151
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Cir-ITCH inhibits gastric cancer migration, invasion and proliferation by regulating the Wnt/β-catenin pathway. Sci Rep 2020; 10:17443. [PMID: 33060778 PMCID: PMC7566509 DOI: 10.1038/s41598-020-74452-8] [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: 03/05/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Circular RNAs (circRNAs) are differentially expressed in various tumours, but the expression and regulatory mechanisms of circular RNA ITCH (cir-ITCH) in gastric cancer remain unclear. For this reason, in the present study, we assessed the expression of cir-ITCH and the associated regulatory mechanism of cir-ITCH in gastric cancer. Through RTq-PCR assays, we observed that cir-ITCH expression was attenuated in gastric cancer cell lines and tissues, with cir-ITCH expression in gastric cancer tissues with lymph node metastasis being considerably lower than that observed in gastric cancer tissues without lymph node metastasis. In addition, we demonstrated that cir-ITCH or linear ITCH may be a useful marker for gastric cancer prognosis by Kaplan–Meier survival analysis. We also showed that cir-ITCH overexpression could increase linear ITCH expression through miR-17 via RNA immunoprecipitation (RIP) and luciferase reporter assays. Moreover, in vivo and in vitro experimental results showed that cir-ITCH can act as a tumour suppressor to prevent gastric cancer tumourgenesis by sponging miR-17. The Wnt/β-catenin pathway plays a crucial role during the carcinogenesis of cancers, and we observed that cir-ITCH could negatively regulate Wnt/β-catenin signalling, which could be restored by miR-17. In summary, cir-ITCH was shown to prevent gastric cancer tumourgenesis through the Wnt/β-catenin signalling pathway by sequestering miR-17.
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152
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Li X, Zhang B, Li F, Yu K, Bai Y. The mechanism and detection of alternative splicing events in circular RNAs. PeerJ 2020; 8:e10032. [PMID: 33033662 PMCID: PMC7521338 DOI: 10.7717/peerj.10032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/03/2020] [Indexed: 01/15/2023] Open
Abstract
Circular RNAs (circRNAs) are considered as functional biomolecules with tissue/development-specific expression patterns. Generally, a single gene may generate multiple circRNA variants by alternative splicing, which contain different combinations of exons and/or introns. Due to the low abundance of circRNAs as well as overlapped with their linear counterparts, circRNA enrichment protocol is needed prior to sequencing. Compared with numerous algorithms, which use back-splicing reads for detection and functional characterization of circRNAs, original bioinformatic analyzing tools have been developed to large-scale determination of full-length circRNAs and accurate quantification. This review provides insights into the complexity of circRNA biogenesis and surveys the recent progresses in the experimental and bioinformatic methodologies that focus on accurately full-length circRNAs identification.
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Affiliation(s)
- Xiaohan Li
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Bing Zhang
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Fuyu Li
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Kequan Yu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu, China
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153
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Beyond Back Splicing, a Still Poorly Explored World: Non-Canonical Circular RNAs. Genes (Basel) 2020; 11:genes11091111. [PMID: 32972011 PMCID: PMC7565381 DOI: 10.3390/genes11091111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/20/2022] Open
Abstract
Most of the circRNAs reported to date originate from back splicing of a pre-mRNA, and these exonic circRNAs are termed canonical circRNAs. Our objective was to provide an overview of all other (non-canonical) circRNAs that do not originate from the junction of two exons and to characterize their common properties. Those generated through a failure of intron lariat debranching are the best known, even though studies on them are rare. These circRNAs retain the 2′–5′ bond derived from the intron lariat, and this feature probably explains the difficulties in obtaining efficient reverse transcription through the circular junction. Here, we provide an unprecedented overview of non-canonical circRNAs (lariat-derived intronic circRNAs, sub-exonic circRNAs, intron circles, tricRNAs), which all derive from non-coding sequences. As there are few data suggesting their involvement in cellular regulatory processes, we believe that it is early to propose a general function for circRNAs, even for lariat-derived circRNAs. We suggest that their small size and probably strong secondary structures could be major obstacles to their reliable detection. Nevertheless, we believe there are still several possible ways to advance our knowledge of this class of non-coding RNA.
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154
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Fan C, Lei X, Pan Y. Prioritizing CircRNA-Disease Associations With Convolutional Neural Network Based on Multiple Similarity Feature Fusion. Front Genet 2020; 11:540751. [PMID: 33193615 PMCID: PMC7525185 DOI: 10.3389/fgene.2020.540751] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022] Open
Abstract
Accumulating evidence shows that circular RNAs (circRNAs) have significant roles in human health and in the occurrence and development of diseases. Biological researchers have identified disease-related circRNAs that could be considered as potential biomarkers for clinical diagnosis, prognosis, and treatment. However, identification of circRNA–disease associations using traditional biological experiments is still expensive and time-consuming. In this study, we propose a novel method named MSFCNN for the task of circRNA–disease association prediction, involving two-layer convolutional neural networks on a feature matrix that fuses multiple similarity kernels and interaction features among circRNAs, miRNAs, and diseases. First, four circRNA similarity kernels and seven disease similarity kernels are constructed based on the biological or topological properties of circRNAs and diseases. Subsequently, the similarity kernel fusion method is used to integrate the similarity kernels into one circRNA similarity kernel and one disease similarity kernel, respectively. Then, a feature matrix for each circRNA–disease pair is constructed by integrating the fused circRNA similarity kernel and fused disease similarity kernel with interactions and features among circRNAs, miRNAs, and diseases. The features of circRNA–miRNA and disease–miRNA interactions are selected using principal component analysis. Finally, taking the constructed feature matrix as an input, we used two-layer convolutional neural networks to predict circRNA–disease association labels and mine potential novel associations. Five-fold cross validation shows that our proposed model outperforms conventional machine learning methods, including support vector machine, random forest, and multilayer perception approaches. Furthermore, case studies of predicted circRNAs for specific diseases and the top predicted circRNA–disease associations are analyzed. The results show that the MSFCNN model could be an effective tool for mining potential circRNA–disease associations.
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Affiliation(s)
- Chunyan Fan
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, China
| | - Yi Pan
- Department of Computer Science, Georgia State University, Atlanta, GA, United States
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155
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He Y, Zhang Q, Zheng Q, Yu X, Guo W. Distinct 5-methylcytosine profiles of circular RNA in human hepatocellular carcinoma. Am J Transl Res 2020; 12:5719-5729. [PMID: 33042451 PMCID: PMC7540146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/20/2020] [Indexed: 06/11/2023]
Abstract
Recent studies have indicated that several circular RNAs (circRNAs) can affect the occurrence and development of hepatocellular carcinoma (HCC). Post-transcriptional methylation modifications, including 5-methylcytosine (m5C) modification, are closely related to the tumorigenesis of cancers. However, the map of m5C modification of circRNA in HCC remains to be investigated. In this study, we performed MeRIP-seq to identify m5C sites on circRNA of human HCC tissues and paired adjacent non-tumor tissues. Further, we analyzed the relationship between m5C and HCC. Moreover, we performed a bioinformatics analysis to predict the function of specific methylated transcripts. We found that there was a significant difference in m5C between HCC tissues and paired non-tumor tissues, suggesting potential critical roles of m5C of circRNA in HCC development. In addition, the Gene Ontology (GO) analysis results indicated that the unique distribution pattern of circRNA m5C in HCC was associated with specific metabolism-associated pathways. In conclusion, our findings suggest a possible association between HCC and m5C of circRNA. Additionally, our results provide new insights into a novel function of m5C RNA methylation of circRNA in HCC progression.
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Affiliation(s)
- Yuting He
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhou 450052, Henan, China
- Henan Key Laboratory of Digestive Organ TransplantationZhengzhou 450052, Henan, China
| | - Qiyao Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhou 450052, Henan, China
- Henan Key Laboratory of Digestive Organ TransplantationZhengzhou 450052, Henan, China
| | - Qingyuan Zheng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhou 450052, Henan, China
- Henan Key Laboratory of Digestive Organ TransplantationZhengzhou 450052, Henan, China
| | - Xiao Yu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhou 450052, Henan, China
- Henan Key Laboratory of Digestive Organ TransplantationZhengzhou 450052, Henan, China
| | - Wenzhi Guo
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Key Laboratory of Hepatobiliary and Pancreatic Surgery and Digestive Organ Transplantation of Henan Province, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
- Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhou 450052, Henan, China
- Henan Key Laboratory of Digestive Organ TransplantationZhengzhou 450052, Henan, China
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156
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Zhang W, Yan H, Deng Y, Lou J, Zhang P, Cui Q, Sun H, Tang H, Sun Y, Yang J, Li D, Sun Y. Expression profile and bioinformatics analysis of circular RNA in intestinal mucosal injury and repair after severe burns. Cell Biol Int 2020; 44:2570-2587. [PMID: 32910511 DOI: 10.1002/cbin.11464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 08/25/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
Circular RNA (circRNA) is a novel noncoding RNA that is mostly found in humans and animals. Although the flux of circRNA research has increased in recent years, its precise function is still unclear. Some studies demonstrate that circRNAs can function as microRNA (miRNA) sponges involved in the regulation of competitive endogenous RNAs networks and play a crucial role in many biological processes. Other studies show that circRNAs play multiple biological roles in gastrointestinal diseases. However, the expression characteristics and function of circRNA in intestinal mucosal injury and repair after severe burn have not been reported. This study aims to screen differentially expressed circRNAs in intestinal mucosal injury and repair after severe burns and understand their underlying mechanisms. To test our hypothesis that circRNA may play a role in promoting repair in intestinal mucosa injury after severe burns, we collected the intestinal tissues of three severely burned mice and three pseudo-scalded mice and evaluated the expression of circRNAs via microarray analysis. Quantitative real-time polymerase chain reaction was also used to validate the circRNA microarray data by selecting six based on different multiples, original values, and p values. The host genes of all differentially expressed circRNAs and the downstream target genes of six selected DEcircRNAs were identified by Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Meanwhile, we also created a circRNA-miRNA-mRNA network to predict the role and function of circRNAs in intestinal mucosal injury and repair after severe burns.
