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Ke X, Liang A, Chen C, Hu T. A one-pot CRISPR-RCA strategy for ultrasensitive and specific detection of circRNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3256-3262. [PMID: 38726809 DOI: 10.1039/d4ay00693c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Accurate and precise detection of circular RNA (circRNA) is imperative for its clinical use. However, the inherent challenges in circRNA detection, arising from its low abundance and potential interference from linear isomers, necessitate innovative solutions. In this study, we introduce, for the first time, the application of the CRISPR/Cas12a system to establish a one-pot, rapid (30 minutes to 2 hours), specific and ultrasensitive circRNA detection strategy, termed RETA-CRISPR (reverse transcription-rolling circle amplification (RT-RCA) with the CRISPR/Cas12a). This method comprises two steps: (1) the RT-RCA process of circRNA amplification, generating repeat units containing the back-splicing junction (BSJ) sequences; and (2) leveraging the protospacer adjacent motif (PAM)-independent Cas12a/crRNA complex to precisely recognize target sequences with BSJ, thereby initiating the collateral cleavage activity of Cas12a to generate a robust fluorescence signal. Remarkably, this approach exhibits the capability to detect circRNAs at a concentration as low as 300 aM. The sensor has been successfully employed for accurate detection of a potential hepatocellular carcinoma biomarker hsa_circ_0001445 (circRNA1445) in various cell lines. In conclusion, RETA-CRISPR seamlessly integrates the advantages of exponential amplification reaction and the robust collateral cleavage activity of Cas12a, positioning it as a compelling tool for practical CRISPR-based diagnostics.
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Affiliation(s)
- Xinxin Ke
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
| | - Ajuan Liang
- Department of Obstetrics, Shanghai First Maternity and Infant Hospital, Obstetrics and Gynecology Hospital, School of Medicine, Tongji University, Shanghai 201204, China
| | - Chuanxia Chen
- School of Materials Science and Engineering, University of Jinan, Jinan 250022, China
| | - Tao Hu
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
- School of Basic Medical Sciences & Forensic Medicine, Hangzhou Medical College, Hangzhou 310000, China
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2
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Rao G, Peng X, Tian Y, Fu X, Zhang Y. Circular RNAs in hepatocellular carcinoma: biogenesis, function, and pathology. Front Genet 2023; 14:1106665. [PMID: 37485335 PMCID: PMC10361733 DOI: 10.3389/fgene.2023.1106665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 06/16/2023] [Indexed: 07/25/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. Both genetic and environmental factors through a multitude of underlying molecular mechanisms participate in the pathogenesis of HCC. Recently, numerous studies have shown that circular RNAs (circRNAs), an emerging class of non-coding RNAs characterized by the presence of covalent bonds linking 3' and 5' ends, play an important role in the initiation and progression of cancers, including HCC. In this review, we outline the current status of the field of circRNAs, with an emphasis on the functions and mechanisms of circRNAs in HCC and its microenvironment. We also summarize and discuss recent advances of circRNAs as biomarkers and therapeutic targets. These efforts are anticipated to throw new insights into future perspectives about circRNAs in basic, translational and clinical research, eventually advancing the diagnosis, prevention and treatment of HCC.
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Affiliation(s)
- Guocheng Rao
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Xi Peng
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yan Tian
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xianghui Fu
- Department of Endocrinology and Metabolism, Cancer Center West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Yuwei Zhang
- Department of Endocrinology and Metabolism, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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Chen Z, Huang Y, Chen Y, Yang X, Zhu J, Xu G, Shen S, Hu Z, Shi P, Ma Y, Fan S. CircFNDC3B regulates osteoarthritis and oxidative stress by targeting miR-525-5p/HO-1 axis. Commun Biol 2023; 6:200. [PMID: 36806251 PMCID: PMC9941484 DOI: 10.1038/s42003-023-04569-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
Osteoarthritis (OA) is a common chronic degenerative joint disease associated with a variety of risk factors including aging, genetics, obesity, and mechanical disturbance. This study aimed to elucidate the function of a newly discovered circular RNA (circRNA), circFNDC3B, in OA progression and its relationship with the NF-κB signaling pathway and oxidative stress. The circFNDC3B/miR-525-5p/HO-1 axis and its relationship with the NF-κB signaling pathway and oxidative stress were investigated and validated using fluorescence in situ hybridization, real-time PCR, western blotting, immunofluorescence analysis, luciferase reporter assays, pull-down assays, and reactive oxygen species analyses. The functions of circFNDC3B in OA was investigated in vitro and in vivo. These evaluations demonstrated that circFNDC3B promotes chondrocyte proliferation and protects the extracellular matrix (ECM) from degradation. We also revealed that circFNDC3B defends against oxidative stress in OA by regulating the circFNDC3B/miR-525-5p/HO-1 axis and the NF-κB signaling pathway. Further, we found that overexpression of circFNDC3B alleviated OA in a rabbit model. In summary, we identified a new circFNDC3B/miR-525-5p/HO-1 signaling pathway that may act to relieve OA by alleviating oxidative stress and regulating the NF-κB pathway, resulting in the protection of the ECM in human chondrocytes, highlighting it as a potential therapeutic target for the treatment of OA.
