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Jiang H, Meng T, Li Z. Role of circular RNAs in preeclampsia (Review). Exp Ther Med 2024; 28:372. [PMID: 39091629 PMCID: PMC11292168 DOI: 10.3892/etm.2024.12661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Preeclampsia (PE) is a hypertensive disorder of pregnancy characterized by new-onset hypertension and proteinuria after 20 weeks of gestation, which affects 3-8% of pregnant individuals worldwide each year. Prevention, diagnosis and treatment of PE are some of the most important problems faced by obstetrics. There is growing evidence that circular RNAs (circRNAs) are involved in the pathogenesis of PE. The present review summarizes the research progress of circRNAs and then describes the expression patterns of circRNAs in PE and their functional mechanisms affecting PE development. The role of circRNAs as biomarkers for the diagnosis of PE, and the research status of circRNAs in PE are summarized in the hope of finding novel strategies for the prevention and treatment of PE.
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Affiliation(s)
- Hengxue Jiang
- Department of Obstetrics, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
- Department of Obstetrics and Gynecology, China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Tao Meng
- Department of Obstetrics, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
| | - Ziwei Li
- Department of Obstetrics, The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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2
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Morandell J, Monziani A, Lazioli M, Donzel D, Döring J, Oss Pegorar C, D'Anzi A, Pellegrini M, Mattiello A, Bortolotti D, Bergonzoni G, Tripathi T, Mattis VB, Kovalenko M, Rosati J, Dieterich C, Dassi E, Wheeler VC, Ellederová Z, Wilusz JE, Viero G, Biagioli M. CircHTT(2,3,4,5,6) - co-evolving with the HTT CAG-repeat tract - modulates Huntington's disease phenotypes. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102234. [PMID: 38974999 PMCID: PMC11225910 DOI: 10.1016/j.omtn.2024.102234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
Circular RNA (circRNA) molecules have critical functions during brain development and in brain-related disorders. Here, we identified and validated a circRNA, circHTT(2,3,4,5,6), stemming from the Huntington's disease (HD) gene locus that is most abundant in the central nervous system (CNS). We uncovered its evolutionary conservation in diverse mammalian species, and a correlation between circHTT(2,3,4,5,6) levels and the length of the CAG-repeat tract in exon-1 of HTT in human and mouse HD model systems. The mouse orthologue, circHtt(2,3,4,5,6), is expressed during embryogenesis, increases during nervous system development, and is aberrantly upregulated in the presence of the expanded CAG tract. While an IRES-like motif was predicted in circH TT (2,3,4,5,6), the circRNA does not appear to be translated in adult mouse brain tissue. Nonetheless, a modest, but consistent fraction of circHtt(2,3,4,5,6) associates with the 40S ribosomal subunit, suggesting a possible role in the regulation of protein translation. Finally, circHtt(2,3,4,5,6) overexpression experiments in HD-relevant STHdh striatal cells revealed its ability to modulate CAG expansion-driven cellular defects in cell-to-substrate adhesion, thus uncovering an unconventional modifier of HD pathology.
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Affiliation(s)
- Jasmin Morandell
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Alan Monziani
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Martina Lazioli
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Deborah Donzel
- Institute of Biophysics Unit at Trento, National Research Council - CNR, 38123 Trento, Italy
| | - Jessica Döring
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Claudio Oss Pegorar
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Angela D'Anzi
- Cellular Reprogramming Unit Fondazione IRCCS, Casa Sollievo Della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Miguel Pellegrini
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Andrea Mattiello
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Dalia Bortolotti
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Guendalina Bergonzoni
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Takshashila Tripathi
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Virginia B Mattis
- Board of Governor's Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Marina Kovalenko
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jessica Rosati
- Cellular Reprogramming Unit Fondazione IRCCS, Casa Sollievo Della Sofferenza, Viale dei Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Vanessa C Wheeler
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zdenka Ellederová
- Research Center PIGMOD, Institute of Animal Physiology and Genetics, Czech Academy of Science, 277 21 Libechov, Czech Republic
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabriella Viero
- Institute of Biophysics Unit at Trento, National Research Council - CNR, 38123 Trento, Italy
| | - Marta Biagioli
- NeuroEpigenetics Laboratory, Department of Cellular, Computational, and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
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Zhou Y, Cui H, Liu D, Wang W. MSTCRB: Predicting circRNA-RBP interaction by extracting multi-scale features based on transformer and attention mechanism. Int J Biol Macromol 2024; 278:134805. [PMID: 39153682 DOI: 10.1016/j.ijbiomac.2024.134805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 08/19/2024]
Abstract
CircRNAs play vital roles in biological system mainly through binding RNA-binding protein (RBP), which is essential for regulating physiological processes in vivo and for identifying causal disease variants. Therefore, predicting interactions between circRNA and RBP is a critical step for the discovery of new therapeutic agents. Application of various deep-learning models in bioinformatics has significantly improved prediction and classification performance. However, most of existing prediction models are only applicable to specific type of RNA or RNA with simple characteristics. In this study, we proposed an attractive deep learning model, MSTCRB, based on transformer and attention mechanism for extracting multi-scale features to predict circRNA-RBP interactions. Therein, K-mer and KNF encoding are employed to capture the global sequence features of circRNA, NCP and DPCP encoding are utilized to extract local sequence features, and the CDPfold method is applied to extract structural features. In order to improve prediction performance, optimized transformer framework and attention mechanism were used to integrate these multi-scale features. We compared our model's performance with other five state-of-the-art methods on 37 circRNA datasets and 31 linear RNA datasets. The results show that the average AUC value of MSTCRB reaches 98.45 %, which is better than other comparative methods. All of above datasets are deposited in https://github.com/chy001228/MSTCRB_database.git and source code are available from https://github.com/chy001228/MSTCRB.git.
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Affiliation(s)
- Yun Zhou
- College of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China; Key Laboratory of Artificial Intelligence and Personalized Learning in Education of Henan Province, College of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China.
| | - Haoyu Cui
- College of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China
| | - Dong Liu
- College of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China; Key Laboratory of Artificial Intelligence and Personalized Learning in Education of Henan Province, College of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China.
| | - Wei Wang
- College of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China; Key Laboratory of Artificial Intelligence and Personalized Learning in Education of Henan Province, College of Computer and Information Engineering, Henan Normal University, Xinxiang 453007, China.
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Hu N, Zheng Y, Liu X, Jia J, Feng J, Zhang C, Liu L, Wang X. CircKat6b Mediates the Antidepressant Effect of Esketamine by Regulating Astrocyte Function. Mol Neurobiol 2024:10.1007/s12035-024-04420-0. [PMID: 39138759 DOI: 10.1007/s12035-024-04420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024]
Abstract
The abundant expression of circular RNAs (circRNAs) in the central nervous system and their contribution to the pathogenesis of depression suggest that circRNAs are promising therapeutic targets for depression. This study explored the role and mechanism of circKat6b in esketamine's antidepressant effect. We found that intravenous administration of esketamine (5 mg/kg) treatment decreased the circKat6b expression in the astrocytes of hippocampus induced by a chronic unpredictable mild stress (CUMS) mouse model, while the overexpression of circKat6b in the hippocampus significantly attenuated the antidepressant effects of esketamine in depressed mice. RNA-sequencing, RT-PCR, and western blot experiments showed that the stat1 and p-stat1 expression were significantly upregulated in mouse astrocytes overexpressing circKat6b. In the CUMS mouse model, overexpression of circKat6b in the hippocampus significantly reversed the downregulation of p-stat1 protein expression caused by esketamine. Our findings demonstrated that a novel mechanism of the antidepressant like effect of esketamine may be achieved by reducing the expression of circKat6b in the astrocyte of the hippocampus of depressed mice.
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Affiliation(s)
- Na Hu
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Yujie Zheng
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Xueru Liu
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Jing Jia
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Jianguo Feng
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Chunxiang Zhang
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Li Liu
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China
| | - Xiaobin Wang
- Department of Anesthesiology, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
- Anesthesiology and Critical Care Medicine Key Laboratory of Luzhou, The Affiliated Hospital, Southwest Medical University, Luzhou, 646000, Sichuan Province, China.
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Mafi A, Khoshnazar SM, Shahpar A, Nabavi N, Hedayati N, Alimohammadi M, Hashemi M, Taheriazam A, Farahani N. Mechanistic insights into circRNA-mediated regulation of PI3K signaling pathway in glioma progression. Pathol Res Pract 2024; 260:155442. [PMID: 38991456 DOI: 10.1016/j.prp.2024.155442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/22/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024]
Abstract
Circular RNAs (CircRNAs) are non-coding RNAs (ncRNAs) characterized by a stable circular structure that regulates gene expression at both transcriptional and post-transcriptional levels. They play diverse roles, including protein interactions, DNA methylation modification, protein-coding potential, pseudogene creation, and miRNA sponging, all of which influence various physiological processes. CircRNAs are often highly expressed in brain tissues, and their levels vary with neural development, suggesting their significance in nervous system diseases such as gliomas. Research has shown that circRNA expression related to the PI3K pathway correlates with various clinical features of gliomas. There is an interact between circRNAs and the PI3K pathway to regulate glioma cell processes such as proliferation, differentiation, apoptosis, inflammation, angiogenesis, and treatment resistance. Additionally, PI3K pathway-associated circRNAs hold potential as biomarkers for cancer diagnosis, prognosis, and treatment. In this study, we reviewed the latest advances in the expression and cellular roles of PI3K-mediated circRNAs and their connections to glioma carcinogenesis and progression. We also highlighted the significance of circRNAs as diagnostic and prognostic biomarkers and therapeutic targets in glioma.
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Affiliation(s)
- Alireza Mafi
- Nutrition and Food Security Research Center, Isfahan University of Medical Sciences, Isfahan, Iran; Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyedeh Mahdieh Khoshnazar
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Amirhossein Shahpar
- Gastroenterology and Hepatology Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Noushin Nabavi
- Independent Researcher, Victoria, British Columbia, Canada
| | - Neda Hedayati
- School of Medicine, Iran University of Medical Science, Tehran, Iran.
| | - Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Najma Farahani
- Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.
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Hou G, Alissa M, Alsuwat MA, Ali Alarjany HM, Alzahrani KJ, Althobaiti FM, Mujalli HM, Alotaiby MM, Al-Doaiss AA, Anthony S. The art of healing hearts: Mastering advanced RNA therapeutic techniques to shape the evolution of cardiovascular medicine in biomedical science. Curr Probl Cardiol 2024; 49:102627. [PMID: 38723793 DOI: 10.1016/j.cpcardiol.2024.102627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of death worldwide and are associated with increasing financial health burden that requires research into novel therapeutic approaches. Since the early 2000s, the availability of next-generation sequencing techniques such as microRNAs, circular RNAs, and long non-coding RNAs have been proven as potential therapeutic targets for treating various CVDs. Therapeutics based on RNAs have become a viable option for addressing the intricate molecular pathways that underlie the pathophysiology of CVDs. We provide an in-depth analysis of the state of RNA therapies in the context of CVDs, emphasizing various approaches that target the various stages of the basic dogma of molecular biology to effect temporary or long-term changes. In this review, we summarize recent methodologies used to screen for novel coding and non-coding RNA candidates with diagnostic and treatment possibilities in cardiovascular diseases. These methods include single-cell sequencing techniques, functional RNA screening, and next-generation sequencing.Lastly, we highlighted the potential of using oligonucleotide-based chemical products such as modified RNA and RNA mimics/inhibitors for the treatment of CVDs. Moreover, there will be an increasing number of potential RNA diagnostic and therapeutic for CVDs that will progress to expand for years to come.
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Affiliation(s)
- Guoliang Hou
- Department of Cardiology, Tengzhou Central People's Hospital, Shandong 277599, China
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
| | - Meshari A Alsuwat
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21974, Saudi Arabia
| | | | - Khalid J Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21974, Saudi Arabia
| | - Fahad M Althobaiti
- Department of Nursing Leadership and Education, Nursing College, Taif University, Taif 21974, Saudi Arabia
| | | | - Monearah M Alotaiby
- Department of Laboratory, King Faisal Medical Complex, Ministry of Health, Taif 26514, Saudi Arabia
| | - Amin A Al-Doaiss
- Biology Department, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Stefan Anthony
- Liaoning Provincial Key Laboratory of Cerebral Diseases, Department of Physiology, Dalian Medical University Liaoning Provence China, China.