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Affiliation(s)
- Wenwen Zhang
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Hao Yan
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Yuequ Deng
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Jiaqi Lou
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Pan Zhang
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Qingwei Cui
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Han Sun
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Hao Tang
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Yuan Sun
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Juan Yang
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Dan Li
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
| | - Yong Sun
- Department of Burn Surgery, The Affiliated Huaihai Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Burn Surgery, The 71st Group Army Hospital of PLA, Xuzhou, Jiangsu, China
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157
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Guerra BS, Lima J, Araujo B, Torres LB, Santos J, Machado D, Cunha E, Serrato JA, de Souza JS, Martins JV, Scalabrin EE, Herai RH. Biogenesis of circular RNAs and their role in cellular and molecular phenotypes of neurological disorders. Semin Cell Dev Biol 2020; 114:1-10. [PMID: 32893132 DOI: 10.1016/j.semcdb.2020.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/28/2020] [Accepted: 08/05/2020] [Indexed: 01/04/2023]
Abstract
Circular RNA (circRNA) is an unusual class of RNA-like structures composed by exonic and/or intronic sequences that are regulated by the backsplicing mechanism and by the spliceosome-mediated machinery. These circular transcripts tend to accumulate during aging in several human tissues, especially in the mammalian brain, and their expression is correlated with the occurrence of several human pathologies, including a broad spectrum of neurological disorders. Previous findings have also shown that circRNAs are significantly present in the neuronal tissue and are up-regulated during neurogenesis, with a significant number been derived from neural genes, suggesting these circular molecules are involved in the cellular and molecular phenotype of our brain. However, the complete biogenesis, the many types of circRNA molecules, and their involvement with neuronal phenotype and with the occurrence of pathologies are still a challenging avenue for researchers. In this updated review, we discuss the current findings of the biogenesis and the diversity of cirRNAs and their molecular involvement in neurological tissue phenotype. We also discuss how some circRNAs can act as sponge molecules, regulating the activity of microRNA expression over gene translation. Finally, we also show the correlation of altered circRNA expression in neurological disorders.
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Affiliation(s)
- B S Guerra
- Experimental Multiuser Laboratory, Graduate Program in Health Sciences (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil
| | - J Lima
- Department of Biotechnology, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil; Immunology Department, Biomedical Science Institute, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Bhs Araujo
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, SP, Brazil
| | - L B Torres
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Research Center, Biosciences Institute, University of São Paulo (USP), São Paulo, SP, Brazil
| | - Jcc Santos
- Neuroscience laboratory, Department of Neurology and Neurosurgery, Federal University of São Paulo - UNIFESP/EPM, São Paulo, SP, 04039-002, Brazil
| | - Djs Machado
- Department of Biotechnology, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil
| | - Ebb Cunha
- Experimental Multiuser Laboratory, Graduate Program in Health Sciences (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil; Division of Genetic Research, AnaclinGENE, Genetics Laboratory, Curitiba, PR, Brazil
| | - J A Serrato
- Department of Biotechnology, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil
| | - J S de Souza
- Departamento de Medicina, Laboratório de Endocrinologia e Medicina Translacional, Universidade Federal de São Paulo, UNIFESP/EPM, Rua Pedro de Toledo, 669 - 11 andar, São Paulo, SP, 04039-032, Brazil; Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - J V Martins
- Graduate Program in Informatics (PPGia), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, Brazil
| | - E E Scalabrin
- Graduate Program in Informatics (PPGia), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, Brazil
| | - R H Herai
- Experimental Multiuser Laboratory, Graduate Program in Health Sciences (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, PR, 80215-901, Brazil; Scientific Department, Lico Kaesemodel Institute (ILK), Curitiba, PR, Brazil.
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158
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Chen C, Zhang X, Deng Y, Cui Q, Zhu J, Ren H, Liu Y, Hu X, Zuo J, Peng Y. Regulatory roles of circRNAs in adipogenesis and lipid metabolism: emerging insights into lipid-related diseases. FEBS J 2020; 288:3663-3682. [PMID: 32798313 DOI: 10.1111/febs.15525] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/06/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022]
Abstract
Disorder of lipid metabolism has become an urgent health problem that brings about a variety of metabolic syndromes, including hepatic steatosis, adipose tissue dysfunction, diabetes and obesity. Circular RNAs (circRNAs), a class of emerging RNA molecules with unique structure and extensive effects, have been verified to participate in various biological programs through distinct mechanisms, especially in lipid-related processes. In this review, the biogenesis, characteristics, and functional mechanisms of circRNAs are discussed. Furthermore, the methods for circRNA identification and expression profiles of circRNAs associated with adipogenesis and lipid metabolism are described. Additionally, we emphasize the regulatory roles of circRNAs in adipogenesis, lipid metabolism, and lipid-related diseases. Finally, the diagnostic and therapeutic potential of circRNAs is highlighted, showing potential for the clinical application of circRNAs in the treatment of lipid-related diseases in the near future.
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Affiliation(s)
- Chen Chen
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Xing Zhang
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Yuan Deng
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Qingming Cui
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Ji Zhu
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Huibo Ren
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Yingying Liu
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Xionggui Hu
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Jianbo Zuo
- Hunan Institute of Animal & Veterinary Science, Changsha, China
| | - Yinglin Peng
- Hunan Institute of Animal & Veterinary Science, Changsha, China.,College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
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159
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Jing L, Wu J, Tang X, Ma M, Long F, Tian B, Lin C. Identification of circular RNA hsa_circ_0044556 and its effect on the progression of colorectal cancer. Cancer Cell Int 2020; 20:427. [PMID: 32884449 PMCID: PMC7465356 DOI: 10.1186/s12935-020-01523-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
Background Circular RNAs (circRNAs) are a novel class of noncoding RNAs. Increasing evidence indicates that circRNAs play an important role in the occurrence and development of tumors. However, the role of circRNA hsa_circ_0044556 in the progression of colorectal cancer (CRC) remains unclear. Methods First, we searched for differentially expressed circRNAs using a circRNA microarray in paired CRC and adjacent normal tissues. The circRNA hsa_circ_0044556 was screened out from the existing CRC circRNA microarray in the Gene Expression Omnibus database and our microarray. The clinical significance of hsa_circ_0044556 expression level in CRC patients was then investigated. Finally, the functions of the targets of this circRNA were determined in CRC cell lines. Results Hsa_circ_0044556 was highly expressed in CRC patients and was positively correlated with tumor stage and lymph node metastasis. In CRC cell lines, the proliferation, migration, and invasion of cancer cells were inhibited by knocking down hsa_circ_0044556 expression. Conclusion Hsa_circ_0044556 promoted the progression of CRC. It is possible that hsa_circ_0044556 will become a novel biomarker or therapeutic target for CRC.
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Affiliation(s)
- Liang Jing
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan China
| | - Junhui Wu
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan China
| | - Xiaocheng Tang
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan China
| | - Min Ma
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan China
| | - Fei Long
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan China
| | - Buning Tian
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, The Third Xiangya Hospital of Central South University, Changsha, Hunan China
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160
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Hayne CK, Schmidt CA, Haque MI, Matera AG, Stanley RE. Reconstitution of the human tRNA splicing endonuclease complex: insight into the regulation of pre-tRNA cleavage. Nucleic Acids Res 2020; 48:7609-7622. [PMID: 32476018 PMCID: PMC7641302 DOI: 10.1093/nar/gkaa438] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/29/2020] [Accepted: 05/12/2020] [Indexed: 01/04/2023] Open
Abstract
The splicing of tRNA introns is a critical step in pre-tRNA maturation. In archaea and eukaryotes, tRNA intron removal is catalyzed by the tRNA splicing endonuclease (TSEN) complex. Eukaryotic TSEN is comprised of four core subunits (TSEN54, TSEN2, TSEN34 and TSEN15). The human TSEN complex additionally co-purifies with the polynucleotide kinase CLP1; however, CLP1's role in tRNA splicing remains unclear. Mutations in genes encoding all four TSEN subunits, as well as CLP1, are known to cause neurodegenerative disorders, yet the mechanisms underlying the pathogenesis of these disorders are unknown. Here, we developed a recombinant system that produces active TSEN complex. Co-expression of all four TSEN subunits is required for efficient formation and function of the complex. We show that human CLP1 associates with the active TSEN complex, but is not required for tRNA intron cleavage in vitro. Moreover, RNAi knockdown of the Drosophila CLP1 orthologue, cbc, promotes biogenesis of mature tRNAs and circularized tRNA introns (tricRNAs) in vivo. Collectively, these and other findings suggest that CLP1/cbc plays a regulatory role in tRNA splicing by serving as a negative modulator of the direct tRNA ligation pathway in animal cells.
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Affiliation(s)
- Cassandra K Hayne
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Casey A Schmidt
- Curriculum in Genetics & Molecular Biology and Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Maira I Haque
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
- Department of Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - A Gregory Matera
- Curriculum in Genetics & Molecular Biology and Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
- Departments of Biology and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, 111 T. W. Alexander Drive, Research Triangle Park, NC 27709, USA
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161
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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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162
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Ashrafizadeh M, Najafi M, Ang HL, Moghadam ER, Mahabady MK, Zabolian A, Jafaripour L, Bejandi AK, Hushmandi K, Saleki H, Zarrabi A, Kumar AP. PTEN, a Barrier for Proliferation and Metastasis of Gastric Cancer Cells: From Molecular Pathways to Targeting and Regulation. Biomedicines 2020; 8:E264. [PMID: 32756305 PMCID: PMC7460532 DOI: 10.3390/biomedicines8080264] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/23/2020] [Accepted: 07/23/2020] [Indexed: 02/06/2023] Open
Abstract
Cancer is one of the life-threatening disorders that, in spite of excellent advances in medicine and technology, there is no effective cure for. Surgery, chemotherapy, and radiotherapy are extensively applied in cancer therapy, but their efficacy in eradication of cancer cells, suppressing metastasis, and improving overall survival of patients is low. This is due to uncontrolled proliferation of cancer cells and their high migratory ability. Finding molecular pathways involved in malignant behavior of cancer cells can pave the road to effective cancer therapy. In the present review, we focus on phosphatase and tensin homolog (PTEN) signaling as a tumor-suppressor molecular pathway in gastric cancer (GC). PTEN inhibits the PI3K/Akt pathway from interfering with the migration and growth of GC cells. Its activation leads to better survival of patients with GC. Different upstream mediators of PTEN in GC have been identified that can regulate PTEN in suppressing growth and invasion of GC cells, such as microRNAs, long non-coding RNAs, and circular RNAs. It seems that antitumor agents enhance the expression of PTEN in overcoming GC. This review focuses on aforementioned topics to provide a new insight into involvement of PTEN and its downstream and upstream mediators in GC. This will direct further studies for evaluation of novel signaling networks and their targeting for suppressing GC progression.