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Affiliation(s)
- Zizheng Chen
- grid.13402.340000 0004 1759 700XDepartment of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016 Zhejiang Province China ,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, 310016 Zhejiang Province China ,grid.13402.340000 0004 1759 700XZhejiang University School of Medicine, Hangzhou, 310016 China
| | - Yizhen Huang
- grid.13402.340000 0004 1759 700XDepartment of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016 Zhejiang Province China ,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, 310016 Zhejiang Province China ,grid.13402.340000 0004 1759 700XZhejiang University School of Medicine, Hangzhou, 310016 China
| | - Yu Chen
- grid.13402.340000 0004 1759 700XDepartment of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016 Zhejiang Province China ,grid.13402.340000 0004 1759 700XZhejiang University School of Medicine, Hangzhou, 310016 China
| | - Xiaodong Yang
- grid.13402.340000 0004 1759 700XDepartment of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016 Zhejiang Province China ,grid.13402.340000 0004 1759 700XZhejiang University School of Medicine, Hangzhou, 310016 China
| | - Jinjin Zhu
- grid.13402.340000 0004 1759 700XDepartment of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016 Zhejiang Province China ,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, 310016 Zhejiang Province China ,grid.13402.340000 0004 1759 700XZhejiang University School of Medicine, Hangzhou, 310016 China
| | - Guang Xu
- grid.13402.340000 0004 1759 700XDepartment of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016 Zhejiang Province China ,grid.13402.340000 0004 1759 700XZhejiang University School of Medicine, Hangzhou, 310016 China
| | - Shuying Shen
- grid.13402.340000 0004 1759 700XDepartment of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016 Zhejiang Province China ,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, 310016 Zhejiang Province China
| | - Ziang Hu
- grid.13402.340000 0004 1759 700XDepartment of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016 Zhejiang Province China ,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, 310016 Zhejiang Province China
| | - Peihua Shi
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China. .,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, 310016, Zhejiang Province, China.
| | - Yan Ma
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China. .,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, 310016, Zhejiang Province, China.
| | - Shunwu Fan
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang Province, China. .,Key Laboratory of Musculoskeletal System Degeneration and Regeneration Translational Research of Zhejiang Province, Hangzhou, 310016, Zhejiang Province, China.
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Zhou Y, Wu Q, Ni G, Hong Y, Xiao S, Liu C, Yu Z. Immune-associated pivotal biomarkers identification and competing endogenous RNA network construction in post-operative atrial fibrillation by comprehensive bioinformatics and machine learning strategies. Front Immunol 2022; 13:974935. [PMID: 36341343 PMCID: PMC9630466 DOI: 10.3389/fimmu.2022.974935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Background Atrial fibrillation (AF) is the most common arrhythmia. Previous studies mainly focused on identifying potential diagnostic biomarkers and treatment strategies for AF, while few studies concentrated on post-operative AF (POAF), particularly using bioinformatics analysis and machine learning algorithms. Therefore, our study aimed to identify immune-associated genes and provide the competing endogenous RNA (ceRNA) network for POAF. Methods Three GSE datasets were downloaded from the GEO database, and we used a variety of bioinformatics strategies and machine learning algorithms to discover candidate hub genes. These techniques included identifying differentially expressed genes (DEGs) and circRNAs (DECs), building protein-protein interaction networks, selecting common genes, and filtering candidate hub genes via three machine learning algorithms. To assess the diagnostic value, we then created the nomogram and receiver operating curve (ROC). MiRNAs targeting DEGs and DECs were predicted using five tools and the competing endogenous RNA (ceRNA) network was built. Moreover, we performed the immune cell infiltration analysis to better elucidate the regulation of immune cells in POAF. Results We identified 234 DEGs (82 up-regulated and 152 down-regulated) of POAF via Limma, 75 node genes were visualized via PPI network, which were mainly enriched in immune regulation. 15 common genes were selected using three CytoHubba algorithms. Following machine learning selection, the nomogram was created based on the four candidate hub genes. The area under curve (AUC) of the nomogram and individual gene were all over 0.75, showing the ideal diagnostic value. The dysregulation of macrophages may be critical in POAF pathogenesis. A novel circ_0007738 was discovered in POAF and the ceRNA network was eventually built. Conclusion We identified four immune-associated candidate hub genes (C1QA, C1R, MET, and SDC4) for POAF diagnosis through the creation of a nomogram and evaluation of its diagnostic value. The modulation of macrophages and the ceRNA network may represent further therapy methods.