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Ji Y, Ni C, Shen Y, Xu Z, Tang L, Yu F, Zhu L, Lu H, Zhang C, Yang S, Wang X. ESRP1-mediated biogenesis of circPTPN12 inhibits hepatocellular carcinoma progression by PDLIM2/ NF-κB pathway. Mol Cancer 2024; 23:143. [PMID: 38992675 PMCID: PMC11238376 DOI: 10.1186/s12943-024-02056-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 06/29/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Emerging evidence indicates the pivotal involvement of circular RNAs (circRNAs) in cancer initiation and progression. Understanding the functions and underlying mechanisms of circRNAs in tumor development holds promise for uncovering novel diagnostic indicators and therapeutic targets. In this study, our focus was to elucidate the function and regulatory mechanism of hsa-circ-0003764 in hepatocellular carcinoma (HCC). METHODS A newly discovered hsa-circ-0003764 (circPTPN12) was identified from the circbase database. QRT-PCR analysis was utilized to assess the expression levels of hsa-circ-0003764 in both HCC tissues and cells. We conducted in vitro and in vivo experiments to examine the impact of circPTPN12 on the proliferation and apoptosis of HCC cells. Additionally, RNA-sequencing, RNA immunoprecipitation, biotin-coupled probe pull-down assays, and FISH were employed to confirm and establish the relationship between hsa-circ-0003764, PDLIM2, OTUD6B, P65, and ESRP1. RESULTS In HCC, the downregulation of circPTPN12 was associated with an unfavorable prognosis. CircPTPN12 exhibited suppressive effects on the proliferation of HCC cells both in vitro and in vivo. Mechanistically, RNA sequencing assays unveiled the NF-κB signaling pathway as a targeted pathway of circPTPN12. Functionally, circPTPN12 was found to interact with the PDZ domain of PDLIM2, facilitating the ubiquitination of P65. Furthermore, circPTPN12 bolstered the assembly of the PDLIM2/OTUD6B complex by promoting the deubiquitination of PDLIM2. ESRP1 was identified to bind to pre-PTPN12, thereby fostering the generation of circPTPN12. CONCLUSIONS Collectively, our findings indicate the involvement of circPTPN12 in modulating PDLIM2 function, influencing HCC progression. The identified ESRP1/circPTPN12/PDLIM2/NF-κB axis shows promise as a novel therapeutic target in the context of HCC.
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Affiliation(s)
- Yang Ji
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
- Medical College, Yangzhou University, Yangzhou, China
| | - Chuangye Ni
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Yanjun Shen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Zhenggang Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Lei Tang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
| | - Fei Yu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China
- Department of General Surgery, Jinhu People's Hospital, Huaian City, China
| | - Lingbang Zhu
- Jiangdu People's Hospital Affiliated to Yangzhou University, Yangzhou, China
| | - Hao Lu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China.
| | - Chuanyong Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China.
| | - Shikun Yang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China.
| | - Xuehao Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, NHC Key Laboratory of Living Donor Liver Transplantation (Nanjing Medical University), No. 300 Guangzhou Road, Nanjing, Jiangsu Province, 210029, China.
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Rossi MN, Fiorucci C, Mariottini P, Cervelli M. Unveiling the hidden players: noncoding RNAs orchestrating polyamine metabolism in disease. Cell Biosci 2024; 14:84. [PMID: 38918813 PMCID: PMC11202255 DOI: 10.1186/s13578-024-01235-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/19/2024] [Indexed: 06/27/2024] Open
Abstract
Polyamines (PA) are polycations with pleiotropic functions in cellular physiology and pathology. In particular, PA have been involved in the regulation of cell homeostasis and proliferation participating in the control of fundamental processes like DNA transcription, RNA translation, protein hypusination, autophagy and modulation of ion channels. Indeed, their dysregulation has been associated to inflammation, oxidative stress, neurodegeneration and cancer progression. Accordingly, PA intracellular levels, derived from the balance between uptake, biosynthesis, and catabolism, need to be tightly regulated. Among the mechanisms that fine-tune PA metabolic enzymes, emerging findings highlight the importance of noncoding RNAs (ncRNAs). Among the ncRNAs, microRNA, long noncoding RNA and circRNA are the most studied as regulators of gene expression and mRNA metabolism and their alteration have been frequently reported in pathological conditions, such as cancer progression and brain diseases. In this review, we will discuss the role of ncRNAs in the regulation of PA genes, with a particular emphasis on the changes of this modulation observed in health disorders.
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Affiliation(s)
| | | | - Paolo Mariottini
- Department of Sciences, University of Roma Tre, 00146, Rome, Italy
| | - Manuela Cervelli
- Department of Sciences, University of Roma Tre, 00146, Rome, Italy.
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Wen K, Chen X, Gu J, Chen Z, Wang Z. Beyond traditional translation: ncRNA derived peptides as modulators of tumor behaviors. J Biomed Sci 2024; 31:63. [PMID: 38877495 PMCID: PMC11177406 DOI: 10.1186/s12929-024-01047-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/24/2024] [Indexed: 06/16/2024] Open
Abstract
Within the intricate tapestry of molecular research, noncoding RNAs (ncRNAs) were historically overshadowed by a pervasive presumption of their inability to encode proteins or peptides. However, groundbreaking revelations have challenged this notion, unveiling select ncRNAs that surprisingly encode peptides specifically those nearing a succinct 100 amino acids. At the forefront of this epiphany stand lncRNAs and circRNAs, distinctively characterized by their embedded small open reading frames (sORFs). Increasing evidence has revealed different functions and mechanisms of peptides/proteins encoded by ncRNAs in cancer, including promotion or inhibition of cancer cell proliferation, cellular metabolism (glucose metabolism and lipid metabolism), and promotion or concerted metastasis of cancer cells. The discoveries not only accentuate the depth of ncRNA functionality but also open novel avenues for oncological research and therapeutic innovations. The main difficulties in the study of these ncRNA-derived peptides hinge crucially on precise peptide detection and sORFs identification. Here, we illuminate cutting-edge methodologies, essential instrumentation, and dedicated databases tailored for unearthing sORFs and peptides. In addition, we also conclude the potential of clinical applications in cancer therapy.
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Affiliation(s)
- Kang Wen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Jingyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China
| | - Zhenyao Chen
- Department of Respiratory Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P.R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210011, P.R. China.
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10
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Digby B, Finn S, Ó Broin P. Computational approaches and challenges in the analysis of circRNA data. BMC Genomics 2024; 25:527. [PMID: 38807085 PMCID: PMC11134749 DOI: 10.1186/s12864-024-10420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Circular RNAs (circRNA) are a class of non-coding RNA, forming a single-stranded covalently closed loop structure generated via back-splicing. Advancements in sequencing methods and technologies in conjunction with algorithmic developments of bioinformatics tools have enabled researchers to characterise the origin and function of circRNAs, with practical applications as a biomarker of diseases becoming increasingly relevant. Computational methods developed for circRNA analysis are predicated on detecting the chimeric back-splice junction of circRNAs whilst mitigating false-positive sequencing artefacts. In this review, we discuss in detail the computational strategies developed for circRNA identification, highlighting a selection of tool strengths, weaknesses and assumptions. In addition to circRNA identification tools, we describe methods for characterising the role of circRNAs within the competing endogenous RNA (ceRNA) network, their interactions with RNA-binding proteins, and publicly available databases for rich circRNA annotation.
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Affiliation(s)
- Barry Digby
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland.
| | - Stephen Finn
- Discipline of Histopathology, School of Medicine, Trinity College Dublin and Cancer Molecular Diagnostic Laboratory, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
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11
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Zhou Q, Song W, Li X, Lin J, Zhu C, Cao L, Li W, Lin S. N6-Methyladenosine reader HNRNPC-mediated downregulation of circITCH prevents miR-224-3p sequestering and contributes to tumorigenesis in nasopharyngeal carcinoma. ENVIRONMENTAL TOXICOLOGY 2024; 39:2893-2907. [PMID: 38299319 DOI: 10.1002/tox.24139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/20/2023] [Accepted: 12/29/2023] [Indexed: 02/02/2024]
Abstract
BACKGROUND N6-Methyladenosine (m6A) RNA methylation modulators are implicated in nasopharyngeal carcinoma (NPC). Circular RNAs (circRNAs) stimulate/inhibit the development of NPC by sponging microRNAs (miRNAs). Herein, m6A modifications affecting the circRNA/miRNA axis in NPC were explored. METHODS Twenty prognostic m6A RNA methylation regulators were identified from 504 head/neck squamous cell carcinoma and 44 normal samples from The Cancer Genome Atlas (TCGA). Differentially expressed miRNAs were screened from the TCGA and Gene Expression Omnibus (GEO) databases. RNA-binding protein (RBP)-circRNA and circRNA-miRNA interactive pairs were verified using RBPmap and RNAhybrid, respectively. The RBP/circRNA/miRNA network was constructed using Cytoscape. Furthermore, CircITCH (hsa_circ_00059948), HNRNPC, and miR-224-3p expressions were detected by western blotting and quantitative polymerase chain reaction. The role of circITCH in NPC was examined using apoptosis, scratch wound healing, transwell invasion, and cell counting kit-8 assays. Finally, CircITCH-miR-224-3p and circITCH-HNRNPC interactions were assessed by dual-luciferase reporter and RNA-immunoprecipitation (RIP) assays, respectively. RESULTS Bioinformatics analysis revealed that high pathological grade, late-stage tumors, and low survival were associated with increased HNRNPC expression. MiR-224-3p was upregulated in NPC and sequestered by circITCH. Construction of the RBP/circRNA/miRNA network highlighted the HNRNPC/circITCH/miR-224-3p axis. In vitro experiments demonstrated decreased circITCH expression and increased HNRNPC and miR-224-3p expressions in NPC. In NPC cells overexpressing circITCH, HNRNPC and miR-224-3p expressions were significantly decreased. Dual-luciferase assays demonstrated a targeting relationship between circITCH and miR-224-3p, and RIP assays demonstrated interaction of HNRNPC targets with circITCH. CONCLUSION CircITCH overexpression inhibited NPC progression by sequestering miR-224-3p, and HNRNPC reduced circITCH expression through direct interaction.
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Affiliation(s)
- Qiang Zhou
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Wei Song
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Xianhui Li
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Jinyan Lin
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Chuansai Zhu
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Longhe Cao
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Wanqing Li
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
| | - Sen Lin
- Department of Otolaryngology, The Third Affiliated Hospital of Wenzhou Medical University (Ruian People's Hospital), Wenzhou, China
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12
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Chen Y, Ye Z, Lin M, Zhu L, Xu L, Wang X. Deciphering the Epigenetic Landscape: Placental Development and Its Role in Pregnancy Outcomes. Stem Cell Rev Rep 2024; 20:996-1014. [PMID: 38457061 DOI: 10.1007/s12015-024-10699-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
The placenta stands out as a unique, transitory, and multifaceted organ, essential to the optimal growth and maturation of the fetus. Functioning as a vital nexus between the maternal and fetal circulatory systems, it oversees the critical exchange of nutrients and waste. This exchange is facilitated by placental cells, known as trophoblasts, which adeptly invade and remodel uterine blood vessels. Deviations in placental development underpin a slew of pregnancy complications, notably fetal growth restriction (FGR), preeclampsia (PE), recurrent spontaneous abortions (RSA), and preterm birth. Central to placental function and development is epigenetic regulation. Despite its importance, the intricate mechanisms by which epigenetics influence the placenta are not entirely elucidated. Recently, the scientific community has turned its focus to parsing out the epigenetic alterations during placental development, such as variations in promoter DNA methylation, genomic imprints, and shifts in non-coding RNA expression. By establishing correlations between epigenetic shifts in the placenta and pregnancy complications, researchers are unearthing invaluable insights into the biology and pathophysiology of these conditions. This review seeks to synthesize the latest findings on placental epigenetic regulation, spotlighting its crucial role in shaping fetal growth trajectories and development. Through this lens, we underscore the overarching significance of the placenta in the larger narrative of gestational health.