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Affiliation(s)
- Milad Ashrafizadeh
- Department of Basic Science, Faculty of Veterinary Medicine, University of Tabriz, Tabriz 5166616471, Iran;
| | - Masoud Najafi
- Radiology and Nuclear Medicine Department, School of Paramedical Sciences, Kermanshah University of Medical Sciences, Kermanshah 6715847141, Iran;
| | - Hui Li Ang
- Cancer Science Institute of Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - Ebrahim Rahmani Moghadam
- Department of Anatomical Sciences, School of Medicine, Student Research Committee, Shiraz University of Medical Sciences, Shiraz 7134814336, Iran;
- Kazerun Health Technology Incubator, Shiraz University of Medical Sciences, Shiraz 6461665145, Iran
| | - Mahmood Khaksary Mahabady
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan 8715988141, Iran;
| | - Amirhossein Zabolian
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran; (A.Z.); (A.K.B.); (H.S.)
| | - Leila Jafaripour
- Department of Anatomy, School of Medicine, Dezful University of Medical Sciences, Dezful 3419759811, Iran;
| | - Atefe Kazemzade Bejandi
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran; (A.Z.); (A.K.B.); (H.S.)
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran 1417414418, Iran;
| | - Hossein Saleki
- Young Researchers and Elite Club, Tehran Medical Sciences, Islamic Azad University, Tehran 1916893813, Iran; (A.Z.); (A.K.B.); (H.S.)
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla 34956, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces (EFSUN), Faculty of Engineering and Natural Sciences, Sabanci University, Tuzla 34956, Istanbul, Turkey
| | - Alan Prem Kumar
- Cancer Science Institute of Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
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163
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Wu Z, Sun H, Li J, Jin H. Circular RNAs in leukemia. Aging (Albany NY) 2020; 11:4757-4771. [PMID: 31306100 PMCID: PMC6660040 DOI: 10.18632/aging.102091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022]
Abstract
In pace with the development of gene sequencing technology and transcriptome research, it has been found that 70 to 90% of the human genome is transcribed into RNAs, while only 2% of RNAs encode proteins. This implies that non-coding RNAs (ncRNAs) may exert vital biological functions and a full analysis of non-coding transcriptomes is needed. Over the past decade, the advance in high-throughput sequencing and transcriptome profiling has enabled the identification of circular RNAs (circRNAs) involved in many biological processes and the occurrence and development of diseases. Accumulating evidence has revealed that circRNAs may serve as new biomarkers for diagnosis as well as provide promising therapeutic approaches and novel drug screening strategies for leukemia. A comprehensive understanding of circRNAs in leukemia is a prerequisite for the development of clinical translational research. In this review, we will discuss the general information of circRNAs and focus on the current advances in understanding the association between dysregulated circRNAs and leukemia.
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Affiliation(s)
- Zijuan Wu
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing 210029, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 210029, China
| | - Handong Sun
- The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jianyong Li
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing 210029, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 210029, China
| | - Hui Jin
- Department of Hematology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu Province Hospital, Nanjing 210029, China.,Key Laboratory of Hematology of Nanjing Medical University, Nanjing 210029, China.,Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing 210029, China
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164
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Chen S, Lu S, Yao Y, Chen J, Yang G, Tu L, Zhang Z, Zhang J, Chen L. Downregulation of hsa_circ_0007580 inhibits non-small cell lung cancer tumorigenesis by reducing miR-545-3p sponging. Aging (Albany NY) 2020; 12:14329-14340. [PMID: 32681720 PMCID: PMC7425484 DOI: 10.18632/aging.103472] [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: 01/06/2020] [Accepted: 05/27/2020] [Indexed: 02/07/2023]
Abstract
Non-small cell lung cancer (NSCLC) is a highly malignant tumor. Many circular RNAs (circRNAs) are reportedly in regulating the progression of NSCLC. To identify potential therapeutic targets for NSCLC, we conducted a bioinformatics analysis of circRNAs differentially expressed between NSCLC tissues and adjacent normal tissues. Hsa_circ_0007580 was upregulated in NSCLC tumor tissues, and the expression of its host gene (protein kinase Ca) correlated negatively with overall survival. Short-hairpin RNAs were used to knock down hsa_circ_0007580 in NSCLC cells, and gene and protein levels were measured with qRT-PCR and Western blotting, respectively. NSCLC cell proliferation, migration and apoptosis were evaluated with CCK-8 assays, Ki-67 staining, Transwell assays and flow cytometry, respectively. Knocking down hsa_circ_0007580 inhibited proliferation and invasion by NSCLC cells and induced their apoptosis. Dual luciferase reporter assays indicated that miR-545-3p can bind to hsa_circ_0007580 (suggesting that hsa_circ_0007580 sponges miR-545-3p) and to protein kinase Ca (suggesting that miR-545-3p directly inhibits this gene). In a xenograft tumor model, downregulating hsa_circ_0007580 inhibited NSCLC tumorigenesis by inactivating p38/mitogen-activated protein kinase signaling. Thus, silencing hsa_circ_0007580 notably inhibited NSCLC progression in vitro and in vivo, suggesting this circRNA could be a novel treatment target for NSCLC.
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Affiliation(s)
- Shuifang Chen
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Shan Lu
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yinan Yao
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Junjun Chen
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Guangdie Yang
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lingfang Tu
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Zeying Zhang
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jianli Zhang
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Lina Chen
- The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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165
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Hao Y, Xi J, Peng Y, Bian B, Hao G, Xi Y, Zhang Z. Circular RNA Circ_0016760 Modulates Non-Small-Cell Lung Cancer Growth Through the miR-577/ZBTB7A Axis. Cancer Manag Res 2020; 12:5561-5574. [PMID: 32753969 PMCID: PMC7354959 DOI: 10.2147/cmar.s243675] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/21/2020] [Indexed: 12/24/2022] Open
Abstract
Background Patients with locally advanced or metastatic non-small-cell lung cancer (NSCLC) have a poor prognosis. Circular RNA circ_0016760 (circ_0016760) is associated with the development of NSCLC. At present, the role and regulatory mechanism of circ_0016760 in NSCLC have not been well explained. Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was executed to detect the expression of circ_0016760, miR-577, and Zinc finger and BTB domain containing 7A (ZBTB7A) mRNA in NSCLC tissues and cells. The colony formation, migration, invasion, and extracellular acidification rate (ECAR) of NSCLC cells were determined through colony formation, transwell, or ECAR assays. The relationship between circ_0016760 or ZBTB7A and miR-577 was analyzed via dual-luciferase reporter and RNA pull-down or RNA immunoprecipitation (RIP) assays. Protein level of ZBTB7A was evaluated with Western blot analysis. Xenograft assay was conducted to confirm the role of circ_0016760 in vivo. Results Circ_0016760 and ZBTB7A were upregulated and miR-577 was downregulated in NSCLC tissues and cells. Circ_0016760 exhaustion curbed the colony formation, migration, invasion, and ECAR of NSCLC cells in vitro and impeded tumor growth in vivo. Mechanically, circ_0016760 modulated ZBTB7A expression via sponging miR-577 in NSCLC cells. MiR-577 downregulation abolished the repressive effects of circ_0016760 silencing on colony formation, migration, invasion, and ECAR of NSCLC cells. Also, ZBTB7A upregulation overturned the repressive impacts of miR-577 elevation on colony formation, migration, invasion, and ECAR of NSCLC cells. Conclusion Circ_0016760 silencing impeded NSCLC advancement through regulation of the miR-577/ZBTB7A axis.
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Affiliation(s)
- Yanhong Hao
- Department of Cardiothoracic Surgery, The First Hospital of Yulin, Yulin City, Shanxi Province, People's Republic of China
| | - Junfeng Xi
- Department of Cardiothoracic Surgery, The First Hospital of Yulin, Yulin City, Shanxi Province, People's Republic of China
| | - Yancai Peng
- Department of Cardiothoracic Surgery, The First Hospital of Yulin, Yulin City, Shanxi Province, People's Republic of China
| | - Burong Bian
- Department of Oncology, The First Hospital of Yulin, Yulin City, Shanxi Province, People's Republic of China
| | - Guangjun Hao
- Department of Oncology, The First Hospital of Yulin, Yulin City, Shanxi Province, People's Republic of China
| | - Yunfeng Xi
- Department of Dermatological Surgery, The First Hospital of Yulin, Yulin City, Shanxi Province, People's Republic of China
| | - Zhibin Zhang
- Department of Cardiothoracic Surgery, The First Hospital of Yulin, Yulin City, Shanxi Province, People's Republic of China
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166
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Fang S, Pan J, Zhou C, Tian H, He J, Shen W, Jin X, Meng X, Jiang N, Gong Z. Circular RNAs Serve as Novel Biomarkers and Therapeutic Targets in Cancers. Curr Gene Ther 2020; 19:125-133. [PMID: 30411680 DOI: 10.2174/1566523218666181109142756] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/20/2018] [Accepted: 10/25/2018] [Indexed: 12/19/2022]
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that structurally form closed loops without 5'-end cap and 3'-end poly(A) tail unlike linear RNAs. CircRNAs are widely present in eukaryotic cells with the capabilities of structural stability, high abundance and cell- /tissue-specific expression. A growing body of researches suggest that the dysregulated circRNAs are intimately relevant to the occurrence and development of cancer. In this review, we mainly discuss the differentially expressed circRNAs in cancer tissues, plasma and exosomes, which makes it possible for clinicians to use certain circRNAs as novel biomarkers for cancer diagnosis and prognosis. In particular, we primarily focus on circRNAs as potential therapeutic targets, which will provide promising applications in cancer gene therapy.
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Affiliation(s)
- Shuai Fang
- Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo
| | - Jinchang Pan
- Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo
| | - Chengwei Zhou
- Department of Thoracic Surgery, The Affiliated Hospital of Medical School of Ningbo University, Ningbo, China
| | - Hui Tian
- Department of Thoracic Surgery, The Affiliated Ningbo Medical Center Lihuili Eastern Hospital of Medical School of Ningbo University, Ningbo, China
| | - Jinxian He
- Department of Thoracic Surgery, The Affiliated Ningbo Medical Center Lihuili Eastern Hospital of Medical School of Ningbo University, Ningbo, China
| | - Weiyu Shen
- Department of Thoracic Surgery, The Affiliated Ningbo Medical Center Lihuili Eastern Hospital of Medical School of Ningbo University, Ningbo, China
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo
| | - Xiaodan Meng
- Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo
| | - Nan Jiang
- Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo
| | - Zhaohui Gong
- Department of Biochemistry and Molecular Biology, Medical School of Ningbo University, Ningbo, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo
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167
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CircFOXO3 rs12196996, a polymorphism at the gene flanking intron, is associated with circFOXO3 levels and the risk of coronary artery disease. Aging (Albany NY) 2020; 12:13076-13089. [PMID: 32614786 PMCID: PMC7377899 DOI: 10.18632/aging.103398] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/25/2020] [Indexed: 01/02/2023]
Abstract
CircFOXO3 plays an important role in the pathogenesis of coronary artery disease (CAD). Single nucleotide polymorphisms (SNPs) at circRNA flanking introns may change its back-splicing and influence circRNA formation. Here, we aimed to investigate the influence of the polymorphisms at the circFOXO3 flanking introns on individual susceptibility to CAD. A total of 1185 individuals were included in the case-control study. In a multivariate logistic regression analysis, we determined that the rs12196996 G variant was significantly associated with increased CAD risk (OR = 1.36, P = 0.014). A similar trend of the association was observed in the recessive model (OR = 2.57, P = 0.003). Stratified analysis revealed a more significant association with CAD risk among younger subjects and non-smokers. Consistent with these results, the haplotype rs12196996G-rs9398171C containing rs12196996G allele was also associated with increased CAD risk (OR = 1.31, P = 0.013). Further investigation revealed that the rs12196996 GG genotype was associated with decreased circFOXO3 expression, but not linear FOXO3 levels. Taken together, our data provide the first evidence that the rs12196996 polymorphism at the circFOXO3 gene flanking intron is associated with CAD risk in the Chinese Han population, which is probably due to influence circFOXO3 levels.
