2019] [Indexed: 10/27/2022]
Abstract
Messenger RNA (mRNA) markers have been extensively investigated for the identification of forensically relevant body fluids and tissues based on their expression profiles among cell types. As products of the backsplicing of pre-mRNAs, circular RNAs (circRNAs) share exonic sequences with their linear counterparts. The inclusion of circRNAs in mRNA profiling is shown to facilitate the detection of biomarkers in the identification of body fluids. In this study, we identified the expression of circRNAs of 14 out of 45 biomarkers from five body fluid types using outward-facing primer sets and revealed the ratio of circular to total transcripts of biomarkers by RNase R treatment. Furthermore, our results of qPCR analysis show that the inclusion of circRNAs in the detection of biomarkers, including HBA and ALAS2 for blood; MMP7 and MMP10 for menstrual blood; HTN3 for saliva; SPINK5, SERPINB3, ESR1, and CYP2B7P1 for vaginal secretions; TGM4, KLK3, and PRM2 for semen; and SLC22A6 and MIOX for urine, does not impair the specificity of these biomarkers. Additionally, a high copy number of targets from linear transcripts could be employed to increase the detection sensitivity of TGM4 and KLK3 with a low expression level of circRNAs in urine samples. Altogether, these results will help with the development of robust multiplex assays for body fluid identification.
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141
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Abstract
As a newly discovered type of RNA, circular RNAs (circRNAs) are widespread throughout the eukaryotic genome. The expression of circRNAs is regulated by both cis-elements and trans-factors, and the expression pattern of circRNAs is cell type- and disease-specific. Similar to other types of non-coding RNAs, functions of circRNAs are also versatile. CircRNAs have been reported previously to function as microRNA (miRNA) sponges, protein sponges, coding RNAs or scaffolds for protein complexes. Recently, several circRNAs have been reported to play important roles in human malignancies, including glioma. Here, we reviewed several reports related to circRNAs and glioma, as well as the potential diagnostic and therapeutic applications of circRNAs in brain cancer. In general, some circRNAs, such as circSMARCA5 and circCFH, are found to be expressed in a glioma-specific pattern, these circRNAs may be used as tumor biomarkers. In addition, some circRNAs have been found to play oncogenic roles in glioma (e.g., circNFIX and circNT5E), whereas others have been reported to function as tumor suppressors (e.g., circFBXW7 and circSHPRH). Furthermore, circRNA is a good tool for protein expression because of its higher stability compared to linear RNAs. Thus, circRNAs may also be an ideal choice for gene/protein delivery in future brain cancer therapies. There are some challenges in circRNA research in glioma and other diseases. Research related to circRNAs in glioma is comparatively new and many mysteries remain to be solved.
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Affiliation(s)
- Jinglei Liu
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou 510080, China
| | - Kun Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou 510080, China
| | - Nunu Huang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou 510080, China
| | - Nu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangzhou 510080, China
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142
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Wang K, Wang C, Guo B, Song K, Shi C, Jiang X, Wang K, Tan Y, Wang L, Wang L, Li J, Li Y, Cai Y, Zhao H, Sun X. CropCircDB: a comprehensive circular RNA resource for crops in response to abiotic stress. Database (Oxford) 2019; 2019:baz053. [PMID: 31058278 PMCID: PMC6501434 DOI: 10.1093/database/baz053] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 11/13/2022]
Abstract
Circular RNA (circRNAs) may mediate mRNA expression as miRNA sponge. Since the community has paid more attention on circRNAs, a lot of circRNA databases have been developed for plant. However, a comprehensive collection of circRNAs in crop response to abiotic stress is still lacking. In this work, we applied a big-data approach to take full advantage of large-scale sequencing data, and developed a rich circRNA resource: CropCircDB for maize and rice, later extending to incorporate more crop species. We also designed a metric: stress detections score, which is specifically for detecting circRNAs under stress condition. In summary, we systematically investigated 244 and 288 RNA-Seq samples for maize and rice, respectively, and found 38 785 circRNAs in maize, and 63 048 circRNAs in rice. This resource not only supports user-friendly JBrowser to visualize genome easily, but also provides elegant view of circRNA structures and dynamic profiles of circRNA expression in all samples. Together, this database will host all predicted and validated crop circRNAs response to abiotic stress.