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Affiliation(s)
- Yujia Chen
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Zhoujie Ye
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Meijia Lin
- Department of Pathology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Liping Zhu
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics and Gynecology and Pediatrics, Fujian Provincial Key Laboratory of Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Xinrui Wang
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.
- National Health Commission (NHC), Key Laboratory of Technical Evaluation of Fertility Regulation for Non-Human Primate, Fujian Maternity and Child Health Hospital, Fuzhou, China.
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13
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Tierno D, Grassi G, Zanconati F, Dapas B, Scaggiante B. Plasma Circular RNAs as Biomarkers for Breast Cancer. Biomedicines 2024; 12:875. [PMID: 38672229 PMCID: PMC11048241 DOI: 10.3390/biomedicines12040875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Breast cancer (BC) is currently the most common neoplasm, the second leading cause of cancer death in women worldwide, and is a major health problem. The discovery of new biomarkers is crucial to improve our knowledge of breast cancer and strengthen our clinical approaches to diagnosis, prognosis, and follow-up. In recent decades, there has been increasing interest in circulating RNA (circRNA) as modulators of gene expression involved in tumor development and progression. The study of circulating circRNAs (ccircRNAs) in plasma may provide new non-invasive diagnostic, prognostic, and predictive biomarkers for BC. This review describes the latest findings on BC-associated ccircRNAs in plasma and their clinical utility. Several ccircRNAs in plasma have shown great potential as BC biomarkers, especially from a diagnostic point of view. Mechanistically, most of the reported BC-associated ccircRNAs are involved in the regulation of cell survival, proliferation, and invasion, mainly via MAPK/AKT signaling pathways. However, the study of circRNAs is a relatively new area of research, and a larger number of studies will be crucial to confirm their potential as plasma biomarkers and to understand their involvement in BC.
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Affiliation(s)
- Domenico Tierno
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, I-34149 Trieste, Italy; (D.T.); (G.G.); (F.Z.)
| | - Gabriele Grassi
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, I-34149 Trieste, Italy; (D.T.); (G.G.); (F.Z.)
| | - Fabrizio Zanconati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Strada di Fiume 447, I-34149 Trieste, Italy; (D.T.); (G.G.); (F.Z.)
| | - Barbara Dapas
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy;
| | - Bruna Scaggiante
- Department of Life Sciences, University of Trieste, Via Valerio 28, I-34127 Trieste, Italy
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14
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Liu Y, Zhao X, Seitz A, Hooijsma AA, Ravanbakhsh R, Sheveleva S, de Jong D, Koerts J, Dzikiewicz-Krawczyk A, van den Berg A, Ziel-Swier LJYM, Kluiver J. Circular ZDHHC11 supports Burkitt lymphoma growth independent of its miR-150 binding capacity. Sci Rep 2024; 14:8730. [PMID: 38627588 PMCID: PMC11021472 DOI: 10.1038/s41598-024-59443-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/10/2024] [Indexed: 04/19/2024] Open
Abstract
We previously showed that MYC promoted Burkitt lymphoma (BL) growth by inhibiting the tumor suppressor miR-150, resulting in release of miR-150 targets MYB and ZDHHC11. The ZDHHC11 gene encodes three different transcripts including a mRNA (pcZDHHC11), a linear long non-coding RNA (lncZDHHC11) and a circular RNA (circZDHHC11). All transcripts contain the same region with 18 miR-150 binding sites. Here we studied the relevance of circZDHHC11, including this miR-150 binding site region, for growth of BL cells. CircZDHHC11 was mainly present in the cytoplasmic fraction in BL cells and its localization was not altered upon miR-150 overexpression. Knockdown of circZDHHC11 caused a strong inhibition of BL growth without affecting the expression levels of MYC, MYB, miR-150 and other genes. Overexpression of circZDHHC11 neither affected cell growth, nor rescued the phenotype induced by miR-150 overexpression. Genomic deletion of the miR-150 binding site region did not affect growth, nor did it change the effect of circZDHHC11 knockdown. This indicated that the miR-150 binding site region is dispensable for the growth promoting role of circZDHHC11. To conclude, our results show that circZDHHC11 is a crucial factor supporting BL cell growth independent of its ability to sponge miR-150.
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Affiliation(s)
- Yichen Liu
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
- Cancer Hospital Academy of Medical Sciences, Peking Union Medical College, Dongcheng, China
| | - Xing Zhao
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Annie A Hooijsma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Reyhaneh Ravanbakhsh
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
- Department of Aquatic Biotechnology, Artemia and Aquaculture Research Institute, Urmia University, Urmia, Iran
| | - Sofia Sheveleva
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | | | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Lotteke J Y M Ziel-Swier
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700 RB, Groningen, The Netherlands.
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15
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Biferali B, Mocciaro E, Runfola V, Gabellini D. Long non-coding RNAs and their role in muscle regeneration. Curr Top Dev Biol 2024; 158:433-465. [PMID: 38670715 DOI: 10.1016/bs.ctdb.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
In mammals, most of the genome is transcribed to generate a large and heterogeneous variety of non-protein coding RNAs, that are broadly grouped according to their size. Long noncoding RNAs include a very large and versatile group of molecules. Despite only a minority of them has been functionally characterized, there is emerging evidence indicating long noncoding RNAs as important regulators of expression at multiple levels. Several of them have been shown to be modulated during myogenic differentiation, playing important roles in the regulation of skeletal muscle development, differentiation and homeostasis, and contributing to neuromuscular diseases. In this chapter, we have summarized the current knowledge about long noncoding RNAs in skeletal muscle and discussed specific examples of long noncoding RNAs (lncRNAs and circRNAs) regulating muscle stem cell biology. We have also discussed selected long noncoding RNAs involved in the most common neuromuscular diseases.
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Affiliation(s)
- Beatrice Biferali
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Emanuele Mocciaro
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Valeria Runfola
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Davide Gabellini
- Gene Expression Regulation Unit, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
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16
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Ni L, Yamada T, Nakatani K. Utility of oligonucleotide in upregulating circular RNA production in a cellular model. Sci Rep 2024; 14:8096. [PMID: 38582789 PMCID: PMC10998836 DOI: 10.1038/s41598-024-58663-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/02/2024] [Indexed: 04/08/2024] Open
Abstract
Circular RNAs (circRNAs), are a covalently closed, single-stranded RNA without 5'- and 3'-termini, commonly stem from the exons of precursor mRNAs (pre-mRNAs). They have recently garnered interest, with studies uncovering their pivotal roles in regulating various aspects of cell functions and disease progressions. A notable feature of circRNA lies in the mechanism of its biogenesis involving a specialized form of splicing: back-splicing. A splicing process that relies on interactions between introns flanking the circularizing exon to bring the up and downstream splice sites in proximity through the formation of a prerequisite hairpin structure, allowing the spliceosomes to join the two splice sites together to produce a circular RNA molecule. Based on this mechanism, we explored the feasibility of facilitating the formation of such a prerequisite hairpin structure by utilizing a newly designed oligonucleotide, CircuLarIzation Promoting OligoNucleotide (CLIP-ON), to promote the production of circRNA in cells. CLIP-ON was designed to hybridize with and physically bridge two distal sequences in the flanking introns of the circularizing exons. The feasibility of CLIP-ON was confirmed in HeLa cells using a model pre-mRNA, demonstrating the applicability of CLIP-ON as a trans-acting modulator to upregulate the production of circRNAs in a cellular environment.
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Affiliation(s)
- Lu Ni
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Takeshi Yamada
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.
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17
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Wu M, Yuan H, Zou W, Xu S, Liu S, Gao Q, Guo Q, Han Y, An X. Circular RNAs: characteristics, functions, mechanisms, and potential applications in thyroid cancer. Clin Transl Oncol 2024; 26:808-824. [PMID: 37864677 DOI: 10.1007/s12094-023-03324-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/08/2023] [Indexed: 10/23/2023]
Abstract
Thyroid cancer (TC) is one of the most common endocrine malignancies, and its incidence has increased globally. Despite extensive research, the underlying molecular mechanisms of TC remain partially understood, warranting continued exploration of molecular markers for diagnostic and prognostic applications. Circular RNAs (circRNAs) have recently garnered significant attention owing to their distinct roles in cancers. This review article introduced the classification and biological functions of circRNAs and summarized their potential as diagnostic and prognostic markers in TC. Further, the interplay of circRNAs with PI3K/Akt/mTOR, Wnt/β-catenin, MAPK/ERK, Notch, JAK/STAT, and AMPK pathways is elaborated upon. The article culminates with an examination of circRNA's role in drug resistance of TC and highlights the challenges in circRNA research in TC.
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Affiliation(s)
- Mengmeng Wu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Haibin Yuan
- Department of Health Management, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Weiwei Zou
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Shujian Xu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Song Liu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Qiang Gao
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Qingqun Guo
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Yong Han
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China.
| | - Xingguo An
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China.
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18
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Dremel SE, Tagawa T, Koparde VN, Hernandez-Perez C, Arbuckle JH, Kristie TM, Krug LT, Ziegelbauer JM. Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection. EMBO Rep 2024; 25:1541-1569. [PMID: 38263330 PMCID: PMC10933408 DOI: 10.1038/s44319-023-00051-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
To globally profile circRNAs, we employ RNA-Sequencing paired with chimeric junction analysis for alpha-, beta-, and gamma-herpesvirus infection. We find circRNAs are, as a population, resistant to host shutoff. We validate this observation using ectopic expression assays of human and murine herpesvirus endoribonucleases. During lytic infection, four circRNAs are commonly induced across all subfamilies of human herpesviruses, suggesting a shared mechanism of regulation. We test one such mechanism, namely how interferon-stimulation influences circRNA expression. 67 circRNAs are upregulated by either interferon-β or -γ treatment, with half of these also upregulated during lytic infection. Using gain and loss of function studies we find an interferon-stimulated circRNA, circRELL1, inhibits lytic Herpes Simplex Virus-1 infection. We previously reported circRELL1 inhibits lytic Kaposi sarcoma-associated herpesvirus infection, suggesting a pan-herpesvirus antiviral activity. We propose a two-pronged model in which interferon-stimulated genes may encode both mRNA and circRNA with antiviral activity. This is critical in cases of host shutoff, such as alpha- and gamma-herpesvirus infection, where the mRNA products are degraded but circRNAs escape.
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Affiliation(s)
- Sarah E Dremel
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, 20892, USA
| | - Takanobu Tagawa
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, 20892, USA
| | - Vishal N Koparde
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, Bethesda, 20892, USA
- Frederick National Laboratory for Cancer Research Advanced Biomedical Computational Sciences, Leidos Biomedical Research, Inc., Frederick, 21701, USA
| | | | - Jesse H Arbuckle
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, 20892, USA
| | - Thomas M Kristie
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, 20892, USA
| | - Laurie T Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, 20892, USA
| | - Joseph M Ziegelbauer
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, 20892, USA.
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19
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Fan X, Zhang Q, Qin S, Ju S. CircBRIP1: a plasma diagnostic marker for non-small-cell lung cancer. J Cancer Res Clin Oncol 2024; 150:83. [PMID: 38329551 PMCID: PMC10853360 DOI: 10.1007/s00432-023-05558-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/12/2023] [Indexed: 02/09/2024]
Abstract
BACKGROUND Circular RNA (circRNA), which has been demonstrated in studies to be abundantly prevalent in tumor cells and bodily fluids and to play a significant role in tumors, has the potential for biological markers to be used to assist tumor diagnosis. This study mainly discusses the potential of circBRIP1 as a biomarker for diagnosing non-small-cell lung cancer (NSCLC). METHODS First, high-throughput sequencing screened the differentially expressed circBRIP1, and real-time fluorescence quantitative PCR (qRT-PCR) verified its expression in NSCLC. Next, sanger sequencing, agarose gel electrophoresis, RNase R assay, and fluorescence in situ hybridization (FISH) were used to verify its molecular characteristics. The diagnostic value was analyzed by the subject operating characteristic curve (ROC), and the cardinality test was analyzed for correlation with clinicopathological parameters. Finally, we tentatively predicted the downstream miRNA- or RNA-binding protein that may bind to circBRIP1. RESULTS CircBRIP1 is highly expressed in NSCLC tissues, cells and plasma with good specificity and stability. CircBRIP1 not only can well-distinguish NSCLC patients from benign pulmonary diseases (BPD) patients, healthy individuals and small cell lung cancer (SCLC) patients, but it also has some potential for dynamic monitoring. Combined with the analysis of clinicopathological data, the high level of circRNA expression was related to the degree of tumor differentiation, TNM stage, T stage, lymph node metastasis and distal metastasis in NSCLC patients. In addition, circBRIP1 has a high diagnostic value. CONCLUSIONS Plasma circBRIP1 is significantly overexpressed in NSCLC patients. It can be used as a sensitive biomarker with unique value for early diagnosis, tumor development and prognosis detection.