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168
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Zhao C, Lv Y, Duan Y, Li G, Zhang Z. Circulating Non-coding RNAs and Cardiovascular Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:357-367. [PMID: 32285424 DOI: 10.1007/978-981-15-1671-9_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The discovery of noncoding RNAs (ncRNAs) including short microRNAs, long ncRNAs and circular RNAs has broaden our knowledge about mammalian genomes and transcriptomes. A growing number of evidence on aberrantly regulated ncRNAs in cardiovascular diseases has indicated that ncRNAs are critical contributors to cardiovascular pathophysiology. Moreover, multiple recent studies have reported that ncRNAs can be detected in the bloodstream that differs between health subjects and diseased patients and some of them are remarkably stable. Although our knowledge about the origin and function of the circulating ncRNAs is still limited, these molecules have been regarded as promising noninvasive biomarker for risk stratification, diagnosis and prognosis of various cardiovascular diseases. In this chapter, we have described biological characteristics of circulating ncRNAs and discussed current trends and future prospects for the usage of circulating ncRNAs as biomarkers for common cardiovascular diseases.
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Affiliation(s)
- Chenglin Zhao
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Yicheng Lv
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Yi Duan
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China
| | - Guoping Li
- Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhongrong Zhang
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, School of Life Science, Shanghai University, Shanghai, China.
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Wang X, Chang X, Jing Y, Zhao J, Fang Q, Sun M, Zhang Y, Li W, Li Y. Identification and functional prediction of soybean CircRNAs involved in low-temperature responses. JOURNAL OF PLANT PHYSIOLOGY 2020; 250:153188. [PMID: 32450394 DOI: 10.1016/j.jplph.2020.153188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 05/22/2023]
Abstract
Circular RNAs (circRNAs) are a newly characterized type of noncoding RNA and play important roles in microRNA (miRNA) function and transcriptional control. To unravel the mechanism of soybean circRNAs in low-temperature (LT) stress response, genome-wide identification of soybean circRNAs was conducted under LT (4 °C) treatment via deep sequencing. In this study, the existence of backsplicing sites was validated and circRNAs exhibited specific expression patterns in response to LT. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that circRNAs could participate in LT-responsive processes. Our study revealed a new circRNA-miRNA-mRNA network, which is involved in LT responses. Furthermore, soybean circRNAs were predicted to have potential to encode polypeptides or protein. Taken together, our results indicate that soybean circRNAs might encode proteins and be involved in the regulation of LT responses, providing clues regarding the molecular LT-responsive mechanisms in soybean.
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Affiliation(s)
- Xuesong Wang
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
| | - Xingchao Chang
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
| | - Ya Jing
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
| | - Jialiang Zhao
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
| | - Qingwei Fang
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
| | - Mingyang Sun
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
| | - Yanzheng Zhang
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
| | - Wenbin Li
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
| | - Yongguang Li
- College of Agronomy, Northeast Agricultural University, Harbin, China; Key Laboratory of Soybean Biology in Chinese Education Ministry (Northeastern Key Laboratory of Soybean Biology and Genetics and Breeding in Chinese Ministry of Agriculture), Northeast Agricultural University, Harbin, China.
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Abstract
Exonic circular RNAs (circRNAs) have been discovered in all kingdoms of life. In many cases, the details of circRNA function and their involvement in cellular processes and diseases are not yet fully understood. However, the past few years have seen significant developments in bioinformatics and in experimental protocols that advance the ongoing research in this still-emerging field. Sophisticated methods for circRNA generation in vitro and in vivo have been developed, allowing model studies into circRNA function and application. We here review the ongoing circRNA research, giving special attention to recent progress in the field.
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Affiliation(s)
| | - Theodor Schnarr
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald, Greifswald, Germany
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171
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Beltrán-García J, Osca-Verdegal R, Nacher-Sendra E, Pallardó FV, García-Giménez JL. Circular RNAs in Sepsis: Biogenesis, Function, and Clinical Significance. Cells 2020; 9:cells9061544. [PMID: 32630422 PMCID: PMC7349763 DOI: 10.3390/cells9061544] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 01/08/2023] Open
Abstract
Sepsis is a life-threatening condition that occurs when the body responds to an infection that damages it is own tissues. The major problem in sepsis is rapid, vital status deterioration in patients, which can progress to septic shock with multiple organ failure if not properly treated. As there are no specific treatments, early diagnosis is mandatory to reduce high mortality. Despite more than 170 different biomarkers being postulated, early sepsis diagnosis and prognosis remain a challenge for clinicians. Recent findings propose that circular RNAs (circRNAs) may play a prominent role in regulating the patients’ immune system against different pathogens, including bacteria and viruses. Mounting evidence also suggests that the misregulation of circRNAs is an early event in a wide range of diseases, including sepsis. Despite circRNA levels being altered in sepsis, the specific mechanisms controlling the dysregulation of these noncoding RNAs are not completely elucidated, although many factors are known to affect circRNA biogenesis. Therefore, there is a need to explore the molecular pathways that lead to this disorder. This review describes the role of this new class of regulatory RNAs in sepsis and the feasibility of using circRNAs as diagnostic biomarkers for sepsis, opening up new avenues for circRNA-based medicine.
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Affiliation(s)
- Jesús Beltrán-García
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.B.-G.); (F.V.P.)
- Instituto de Investigación Sanitaria INCLIVA, 46010 Valencia, Spain;
- Departamento de Fisiología, Facultad de Medicina y Odontología, Universitat de València, 46010 València, Spain;
| | - Rebeca Osca-Verdegal
- Instituto de Investigación Sanitaria INCLIVA, 46010 Valencia, Spain;
- Departamento de Fisiología, Facultad de Medicina y Odontología, Universitat de València, 46010 València, Spain;
| | - Elena Nacher-Sendra
- Departamento de Fisiología, Facultad de Medicina y Odontología, Universitat de València, 46010 València, Spain;
| | - Federico V. Pallardó
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.B.-G.); (F.V.P.)
- Instituto de Investigación Sanitaria INCLIVA, 46010 Valencia, Spain;
- Departamento de Fisiología, Facultad de Medicina y Odontología, Universitat de València, 46010 València, Spain;
| | - José Luis García-Giménez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain; (J.B.-G.); (F.V.P.)
- Instituto de Investigación Sanitaria INCLIVA, 46010 Valencia, Spain;
- Departamento de Fisiología, Facultad de Medicina y Odontología, Universitat de València, 46010 València, Spain;
- Correspondence:
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172
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Qi L, Li J, Jia J, Yue L, Dong X. Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea. RNA Biol 2020; 17:1427-1441. [PMID: 32449429 DOI: 10.1080/15476286.2020.1771946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The ribosomal RNA (rRNA) genes are generally organized as an operon and cotranscribed into a polycistronic precursor; therefore, processing and maturation of pre-rRNAs are essential for ribosome biogenesis. However, rRNA maturation pathways of archaea, particularly of methanoarchaea, are scarcely known. Here, we thoroughly elucidated the maturation pathway of the rRNA operon (16S-tRNAAla-23S-tRNACys-5S) in Methanolobus psychrophilus, one representative of methanoarchaea. Enzymatic assay demonstrated that EndA, a tRNA splicing endoribonuclease, cleaved bulge-helix-bulge (BHB) motifs buried in the processing stems of pre-16S and pre-23S rRNAs. Northern blot and quantitative PCR detected splicing-coupled circularization of pre-16S and pre-23S rRNAs, which accounted for 2% and 12% of the corresponding rRNAs, respectively. Importantly, endoribonuclease Nob1 was determined to linearize circular pre-16S rRNA at the mature 3' end so to expose the anti-Shine-Dalgarno sequence, while circular pre-23S rRNA was linearized at the mature 5' end by an unknown endoribonuclease. The resultant 5' and 3' extension in linearized pre-16S and pre-23S rRNAs were finally matured through 5'-3' and 3'-5' exoribonucleolytic trimming, respectively. Additionally, a novel processing pathway of endoribonucleolysis coupled with exoribonucleolysis was identified for the pre-5S rRNA maturation in this methanogen, which could be also conserved in most methanogenic euryarchaea. Based on evaluating the phylogenetic conservation of the key elements that are involved in circularization and linearization of pre-rRNA maturation, we predict that the rRNA maturation mode revealed here could be prevalent among archaea.
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Affiliation(s)
- Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China
| | - Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, PR China
| | - Jia Jia
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, PR China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences , Beijing, PR China.,College of Life Sciences, University of Chinese Academy of Sciences , Beijing, PR China
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173
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Zhang L, Hou C, Chen C, Guo Y, Yuan W, Yin D, Liu J, Sun Z. The role of N 6-methyladenosine (m 6A) modification in the regulation of circRNAs. Mol Cancer 2020; 19:105. [PMID: 32522202 PMCID: PMC7285594 DOI: 10.1186/s12943-020-01224-3] [Citation(s) in RCA: 185] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/28/2020] [Indexed: 01/17/2023] Open
Abstract
N6-methyladenosine (m6A), the most abundant modification in eukaryotic cells, regulates RNA transcription, processing, splicing, degradation, and translation. Circular RNA (circRNA) is a class of covalently closed RNA molecules characterized by universality, diversity, stability and conservatism of evolution. Accumulating evidence shows that both m6A modification and circRNAs participate in the pathogenesis of multiple diseases, such as cancers, neurological diseases, autoimmune diseases, and infertility. Recently, m6A modification has been identified for its enrichment and vital biological functions in regulating circRNAs. In this review, we summarize the role of m6A modification in the regulation and function of circRNAs. Moreover, we discuss the potential applications and possible future directions in the field.