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Affiliation(s)
- Kai Wang
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Chong Wang
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Baohuan Guo
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Kun Song
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Chuanhong Shi
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Xin Jiang
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Keyi Wang
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Yacong Tan
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Lequn Wang
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Lin Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Jiangjiao Li
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Ying Li
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Yu Cai
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
| | - Hongwei Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Xiaoyong Sun
- Agricultural Big-Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian, China
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143
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Meng X, Hu D, Zhang P, Chen Q, Chen M. CircFunBase: a database for functional circular RNAs. Database (Oxford) 2019; 2019:5306167. [PMID: 30715276 PMCID: PMC6360206 DOI: 10.1093/database/baz003] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 12/23/2018] [Accepted: 01/07/2019] [Indexed: 01/26/2023]
Abstract
Increasing evidence reveals that circular RNAs (circRNAs) are widespread in eukaryotes and play important roles in diverse biological processes. However, a comprehensive functionally annotated circRNA database is still lacking. CircFunBase is a web-accessible database that aims to provide a high-quality functional circRNA resource including experimentally validated and computationally predicted functions. The current version of CircFunBase documents more than 7000 manually curated functional circRNA entries, mainly including Homo sapiens, Mus musculus etc. CircFunBase provides visualized circRNA-miRNA interaction networks. In addition, a genome browser is provided to visualize the genome context of circRNAs. As a biological information platform for circRNAs, CircFunBase will contribute for circRNA studies and bridge the gap between circRNAs and their functions.
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Affiliation(s)
- Xianwen Meng
- Department of Bioinformatics, the State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, China
- The State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, China
| | - Dahui Hu
- Department of Bioinformatics, the State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Peijing Zhang
- Department of Bioinformatics, the State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qi Chen
- Department of Bioinformatics, the State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming Chen
- Department of Bioinformatics, the State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Science, College of Life Sciences, Zhejiang University, Hangzhou, China
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144
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Abstract
BACKGROUND Many evidences have demonstrated that circRNAs (circular RNA) play important roles in controlling gene expression of human, mouse and nematode. More importantly, circRNAs are also involved in many diseases through fine tuning of post-transcriptional gene expression by sequestering the miRNAs which associate with diseases. Therefore, identifying the circRNA-disease associations is very appealing to comprehensively understand the mechanism, treatment and diagnose of diseases, yet challenging. As the complex mechanism between circRNAs and diseases, wet-lab experiments are expensive and time-consuming to discover novel circRNA-disease associations. Therefore, it is of dire need to employ the computational methods to discover novel circRNA-disease associations. RESULT In this study, we develop a method (DWNN-RLS) to predict circRNA-disease associations based on Regularized Least Squares of Kronecker product kernel. The similarity of circRNAs is computed from the Gaussian Interaction Profile(GIP) based on known circRNA-disease associations. In addition, the similarity of diseases is integrated by the mean of GIP similarity and sematic similarity which is computed by the direct acyclic graph (DAG) representation of diseases. The kernels of circRNA-disease pairs are constructed from the Kronecker product of the kernels of circRNAs and diseases. DWNN (decreasing weight k-nearest neighbor) method is adopted to calculate the initial relational score for new circRNAs and diseases. The Kronecker product kernel based regularised least squares approach is used to predict new circRNA-disease associations. We adopt 5-fold cross validation (5CV), 10-fold cross validation (10CV) and leave one out cross validation (LOOCV) to assess the prediction performance of our method, and compare it with other six competing methods (RLS-avg, RLS-Kron, NetLapRLS, KATZ, NBI, WP). CONLUSION The experiment results show that DWNN-RLS reaches the AUC values of 0.8854, 0.9205 and 0.9701 in 5CV, 10CV and LOOCV, respectively, which illustrates that DWNN-RLS is superior to the competing methods RLS-avg, RLS-Kron, NetLapRLS, KATZ, NBI, WP. In addition, case studies also show that DWNN-RLS is an effective method to predict new circRNA-disease associations.