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Affiliation(s)
- Yufei Zhou
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qianyun Wu
- Department of Cardiology, The First People’s Hospital of Kunshan Affiliated to Jiangsu University, Suzhou, China
| | - Gehui Ni
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yulu Hong
- Department of Computer Science and Technology, Central South University, Changsha, China
| | - Shengjue Xiao
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Chunjiang Liu
- Department of General Surgery, Shaoxing People’s Hospital (Shaoxing Hospital of Zhejiang University), Shaoxing, China
| | - Zongliang Yu
- Department of Cardiology, The First People’s Hospital of Kunshan Affiliated to Jiangsu University, Suzhou, China
- *Correspondence: Zongliang Yu,
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Circular RNA circ-BNC2 (hsa_circ_0008732) inhibits the progression of ovarian cancer through microRNA-223-3p/ FBXW7 axis. J Ovarian Res 2022; 15:95. [PMID: 35965327 PMCID: PMC9377053 DOI: 10.1186/s13048-022-01025-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background Circular RNAs (circRNAs) are reported to be key regulators in the progression of human cancers. This work focuses on the function and molecular mechanism of circRNA-BNC2 (circ-BNC2) (also known as hsa_circ_0008732) in ovarian cancer (OC). Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to detect circ-BNC2, microRNA-223-3p (miR-223-3p) and F-box and WD repeat domain containing 7 (FBXW7) mRNA expressions in OC tissues and cells. Besides, cell counting kit 8 (CCK-8), transwell assay and cell cycle assays were executed to assess the proliferative, migrative, invasive abilities, and cell cycle progression of OC cells, respectively. Dual-luciferase reporter gene assay and RNA pull-down assay were used to validate the targeting relationships between miR-223-3p and circ-BNC2 or FBXW7. Western blot was adopted to determine FBXW7 protein levels in OC cells. Results Circ-BNC2 expression was downregulated in OC tissues and cell lines, which was associated with higher FIGO stage and lymph node metastasis of OC patients. Circ-BNC2 overexpression repressed the proliferation, migration, invasion of OC cells and induced cell cycle arrest, while silencing circ-BNC2 worked oppositely. Mechanistically, circ-BNC2 could upregulate FBXW7 expression in OC cells via sponging miR-223-3p. Conclusion Circ-BNC2 suppresses the progression of OC via regulating miR-223-3p / FBXW7 axis. Our findings provided potential biomarker for OC therapy.
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Braghini MR, Lo Re O, Romito I, Fernandez-Barrena MG, Barbaro B, Pomella S, Rota R, Vinciguerra M, Avila MA, Alisi A. Epigenetic remodelling in human hepatocellular carcinoma. J Exp Clin Cancer Res 2022; 41:107. [PMID: 35331312 PMCID: PMC8943959 DOI: 10.1186/s13046-022-02297-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/19/2022] [Indexed: 04/13/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most frequent primary liver cancer, being the sixth most commonly diagnosed cancer and the fourth leading cause of cancer-related death. As other heterogeneous solid tumours, HCC results from a unique synergistic combination of genetic alterations mixed with epigenetic modifications.In HCC the patterns and frequencies of somatic variations change depending on the nearby chromatin. On the other hand, epigenetic alterations often induce genomic instability prone to mutations. Epigenetics refers to heritable states of gene expression without alteration to the DNA sequence itself and, unlike genetic changes, the epigenetic modifications are reversible and affect gene expression more extensively than genetic changes. Thus, studies of epigenetic regulation and the involved molecular machinery are greatly contributing to the understanding of the mechanisms that underline HCC onset and heterogeneity. Moreover, this knowledge may help to identify biomarkers for HCC diagnosis and prognosis, as well as future new targets for more efficacious therapeutic approaches.In this comprehensive review we will discuss the state-of-the-art knowledge about the epigenetic landscape in hepatocarcinogenesis, including evidence on the diagnostic and prognostic role of non-coding RNAs, modifications occurring at the chromatin level, and their role in the era of precision medicine.Apart from other better-known risk factors that predispose to the development of HCC, characterization of the epigenetic remodelling that occurs during hepatocarcinogenesis could open the way to the identification of personalized biomarkers. It may also enable a more accurate diagnosis and stratification of patients, and the discovery of new targets for more efficient therapeutic approaches.