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Affiliation(s)
- Lele Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,Department of Colorectal Surgery, Zhengzhou Central Hospital, Zhengzhou University, Zhengzhou, 450007, Henan, China.,Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Chaofeng Hou
- Department of Colorectal Surgery, Zhengzhou Central Hospital, Zhengzhou University, Zhengzhou, 450007, Henan, China
| | - Chen Chen
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Yaxin Guo
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, Henan, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450002, Henan, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Detao Yin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China. .,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450002, Henan, China.
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174
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De Majo F, da Costa Martins PA. CircRNAs in the heart: bricks in Brunelleschi's Dome. Cardiovasc Res 2020; 116:1240-1241. [PMID: 32031589 PMCID: PMC7243273 DOI: 10.1093/cvr/cvaa020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Federica De Majo
- Department of Molecular Genetics, Faculty of Science and Engineering, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands.,CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands
| | - Paula A da Costa Martins
- Department of Molecular Genetics, Faculty of Science and Engineering, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands.,CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Universiteitssingel 50, 6200 MD Maastricht, The Netherlands.,Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
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175
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Chen H, Cheng K, Liu X, An R, Komiyama M, Liang X. Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand. Nucleic Acids Res 2020; 48:e54. [PMID: 32232357 PMCID: PMC7229815 DOI: 10.1093/nar/gkaa181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/04/2020] [Accepted: 03/11/2020] [Indexed: 12/04/2022] Open
Abstract
Rings of single-stranded RNA are promising for many practical applications, but the methods to prepare them in preparative scale have never been established. Previously, RNA circularization was achieved by T4 RNA ligase 2 (Rnl2, a dsRNA ligase) using splints, but the yield was low due to concurrent intermolecular polymerization. Here, various functional RNAs (siRNA, miRNA, ribozyme, etc.) are dominantly converted by Rnl2 to the rings without significant limitations in sizes and sequences. The key is to design a precursor RNA, which is highly activated for the efficient circularization without any splint. First, secondary structure of target RNA ring is simulated by Mfold, and then hypothetically cut at one site so that a few intramolecular base pairs are formed at the terminal. Simply by treating this RNA with Rnl2, the target ring was selectively and efficiently produced. Unexpectedly, circular RNA can be obtained in high yield (>90%), even when only 2 bp form in the 3'-OH side and no full match base pair forms in the 5'-phosphate side. Formation of polymeric by-products was further suppressed by diluting conventional Rnl2 buffer to abnormally low concentrations. Even at high-RNA concentrations (e.g. 50 μM), enormously high selectivity (>95%) was accomplished.
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Affiliation(s)
- Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Kai Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiaoli Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
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176
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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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177
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Zhang P, Li S, Chen M. Characterization and Function of Circular RNAs in Plants. Front Mol Biosci 2020; 7:91. [PMID: 32509801 PMCID: PMC7248317 DOI: 10.3389/fmolb.2020.00091] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/22/2020] [Indexed: 12/14/2022] Open
Abstract
CircRNAs are covalently closed-loop single-stranded RNA molecules ubiquitously expressing in eukaryotes. As an important member of the endogenous ncRNA family, circRNAs are associated with diverse biological processes and can regulate transcription, modulate alternative splicing, and interact with miRNAs or proteins. Compared to abundant advances in animals, studies of circRNAs in plants are rapidly emerging. The databases and analysis tools for plant circRNAs are constantly being developed. Large numbers of circRNAs have been identified and characterized in plants and proved to play regulatory roles in plant growth, development, and stress responses. Here, we review the biogenesis, characteristics, bioinformatics resources, and biological functions of plant circRNAs, and summarize the distinct circularization features and differentially expression patterns comparison with animal-related results.
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Affiliation(s)
- Peijing Zhang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Sida Li
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
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178
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Intracranial Infections in Neurological Surgery: The Changes of Circular RNA Expression and Their Possible Function Mechanism. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2536272. [PMID: 32461970 PMCID: PMC7222609 DOI: 10.1155/2020/2536272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022]
Abstract
Methods circRNA expression was analysed in six cerebrospinal fluid (CSF) samples from three patients of the infectious and noninfectious phases using an Arraystar Human circRNA Array. Differentially altered circRNAs were validated by quantitative real-time polymerase chain reaction (qRT-PCR) in the 66 CSF samples of 33 patients of the infectious and noninfectious phases. t-test was used for statistical analysis. A bioinformatics analysis was employed to investigate the function mechanism of the circRNAs. Results Firstly, 142 circRNAs were found significantly different in 6 CSF samples of the infection and noninfection phases of 3 patients. Fourteen circRNAs with the top largest fold changes were chosen from the 142 circRNAs for PCR validation in the same 6 CSF samples of 3 patients. Three circRNAs were selected to be validated in 60 CSF samples of 30 patients using the PCR test. In infection CSF, an upregulated hsa_circRNA_402632 and downregulated hsa_circRNA_008636 and hsa_circRNA_405481 were confirmed by PCR test. A bioinformatics analysis was used to investigate the function mechanism of the 3 circRNAs. hsa_circRNA_402632 is enriched in the insulin resistance pathway, the FoxO and AMPK signaling pathways are the most important pathways for hsa_circRNA_008636 gene expression, and hsa_circRNA_405481 is enriched in the endometrial cancer signaling pathway, Fc epsilon RI signaling pathway, and TGF-beta signaling pathway. Conclusions hsa_circRNA_402632, hsa_circRNA_008636, and hsa_circRNA_405481 may be potential diagnostic markers for central nervous system infection after neurological surgery.
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179
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Li R, Jiang J, Shi H, Qian H, Zhang X, Xu W. CircRNA: a rising star in gastric cancer. Cell Mol Life Sci 2020; 77:1661-1680. [PMID: 31659415 PMCID: PMC11104848 DOI: 10.1007/s00018-019-03345-5] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 01/17/2023]
Abstract
In recent years, a large number of circRNAs have been identified in mammalian cells with high-throughput sequencing technologies and bioinformatics. The aberrant expression of circRNAs has been reported in many human diseases including gastric cancer (GC). The number of GC-related circRNAs with validated biological functions and mechanisms of action is growing. CircRNAs are critically involved in GC cell proliferation, apoptosis, migration, and invasion. CircRNAs have been shown to function as regulators of parental gene transcription and alternative splicing and miRNA sponges. Moreover, circRNAs have been suggested to interact with proteins to regulate their expression level and activities. Several circRNAs have been identified to encode functional proteins. Due to their great abundance, high stability, tissue- and developmental-stage-specific expression patterns, and wide distribution in various body fluids and exosomes, circRNAs exhibit a great potential to be utilized as biomarkers for GC. Herein, we briefly summarize their biogenesis, properties and biological functions and discuss about the current research progress of circRNAs in GC with a focus on the potential application for GC diagnosis and therapy.
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Affiliation(s)
- Rong Li
- Aoyang Institute of Cancer, Jiangsu University, 279 Jingang Road, Suzhou, 215600, Jiangsu, China
- Zhenjiang Key Laboratory of High Technology Research on Exosomes Foundation and Transformation Application, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
| | - Jiajia Jiang
- Aoyang Institute of Cancer, Jiangsu University, 279 Jingang Road, Suzhou, 215600, Jiangsu, China
| | - Hui Shi
- Zhenjiang Key Laboratory of High Technology Research on Exosomes Foundation and Transformation Application, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
| | - Hui Qian
- Aoyang Institute of Cancer, Jiangsu University, 279 Jingang Road, Suzhou, 215600, Jiangsu, China
- Zhenjiang Key Laboratory of High Technology Research on Exosomes Foundation and Transformation Application, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
| | - Xu Zhang
- Aoyang Institute of Cancer, Jiangsu University, 279 Jingang Road, Suzhou, 215600, Jiangsu, China.
- Zhenjiang Key Laboratory of High Technology Research on Exosomes Foundation and Transformation Application, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
| | - Wenrong Xu
- Aoyang Institute of Cancer, Jiangsu University, 279 Jingang Road, Suzhou, 215600, Jiangsu, China.
- Zhenjiang Key Laboratory of High Technology Research on Exosomes Foundation and Transformation Application, Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
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180
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Kong S, Tao M, Shen X, Ju S. Translatable circRNAs and lncRNAs: Driving mechanisms and functions of their translation products. Cancer Lett 2020; 483:59-65. [PMID: 32360179 DOI: 10.1016/j.canlet.2020.04.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/29/2020] [Accepted: 04/05/2020] [Indexed: 12/16/2022]
Abstract
Long non-coding RNA (lncRNAs) are functional RNA segments longer than 200 nucleotides, which are considered a redundant transcriptional product. Recently, lncRNAs have been shown to harbor open reading frame (ORF) sequences and encode proteins/peptides. Circular RNAs (circRNAs) have long been considered as another type of non-coding RNA (ncRNA) due to the absence of the 5' cap structure. However, recent studies have shown that they also have ORFs in their sequences. CircRNAs can be translated into proteins via internal ribosome entry site (IRES)-driven or N6-methyladenosine (m6A)-mediated initiation. To date, several translatable circRNAs and lncRNAs have been identified in Drosophila, mice, and human myoblasts, as well as in different cancers, such as glioma, hepatocellular carcinoma, and colon cancer. In this article, we review the mechanisms that drive translation of circRNAs and lncRNAs. Moreover, we discuss the research methods and tools available to identify their translation products and validate the function of these bioactive proteins/peptides in physiology and cancer.
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Affiliation(s)
- Shan Kong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China; Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Mei Tao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China; Medical School of Nantong University, Nantong University, Nantong, 226001, Jiangsu, China
| | - Xianjuan Shen
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China; Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.
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181
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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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182
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Das A, Das A, Das D, Abdelmohsen K, Panda AC. Circular RNAs in myogenesis. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2020; 1863:194372. [PMID: 30946990 PMCID: PMC6773529 DOI: 10.1016/j.bbagrm.2019.02.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/09/2019] [Accepted: 02/21/2019] [Indexed: 01/08/2023]
Abstract
Skeletal muscles have an immense ability to regenerate from the muscle stem cells called satellite cells. The process of skeletal muscle regeneration is called myogenesis, which starts with activation of quiescent satellite cells immediately after muscle injury followed by proliferation and fusion of myoblasts into myotubes. Myogenesis is orchestrated through the expression of a specific set of genes which, at each step regulated by complex gene regulatory networks. Besides the well-established roles of transcription factors, increasing evidence demonstrated that circular (circ)RNAs modulate gene expression during myogenesis and are involved in muscle-related diseases. Here we review the recent findings of circRNAs involved in myogenesis.
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Affiliation(s)
- Arundhati Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Aniruddha Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Debojyoti Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, USA
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India.