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Affiliation(s)
- Cheng Yan
- School of Information Science and Engineering, Central South University, 932 South Lushan Rd, ChangSha, 410083 China
- School of Computer and Information,Qiannan Normal University for Nationalities, Longshan Road, DuYun, 558000 China
| | - Jianxin Wang
- School of Information Science and Engineering, Central South University, 932 South Lushan Rd, ChangSha, 410083 China
| | - Fang-Xiang Wu
- Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SKS7N5A9 Canada
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145
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Fan C, Lei X, Fang Z, Jiang Q, Wu FX. CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4992948. [PMID: 29741596 PMCID: PMC5941138 DOI: 10.1093/database/bay044] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/16/2018] [Indexed: 12/18/2022]
Abstract
CircR2Disease is a manually curated database, which provides a comprehensive resource for circRNA deregulation in various diseases. Increasing evidences have shown that circRNAs play critical roles in transcriptional, post-transcriptional and translational regulation. Therefore, the aberrant expression of circRNAs has been associated with a group of diseases. It is significant to develop a high-quality database to deposit the deregulated circRNAs in diseases. The current version of CircR2Disease contains 725 associations between 661 circRNAs and 100 diseases by reviewing existing literatures. Each entry in the CircR2Disease contains detailed information for the circRNA–disease relationship, including circRNA name, coordinates and gene symbol, disease name, expression patterns of circRNA, experimental techniques, a brief description of the circRNA–disease relationship, year of publication and the PubMed ID. CircR2Disease provides a user-friendly interface to browse, search and download as well as to submit novel disease-related circRNAs. CircR2Disease could be very beneficial for researches to investigate the mechanism of disease-related circRNAs and explore the appropriate algorithms for predicting novel associations. Database URL: http://bioinfo.snnu.edu.cn/CircR2Disease/
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Affiliation(s)
- Chunyan Fan
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Zengqiang Fang
- School of Computer Science, Shaanxi Normal University, Xi'an 710119, China
| | - Qinghua Jiang
- Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China
| | - Fang-Xiang Wu
- Department of Mechanical Engineering and Division of Biomedical Engineering, University of Saskatchewan, Saskatoon, SK S7N 5A9, Canada
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146
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Carrara M, Fuschi P, Ivan C, Martelli F. Circular RNAs: Methodological challenges and perspectives in cardiovascular diseases. J Cell Mol Med 2018; 22:5176-5187. [PMID: 30277664 PMCID: PMC6201346 DOI: 10.1111/jcmm.13789] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/03/2018] [Accepted: 06/12/2018] [Indexed: 12/22/2022] Open
Abstract
Circular RNAs are generated by back‐splicing of precursor‐mRNAs. Although they have been known for many years, only recently we have started to appreciate their widespread expression and their regulatory functions in a variety of biological processes. Not surprisingly, circular RNA dysregulation and participation in the pathogenic mechanisms have started to emerge in many instances, including cardiovascular diseases. Detection, differential expression analysis and validation are the three critical points for the characterization of any RNA, and circular RNAs are no exception. Their characteristics, however, generate several problems that are yet to be completely addressed, and literature still lacks comprehensive definitions of well‐defined best practices. We present a map of the current knowledge regarding circular RNAs and the critical issues limiting our understanding of their regulation and function. The goal was to provide the readers with the tools to critically decide which of the many approaches available is most suitable to their experimental plan. Although particularly focused on cardiovascular diseases, most critical issues concerning circular RNAs are common to many other fields of investigation.
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Affiliation(s)
- Matteo Carrara
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Milan, Italy
| | - Paola Fuschi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Milan, Italy
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Milan, Italy
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147
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Lim MCJ, Baird AM, Aird J, Greene J, Kapoor D, Gray SG, McDermott R, Finn SP. RNAs as Candidate Diagnostic and Prognostic Markers of Prostate Cancer-From Cell Line Models to Liquid Biopsies. Diagnostics (Basel) 2018; 8:E60. [PMID: 30200254 PMCID: PMC6163368 DOI: 10.3390/diagnostics8030060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 12/19/2022] Open
Abstract
The treatment landscape of prostate cancer has evolved rapidly over the past five years. The explosion in treatment advances has been witnessed in parallel with significant progress in the field of molecular biomarkers. The advent of next-generation sequencing has enabled the molecular profiling of the genomic and transcriptomic architecture of prostate and other cancers. Coupled with this, is a renewed interest in the role of non-coding RNA (ncRNA) in prostate cancer biology. ncRNA consists of several different classes including small non-coding RNA (sncRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). These families are under active investigation, given their essential roles in cancer initiation, development and progression. This review focuses on the evidence for the role of RNAs in prostate cancer, and their use as diagnostic and prognostic markers, and targets for treatment in this disease.
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Affiliation(s)
- Marvin C J Lim
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
- Department of Medical Oncology, Tallaght University Hospital, Dublin D24 NR0A, Ireland.
| | - Anne-Marie Baird
- Cancer and Ageing Research Programme, Queensland University of Technology, Brisbane, QLD 4000, Australia.