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Affiliation(s)
- Xinfeng Fan
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, Nantong, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Qi Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, Nantong, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Shiyi Qin
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, Nantong, 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, Medical School of Nantong University, Nantong, 226001, Jiangsu, China.
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.
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20
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Jafarbeik-Iravani N, Kolahdozan S, Esmaeili R. The role of ASXL1 mutations and ASXL1 CircRNAs in cancer. Biomarkers 2024; 29:1-6. [PMID: 38193494 DOI: 10.1080/1354750x.2024.2304187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/06/2024] [Indexed: 01/10/2024]
Abstract
BACKGROUND Mutations in the Additional Sex Combs Like 1 (ASXL1) gene were first reported in myelodysplastic syndromes. Recent studies have clarified the relationship between ASXL1 mutations and the development of cancers. OBJECTIVE This study aims to review the roles of ASXL1 and ASXL1 CircRNAs, such as epigenetic regulation, chromatin modification, and transcription factor function in malignancies. METHOD This study is a review of articles related to the role of ASXL1 and ASXL1 CircRNAs in malignancies, retrieved from PubMed and Scopus. RESULTS ASXL1 plays a role in malignancies and is also related to poor overall survival and cancer metastasis. ASXL1 encodes conserved and abundant Circular RNAs (circRNAs) that act as post-transcriptional regulators, regulating tumorigenesis and progression in cancer. ASXL1 circRNA was identified in the top 10% of differentially expressed circRNAs in clinically relevant tissues. Additionally, the role of ASXL1 gene circRNAs in cancer development is reviewed in this study. CONCLUSION ASXL1 and ASXL1circRNA have dual functions in combination with different proteins, being involved in both transcriptional activation and repression in a context-dependent manner. Moreover, studies indicate these genes play an important role in epithelial-mesenchymal transition (EMT) and metastasis. Ongoing research is aimed at determining this gene family's function in biological events.
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Affiliation(s)
- Narges Jafarbeik-Iravani
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Sara Kolahdozan
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Rezvan Esmaeili
- Genetics Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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21
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Yuan H, Chen C, Li H, Qu G, Chen L, Liu Y, Zhang Y, Zhao Q, Lian C, Ji A, Hou X, Liu X, Jiang K, Zhu Y, He Y. Role of a novel circRNA-CGNL1 in regulating pancreatic cancer progression via NUDT4-HDAC4-RUNX2-GAMT-mediated apoptosis. Mol Cancer 2024; 23:27. [PMID: 38297362 PMCID: PMC10829403 DOI: 10.1186/s12943-023-01923-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/20/2023] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is an extremely malignant tumor with low survival rate. Effective biomarkers and therapeutic targets for PC are lacking. The roles of circular RNAs (circRNAs) in cancers have been explored in various studies, however more work is needed to understand the functional roles of specific circRNAs. In this study, we explore the specific role and mechanism of circ_0035435 (termed circCGNL1) in PC. METHODS qRT-PCR analysis was performed to detect circCGNL1 expression, indicating circCGNL1 had low expression in PC cells and tissues. The function of circCGNL1 in PC progression was examined both in vitro and in vivo. circCGNL1-interacting proteins were identified by performing RNA pulldown, co-immunoprecipitation, GST-pulldown, and dual-luciferase reporter assays. RESULTS Overexpressing circCGNL1 inhibited PC proliferation via promoting apoptosis. CircCGNL1 interacted with phosphatase nudix hydrolase 4 (NUDT4) to promote histone deacetylase 4 (HDAC4) dephosphorylation and subsequent HDAC4 nuclear translocation. Intranuclear HDAC4 mediated RUNX Family Transcription Factor 2 (RUNX2) deacetylation and thereby accelerating RUNX2 degradation. The transcription factor, RUNX2, inhibited guanidinoacetate N-methyltransferase (GAMT) expression. GAMT was further verified to induce PC cell apoptosis via AMPK-AKT-Bad signaling pathway. CONCLUSIONS We discovered that circCGNL1 can interact with NUDT4 to enhance NUDT4-dependent HDAC4 dephosphorylation, subsequently activating HDAC4-RUNX2-GAMT-mediated apoptosis to suppress PC cell growth. These findings suggest new therapeutic targets for PC.
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Affiliation(s)
- Hao Yuan
- Department of General Surgery, Pancreas Centre, the First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Road, Nanjing, P. R. China
- Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Chuang Chen
- Department of Hepatopancreatobiliary Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Haonan Li
- Changzhi Medical College, Changzhi, China
| | - Gexi Qu
- Changzhi Medical College, Changzhi, China
| | - Luyao Chen
- Changzhi Medical College, Changzhi, China
| | - Yaxing Liu
- Changzhi Medical College, Changzhi, China
| | - Yufeng Zhang
- Department of General Surgery, Pancreas Centre, the First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Road, Nanjing, P. R. China
| | - Qiang Zhao
- Heping Hospital, Changzhi Medical College, Changzhi, China
| | - Changhong Lian
- Heping Hospital, Changzhi Medical College, Changzhi, China
| | - Aifang Ji
- Heping Hospital, Changzhi Medical College, Changzhi, China
| | | | - Xinjian Liu
- Department of Pathogen Biology, Nanjing Medical University, Nanjing, China
| | - Kuirong Jiang
- Department of General Surgery, Pancreas Centre, the First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Road, Nanjing, P. R. China.
- Pancreas Institute, Nanjing Medical University, Nanjing, China.
| | - Yi Zhu
- Department of General Surgery, Pancreas Centre, the First Affiliated Hospital With Nanjing Medical University, 300 Guangzhou Road, Nanjing, P. R. China.
- Pancreas Institute, Nanjing Medical University, Nanjing, China.
| | - Yuan He
- Changzhi Medical College, Changzhi, China.
- Heping Hospital, Changzhi Medical College, Changzhi, China.
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22
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Guo N, Zhou H, Zhang Q, Fu Y, Jia Q, Gan X, Wang Y, He S, Li C, Tao Z, Liu J, Jia E. Exploration and bioinformatic prediction for profile of mRNA bound to circular RNA BTBD7_hsa_circ_0000563 in coronary artery disease. BMC Cardiovasc Disord 2024; 24:71. [PMID: 38267845 PMCID: PMC10809658 DOI: 10.1186/s12872-024-03711-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND As a novel circRNA, BTBD7_hsa_circ_0000563 has not been fully investigated in coronary artery disease (CAD). Our aim is to reveal the possible functional role and regulatory pathway of BTBD7_hsa_circ_0000563 in CAD via exploring genes combined with BTBD7_hsa_circ_0000563. METHODS A total of 45 peripheral blood mononuclear cell (PBMC) samples of CAD patients were enrolled. The ChIRP-RNAseq assay was performed to directly explore genes bound to BTBD7_hsa_circ_0000563. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted to reveal possible functions of these genes. The interaction network was constructed by the STRING database and the Cytoscape software. The Cytoscape software were used again to identify clusters and hub genes of genes bound to BTBD7_hsa_circ_0000563. The target miRNAs of hub genes were predicted via online databases. RESULTS In this study, a total of 221 mRNAs directly bound to BTBD7_hsa_circ_0000563 were identified in PBMCs of CAD patients via ChIRP-RNAseq. The functional enrichment analysis revealed that these mRNAs may participate in translation and necroptosis. Moreover, the interaction network showed that there may be a close relationship between these mRNAs. Eight clusters can be further subdivided from the interaction network. RPS3 and RPSA were identified as hub genes and hsa-miR-493-5p was predicted to be the target miRNA of RPS3. CONCLUSIONS BTBD7_hsa_circ_0000563 and mRNAs directly bound to it may influence the initiation and progression of CAD, among which RPS3 and RPSA may be hub genes. These findings may provide innovative ideas for further research on CAD.
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Affiliation(s)
- Ning Guo
- Suzhou Hospital of Integrated Traditional Chinese and Western Medicine, Suzhou, 215101, Jiangsu Province, China
| | - Hanxiao Zhou
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Qian Zhang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Yahong Fu
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Qiaowei Jia
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Xiongkang Gan
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Yanjun Wang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Shu He
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Chengcheng Li
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Zhengxian Tao
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China
| | - Jun Liu
- Department of Cardiology, Jurong City People's Hospital, Ersheng Road 66, Jurong, 212400, Jiangsu Province, China.
| | - Enzhi Jia
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Nanjing Medical University, Guangzhou Road 300, Nanjing, 210029, Jiangsu Province, China.
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23
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Caponnetto A, Ferrara C, Fazzio A, Agosta N, Scribano M, Vento ME, Borzì P, Barbagallo C, Stella M, Ragusa M, Scollo P, Barbagallo D, Purrello M, Di Pietro C, Battaglia R. A Circular RNA Derived from the Pumilio 1 Gene Could Regulate PTEN in Human Cumulus Cells. Genes (Basel) 2024; 15:124. [PMID: 38275605 PMCID: PMC10815046 DOI: 10.3390/genes15010124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
CircRNAs are a class of non-coding RNAs able to regulate gene expression at multiple levels. Their involvement in physiological processes, as well as their altered regulation in different human diseases, both tumoral and non-tumoral, is well documented. However, little is known about their involvement in female reproduction. This study aims to identify circRNAs potentially involved in reproductive women's health. Candidate circRNAs expressed in ovary and sponging miRNAs, already known to be expressed in the ovary, were selected by a computational approach. Using real time PCR, we verified their expression and identified circPUM1 as the most interesting candidate circRNA for further analyses. We assessed the expression of circPUM1 and its linear counterpart in all the follicle compartments and, using a computational and experimental approach, identified circPUM1 direct and indirect targets, miRNAs and mRNAs, respectively, in cumulus cells. We found that both circPUM1 and its mRNA host gene are co-expressed in all the follicle compartments and proposed circPUM1 as a potential regulator of PTEN, finding a strong positive correlation between circPUM1 and PTEN mRNA. These results suggest a possible regulation of PTEN by circPUM1 in cumulus cells and point out the important role of circRNA inside the pathways related to follicle growth and oocyte maturation.
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Affiliation(s)
- Angela Caponnetto
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Carmen Ferrara
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Anna Fazzio
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Noemi Agosta
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy; (N.A.); (M.S.)
| | - Marianna Scribano
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123 Catania, Italy; (N.A.); (M.S.)
| | - Maria Elena Vento
- IVF Unit, Cannizzaro Hospital, 95123 Catania, Italy; (M.E.V.); (P.B.)
| | - Placido Borzì
- IVF Unit, Cannizzaro Hospital, 95123 Catania, Italy; (M.E.V.); (P.B.)
| | - Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Michele Stella
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Paolo Scollo
- Department of Medicine and Surgery, Kore University, 94100 Enna, Italy;
- Maternal and Child Department, Obstetrics and Gynecology Unit, Cannizzaro Hospital, 95123 Catania, Italy
| | - Davide Barbagallo
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Michele Purrello
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Cinzia Di Pietro
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
| | - Rosalia Battaglia
- Department of Biomedical and Biotechnological Sciences, Section of Biology and Genetics “G. Sichel”, University of Catania, 95123 Catania, Italy; (C.F.); (A.F.); (C.B.); (M.S.); (M.R.); (D.B.); (M.P.); (C.D.P.); (R.B.)