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183
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Jiang R, Li H, Yang J, Shen X, Song C, Yang Z, Wang X, Huang Y, Lan X, Lei C, Chen H. circRNA Profiling Reveals an Abundant circFUT10 that Promotes Adipocyte Proliferation and Inhibits Adipocyte Differentiation via Sponging let-7. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 20:491-501. [PMID: 32305019 PMCID: PMC7163053 DOI: 10.1016/j.omtn.2020.03.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 02/07/2023]
Abstract
Adipose development is regulated by a series of complex processes, and non-coding RNAs (ncRNAs), including circular RNAs (circRNAs), play important roles in regulating proliferation and differentiation of adipocytes. In this study, we profiled circRNA expression in cattle fat tissue during calf and adult developmental stages and detected 14,274 circRNA candidates. Some circRNAs are differentially expressed between two developmental stages. We characterized circFUT10, named for its host gene FUT10, a highly expressed and abundant circRNA. Luciferase screening, an RNA-binding protein immunoprecipitation (RIP) assay, quantitative real-time PCR, and western blotting assays indicated that circFUT10 directly binds let-7c/let-e, and PPARGC1B (peroxisome proliferator-activated receptor γ coactivator 1-β) is identified as a target of let-7c. Flow cytometry, EdU (5-ethynyl-2′-deoxyuridine) incorporation, a CCK-8 (cell counting kit-8) assay, oil red O staining, and western blotting assays demonstrated that circFUT10 promotes adipocyte proliferation and inhibits cell differentiation by sponging let-7c. The results demonstrate that circFUT10 binding of let-7c promotes cell proliferation and inhibits cell differentiation by targeting PPARGC1B in cattle adipocytes.
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Affiliation(s)
- Rui Jiang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hui Li
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Jiameng Yang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xuemei Shen
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chengchuang Song
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhaoxin Yang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiaogang Wang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Yongzhen Huang
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xianyong Lan
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chuzhao Lei
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hong Chen
- Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China.
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Yu C, Cheng Z, Cui S, Mao X, Li B, Fu Y, Wang H, Jin H, Ye Q, Zhao X, Jiang L, Qin W. circFOXM1 promotes proliferation of non-small cell lung carcinoma cells by acting as a ceRNA to upregulate FAM83D. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:55. [PMID: 32228656 PMCID: PMC7106704 DOI: 10.1186/s13046-020-01555-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/08/2020] [Indexed: 01/26/2023]
Abstract
Background Biological role and clinical significance of circular RNAs (circRNAs) remain largely unknown. Herein, we aimed to investigate biological function, molecular mechanism, and clinical significance of a circular RNA FOXM1 (circFOXM1) in non-small cell lung cancer (NSCLC). Methods Expression of circFOXM1 was measured in 48 paired samples of NSCLC by qRT-PCR. Functional roles of circFOXM1 on tumor cells were explored by in vitro and in vivo assays. Transcriptome sequencing was employed to screen the molecules involved in circFOXM1 regulatory network. RNA immunoprecipitation, luciferase analysis, RNA pull-down, and rescue assay were used to investigate potential mechanisms of circFOXM1. Results We found that circFOXM1 was significantly upregulated in NSCLC tissues, and its upregulation was positively correlated with advanced clinical stage and poor prognosis of NSCLC patients. Gain or loss-of-function assay showed that circFOXM1 promoted cell proliferation and cell cycle progression. In vivo assays showed that silencing circFOXM1 inhibited xenograft tumor growth. Mechanically, transcriptome sequencing data indicated that silencing circFOXM1 led to the downregulation of cell cycle-related mRNAs. RNA pull-down and dual-luciferase reporter assay suggested that circFOXM1 could bind to miR-614, and FAM83D was an essential gene involved in the circFOXM1/miR-614 regulatory network. Conclusions circFOXM1promotes NSCLC progression by interacting with miR-614 and thus inactivating the function of miR-614, which will further release the suppression of FAM83D. circFOXM1/miR-614/FAM83D regulatory network may serve as a potential therapeutic target for NSCLC patients.
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Affiliation(s)
- Chengtao Yu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Biomedical Engineering, Shanghai, 200032, China
| | - Zhuoan Cheng
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Biomedical Engineering, Shanghai, 200032, China
| | - Shaohua Cui
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Xiaowei Mao
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Botai Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Biomedical Engineering, Shanghai, 200032, China
| | - Yujie Fu
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Hui Wang
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Haojie Jin
- Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Qing Ye
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Xiaojing Zhao
- Department of Thoracic Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China
| | - Liyan Jiang
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Wenxin Qin
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Biomedical Engineering, Shanghai, 200032, China. .,Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200032, China.
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185
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Nedoluzhko A, Sharko F, Rbbani MG, Teslyuk A, Konstantinidis I, Fernandes JMO. CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. PeerJ 2020; 8:e8757. [PMID: 32211235 PMCID: PMC7081776 DOI: 10.7717/peerj.8757] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 02/16/2020] [Indexed: 01/07/2023] Open
Abstract
Circular RNAs (circRNAs) are long noncoding RNAs that play a significant role in various biological processes, including embryonic development and stress responses. These regulatory molecules can modulate microRNA activity and are involved in different molecular pathways as indirect regulators of gene expression. Thousands of circRNAs have been described in diverse taxa due to the recent advances in high throughput sequencing technologies, which led to a huge variety of total RNA sequencing being publicly available. A number of circRNA de novo and host gene prediction tools are available to date, but their ability to accurately predict circRNA host genes is limited in the case of low-quality genome assemblies or annotations. Here, we present CircParser, a simple and fast Unix/Linux pipeline that uses the outputs from the most common circular RNAs in silico prediction tools (CIRI, CIRI2, CircExplorer2, find_circ, and circFinder) to annotate circular RNAs, assigning presumptive host genes from local or public databases such as National Center for Biotechnology Information (NCBI). Also, this pipeline can discriminate circular RNAs based on their structural components (exonic, intronic, exon-intronic or intergenic) using a genome annotation file.
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Affiliation(s)
- Artem Nedoluzhko
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Bodø, Norway
| | - Fedor Sharko
- Complex of NBICS Technologies, National Research Centre "Kurchatov Institute", Moscow, Russia.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia, Russia
| | - Md Golam Rbbani
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Bodø, Norway
| | - Anton Teslyuk
- Complex of NBICS Technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
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186
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Bhat AA, Younes SN, Raza SS, Zarif L, Nisar S, Ahmed I, Mir R, Kumar S, Sharawat SK, Hashem S, Elfaki I, Kulinski M, Kuttikrishnan S, Prabhu KS, Khan AQ, Yadav SK, El-Rifai W, Zargar MA, Zayed H, Haris M, Uddin S. Role of non-coding RNA networks in leukemia progression, metastasis and drug resistance. Mol Cancer 2020; 19:57. [PMID: 32164715 PMCID: PMC7069174 DOI: 10.1186/s12943-020-01175-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Early-stage detection of leukemia is a critical determinant for successful treatment of the disease and can increase the survival rate of leukemia patients. The factors limiting the current screening approaches to leukemia include low sensitivity and specificity, high costs, and a low participation rate. An approach based on novel and innovative biomarkers with high accuracy from peripheral blood offers a comfortable and appealing alternative to patients, potentially leading to a higher participation rate. Recently, non-coding RNAs due to their involvement in vital oncogenic processes such as differentiation, proliferation, migration, angiogenesis and apoptosis have attracted much attention as potential diagnostic and prognostic biomarkers in leukemia. Emerging lines of evidence have shown that the mutational spectrum and dysregulated expression of non-coding RNA genes are closely associated with the development and progression of various cancers, including leukemia. In this review, we highlight the expression and functional roles of different types of non-coding RNAs in leukemia and discuss their potential clinical applications as diagnostic or prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Ajaz A Bhat
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Salma N Younes
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar.,Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Syed Shadab Raza
- Laboratory for Stem Cell & Restorative Neurology, Era's Lucknow Medical College and Hospital, Lucknow, Uttar Pradesh, India
| | - Lubna Zarif
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar.,Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Sabah Nisar
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Ikhlak Ahmed
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Rashid Mir
- Department of Medical Lab Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Sachin Kumar
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Surender K Sharawat
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sheema Hashem
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Michal Kulinski
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Shilpa Kuttikrishnan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Kirti S Prabhu
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Santosh K Yadav
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Wael El-Rifai
- Department of Surgery, University of Miami, Miami, Florida, USA
| | - Mohammad A Zargar
- Department of Biotechnology, Central University of Kashmir, Ganderbal, Jammu and Kashmir, India
| | - Hatem Zayed
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar
| | - Mohammad Haris
- Translational Medicine, Sidra Medicine, P.O. Box 26999, Doha, Qatar. .,Laboratory Animal Research Center, Qatar University, Doha, Qatar.
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar.
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187
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Cavalcante GC, Magalhães L, Ribeiro-dos-Santos Â, Vidal AF. Mitochondrial Epigenetics: Non-Coding RNAs as a Novel Layer of Complexity. Int J Mol Sci 2020; 21:E1838. [PMID: 32155913 PMCID: PMC7084767 DOI: 10.3390/ijms21051838] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 01/29/2020] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
Mitochondria are organelles responsible for several functions involved in cellular balance, including energy generation and apoptosis. For decades now, it has been well-known that mitochondria have their own genetic material (mitochondrial DNA), which is different from nuclear DNA in many ways. More recently, studies indicated that, much like nuclear DNA, mitochondrial DNA is regulated by epigenetic factors, particularly DNA methylation and non-coding RNAs (ncRNAs). This field is now called mitoepigenetics. Additionally, it has also been established that nucleus and mitochondria are constantly communicating to each other to regulate different cellular pathways. However, little is known about the mechanisms underlying mitoepigenetics and nuclei-mitochondria communication, and also about the involvement of the ncRNAs in mitochondrial functions and related diseases. In this context, this review presents the state-of-the-art knowledge, focusing on ncRNAs as new players in mitoepigenetic regulation and discussing future perspectives of these fields.
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Affiliation(s)
- Giovanna C. Cavalcante
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Researches, Federal University of Pará, Rua dos Mundurucus, 4487, 66073-005 Belém, PA, Brazil
| | - Amanda F. Vidal
- Laboratory of Human and Medical Genetics, Federal University of Pará, Av. Augusto Correa, 01, 66075-970 Belém, PA, Brazil; (G.C.C.); (L.M.); (Â.R.-d.-S.)