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Affiliation(s)
- Maria Rita Braghini
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Oriana Lo Re
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Ilaria Romito
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Maite G Fernandez-Barrena
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Barbara Barbaro
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy
| | - Silvia Pomella
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Paediatric Haematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Manlio Vinciguerra
- Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Matias A Avila
- Hepatology Program, CIMA, University of Navarra, Pamplona, Spain
- Center for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health, Madrid, Spain
| | - Anna Alisi
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Viale S. Paolo, 15, 00146, Rome, Italy.
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Liu Q, Yu J, Cai Y, Zhang G, Dai X. SAAED: Embedding and Deep Learning Enhance Accurate Prediction of Association Between circRNA and Disease. Front Genet 2022; 13:832244. [PMID: 35273640 PMCID: PMC8902643 DOI: 10.3389/fgene.2022.832244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Emerging evidence indicates that circRNA can regulate various diseases. However, the mechanisms of circRNA in these diseases have not been fully understood. Therefore, detecting potential circRNA–disease associations has far-reaching significance for pathological development and treatment of these diseases. In recent years, deep learning models are used in association analysis of circRNA–disease, but a lack of circRNA–disease association data limits further improvement. Therefore, there is an urgent need to mine more semantic information from data. In this paper, we propose a novel method called Semantic Association Analysis by Embedding and Deep learning (SAAED), which consists of two parts, a neural network embedding model called Entity Relation Network (ERN) and a Pseudo-Siamese network (PSN) for analysis. ERN can fuse multiple sources of data and express the information with low-dimensional embedding vectors. PSN can extract the feature between circRNA and disease for the association analysis. CircRNA–disease, circRNA–miRNA, disease–gene, disease–miRNA, disease–lncRNA, and disease–drug association information are used in this paper. More association data can be introduced for analysis without restriction. Based on the CircR2Disease benchmark dataset for evaluation, a fivefold cross-validation experiment showed an AUC of 98.92%, an accuracy of 95.39%, and a sensitivity of 93.06%. Compared with other state-of-the-art models, SAAED achieves the best overall performance. SAAED can expand the expression of the biological related information and is an efficient method for predicting potential circRNA–disease association.
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Affiliation(s)
- Qingyu Liu
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, China
| | - Junjie Yu
- Macquarie Business School, Macquarie University, Sydney, NSW, Australia
| | - Yanning Cai
- College of Information Science and Technology, Jinan University, Guangzhou, China
| | - Guishan Zhang
- College of Engineering, Shantou University, Shantou, China
| | - Xianhua Dai
- School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, China
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Li P, Song R, Yin F, Liu M, Liu H, Ma S, Jia X, Lu X, Zhong Y, Yu L, Li X, Li X. circMRPS35 promotes malignant progression and cisplatin resistance in hepatocellular carcinoma. Mol Ther 2022; 30:431-447. [PMID: 34450251 PMCID: PMC8753434 DOI: 10.1016/j.ymthe.2021.08.027] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 01/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the major causes of cancer-related death worldwide. Circular RNAs (circRNAs), a novel class of non-coding RNA, have been reported to be involved in the etiology of various malignancies. However, the underlying cellular mechanisms of circRNAs implicated in the pathogenesis of HCC remain unknown. In this study, we identified a functional RNA, hsa_circ_0000384 (circMRPS35), from public tumor databases using a set of computational analyses, and we further identified that circMRPS35 was highly expressed in 35 pairs of HCC from patients. Moreover, knockdown of the expression of circMRPS35 in Huh-7 and HCC-LM3 cells suppressed their proliferation, migration, invasion, clone formation, and cell cycle in vitro, and it suppressed tumor growth in vivo as well. Mechanically, circMRPS35 sponged microRNA-148a-3p (miR-148a), regulating the expression of Syntaxin 3 (STX3), which modulated the ubiquitination and degradation of phosphatase and tensin homolog (PTEN). Unexpectedly, we detected a peptide encoded by circMRPS35 (circMRPS35-168aa), which was significantly induced by chemotherapeutic drugs and promoted cisplatin resistance in HCC. These results demonstrated that circMRPS35 might be a novel mediator in HCC progress, and they raise the potential of a new biomarker for HCC diagnosis and prognosis, as well as a novel therapeutic target for HCC patients.