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24
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Diallo LH, Mariette J, Laugero N, Touriol C, Morfoisse F, Prats AC, Garmy-Susini B, Lacazette E. Specific Circular RNA Signature of Endothelial Cells: Potential Implications in Vascular Pathophysiology. Int J Mol Sci 2024; 25:680. [PMID: 38203852 PMCID: PMC10779679 DOI: 10.3390/ijms25010680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Circular RNAs (circRNAs) are a recently characterized family of gene transcripts forming a covalently closed loop of single-stranded RNA. The extent of their potential for fine-tuning gene expression is still being discovered. Several studies have implicated certain circular RNAs in pathophysiological processes within vascular endothelial cells and cancer cells independently. However, to date, no comparative study of circular RNA expression in different types of endothelial cells has been performed and analysed through the lens of their central role in vascular physiology and pathology. In this work, we analysed publicly available and original RNA sequencing datasets from arterial, veinous, and lymphatic endothelial cells to identify common and distinct circRNA expression profiles. We identified 4713 distinct circRNAs in the compared endothelial cell types, 95% of which originated from exons. Interestingly, the results show that the expression profile of circular RNAs is much more specific to each cell type than linear RNAs, and therefore appears to be more suitable for distinguishing between them. As a result, we have discovered a specific circRNA signature for each given endothelial cell type. Furthermore, we identified a specific endothelial cell circRNA signature that is composed four circRNAs: circCARD6, circPLXNA2, circCASC15 and circEPHB4. These circular RNAs are produced by genes that are related to endothelial cell migration pathways and cancer progression. More detailed studies of their functions could lead to a better understanding of the mechanisms involved in physiological and pathological (lymph)angiogenesis and might open new ways to tackle tumour spread through the vascular system.
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Affiliation(s)
- Leïla Halidou Diallo
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Jérôme Mariette
- MIAT, University of Toulouse, INRAE, 31326 Castanet-Tolosan, France;
| | - Nathalie Laugero
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Christian Touriol
- UMR1037 INSERM, University of Toulouse, 2 Avenue Hubert Curien, 31100 Toulouse, France;
| | - Florent Morfoisse
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Anne-Catherine Prats
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Barbara Garmy-Susini
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
| | - Eric Lacazette
- U1297-I2MC, INSERM, University of Toulouse, 1 Avenue Jean Poulhes, BP 84225, 31432 Toulouse, France; (L.H.D.); (N.L.); (F.M.); (A.-C.P.); (B.G.-S.)
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Kaisai T, Mantang Z, Tailei Y, Liying Z, Xiaoping C, Mingming J, Yi Z. Hsa_circ_0013561 promotes progression of nasopharyngeal carcinoma by activating JAK2/STAT3 signaling pathway. Braz J Otorhinolaryngol 2024; 90:101362. [PMID: 38006726 PMCID: PMC10709185 DOI: 10.1016/j.bjorl.2023.101362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/15/2023] [Accepted: 11/03/2023] [Indexed: 11/27/2023] Open
Abstract
OBJECTIVE Nasopharyngeal Carcinoma (NPC) is a malignancy of epithelium of epithelium of the nasopharynx, with the highest incidence of otolaryngeal malignancies. A growing number of studies confirm that Circular RNA (circRNA) plays an important role in tumor development, including Hsa_circ_0013561. This study aims to elucidate the process and mechanism of NPC regulation hsa_circ_0013561. METHODS In this study, circRNA expression nodes and subcellular localization in NPC tissues were analyzed by fluorescence in situ hybridization. The expression of hsa_circ_0013561 in NPC cells was further clarified by RT-qPCR. At the same time, the lentivirus vector interfered by hsa_circ_0013561 was constructed and transfected. The cell proliferation was detected by CCK-8 method, EdU assay and plate cloning assay. The cell cycle and apoptosis were detected by flow cytometry, and the cell migration ability was detected by wound healing assay and Transwell assay. Western blotting examined the expression of apoptosis, Epithelial-Mesenchymal Transition (EMT)-associated proteins, and Janus Kinase/Signal Transductor and Activator of Transcription (JAK/STAT) signaling pathway-related proteins. RESULTS The results showed that the expression of hsa_circ_0013561 in NPC samples was significantly upregulated and hsa_circ_0013561 localized in the cytoplasm. After down-regulating hsa_circ_0013561 expression, it significantly inhibited the proliferation and metastasis ability of NPC, inhibited EMT progression, and promoted apoptosis. Further studies showed that interference hsa_circ_0013561 significantly inhibited JAK2/STAT3 signaling pathway activation and induced the expression of apoptosis-related proteins. CONCLUSION In summary, we found that hsa_circ_0013561 is a pro-tumor circRNA in NPC, which can reduce the activation of JAK2/STAT3 pathway by knocking down hsa_circ_0013561, thereby slowing down the malignant progression of NPC. OXFORD CENTRE FOR EVIDENCE-BASED MEDICINE 2011 LEVELS OF EVIDENCE: Level 4.
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Affiliation(s)
- Tian Kaisai
- Ningxia Medical University, Postgraduate Training Base in Shanghai Gongli Hospital, Shanghai, China; Shanghai Pudong New Area Gongli Hospital, Department of Otorhinolaryngology & Head and Neck Surgery, Shanghai, China; Shanghai University of Medicine and Health Sciences, Shanghai Key Laboratory of Molecular Imaging, Shanghai, China
| | - Zheng Mantang
- Affiliated Hospital of Hebei University, Baoding, China
| | - Yuan Tailei
- Ningxia Medical University, Postgraduate Training Base in Shanghai Gongli Hospital, Shanghai, China; Shanghai University of Medicine and Health Sciences, Shanghai Key Laboratory of Molecular Imaging, Shanghai, China
| | - Zheng Liying
- Ningxia Medical University, Postgraduate Training Base in Shanghai Gongli Hospital, Shanghai, China; Shanghai Pudong New Area Gongli Hospital, Department of Otorhinolaryngology & Head and Neck Surgery, Shanghai, China; Shanghai University of Medicine and Health Sciences, Shanghai Key Laboratory of Molecular Imaging, Shanghai, China
| | - Chen Xiaoping
- Shanghai Pudong New Area Gongli Hospital, Department of Otorhinolaryngology & Head and Neck Surgery, Shanghai, China
| | - Jin Mingming
- Shanghai University of Medicine and Health Sciences, Shanghai Key Laboratory of Molecular Imaging, Shanghai, China
| | - Zhang Yi
- Shanghai Pudong New Area Gongli Hospital, Department of Otorhinolaryngology & Head and Neck Surgery, Shanghai, China.
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Zeng Q, Liu CH, Ampuero J, Wu D, Jiang W, Zhou L, Li H, Bai L, Romero-Gómez M, Tang H. Circular RNAs in non-alcoholic fatty liver disease: Functions and clinical significance. RNA Biol 2024; 21:1-15. [PMID: 38113132 PMCID: PMC10761141 DOI: 10.1080/15476286.2023.2290769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 12/21/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD), which affects approximately 25% of the global population, is an urgent health issue leading to various metabolic comorbidities. Circular RNAs (circRNAs), covalently closed RNA molecules, are characterized by ubiquity, diversity, stability, and conservatism. Indeed, they participate in various biological processes via distinct mechanisms that could modify the natural history of NAFLD. In this review, we briefly introduce the biogenesis, characteristics, and biological functions of circRNAs. Furthermore, we summarize circRNAs expression profiles in NAFLD by intersecting seven sequencing data sets and describe the cellular roles of circRNAs and their potential advantages as biomarkers of NAFLD. In addition, we emphatically discuss the exosomal non-coding RNA sorting mechanisms and possible functions in recipient cells. Finally, we extensively discuss the potential application of targeting disease-related circRNAs and competing endogenous RNA networks through gain-of-function and loss-of-function approaches in targeted therapy of NAFLD.
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Affiliation(s)
- Qingmin Zeng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Chang-Hai Liu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Javier Ampuero
- Digestive Diseases Unit, Virgen del Rocío University Hospital. SeLiver group at Institute of Biomedicine of Seville (IBIS: HUVRocío/CSIC/US). University of Seville, Seville, Spain
| | - Dongbo Wu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Jiang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Lingyun Zhou
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Li
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Lang Bai
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
| | - Manuel Romero-Gómez
- Digestive Diseases Unit, Virgen del Rocío University Hospital. SeLiver group at Institute of Biomedicine of Seville (IBIS: HUVRocío/CSIC/US). University of Seville, Seville, Spain
| | - Hong Tang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Disease, West China Hospital, Sichuan University, Chengdu, China
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27
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Baulina NM, Kiselev IS, Chumakova OS, Favorova OO. Circular RNAs: Biogenesis, Functions, and Role in Myocardial Hypertrophy. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S1-S13. [PMID: 38621741 DOI: 10.1134/s0006297924140013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 04/17/2024]
Abstract
Circular RNAs (circRNAs) are a large class of endogenous single-stranded covalently closed RNA molecules. High-throughput RNA sequencing and bioinformatic algorithms have identified thousands of eukaryotic circRNAs characterized by high stability and tissue-specific expression pattern. Recent studies have shown that circRNAs play an important role in the regulation of physiological processes in the norm and in various diseases, including cardiovascular disorders. The review presents current concepts of circRNA biogenesis, structural features, and biological functions, describes the methods of circRNA analysis, and summarizes the results of studies on the role of circRNAs in the pathogenesis of hypertrophic cardiomyopathy, the most common inherited heart disease.
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Affiliation(s)
- Natalia M Baulina
- Chazov National Medical Research Centre of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia.
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Ivan S Kiselev
- Chazov National Medical Research Centre of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Olga S Chumakova
- Chazov National Medical Research Centre of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
| | - Olga O Favorova
- Chazov National Medical Research Centre of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
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Wang X, Huang R, Yu J, Zhu F, Xi X, Huang Y, Zhang C, Hu H. Identification of differentially expressed circRNAs in prostate cancer of different clinical stages by RNA sequencing. Sci Rep 2023; 13:21175. [PMID: 38040819 PMCID: PMC10692156 DOI: 10.1038/s41598-023-48521-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Circular RNAs (circRNAs) are linked to cancer, but it's still not clear what role they play in prostatic cancer. Through high-throughput sequencing, the goal of this study was to compare how circRNAs are expressed at different stages of prostate cancer. 12 patients attending the Department of Urology at the Second Affiliated Hospital of Nanchang University between June 2020 and October 2021 were used for RNA sequencing, and 14 patients were used for real-time fluorescent quantitative PCR (qRT-PCR). The expression profiles of prostate cancer circRNAs were constructed by sequencing with the help of next-generation high-throughput sequencing technology, and the differentially expressed circRNAs were analyzed by targeting microRNA (miRNA) loci and Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the genes from which circRNAs originated. Finally, the expression of target circRNAs in two prostate tissues was verified by qRT-PCR. Following high-throughput sequencing, 13,047 circRNAs were identified, and 605 circRNAs with significant differential expression were identified, of which 361 circRNAs were up-regulated, and 244 circRNAs were down-regulated. Analysis of circRNA-originated genes using GO and the KEGG enrichment analysis showed that circRNA host genes can regulate and influence multiple signaling pathways in prostate cancer with important biological functions. And the circRNA-miRNA network was constructed. The highest number of differentially expressed circRNA-binding miRNAs were: hsa_circ_000 7582 (52), hsa_circ_000 6198 (37), hsa_circ_000 6759 (28), hsa_circ_000 5675 (25), and hsa_circ_000 2172 (22). Moreover, we further screened out the circRNA (hsa_circ_0005692) that was significantly differentially expressed and common to all groups and verified by qRT-PCR that the expression of the target circRNA (hsa_circ_0005692) was significantly downregulated in prostate cancer compared with benign prostatic hyperplasia (BPH) tissues.
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Affiliation(s)
- Xing Wang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
- Northeast Yunnan Regional Center Hospital, Zhaotong, 657000, China
| | - Ruizhen Huang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Juhui Yu
- Department of Urology, People's Hospital of Wuyuan County, Shangrao, 33320, China
| | - Fei Zhu
- Department of Urology, People's Hospital of Wuyuan County, Shangrao, 33320, China
| | - Xiaoqing Xi
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Yawei Huang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Chiyu Zhang
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Honglin Hu
- Department of Urology, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China.