- Department of Clinical Medicine, Trinity College Dublin, College Green, Dublin D02 PN40, Ireland.
- Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin 08 W9RT, Ireland.
| | - John Aird
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - John Greene
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - Dhruv Kapoor
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
| | - Steven G Gray
- Department of Clinical Medicine, Trinity College Dublin, College Green, Dublin D02 PN40, Ireland.
- Thoracic Oncology Research Group, Labmed Directorate, St. James's Hospital, Dublin 08 W9RT, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, Dublin D08 NF82, Ireland.
| | - Ray McDermott
- Department of Medical Oncology, Tallaght University Hospital, Dublin D24 NR0A, Ireland.
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin D04 YN26, Ireland.
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, Dublin D08 W9RT, Ireland.
- Department of Histopathology, St. James's Hospital, P.O. Box 580, James's Street, Dublin D08 X4RX, Ireland.
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148
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Wang X, Fang L. Advances in circular RNAs and their roles in breast Cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:206. [PMID: 30157902 PMCID: PMC6116371 DOI: 10.1186/s13046-018-0870-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Accepted: 04/08/2018] [Indexed: 12/21/2022]
Abstract
Circular RNAs (circRNAs) are a type of noncoding RNAs with a closed loop structure. With the development of high-throughput sequencing, massive circRNAs have been discovered in tumorous tissues. Emerging evidence suggests that the biological functions of circRNAs including serving as ceRNAs or miRNA sponges, interacting with proteins, regulating gene transcription and translation, suggesting that circRNAs will be novel biomarkers and targets for the diagnosis and prognosis of diseases. Breast cancer is the most frequently occurring cancer and the leading cause of cancer-related death among women worldwide. It is vital to understand the molecular pathways involved in the pathogenesis of proliferation and progression. In this review, we summarize the current knowledge on human circRNAs and their potential clinical implications on breast cancer.
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Affiliation(s)
- Xuehui Wang
- Nanjing Medical University, Nanjing, 211166, China.,Department of Thyroid and Breast Surgery, Shanghai Tenth People's Hospital, Shanghai, 200070, China
| | - Lin Fang
- Department of Thyroid and Breast Surgery, Shanghai Tenth People's Hospital, Shanghai, 200070, China.
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149
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Xu S, Zhou L, Ponnusamy M, Zhang L, Dong Y, Zhang Y, Wang Q, Liu J, Wang K. A comprehensive review of circRNA: from purification and identification to disease marker potential. PeerJ 2018; 6:e5503. [PMID: 30155370 PMCID: PMC6110255 DOI: 10.7717/peerj.5503] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/01/2018] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is an endogenous noncoding RNA with a covalently closed cyclic structure. Based on their components, circRNAs are divided into exonic circRNAs, intronic circRNAs, and exon-intron circRNAs. CircRNAs have well-conserved sequences and often have high stability due to their resistance to exonucleases. Depending on their sequence, circRNAs are involved in different biological functions, including microRNA sponge activity, modulation of alternative splicing or transcription, interaction with RNA-binding proteins, and rolling translation, and are a derivative of pseudogenes. CircRNAs are involved in the development of a variety of pathological conditions, such as cardiovascular diseases, diabetes, neurological diseases, and cancer. Emerging evidence has shown that circRNAs are likely to be new potential clinical diagnostic markers or treatments for many diseases. Here we describe circRNA research methods and biological functions, and discuss the potential relationship between circRNAs and disease progression.
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Affiliation(s)
- Sheng Xu
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - LuYu Zhou
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Murugavel Ponnusamy
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - LiXia Zhang
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, Shandong, China
| | - YanHan Dong
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - YanHui Zhang
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Qi Wang
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Jing Liu
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Kun Wang
- Center for Developmental Cardiology, Institute of Translational Medicine and School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
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150
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Zhou J, Ge Y, Hu Y, Rong D, Fu K, Wang H, Cao H, Tang W. Circular RNAs as novel rising stars with huge potentials in development and disease. Cancer Biomark 2018; 22:597-610. [PMID: 29914009 DOI: 10.3233/cbm-181296] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jian Zhou
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuyuan Ge
- Department of Neurosurgery, Hospital of Integrated Traditional Chinese and Western Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yun Hu
- Department of General Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Dawei Rong
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kai Fu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hanjin Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiwei Tang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
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