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Affiliation(s)
- Peng Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Runjie Song
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Fan Yin
- Department of Oncology, The Second Medical Centre & National Clinical Research Center of Geriatric Disease, Chinese PLA General Hospital, Beijing 100071, China
| | - Mei Liu
- Department of Pathology, Chinese PLA General Hospital, Beijing 100071, China
| | - Huijiao Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shuoqian Ma
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaomeng Jia
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaohui Lu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yuting Zhong
- Department of Surgery, Chinese PLA General Hospital, Beijing, 100071, China
| | - Lei Yu
- Department of Thoracic Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100005, China
| | - Xiru Li
- Department of Surgery, Chinese PLA General Hospital, Beijing, 100071, China
| | - Xiangdong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China,Department of Reproduction and Gynecological Endocrinology, Medical University of Bialystok, Bialystok, Poland,Department of Nutrition and Health, China Agricultural University, Beijing 100193, China,Corresponding author: Xiangdong Li, State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Li Y, Gong H, Wang P, Zhu Y, Peng H, Cui Y, Li H, Liu J, Wang Z. The emerging role of ISWI chromatin remodeling complexes in cancer. J Exp Clin Cancer Res 2021; 40:346. [PMID: 34736517 PMCID: PMC8567610 DOI: 10.1186/s13046-021-02151-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022] Open
Abstract
Disordered chromatin remodeling regulation has emerged as an essential driving factor for cancers. Imitation switch (ISWI) family are evolutionarily conserved ATP-dependent chromatin remodeling complexes, which are essential for cellular survival and function through multiple genetic and epigenetic mechanisms. Omics sequencing and a growing number of basic and clinical studies found that ISWI family members displayed widespread gene expression and genetic status abnormalities in human cancer. Their aberrant expression is closely linked to patient outcome and drug response. Functional or componential alteration in ISWI-containing complexes is critical for tumor initiation and development. Furthermore, ISWI-non-coding RNA regulatory networks and some non-coding RNAs derived from exons of ISWI member genes play important roles in tumor progression. Therefore, unveiling the transcriptional regulation mechanism underlying ISWI family sparked a booming interest in finding ISWI-based therapies in cancer. This review aims at describing the current state-of-the-art in the role of ISWI subunits and complexes in tumorigenesis, tumor progression, immunity and drug response, and presenting deep insight into the physiological and pathological implications of the ISWI transcription machinery in cancers.
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Affiliation(s)
- Yanan Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Han Gong
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Pan Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Yu Zhu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Hongling Peng
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Yajuan Cui
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Heng Li
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China
| | - Jing Liu
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Zi Wang
- Department of Hematology, Institute of Molecular Hematology, The Second Xiangya Hospital, Central South University, Changsha, 410011, Hunan, China.
- Molecular Biology Research Center and Hunan Province Key Laboratory of Basic and Applied Hematology, School of Life Sciences, Central South University, Changsha, 410078, Hunan, China.
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Shen HY, Shi LX, Wang L, Fang LP, Xu W, Xu JQ, Fan BQ, Fan WF. Hsa_circ_0001361 facilitates the progress of lung adenocarcinoma cells via targeting miR-525-5p/VMA21 axis. J Transl Med 2021; 19:389. [PMID: 34507559 PMCID: PMC8434718 DOI: 10.1186/s12967-021-03045-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is a common subtype of lung cancer with high recurrence rate and fatality. Circ_0001361 has been recognized as key regulators in various malignancies, but its roles in LUAD remain ambiguous. Methods Circ_0001361, miR-525-5p, and VMA21 levels were assessed by RT-qPCR. The growth and metastasis of LUAD cells were detected by MTT, colony formation, wound scratch, and transwell assays, respectively. The interaction between circ_0001361/VMA21 and miR-525-5p was detected by dual luciferase, RNA immunoprecipitation, and RNA pull-down assays. VMA21 protein level was detected by Western blotting. Nude mouse xenograft model was established to determine the role of circ_0001361 in tumor growth in vivo. Results Circ_0001361 was up-regulated, while miR-525-5p was down-regulated in LUAD tissues and cells. Functional experiments demonstrated that circ_0001361 drove LUAD cell growth and metastasis. Mechanistically, circ_0001361 functioned as a sponge of miR-525-5p to up-regulate downstream target VMA21 level. MiR-525-5p/VMA21 axis was involved in circ_0001361-mediated malignant phenotypes of LUAD cells. Finally, inhibition of circ_0001361 restrained in vivo xenograft tumor growth via regulating miR-525-5p/VMA21 axis. Conclusion Our findings elucidate that circ_0001361 facilitates the tumorigenesis and development of LUAD through miR-525-5p/VMA21 axis, providing evidence for circ_0001361 as a potential prognosis biomarker and therapeutic target for clinical treatment of LUAD. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03045-4.