- Graduate Program in Genetics and Molecular Biology, Federal University of Pará, Av. Augusto Correa, 01, 66075-110 Belém, PA, Brazil
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188
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Abstract
AbstractFollowing improvement and integration of novel genome sequencing techniques, a new stage light has been shone upon circular RNAs (circRNA) in regard to their structure and functionality. In comparison to their linear counterparts, circRNA possess a multitude of remarkable functions such as microRNA (miRNA) sponging, RNA-binding protein (RBP) regulation and translational capabilities whose research have recently gained traction. Comprehensive computational modelling and analysis have revealed the relationship between the sequence composition of circRNAs and their biogenesis and structural formation as well as spatial identification. Due to fluctuations in expressional activity in tissue-specific environments and stimulations by tumour cells, circRNAs have sparked considerable interest in being employed as plausible biomarkers in disease control and treatment as consequence of their impressive specificity and biocompatibility. Additionally, an increasing number of studies have proposed them as viable solutions to be just as competent as presently used disease markers and medicine, if not better. In this review, I briefly summarized the characteristics, biogenesis and function of circRNA and introduced the potential applications and prospects of circRNA. With vigorous research being carried out regarding their still unclear diversified roles and precise molecular structure, circRNAs are bound to become the new revolutionary perspective on cellular regulation, protein signalling and disease pathogenesis.
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189
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Mehta SL, Dempsey RJ, Vemuganti R. Role of circular RNAs in brain development and CNS diseases. Prog Neurobiol 2020; 186:101746. [PMID: 31931031 PMCID: PMC7024016 DOI: 10.1016/j.pneurobio.2020.101746] [Citation(s) in RCA: 184] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/13/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
In mammals, many classes of noncoding RNAs (ncRNAs) are expressed at a much higher level in the brain than in other organs. Recent studies have identified a new class of ncRNAs called circular RNAs (circRNAs), which are produced by back-splicing and fusion of either exons, introns, or both exon-intron into covalently closed loops. The circRNAs are also highly enriched in the brain and increase continuously from the embryonic to the adult stage. Although the functional significance and mechanism of action of circRNAs are still being actively explored, they are thought to regulate the transcription of their host genes and sequestration of miRNAs and RNA binding proteins. Some circRNAs are also shown to have translation potential to form peptides. The expression and abundance of circRNAs seem to be spatiotemporally maintained in a normal brain. Altered expression of circRNAs is also thought to mediate several disorders, including brain-tumor growth, and acute and chronic neurodegenerative disorders by affecting mechanisms such as angiogenesis, neuronal plasticity, autophagy, apoptosis, and inflammation. This review discusses the involvement of various circRNAs in brain development and CNS diseases. A better understanding of the circRNA function will help to develop novel therapeutic strategies to treat CNS complications.
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Affiliation(s)
- Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States
| | - Robert J Dempsey
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States
| | - Raghu Vemuganti
- Department of Neurological Surgery, University of Wisconsin, Madison, WI, United States; William S. Middleton Veterans Hospital, Madison, WI, United States.
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190
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Identification and characterization of circRNAs in the skin during wool follicle development in Aohan fine wool sheep. BMC Genomics 2020; 21:187. [PMID: 32111155 PMCID: PMC7048093 DOI: 10.1186/s12864-020-6599-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/20/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Aohan fine wool sheep (AFWS) is a historically bred fine wool sheep, cultivated in China. The wool has excellent quality and good textile performance. Investigating the molecular mechanisms that regulate wool growth is important to improve wool quality and yield. Circular RNAs (circRNAs) are widely expressed non-coding RNAs that can act as competitive endogenous RNAs (ceRNAs) to bind to miRNAs. Although circRNAs have been studied in many fields, research on their activity in sheep wool follicles is limited. To understand the regulation of circRNAs in the growth of fine wool in sheep, we used RNA-Seq to identify circRNAs in sheep shoulder skin samples at three developmental stages: embryonic day 90 (E90d), embryonic day 120 (E120d), and at birth (Birth). RESULTS We identified 8753 circRNAs and found that 918 were differentially-expressed. We then analyzed the classification and characteristic of the circRNAs in sheep shoulder skin. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we identified the source genes of circRNAs, which were mainly enriched in cellular component organization, regulation of primary metabolic processes, tight junctions, and the cGMP-PKG and AMPK signaling pathways. In addition, we predicted interactions between 17 circRNAs and eight miRNAs, using miRanda software. Based on the significant pathways, we speculate that circ_0005720, circ_0001754, circ_0008036, circ_0004032, circ_0005174, circ_0005519, and circ_0007826 might play an important role in regulating wool follicle growth in AFWS. Seven circRNAs were randomly selected to validate the RNA-Seq results, using qRT-PCR. CONCLUSION Our results provide more information about circRNAs regulation of wool follicle development in AFWS, and establish a solid foundation for future research.
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191
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Jüttner M, Weiß M, Ostheimer N, Reglin C, Kern M, Knüppel R, Ferreira-Cerca S. A versatile cis-acting element reporter system to study the function, maturation and stability of ribosomal RNA mutants in archaea. Nucleic Acids Res 2020; 48:2073-2090. [PMID: 31828323 PMCID: PMC7038931 DOI: 10.1093/nar/gkz1156] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/12/2019] [Accepted: 11/30/2019] [Indexed: 12/17/2022] Open
Abstract
General molecular principles of ribosome biogenesis have been well explored in bacteria and eukaryotes. Collectively, these studies have revealed important functional differences and few similarities between these processes. Phylogenetic studies suggest that the information processing machineries from archaea and eukaryotes are evolutionary more closely related than their bacterial counterparts. These observations raise the question of how ribosome synthesis in archaea may proceed in vivo. In this study, we describe a versatile plasmid-based cis-acting reporter system allowing to analyze in vivo the consequences of ribosomal RNA mutations in the model archaeon Haloferax volcanii. Applying this system, we provide evidence that the bulge-helix-bulge motif enclosed within the ribosomal RNA processing stems is required for the formation of archaeal-specific circular-pre-rRNA intermediates and mature rRNAs. In addition, we have collected evidences suggesting functional coordination of the early steps of ribosome synthesis in H. volcanii. Together our investigation describes a versatile platform allowing to generate and functionally analyze the fate of diverse rRNA variants, thereby paving the way to better understand the cis-acting molecular determinants necessary for archaeal ribosome synthesis, maturation, stability and function.
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Affiliation(s)
- Michael Jüttner
- Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Matthias Weiß
- Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Nina Ostheimer
- Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Corinna Reglin
- Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Michael Kern
- Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Robert Knüppel
- Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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192
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Lohani N, Jain D, Singh MB, Bhalla PL. Engineering Multiple Abiotic Stress Tolerance in Canola, Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:3. [PMID: 32161602 PMCID: PMC7052498 DOI: 10.3389/fpls.2020.00003] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/03/2020] [Indexed: 05/22/2023]
Abstract
Impacts of climate change like global warming, drought, flooding, and other extreme events are posing severe challenges to global crop production. Contribution of Brassica napus towards the oilseed industry makes it an essential component of international trade and agroeconomics. Consequences from increasing occurrences of multiple abiotic stresses on this crop are leading to agroeconomic losses making it vital to endow B. napus crop with an ability to survive and maintain yield when faced with simultaneous exposure to multiple abiotic stresses. For an improved understanding of the stress sensing machinery, there is a need for analyzing regulatory pathways of multiple stress-responsive genes and other regulatory elements such as non-coding RNAs. However, our understanding of these pathways and their interactions in B. napus is far from complete. This review outlines the current knowledge of stress-responsive genes and their role in imparting multiple stress tolerance in B. napus. Analysis of network cross-talk through omics data mining is now making it possible to unravel the underlying complexity required for stress sensing and signaling in plants. Novel biotechnological approaches such as transgene-free genome editing and utilization of nanoparticles as gene delivery tools are also discussed. These can contribute to providing solutions for developing climate change resilient B. napus varieties with reduced regulatory limitations. The potential ability of synthetic biology to engineer and modify networks through fine-tuning of stress regulatory elements for plant responses to stress adaption is also highlighted.
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Affiliation(s)
| | | | | | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC, Australia
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193
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Yuan X, Xu Y, Wei Z, Ding Q. CircAP2A2 acts as a ceRNA to participate in infantile hemangiomas progression by sponging miR-382-5p via regulating the expression of VEGFA. J Clin Lab Anal 2020; 34:e23258. [PMID: 32091151 PMCID: PMC7370729 DOI: 10.1002/jcla.23258] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background Increasing evidences reveal that circular RNAs (circRNAs) play crucial functions in cancer development. However, the expression pattern and roles of circRNAs in infantile hemangiomas (IH) remain unclear. Methods In this study, qRT‐PCR was performed to determine the expression of circAP2A2, miR‐382‐5p, and VEGFA in IH tissues and cell lines. Moreover, MTT assay, colony formation, transwell assay, and Western blot analysis were conducted to assess the function of circAP2A2 or miR‐382‐5p on cell proliferation, and migration in vitro, respectively. Also, dual luciferase assay was used to confirm the interactions among circAP2A2, miR‐382‐5p, and VEGFA. Results CircAP2A2 was confirmed to be highly expressed in IH. CircAP2A2 knockdown or miR‐382‐5p overexpression decreased the proliferation, colony formation, migration, and invasion of HemECs and HUVEC cells. Conclusion CircAP2A2 could promote proliferation and invasion of IH by regulating miR‐382‐5p/VEGFA axis.
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Affiliation(s)
- Xiaoqi Yuan
- The Ningbo Women and Children's Hospital, Ningbo, China
| | - Yanan Xu
- The Ningbo Women and Children's Hospital, Ningbo, China
| | - Zhiqiang Wei
- The Ningbo Women and Children's Hospital, Ningbo, China
| | - Qi Ding
- Department of Diagnosis, Ningbo Diagnostic Pathology Center, Ningbo, China
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194
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Vélez JL, Morocho P, Montalvo M, Aguayo S, Vélez PA, Velarde G, Jara F, Paz y Miño C. The micro RNAs in human pathology: clinical utility and translational approach. BIONATURA 2020. [DOI: 10.21931/rb/2020.05.01.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In human clinics, pathologies as diverse as cancer, sepsis, autoimmune diseases, among others; of different etiology and a different pathophysiological behavior, converge in a failure of gene repression that allows the phenotypic expression of the disease; The possibility of having a biological marker that shows these events to the clinician is desirable since it would allow early diagnostic and therapeutic strategies. Micro RNAs are small and non-coding RNAs that fulfill that “genetic silencing” role, however, the step from basic research to clinical applicability, that is, their translational utility is still little diffused in specialties other than oncology. The objective of this review is to explain in a more precise way.