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Soslau G. Platelet protein synthesis, regulation, and post-translational modifications: mechanics and function. Crit Rev Biochem Mol Biol 2023; 58:99-117. [PMID: 37347996 DOI: 10.1080/10409238.2023.2224532] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/08/2023] [Indexed: 06/24/2023]
Abstract
Dogma had been firmly entrenched in the minds of the scientific community that the anucleate mammalian platelet was incapable of protein biosynthesis since their identification in the late 1880s. These beliefs were not challenged until the 1960s when several reports demonstrated that platelets possessed the capacity to biosynthesize proteins. Even then, many still dismissed the synthesis as trivial and unimportant for at least another two decades. Research in the field expanded after the 1980s and numerous reports have since been published that now clearly demonstrate the potential significance of platelet protein synthesis under normal, pathological, and activating conditions. It is now clear that the platelet proteome is not a static entity but can be altered slowly or rapidly in response to external signals to support physiological requirements to maintain hemostasis and other biological processes. All the necessary biological components to support protein synthesis have been identified in platelets along with post-transcriptional processing of mRNAs, regulators of translation, and post-translational modifications such as glycosylation. The last comprehensive review of the subject appeared in 2009 and much work has been conducted since that time. The current review of the field will briefly incorporate the information covered in earlier reviews and then bring the reader up to date with more recent findings.
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Affiliation(s)
- Gerald Soslau
- Department of Biochemistry and Molecular Biology Drexel University College of Medicine, Philadelphia, PA, United States
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LIU SS, GUO HY, ZHU J, MA JL, LIU SZ, HE KL, BIAN SY. Circulating circRNA expression profile and its potential role in late recurrence of paroxysmal atrial fibrillation post catheter ablation. J Geriatr Cardiol 2023; 20:788-800. [PMID: 38098469 PMCID: PMC10716615 DOI: 10.26599/1671-5411.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Catheter-based pulmonary vein isolation (PVI) is an effective and well-established intervention for symptomatic paroxysmal atrial fibrillation (PAF). Nevertheless, late recurrences of atrial fibrillation (LRAF) occurring during 3 to 12 months are common, and the underlying mechanisms remain elusive. Circular RNAs (circRNAs) in atrial tissue have been linked to the pathophysiological mechanisms and progression of PAF in a few studies. However, their expression patterns in peripheral blood and regulatory function in LRAF are not clear. METHODS In the present study, the expression profile of circulating circRNAs in three paired nonvalvular PAF patients with or without LRAF was investigated by high-throughput sequencing and validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and circRNA/miRNA regulatory network, were performed to predict the functions and potential regulatory roles of differentially expressed (DE) circRNAs. RESULTS A total of 12,834 circRNAs, comprising 5,491 down-regulated and 7,343 up-regulated circRNAs, were found to be DE in blood smaples from the two groups in peripheral blood between LRAF and non-recurrence control individuals. The most enriched GO categories in terms of molecular function, biological process, and cellular component features were catalytic activity, cellular metabolic process, and intracellular part, respectively. The KEGG enrichment study revealed that the most important metabolic process controlled by DE circRNAs is endocytosis. In the circRNA/microRNAs interaction network, four up-regulated circRNAs (hsa_circ_0002665, hsa_circ_0001953, hsa_circ_0003831, and hsa_circ_0040533) and one down-regulated circRNA (hsa_circ_0041103) were predicted to play potential regulatory roles in the pathogenesis of LRAF. CONCLUSIONS This investigation discovered the expression pattern of circulating circRNAs that is indicative of PAF late recurrence, which may serve as risk markers or therapeutic targets for LRAF after PVI.
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Affiliation(s)
- Shan-Shan LIU
- Department of Cardiology, the Second Medical Center, National Clinical Research Center of Geriatric Disease, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
| | - Hong-Yang GUO
- Department of Cardiology, the Six Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Jian ZHU
- Department of Cardiology, the Second Medical Center, National Clinical Research Center of Geriatric Disease, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
| | - Jin-Ling MA
- Department of Cardiology, the Second Medical Center, National Clinical Research Center of Geriatric Disease, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
| | - Sai-Zhe LIU
- Department of Cardiology, the Six Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Kun-Lun HE
- Medical Big Data Research Center, Medical Innovation Research Department, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
| | - Su-Yan BIAN
- Department of Cardiology, the Second Medical Center, National Clinical Research Center of Geriatric Disease, Beijing Key Laboratory of Chronic Heart Failure Precision Medicine, Chinese PLA General Hospital, Beijing, China
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Rengganaten V, Huang CJ, Wang ML, Chien Y, Tsai PH, Lan YT, Ong HT, Chiou SH, Choo KB. Circular RNA ZNF800 (hsa_circ_0082096) regulates cancer stem cell properties and tumor growth in colorectal cancer. BMC Cancer 2023; 23:1088. [PMID: 37950151 PMCID: PMC10636831 DOI: 10.1186/s12885-023-11571-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Cancer stem cells form a rare cell population in tumors that contributes to metastasis, recurrence and chemoresistance in cancer patients. Circular RNAs (circRNAs) are post-transcriptional regulators of gene expression that sponge targeted microRNA (miRNAs) to affect a multitude of downstream cellular processes. We previously showed in an expression profiling study that circZNF800 (hsa_circ_0082096) was up-regulated in cancer stem cell-enriched spheroids derived from colorectal cancer (CRC) cell lines. METHODS Spheroids were generated in suspension spheroidal culture. The ZNF800 mRNA, pluripotency stem cell markers and circZNF800 levels were determined by quantitative RT-PCR. CircZNF800-miRNA interactions were shown in RNA pulldown assays and the miRNA levels determined by stem-loop qRT-PCR. The effects of circZNF800 on cell proliferation were tested by EdU staining followed by flowcytometry. Expression of stem cell markers CD44/CD133, Lgr5 and SOX9 was demonstrated in immunofluorescence microscopy. To manipulate the cellular levels of circZNF800, circZNF800 over-expression was achieved via transfection of in vitro synthesized and circularized circZNF800, and knockdown attained using a CRISPR-Cas13d-circZNF800 vector system. Xenografted nude mice were used to demonstrate effects of circZNF800 over-expression and knockdown on tumor growth in vivo. RESULTS CircZNF800 was shown to be over-expressed in late-stage tumor tissues of CRC patients. Data showed that circZNF800 impeded expression of miR-140-3p, miR-382-5p and miR-579-3p while promoted the mRNA levels of ALK/ACVR1C, FZD3 and WNT5A targeted by the miRNAs, as supported by alignments of seed sequences between the circZNF800-miRNA, and miRNA-mRNA paired interactions. Analysis in CRC cells and biopsied tissues showed that circZNF800 positively regulated the expression of intestinal stem cell, pluripotency and cancer stem cell markers, and promoted CRC cell proliferation, spheroid and colony formation in vitro, all of which are cancer stem cell properties. In xenografted mice, circZNF800 over-expression promoted tumor growth, while circZNF800 knockdown via administration of CRISPR Cas13d-circZNF800 viral particles at the CRC tumor sites impeded tumor growth. CONCLUSIONS CircZNF800 is an oncogenic factor that regulate cancer stem cell properties to lead colorectal tumorigenesis, and may be used as a predictive marker for tumor progression and the CRISPR Cas13d-circZNF800 knockdown strategy for therapeutic intervention of colorectal cancer.
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Affiliation(s)
- Vimalan Rengganaten
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia
- Postgraduate Program, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, 43000, Kajang, Malaysia
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chiu-Jung Huang
- Department of Animal Science & Graduate Institute of Biotechnology, Chinese Culture University, Taipei, 11221, Taiwan
| | - Mong-Lien Wang
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 11221, Taiwan
- Institute of Food Safety and Health Risk Assessment, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Yueh Chien
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 11221, Taiwan
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 11221, Taiwan
| | - Yuan-Tzu Lan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
- Division of Colon & Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, 11221, Taiwan
| | - Hooi Tin Ong
- Centre for Cancer Research, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia
- Department of Preclinical Sciences, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Sg Long, 43000, Kajang, Selangor, Malaysia
| | - Shih-Hwa Chiou
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 11221, Taiwan.
| | - Kong Bung Choo
- Centre for Stem Cell Research, Universiti Tunku Abdul Rahman, 43000, Kajang, Selangor, Malaysia.
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 11221, Taiwan.
- Department of Preclinical Sciences, M. Kandiah Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Sg Long, 43000, Kajang, Selangor, Malaysia.
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Zeng M, Yan S, Yang P, Li Q, Li J, Fan X, Liu X, Yao Y, Wang W, Chen R, Han G, Yang Y, Tang Z. Circular RNA transcriptome across multiple tissues reveal skeletal muscle-specific circPSME4 regulating myogenesis. Int J Biol Macromol 2023; 251:126322. [PMID: 37591436 DOI: 10.1016/j.ijbiomac.2023.126322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023]
Abstract
There are significant differences in meat production, growth rate and other traits between Western commercial pigs and Chinese local pigs. Comparative transcriptome approaches have identified many coding and non-coding candidate genes associated various traits. However, the expression and function of circular RNAs (circRNAs) in different pig tissues are largely unknown. In this study, we conducted a comprehensive analysis of the genome-wide circRNA expression profile across ten tissues in Luchuan (a Chinese local breed) and Duroc (a Western commercial breed) pigs. We identified a total of 56,254 circRNAs, of which 42.9 % were not previously annotated. We found that 33.7 % of these circRNAs were differentially expressed. Enrichment analysis revealed that differentially expressed circRNAs might contribute to the phenotypic differentiation between Luchuan and Duroc pigs. We identified 538 tissue-specific circRNAs, most of which were specifically expressed in the brain and skeletal muscle. Competitive endogenous RNA network analysis suggested that skeletal muscle-specific circPSME4 was co-expressed with MYOD1 and targeted by ssc-miR-181d-3p. Functional analysis revealed that circPSME4 knockdown could promote the proliferation and differentiation of myoblasts. Together, our findings provide valuable resources of circRNAs for animal breeding and biomedical research. We demonstrated that circPSME4 is a novel regulator of skeletal muscle development.
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Affiliation(s)
- Mu Zeng
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Shanying Yan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Peng Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Qiaowei Li
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; School of Veterinary Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Jiju Li
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xinhao Fan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoqin Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yilong Yao
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wei Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Ruipu Chen
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Guohao Han
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yalan Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan 528226, China; School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
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Shi M, Fang Y, Liang Y, Hu Y, Huang J, Xia W, Bian H, Zhuo Q, Wu L, Zhao C. Identification and characterization of differentially expressed circular RNAs in extraocular muscle of oculomotor nerve palsy. BMC Genomics 2023; 24:617. [PMID: 37848864 PMCID: PMC10583365 DOI: 10.1186/s12864-023-09733-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Oculomotor nerve palsy (ONP) is a neuroparalytic disorder resulting in dysfunction of innervating extraocular muscles (EOMs), of which the pathological characteristics remain underexplored. METHODS In this study, medial rectus muscle tissue samples from four ONP patients and four constant exotropia (CXT) patients were collected for RNA sequencing. Differentially expressed circular RNAs (circRNAs) were identified and included in functional enrichment analysis, followed by interaction analysis with microRNAs and mRNAs as well as RNA binding proteins. Furthermore, RT-qPCR was used to validate the expression level of the differentially expressed circRNAs. RESULTS A total of 84 differentially expressed circRNAs were identified from 10,504 predicted circRNAs. Functional enrichment analysis indicated that the differentially expressed circRNAs significantly correlated with skeletal muscle contraction. In addition, interaction analyses showed that up-regulated circRNA_03628 was significantly interacted with RNA binding protein AGO2 and EIF4A3 as well as microRNA hsa-miR-188-5p and hsa-miR-4529-5p. The up-regulation of circRNA_03628 was validated by RT-qPCR, followed by further elaboration of the expression, location and clinical significance of circRNA_03628 in EOMs of ONP. CONCLUSIONS Our study may shed light on the role of differentially expressed circRNAs, especially circRNA_03628, in the pathological changes of EOMs in ONP.
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Affiliation(s)
- Mingsu Shi
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yanxi Fang
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yu Liang
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Yuxiang Hu
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Jiaqiu Huang
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Weiyi Xia
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Hewei Bian
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Qiao Zhuo
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China
| | - Lianqun Wu
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China.
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China.
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China.
| | - Chen Zhao
- Eye Institute, Department of Ophthalmology, Eye & ENT Hospital, Fudan University, 83 Fenyang Road, Shanghai, 200031, China.
- NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, 83 Fenyang Road, Shanghai, 200031, China.
- Shanghai Key Laboratory of Visual Impairment and Restoration, 83 Fenyang Road, Shanghai, 200031, China.
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Feng XY, Zhu SX, Pu KJ, Huang HJ, Chen YQ, Wang WT. New insight into circRNAs: characterization, strategies, and biomedical applications. Exp Hematol Oncol 2023; 12:91. [PMID: 37828589 PMCID: PMC10568798 DOI: 10.1186/s40164-023-00451-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed, endogenous ncRNAs. Most circRNAs are derived from exonic or intronic sequences by precursor RNA back-splicing. Advanced high-throughput RNA sequencing and experimental technologies have enabled the extensive identification and characterization of circRNAs, such as novel types of biogenesis, tissue-specific and cell-specific expression patterns, epigenetic regulation, translation potential, localization and metabolism. Increasing evidence has revealed that circRNAs participate in diverse cellular processes, and their dysregulation is involved in the pathogenesis of various diseases, particularly cancer. In this review, we systematically discuss the characterization of circRNAs, databases, challenges for circRNA discovery, new insight into strategies used in circRNA studies and biomedical applications. Although recent studies have advanced the understanding of circRNAs, advanced knowledge and approaches for circRNA annotation, functional characterization and biomedical applications are continuously needed to provide new insights into circRNAs. The emergence of circRNA-based protein translation strategy will be a promising direction in the field of biomedicine.
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Affiliation(s)
- Xin-Yi Feng
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shun-Xin Zhu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Ke-Jia Pu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Heng-Jing Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of 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, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
| | - Wen-Tao Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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Zhu M, Chen D, Ruan C, Yang P, Zhu J, Zhang R, Li Y. CircRNAs: A Promising Star for Treatment and Prognosis in Oral Squamous Cell Carcinoma. Int J Mol Sci 2023; 24:14194. [PMID: 37762497 PMCID: PMC10532269 DOI: 10.3390/ijms241814194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
CircRNAs are a class of endogenous long non-coding RNAs with a single-stranded circular structure. Most circRNAs are relatively stable, highly conserved, and specifically expressed in tissue during the cell and developmental stages. Many circRNAs have been discovered in OSCC. OSCC is one of the most severe and frequent forms of head and neck cancer today, with a poor prognosis and low overall survival rate. Due to its prevalence, OSCC is a global health concern, characterized by genetic and epigenomic changes. However, the mechanism remains vague. With the advancement of biotechnology, a large number of circRNAs have been discovered in mammalian cells. CircRNAs are dysregulated in OSCC tissues and thus associated with the clinicopathological characteristics and prognosis of OSCC patients. Research studies have demonstrated that circRNAs can serve as biomarkers for OSCC diagnosis and treatment. Here, we summarized the properties, functions, and biogenesis of circRNAs, focusing on the progress of current research on circRNAs in OSCC.
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Affiliation(s)
| | | | | | | | | | - Rongxin Zhang
- Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China; (M.Z.); (D.C.); (C.R.); (J.Z.)
| | - Yan Li
- Department of Biotechnology, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China; (M.Z.); (D.C.); (C.R.); (J.Z.)
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Galang JN, Shen Y, Koitzsch U, Yu X, Eischeid-Scholz H, Bachurski D, Rau TT, Neppl C, Herling M, Bulimaga B, Vasyutina E, Schweiger MR, Büttner R, Odenthal M, Anokhina MM. Vesicular Release and Uptake of Circular LSD1-RNAs from Non-Cancer and Cancer Lung Cells. Int J Mol Sci 2023; 24:13981. [PMID: 37762282 PMCID: PMC10530930 DOI: 10.3390/ijms241813981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is highly expressed in many cancer types and strongly associated with cancer progression and metastasis. Circular RNAs (circRNAs) are produced by back-splicing and influence the interactive RNA network by microRNA and protein sponging. In the present study, we aimedto identify circRNAs that derive from the LSD1-encoding KDM1A gene, and to investigate their potential to be released and uptaken by lung cancer versus non-cancer epithelial cells. We identified four circLSD1-RNAs by RT-PCR with divergent primers, followed by sequencing. The expression level of circLSD1-RNAs was then studied by quantitative PCR on cellular and extracellular fractions of lung cancer (PC9) and non-cancer primary small airway epithelial (PSAE) cells. Moreover, we established the transgenic overexpression of circLSD1-RNAs. We show that circLSD1-RNAs are primarily located in the cytoplasm, but are packaged and released from lung cancer and non-cancer cells by extracellular vesicles (EVs) and ribonucleoprotein (RNP) complexes, respectively. Proteomics demonstrated a different protein pattern of EV fractions released from PC9 versus PSAE cells. Importantly, released circLSD1-RNAs were differently taken up by PSAE and PC9 cells. In conclusion, our findings provide primary evidence that circLSD1-RNAs participate in the intercellular communication of lung cancer cells with the tumor environment.
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Affiliation(s)
- Joelle Noriko Galang
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Yefeng Shen
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Ulrike Koitzsch
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Xiaojie Yu
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Hannah Eischeid-Scholz
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Daniel Bachurski
- CECAD Center of Excellence on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, 50937 Cologne, Germany;
- Department I of Internal Medicine, University Hospital of Cologne, 50937 Cologne, Germany; (M.H.)
| | - Tilman T. Rau
- Institute of Pathology, University Hospital of Duesseldorf, 40225 Duesseldorf, Germany; (T.T.R.); (C.N.)
| | - Christina Neppl
- Institute of Pathology, University Hospital of Duesseldorf, 40225 Duesseldorf, Germany; (T.T.R.); (C.N.)
| | - Marco Herling
- Department I of Internal Medicine, University Hospital of Cologne, 50937 Cologne, Germany; (M.H.)
- Department of Hematology, Cellular Therapy and Hemostaseology, University of Leipzig, 04103 Leipzig, Germany
| | - Bianca Bulimaga
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Elena Vasyutina
- Department I of Internal Medicine, University Hospital of Cologne, 50937 Cologne, Germany; (M.H.)
- Department of Hematology, Cellular Therapy and Hemostaseology, University of Leipzig, 04103 Leipzig, Germany
| | - Michal R. Schweiger
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
- Institute for Epigenetics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Margarete Odenthal
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
| | - Maria M. Anokhina
- Institute of Pathology, University Hospital of Cologne, 50937 Cologne, Germany; (J.N.G.); (Y.S.); (X.Y.); (H.E.-S.); (B.B.); (R.B.)
- Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany;
- Institute of Pathology, University Hospital of Duesseldorf, 40225 Duesseldorf, Germany; (T.T.R.); (C.N.)
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Dremel SE, Tagawa T, Koparde VN, Arbuckle JH, Kristie TM, Krug LT, Ziegelbauer JM. Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.07.556698. [PMID: 37886542 PMCID: PMC10602050 DOI: 10.1101/2023.09.07.556698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
A first line of defense during infection is expression of interferon (IFN)-stimulated gene products which suppress viral lytic infection. To combat this, herpesviruses express endoribonucleases to deplete host RNAs. Here we demonstrate that IFN-induced circular RNAs (circRNAs) can escape viral-mediated degradation. We performed comparative circRNA expression profiling for representative alpha- (Herpes simplex virus-1, HSV-1), beta- (human cytomegalovirus, HCMV), and gamma-herpesviruses (Kaposi sarcoma herpesvirus, KSHV; murine gamma-herpesvirus 68, MHV68). Strikingly, we found that circRNAs are, as a population, resistant to host shutoff. This observation was confirmed by ectopic expression assays of human and murine herpesvirus endoribonucleases. During primary lytic infection, ten circRNAs were commonly regulated across all subfamilies of human herpesviruses, suggesting a common mechanism of regulation. We tested one such mechanism, namely how interferon-stimulation influences circRNA expression. 67 circRNAs were upregulated by either IFN-β or -γ treatment, with half of these also upregulated during lytic infection. Using gain and loss of function studies we found an interferon-stimulated circRNA, circRELL1, inhibited lytic HSV-1 infection. We have previously reported circRELL1 inhibits lytic KSHV infection, suggesting a pan-herpesvirus antiviral activity. We propose a two-pronged model in which interferon-stimulated genes may encode both mRNA and circRNA with antiviral activity. This is critical in cases of host shutoff, such as alpha- and gamma-herpesvirus infection, where the mRNA products are degraded but circRNAs escape.
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Affiliation(s)
- Sarah E. Dremel
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, United States
| | - Takanobu Tagawa
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, United States
| | - Vishal N. Koparde
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Jesse H. Arbuckle
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Thomas M. Kristie
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, United States
| | - Joseph M. Ziegelbauer
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, United States
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Campolo F, Sesti F, Feola T, Puliani G, Faggiano A, Tarsitano MG, Tenuta M, Hasenmajer V, Ferretti E, Verrico M, Gianfrilli D, Venneri MA, Isidori AM, Giannetta E. Platelet-derived circRNAs signature in patients with gastroenteropancreatic neuroendocrine tumors. J Transl Med 2023; 21:548. [PMID: 37587471 PMCID: PMC10428534 DOI: 10.1186/s12967-023-04417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Neuroendocrine tumors (NETs) early diagnosis is a clinical challenge that require a deep understanding of molecular and genetic features of this heterogeneous group of neoplasms. However, few biomarkers exist to aid diagnosis and to predict prognosis and treatment response. In the oncological field, tumor-educated platelets (TEPs) have been implicated as central players in the systemic and local responses to tumor growth, thereby altering tumor specific RNA profile. Although TEPs have been found to be enriched in RNAs, few studies have investigated the potential of a type of RNA, circular RNAs (circRNA), as platelet-derived biomarkers for cancer. In this proof-of-concept study, we aim to demonstrate whether the circRNAs signature of tumor educated platelets can be used as a liquid biopsy biomarker for the detection of gastroenteropancreatic (GEP)-NETs and the prediction of the early response to treatment. METHODS We performed a 24-months, prospective proof-of-concept study in men and women with histologically proven well-differentiated G1-G2 GEP-NET, aged 18-80 years, naïve to treatment. We performed a RNAseq analysis of circRNAs obtained from TEPs samples of 10 GEP-NETs patients at baseline and after 3 months from therapy (somatostatin analogs or surgery) and from 5 patients affected by non-malignant endocrinological diseases enrolled as a control group. RESULTS Statistical analysis based on p < 0.05 resulted in the identification of 252 circRNAs differentially expressed between GEP-NET and controls of which 109 were up-regulated and 143 were down-regulated in NET patients. Further analysis based on an FDR value ≤ 0.05 resulted in the selection of 5 circRNAs all highly significant downregulated. The same analysis on GEP-NETs at baseline and after therapy in 5 patients revealed an average of 4983 remarkably differentially expressed circRNAs between follow-up and baseline samples of which 2648 up-regulated and 2334 down-regulated, respectively. Applying p ≤ 0.05 and FDR ≤ 0.05 filters, only 3/5 comparisons gave statistically significant results. CONCLUSIONS Our findings identified for the first time a circRNAs signature from TEPs as potential diagnostic and predictive biomarkers for GEP-NETs.