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Affiliation(s)
- Hong-Yu Shen
- Department of Hematology and Oncology, Department of Geriatric Lung Cancer Laboratory, Geriatric Hospital of Nanjing Medical University, Jiangsu Province Geriatric Hospital, No.65 Jiangsu Road, Gulou District, Nanjing, 210000, Jiangsu Province, People's Republic of China
| | - Liu-Xi Shi
- GCP office, The Second Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu Province, People's Republic of China
| | - Lin Wang
- Department of Hematology and Oncology, Department of Geriatric Lung Cancer Laboratory, Geriatric Hospital of Nanjing Medical University, Jiangsu Province Geriatric Hospital, No.65 Jiangsu Road, Gulou District, Nanjing, 210000, Jiangsu Province, People's Republic of China
| | - Le-Ping Fang
- Department of Hematology and Oncology, Department of Geriatric Lung Cancer Laboratory, Geriatric Hospital of Nanjing Medical University, Jiangsu Province Geriatric Hospital, No.65 Jiangsu Road, Gulou District, Nanjing, 210000, Jiangsu Province, People's Republic of China
| | - Wei Xu
- Department of Hematology and Oncology, Department of Geriatric Lung Cancer Laboratory, Geriatric Hospital of Nanjing Medical University, Jiangsu Province Geriatric Hospital, No.65 Jiangsu Road, Gulou District, Nanjing, 210000, Jiangsu Province, People's Republic of China
| | - Ju-Qing Xu
- Department of Hematology and Oncology, Department of Geriatric Lung Cancer Laboratory, Geriatric Hospital of Nanjing Medical University, Jiangsu Province Geriatric Hospital, No.65 Jiangsu Road, Gulou District, Nanjing, 210000, Jiangsu Province, People's Republic of China
| | - Bo-Qiang Fan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, Jiangsu Province, People's Republic of China.
| | - Wei-Fei Fan
- Department of Hematology and Oncology, Department of Geriatric Lung Cancer Laboratory, Geriatric Hospital of Nanjing Medical University, Jiangsu Province Geriatric Hospital, No.65 Jiangsu Road, Gulou District, Nanjing, 210000, Jiangsu Province, People's Republic of China.
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11
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Han J, Thurnherr T, Chung AYF, Goh BKP, Chow PKH, Chan CY, Cheow PC, Lee SY, Lim TKH, Chong SS, Ooi LLPJ, Lee CG. Clinicopathological-Associated Regulatory Network of Deregulated circRNAs in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13112772. [PMID: 34199580 PMCID: PMC8199648 DOI: 10.3390/cancers13112772] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/01/2023] Open
Abstract
Simple Summary Here, we present a novel strategy to identify key signatures of clinically-relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate the prognosis of HCC patients, by integrating clinicopathological features, circRNA and mRNA expression profiles. Five master circRNAs were identified and experimentally demonstrated to upregulate proliferate and promote transformation. Through further integration with miRNA-expression profiles, clinically-relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. The most up-regulated nodal-circRNA, circGPC3 was experimentally demonstrated to up-regulate cell-cycle, migration and invasion. circGPC3 was found to act as a sponge of miR-378a-3p to regulate ASPM expression and modulate cell transformation. These 5 nodal circRNAs has potential to be good prognostic biomarkers with good prognostic performance. circGPC3 has great potential to be a promising non-invasive prognostic biomarker for early HCC. We have thus demonstrated the robustness of bioinformatically-predicted master circRNAs in clinically-relevant, circRNA-mRNA networks, underscoring the important roles that these identified deregulated key/master circRNAs play in HCC. Abstract Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. Here, we present a novel strategy to identify key circRNA signatures of clinically relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate prognosis of HCC patients, by integrating clinic-pathological features, circRNA and mRNA expression profiles. Through further integration with miRNA expression profiles, clinically relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. At least five clinically relevant nodal-circRNAs, co-expressed with numerous genes, were identified from the circRNA-mRNA networks. These nodal circRNAs upregulated proliferation (except circRaly) and transformation in cells. The most upregulated nodal-circRNA, circGPC3, associated with higher-grade tumors and co-expressed with 33 genes, competes with 11 mRNAs for two shared miRNAs. circGPC3 was experimentally demonstrated to upregulate cell-cycle and migration/invasion in both transformed and non-transformed liver cell-lines. circGPC3 was further shown to act as a sponge of miR-378a-3p to regulate APSM (Abnormal spindle-like microcephaly associated) expression and modulate cell transformation. This study identifies 5 key nodal master circRNAs in a clinically relevant circRNA-centric network that are significantly associated with poorer prognosis of HCC patients and promotes tumorigenesis in cell-lines. The identification and characterization of these key circRNAs in clinically relevant circRNA-mRNA and ceRNA networks may facilitate the design of novel strategies targeting these important regulators for better HCC prognosis.