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195
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Yao L, Xu B, Li X. Neisseria gonorrhoeae-induced salpingitis is targeted by circular RNA EIF3K via miR-139-5p and regulating MAPK/NF-κB signaling pathway to promotes apoptosis and autophagy bacterial cells. Microb Pathog 2020; 142:104051. [PMID: 32045642 DOI: 10.1016/j.micpath.2020.104051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Salpingitis is a part of pelvic inflammation, which is a threat for women's health. With development of genetic engineering, circular RNAs were discovered to have connections with diseases of human. METHODS RT-qPCR was for analyzing expressions of EIF3K, miR-139-5p and RNAs related to apoptosis. CCK-8 was applied for detecting cell viabilities. Expressions of proteins in autophagy and MAPK/NF-κB signaling pathway was detected by western blot. Luciferase report assay was used to make sure binding situation between circEIF3K and miR-139-5p in cells. RESULTS Circular EIF3K expressed lower in inflammatory cells with suppressing cell viabilities and promoting apoptosis and autophagy. MiR-139-5p could bind circEIF3K and promoted cell viabilities. Meanwhile, miR-139-5p could suppress apoptosis and autophagy. Functions of overexpressed EIF3K were restored by miR-139-5p in cell viabilities, apoptosis and autophagy. Proteins in MAPK/NF-κB signaling pathway expressed higher in inflammatory cells and overexpressed EIF3K could down regulate expressions of proteins. Inhibition then was resumed by up-regulated miR-139-5p. After proteins in MAPK signaling pathway was activated, apoptosis and autophagy was suppressed. CONCLUSION Circular EIF3K suppressed cell growth in salpingitis through inhibiting MAPK/NK-κB signaling pathway, which could be a potential factor for further studies in slpingitis.
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Affiliation(s)
- Li Yao
- Department of Gynaecology, Zaozhuang Municipal Hospital, Shandong Province, China.
| | - Bo Xu
- Department of Obstetrics, Zaozhuang Municipal Hospital, Shandong Province, China.
| | - Xuepeng Li
- Department of Gynaecology, Zaozhuang Municipal Hospital, Zaozhuang City, shandong province, China.
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196
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Lei X, Bian C. Integrating random walk with restart and k-Nearest Neighbor to identify novel circRNA-disease association. Sci Rep 2020; 10:1943. [PMID: 32029856 PMCID: PMC7005057 DOI: 10.1038/s41598-020-59040-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/23/2020] [Indexed: 01/21/2023] Open
Abstract
CircRNA is a special type of non-coding RNA, which is closely related to the occurrence and development of many complex human diseases. However, it is time-consuming and expensive to determine the circRNA-disease associations through experimental methods. Therefore, based on the existing databases, we propose a method named RWRKNN, which integrates the random walk with restart (RWR) and k-nearest neighbors (KNN) to predict the associations between circRNAs and diseases. Specifically, we apply RWR algorithm on weighting features with global network topology information, and employ KNN to classify based on features. Finally, the prediction scores of each circRNA-disease pair are obtained. As demonstrated by leave-one-out, 5-fold cross-validation and 10-fold cross-validation, RWRKNN achieves AUC values of 0.9297, 0.9333 and 0.9261, respectively. And case studies show that the circRNA-disease associations predicted by RWRKNN can be successfully demonstrated. In conclusion, RWRKNN is a useful method for predicting circRNA-disease associations.
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Affiliation(s)
- Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China.
| | - Chen Bian
- School of Computer Science, Shaanxi Normal University, Xi'an, 710119, China
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197
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Pan G, Mao A, Liu J, Lu J, Ding J, Liu W. Circular RNA hsa_circ_0061825 (circ-TFF1) contributes to breast cancer progression through targeting miR-326/TFF1 signalling. Cell Prolif 2020; 53:e12720. [PMID: 31961997 PMCID: PMC7048212 DOI: 10.1111/cpr.12720] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/22/2019] [Accepted: 10/15/2019] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES Circular RNAs (circRNAs) are RNA transcripts that belong to non-coding RNAs (ncRNAs), whose implication in human cancers has been recently demonstrated. However, the specific role of multiple circRNAs in breast cancer remains unidentified. MATERIALS AND METHODS Microarray analysis and bioinformatics analysis were applied to select circRNA and miRNA, respectively. The loop structure of circ-TFF1 was confirmed using RNase R treatment, divergent primer PCR and Sanger sequencing. qRT-PCR and Western blot were employed for gene expressions. In vitro and in vivo experiments were conducted to assess the function of circ-TFF1 in biological processes in breast cancer cells. FISH and subcellular separation indicated circ-TFF1 cellular distribution. Luciferase reporter and RIP assays and Pearson's correlation analysis were performed to evaluate relationships between genes. RESULTS Circ-TFF1 and TFF1 were both upregulated and positively associated with each other in breast cancer. Knockdown of circ-TFF1 hindered breast cancer cell proliferation, migration, invasion and EMT in vitro and controlled tumour growth in vivo. Circ-TFF1 acted as a ceRNA of TFF1 by sponging miR-326, and its contribution to breast cancer progression was mediated by miR-326/TFF1 axis. CONCLUSIONS Circ-TFF1 is a facilitator in breast cancer relying on TFF1 by absorbing miR-326, providing a novel promising target for BC treatment.
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Affiliation(s)
- Gaofeng Pan
- Minhang HospitalFudan UniversityShanghaiChina
| | - Anwei Mao
- Minhang HospitalFudan UniversityShanghaiChina
| | - Jiazhe Liu
- Minhang HospitalFudan UniversityShanghaiChina
| | - Jingfeng Lu
- Minhang HospitalFudan UniversityShanghaiChina
| | - Junbin Ding
- Minhang HospitalFudan UniversityShanghaiChina
| | - Weiyan Liu
- Minhang HospitalFudan UniversityShanghaiChina
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198
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Lu HC, Yao JQ, Yang X, Han J, Wang JZ, Xu K, Zhou R, Yu H, Lv Q, Gu M. Identification of a potentially functional circRNA-miRNA-mRNA regulatory network for investigating pathogenesis and providing possible biomarkers of bladder cancer. Cancer Cell Int 2020; 20:31. [PMID: 32015691 PMCID: PMC6990554 DOI: 10.1186/s12935-020-1108-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) have received considerable attention in human cancer research. However, many circRNAs remain to be detected. In our study, we determined novel circRNAs and investigated their effects on bladder cancer (BCa). METHODS Microarray dataset GSE92675 was downloaded from Gene Expression Omnibus (GEO). Then, we combined computational biology with quantitative real-time polymerase chain reaction (qRT-PCR) to select related circRNAs in BCa. The selected circRNA-microRNA (miRNA)-messenger RNA (mRNA) regulatory subnetwork was determined by Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. RESULTS The regulatory network constructed from the microarray dataset (GSE92675) contained 49 differentially expressed circRNAs (DECs). GO and KEGG analyses showed that the MAPK and PI3K-AKT signaling pathways were statistically significant. On the basis of qRT-PCR and the degree value calculated by the cytoHubba plugin of Cytoscape, hsa_circ_0011385 was finally confirmed. The subnetwork around hsa_circ_0011385 was constructed. In addition, we created a protein-protein interaction (PPI) network composed of 67 nodes and 274 edges after removing independent nodes. GO and KEGG analyses showed that hubgenes were involved in cell cycle activities. Moreover, they could be regulated by miRNAs and play an eventful role in BCa pathogenesis. CONCLUSIONS We proposed a novel circRNA-miRNA-mRNA network related to BCa pathogenesis. This network might be a new molecular biomarker and could be used to develop potential treatment strategies for BCa.
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Affiliation(s)
- Hong-cheng Lu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Jia-qi Yao
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Xiao Yang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Jie Han
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Jing-zi Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Kun Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Rui Zhou
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Hao Yu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Qiang Lv
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
| | - Min Gu
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, 300, Guangzhou Road, Nanjing, 210029 Jiangsu China
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199
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Jahani S, Nazeri E, Majidzadeh-A K, Jahani M, Esmaeili R. Circular RNA; a new biomarker for breast cancer: A systematic review. J Cell Physiol 2020; 235:5501-5510. [PMID: 31985056 DOI: 10.1002/jcp.29558] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/10/2020] [Indexed: 12/22/2022]
Abstract
Circular RNAs (circRNAs) were recently discovered as a looped subset of competing endogenous RNAs, with an ability to regulate gene expression by microRNA sponging. There are several studies on their potential roles in cancer development, such as colorectal cancer and basal cell carcinoma. However, there is still a significant gap in the knowledge about circRNA functions in breast cancer (BC) progression. The current study systematically reviewed circRNA biogenesis and their potential roles as a novel biomarker in BC on published studies of the MEDLINE®/PubMed, Cochrane®, and Scopus® databases. The obtained results showed a general dysregulation of circRNAs expression in BC cells with a cell-type and stage-specific manner. The potential connection between circRNAs and BC cell proliferation, apoptosis, metastasis, and chemotherapy sensitivity and resistance were discussed.
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Affiliation(s)
- Shima Jahani
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.,Students Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Elahe Nazeri
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Keivan Majidzadeh-A
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Mona Jahani
- Department of Crop Protection, Laboratory of Agrozoology, Ghent University, Ghent, Belgium
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
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200
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Zhang Q, Wang W, Zhou Q, Chen C, Yuan W, Liu J, Li X, Sun Z. Roles of circRNAs in the tumour microenvironment. Mol Cancer 2020; 19:14. [PMID: 31973726 PMCID: PMC6977266 DOI: 10.1186/s12943-019-1125-9] [Citation(s) in RCA: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/26/2019] [Indexed: 02/06/2023] Open
Abstract
The tumour microenvironment (TME) constitutes the area surrounding the tumour during its development and has been demonstrated to play roles in cancer-related diseases through crosstalk with tumour cells. Circular RNAs (circRNAs) are a subpopulation of endogenous noncoding RNAs (ncRNAs) that are ubiquitously expressed in eukaryotes and have multiple biological functions in the regulation of cancer onset and progression. An increasing number of studies have shown that circRNAs participate in the multifaceted biological regulation of the TME. However, details on the mechanisms involved have remained elusive until now. In this review, we analyse the effects of circRNAs on the TME from various perspectives, including immune surveillance, angiogenesis, hypoxia, matrix remodelling, exo-circRNAs and chemoradiation resistance. Currently, the enormous potential for circRNA use in targeted therapy and as noninvasive biomarkers have drawn our attention. We emphasize the prospect of targeting circRNAs as an essential strategy to regulate TME, overcome cancer resistance and improve therapeutic outcomes.
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Affiliation(s)
- Qiuge Zhang
- Department of Geriatric Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, 450052, China
| | - Quanbo Zhou
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chen Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Weitang Yuan
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jinbo Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Xiaoli Li
- Department of Geriatric Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Zhenqiang Sun
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China. .,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China.
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