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Affiliation(s)
- Jian Han
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore;
| | - Alexander Y. F. Chung
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Brian K. P. Goh
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Pierce K. H. Chow
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Chung Yip Chan
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Peng Chung Cheow
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Ser Yee Lee
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Tony K. H. Lim
- Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore;
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - London L. P. J. Ooi
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Caroline G. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore;
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Level 6, Lab 5, 11 Hospital Drive, Singapore 169610, Singapore
- Correspondence: ; Tel.: +65-65163251
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Ely A, Bloom K, Maepa MB, Arbuthnot P. Recent Update on the Role of Circular RNAs in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2021; 8:1-17. [PMID: 33542907 PMCID: PMC7851377 DOI: 10.2147/jhc.s268291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
After being overlooked for decades, circular RNAs (circRNAs) have recently generated considerable interest. circRNAs play a role in a variety of normal and pathological biological processes, including hepatocarcinogenesis. Many circRNAs contribute to hepatocarcinogenesis through sponging of microRNAs (miRs) and disruption of cellular signaling pathways that play a part in control of cell proliferation, metastasis and apoptosis. In most cases, overexpressed circRNAs sequester miRs to cause de-repressed translation of mRNAs that encode oncogenic proteins. Conversely, low expression of circRNAs has also been described in hepatocellular carcinoma (HCC) and is associated with inhibited production of tumor suppressor proteins. Other functions of circRNAs that contribute to hepatocarcinogenesis include translation of truncated proteins and acting as adapters to regulate influence of transcription factors on target gene expression. circRNAs also affect hepatocyte transformation indirectly. For example, the molecules regulate immune surveillance of cancerous cells and influence the liver fibrosis that commonly precedes HCC. Marked over- or under-expression of circRNA expression in HCC, with correlating plasma concentrations, has diagnostic utility and assays of these RNAs are being developed as biomarkers of HCC. Although knowledge in the field has recently surged, the myriad of described effects suggests that not all may be vital to hepatocarcinogenesis. Nevertheless, investigation of the role of circRNAs is providing valuable insights that are likely to contribute to improved management of a serious and highly aggressive cancer.
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Affiliation(s)
- Abdullah Ely
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mohube Betty Maepa
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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13
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Xu Q, Zhou L, Yang G, Meng F, Wan Y, Wang L, Zhang L. Overexpression of circ_0001445 decelerates hepatocellular carcinoma progression by regulating miR-942-5p/ALX4 axis. Biotechnol Lett 2020; 42:2735-2747. [PMID: 32856218 DOI: 10.1007/s10529-020-02985-z] [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: 04/02/2020] [Accepted: 08/08/2020] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) have been verified to have essential regulatory roles in diverse human cancers, including hepatocellular carcinoma (HCC). In this study, we aimed to explore the roles of circ_0001445 in HCC. Herein, circ_0001445 was decreased and miR-942-5p was increased in HCC tissues and cells. Circ_0001445 overexpression or miR-942-5p inhibition repressed cell cycle process, migration, invasion, epithelial-mesenchymal transition and glycolysis in HCC cells. Mechanistically, circ_0001445 could promote ALX4 expression through targeting miR-942-5p. Moreover, miR-942-5p overexpression reversed the inhibitory effect of circ_0001445 on HCC cell progression. The effect of miR-942-5p on HCC cell development was rescued following the elevation of ALX4. In addition, circ_0001445 overexpression restrained tumorigenesis in vivo. In conclusion, circ_0001445 played a negative role in HCC progression by modulating miR-942-5p/ALX4 axis, which might provide a novel target for HCC therapy.
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Affiliation(s)
- Qinhong Xu
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Lijing Zhou
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Ganghua Yang
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Fandi Meng
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Yong Wan
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Lin Wang
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, 710061, Shaanxi, China
| | - Lei Zhang
- Department of Geriatric Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277, Yanta West Road, Xi'an, 710061, Shaanxi, China.
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Yao J, Qian K, Chen C, Liu X, Yu D, Yan X, Liu T, Li S. ZNF139/ circZNF139 promotes cell proliferation, migration and invasion via activation of PI3K/AKT pathway in bladder cancer. Aging (Albany NY) 2020; 12:9915-9934. [PMID: 32454461 PMCID: PMC7288921 DOI: 10.18632/aging.103256] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/29/2020] [Indexed: 02/07/2023]
Abstract
Existing reports identify the involved roles of ZNF139 and its one circular RNA (circRNA), circZNF139, in the progression of various tumors. However, their relevance and function role in bladder cancer (BC) remain largely unexplored. Herein, we aimed to reconnoiter the role and potential mechanism of ZNF139 and circZNF139 in the progression of BC. Firstly, bioinformatics analyses indicated ZNF139 was upregulated in BC tissues and correlated with disease-free survival of BC patients. The subcellular localization and structural analyses of ZNF139 conveyed the possibility of ZNF139 functioning as a transcription factor. Secondly, circZNF139 was validated by bioinformatics analyses and RNase R tests. ZNF139 and circZNF139 were both significantly upregulated in BC cell lines. Functionally, ZNF139/circZNF139 had facilitated effects on the proliferative, clonal, migratory, and invasive potential of BC cells. Mechanistically, GO, KEGG pathway analyses and western blot assays altogether unveiled ZNF139/circZNF139 activated PI3K/AKT pathway in BC cells, supported by the alteration of AKT at phosphorylation level and PI3K at the protein level. Collectively, this work reveals ZNF139 and circZNF139 cooperate closely with each other to promote cell proliferation, migration and invasion via activation of PI3K/AKT pathway in BC.
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Affiliation(s)
- Jie Yao
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Kaiyu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China
| | - Chen Chen
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China
| | - Xiaoping Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Donghu Yu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xin Yan
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Tongzu Liu
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Sheng Li
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan 430071, China.,Human Genetics Resource Preservation Center of Hubei Province, Wuhan 430071, China.,Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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15
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Zhang S, Zhou Y, Wang Y, Wang Z, Xiao Q, Zhang Y, Lou Y, Qiu Y, Zhu F. The mechanistic, diagnostic and therapeutic novel nucleic acids for hepatocellular carcinoma emerging in past score years. Brief Bioinform 2020; 22:1860-1883. [PMID: 32249290 DOI: 10.1093/bib/bbaa023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/09/2020] [Accepted: 02/12/2020] [Indexed: 02/07/2023] Open
Abstract
Despite The Central Dogma states the destiny of gene as 'DNA makes RNA and RNA makes protein', the nucleic acids not only store and transmit genetic information but also, surprisingly, join in intracellular vital movement as a regulator of gene expression. Bioinformatics has contributed to knowledge for a series of emerging novel nucleic acids molecules. For typical cases, microRNA (miRNA), long noncoding RNA (lncRNA) and circular RNA (circRNA) exert crucial role in regulating vital biological processes, especially in malignant diseases. Due to extraordinarily heterogeneity among all malignancies, hepatocellular carcinoma (HCC) has emerged enormous limitation in diagnosis and therapy. Mechanistic, diagnostic and therapeutic nucleic acids for HCC emerging in past score years have been systematically reviewed. Particularly, we have organized recent advances on nucleic acids of HCC into three facets: (i) summarizing diverse nucleic acids and their modification (miRNA, lncRNA, circRNA, circulating tumor DNA and DNA methylation) acting as potential biomarkers in HCC diagnosis; (ii) concluding different patterns of three key noncoding RNAs (miRNA, lncRNA and circRNA) in gene regulation and (iii) outlining the progress of these novel nucleic acids for HCC diagnosis and therapy in clinical trials, and discuss their possibility for clinical applications. All in all, this review takes a detailed look at the advances of novel nucleic acids from potential of biomarkers and elaboration of mechanism to early clinical application in past 20 years.
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Affiliation(s)
- Song Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China.,College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China
| | - Yanan Wang
- School of Life Sciences in Nanchang University, China
| | - Zhengwen Wang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Qitao Xiao
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Ying Zhang
- College of Pharmaceutical Sciences in Zhejiang University, China
| | - Yan Lou
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China
| | - Yunqing Qiu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China
| | - Feng Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital in Zhejiang University, China.,College of Pharmaceutical Sciences in Zhejiang University, China
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