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Affiliation(s)
- Federica Campolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Franz Sesti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tiziana Feola
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Neuroendocrinology, Neuromed Institute, IRCCS, Pozzilli, Italy
| | - Giulia Puliani
- Oncological Endocrinology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Antongiulio Faggiano
- Department of Clinical and Molecular Medicine, Sant'Andrea Hospital, ENETS Center of Excellence, Sapienza University of Rome, Rome, Italy
| | | | - Marta Tenuta
- UOC Endocrinology, Metabolic Diseases, Andrology SMIC08, Policlinico Umberto I, Rome, Italy
| | - Valeria Hasenmajer
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Elisabetta Ferretti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Monica Verrico
- Department of Radiological, Oncological and Anatomo-Pathological Sciences, Sapienza University of Rome, Rome, Italy
| | - Daniele Gianfrilli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Mary Anna Venneri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Andrea M Isidori
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
- Centre for Rare Diseases (ENDO-ERN Accredited), Policlinico Umberto I, Rome, Italy
| | - Elisa Giannetta
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
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Min J, Li Y, Li X, Wang M, Li H, Bi Y, Xu P, Liu W, Ye X, Li J. The circRNA circVAMP3 restricts influenza A virus replication by interfering with NP and NS1 proteins. PLoS Pathog 2023; 19:e1011577. [PMID: 37603540 PMCID: PMC10441791 DOI: 10.1371/journal.ppat.1011577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Circular RNAs (circRNAs) are involved in various biological roles, including viral infection and antiviral immune responses. To identify influenza A virus (IAV) infection-related circRNAs, we compared the circRNA profiles of A549 cells upon IAV infection. We found that circVAMP3 is substantially upregulated after IAV infection or interferon (IFN) stimulation. Furthermore, IAV and IFN-β induced the expression of QKI-5, which promoted the biogenesis of circVAMP3. Overexpression of circVAMP3 inhibited IAV replication, while circVAMP3 knockdown promoted viral replication, suggesting that circVAMP3 restricts IAV replication. We verified the effect of circVAMP3 on viral infection in mice and found that circVAMP3 restricted IAV replication and pathogenesis in vivo. We also found that circVAMP3 functions as a decoy to the viral proteins nucleoprotein (NP) and nonstructural protein 1 (NS1). Mechanistically, circVAMP3 interfered with viral ribonucleoprotein complex activity by reducing the interaction of NP with polymerase basic 1, polymerase basic 2, or vRNA and restored the activation of IFN-β by alleviating the inhibitory effect of NS1 to RIG-I or TRIM25. Our study provides new insights into the roles of circRNAs, both in directly inhibiting virus replication and in restoring innate immunity against IAV infection.
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Affiliation(s)
- Jie Min
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yucen Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Department of Microbiology and Parasitology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xinda Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mingge Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Science and Technology of China, Anhui, China
| | - Huizi Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Ping Xu
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Wenjun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Xin Ye
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
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Puri S, Hu J, Sun Z, Lin M, Stein TD, Farrer LA, Wolozin B, Zhang X. Identification of circRNAs linked to Alzheimer's disease and related dementias. Alzheimers Dement 2023; 19:3389-3405. [PMID: 36795937 PMCID: PMC10427739 DOI: 10.1002/alz.12960] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/21/2022] [Accepted: 12/27/2022] [Indexed: 02/18/2023]
Abstract
INTRODUCTION Circular RNAs (circRNAs) exhibit selective expression in the brain and differential regulation in Alzheimer's disease (AD). To explore the role of circRNAs in AD, we investigated how circRNA expression varies between brain regions and with AD-related stress in human neuronal precursor cells (NPCs). METHODS Ribosomal RNA-depleted hippocampus RNA-sequencing data were generated. Differentially regulated circRNAs in AD and related dementias were detected using CIRCexplorer3 and limma. circRNA results were validated using quantitative real-time PCR of cDNA from the brain and NPCs. RESULTS We identified 48 circRNAs that were significantly associated with AD. We observed that circRNA expression differed by dementia subtype. Using NPCs, we demonstrated that exposure to oligomeric tau elicits downregulation of circRNA similar to that observed in the AD brain. DISCUSSION Our study shows that differential expression of circRNA can vary by dementia subtype and brain region. We also demonstrated that circRNAs can be regulated by AD-linked neuronal stress independently from their cognate linear messenger RNAs (mRNAs).
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Affiliation(s)
- Sambhavi Puri
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Junming Hu
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Zhuorui Sun
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Mintao Lin
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
| | - Thor D. Stein
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
- Alzheimer’s Disease Research Center, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Boston University School of Medicine, Framingham, MA, USA
- VA Boston Healthcare System, Boston, MA, USA
| | - Lindsay A. Farrer
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Department of Ophthalmology, Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Alzheimer’s Disease Research Center, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Boston University School of Medicine, Framingham, MA, USA
| | - Benjamin Wolozin
- Department of Pharmacology & Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Xiaoling Zhang
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, Boston University School of Medicine, Framingham, MA, USA
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Zhou J, Zhao Y, An P, Zhao H, Li X, Xiong Y. Hsa_circ_0002348 regulates trophoblast proliferation and apoptosis through miR-126-3p/BAK1 axis in preeclampsia. J Transl Med 2023; 21:509. [PMID: 37507742 PMCID: PMC10375637 DOI: 10.1186/s12967-023-04240-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/31/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Preeclampsia is a common pregnancy complication characterized by high blood pressure and damage to organs. Abnormal placenta and vascular function can lead to preeclampsia. Accumulating evidence has suggested a potential link between circular RNAs (circRNAs) and preeclampsia. As a placenta and endothelial-expressed circRNA, hsa_circ_0002348, may be promising to be the novel molecular target for preeclampsia. However, the function and mechanism of hsa_circ_0002348 in preeclampsia has not been elucidated. MATERIALS AND METHODS An overlap analysis of two circRNA profiles from placenta and endothelial cells was used to identify a functionally unknown circRNA, hsa_circ_0002348. Quantitative real-time PCR (qRT-PCR) and in situ hybridization (ISH) were used to detect its expression in the trophoblast cells and placental tissues. The mouse model of lipopolysaccharide (LPS)-induced preeclampsia was established to determine the in vivo role of hsa_circ_0002348. RNA immunoprecipitation (RIP), Luciferase reporter assay, qRT-PCR, western blot, gain- and loss-of-function and rescue experiments were conducted to uncover the role of hsa_circ_0002348 and its interaction with miR-126-3p and BAK1 in regulating trophoblast proliferation and apoptosis. Fluorescence in situ hybridization (FISH) and Immunohistochemistry (IHC) were performed to examine the expression of miR-126-3p and BAK1 in mice and human placentas, respectively. RESULTS Hsa_circ_0002348 was significantly increased in the preeclampsia placentas, and positively correlated with the severity of preeclampsia patients' clinical manifestations. Its overexpression exacerbated preeclampsia-like features in the mouse model of LPS-induced preeclampsia. Functionally, hsa_circ_0002348 was found to inhibit trophoblast proliferation and promote trophoblast apoptosis. Mechanistically, hsa_circ_0002348, as an endogenous miR-126-3p sponge, upregulated the expression of BAK1. Additionally, both hsa_circ_0002348 knockdown and miR-126-3p overexpression enhanced the mammalian target of rapamycin (mTOR) and ERK1/2 signaling pathway. CONCLUSIONS Hsa_circ_0002348 might be a novel regulator of trophoblast proliferation and apoptosis through miR-126-3p/BAK1 axis in preeclampsia, which may serve as a potential target for detecting and treating preeclampsia.
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Affiliation(s)
- Jizi Zhou
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Ying Zhao
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Ping An
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Huanqiang Zhao
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China.
- Institute of Biomedical Sciences, Fudan University, Shanghai, China.
| | - Yu Xiong
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China.
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Miao S, Zhang Q. Circulating circRNA: a social butterfly in tumors. Front Oncol 2023; 13:1203696. [PMID: 37546422 PMCID: PMC10401440 DOI: 10.3389/fonc.2023.1203696] [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: 04/11/2023] [Accepted: 06/20/2023] [Indexed: 08/08/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of single-stranded non-coding RNAs that form circular structures through irregular splicing or post-splicing events. CircRNAs are abnormally expressed in many cancers and regulate the occurrence and development of tumors. Circulating circRNAs are cell-free circRNAs present in peripheral blood, they are considered promising biomarkers due to their high stability. In recent years, more and more studies have revealed that circulating circRNAs participate in various cellular communication and regulate the occurrence and development of tumors, which involve many pathological processes such as tumorigenesis, tumor-related immunity, tumor angiogenesis, and tumor metastasis. Understanding the role of cell communication mediated by circulating circRNAs in tumor will further reveal the value and significance behind their use as biomarkers and potential therapeutic targets. In this review, we summarize the recent findings and provide an overview of the cell-cell communication mediated by circulating circRNAs, aiming to explore the role and application value of circulating circRNAs in tumors.
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Affiliation(s)
- Shuo Miao
- Department of Urology, Affiliated Hospital of Qingdao University, Qingdao, China
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Qingsong Zhang
- Department of Urology, Affiliated Hospital of Qingdao University, Qingdao, China
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Yang J, Long Q, Zhang Y, Liu Y, Wu J, Zhao X, You X, Li X, Liu J, Teng Z, Zeng Y, Luo XJ. Whole transcriptome analysis reveals dysregulation of molecular networks in schizophrenia. Asian J Psychiatr 2023; 85:103649. [PMID: 37267675 DOI: 10.1016/j.ajp.2023.103649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023]
Abstract
To characterize the regulatory relationships between different types of transcripts and the altered molecular networks in schizophrenia (SCZ), we performed a whole transcriptome study by quantifying mRNAs, long noncoding RNAs (lncRNAs), miRNAs, and circular RNAs (circRNAs) in the same individuals simultaneously. A total of 807 dysregulated genes showed differential expression in SCZ cases compared with controls. Network-based analysis revealed dysregulation of molecular networks in SCZ. Finally, integration of the transcriptome data with published data identified promising SCZ candidate genes. Our study reveals that dysregulated molecular networks and regulatory relationships between different types of transcript may have a role in SCZ.
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Affiliation(s)
- Jinfeng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Qing Long
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China
| | - Yunqiao Zhang
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China; Honghe Second People's Hospital, Honghe, Yunnan 654399, China; The Sixth Affiliated Hospital, Kunming Medical University, Yuxi, Yunnan 653100, China
| | - Yilin Liu
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China
| | - Jie Wu
- The Affiliated Mental Health Center, Kunming Medical University, Kunming, Yunnan 650224, China
| | - Xinling Zhao
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China
| | - Xu You
- Honghe Second People's Hospital, Honghe, Yunnan 654399, China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zhaowei Teng
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China.
| | - Yong Zeng
- The Second Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650101, China.
| | - Xiong-Jian Luo
- Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing 210096, China; Department of Neurology, Zhongda Hospital, School of Medicine, Advanced Institute for Life and Health, Southeast University, Nanjing, China.
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Hosaka T, Tsuji H, Kwak S. Roles of Aging, Circular RNAs, and RNA Editing in the Pathogenesis of Amyotrophic Lateral Sclerosis: Potential Biomarkers and Therapeutic Targets. Cells 2023; 12:1443. [PMID: 37408276 DOI: 10.3390/cells12101443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 07/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable motor neuron disease caused by upper and lower motor neuron death. Despite advances in our understanding of ALS pathogenesis, effective treatment for this fatal disease remains elusive. As aging is a major risk factor for ALS, age-related molecular changes may provide clues for the development of new therapeutic strategies. Dysregulation of age-dependent RNA metabolism plays a pivotal role in the pathogenesis of ALS. In addition, failure of RNA editing at the glutamine/arginine (Q/R) site of GluA2 mRNA causes excitotoxicity due to excessive Ca2+ influx through Ca2+-permeable α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors, which is recognized as an underlying mechanism of motor neuron death in ALS. Circular RNAs (circRNAs), a circular form of cognate RNA generated by back-splicing, are abundant in the brain and accumulate with age. Hence, they are assumed to play a role in neurodegeneration. Emerging evidence has demonstrated that age-related dysregulation of RNA editing and changes in circRNA expression are involved in ALS pathogenesis. Herein, we review the potential associations between age-dependent changes in circRNAs and RNA editing, and discuss the possibility of developing new therapies and biomarkers for ALS based on age-related changes in circRNAs and dysregulation of RNA editing.
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Affiliation(s)
- Takashi Hosaka
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
- University of Tsukuba Hospital/Jichi Medical University Joint Ibaraki Western Regional Clinical Education Center, Chikusei 308-0813, Japan
- Department of Internal Medicine, Ibaraki Western Medical Center, Chikusei 308-0813, Japan
| | - Hiroshi Tsuji
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Shin Kwak
- Department of Neurology, Tokyo Medical University, Tokyo 160-0023, Japan
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Feng H, Deng Z, Peng W, Wei X, Liu J, Wang T. Circular RNA EPHA3 suppresses progression and metastasis in prostate cancer through the miR-513a-3p/BMP2 axis. J Transl Med 2023; 21:288. [PMID: 37118847 PMCID: PMC10148471 DOI: 10.1186/s12967-023-04132-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) may regulate the onset and progression of human malignancies by competitively binding to microRNA (miRNA) sponges, thus regulating the downstream genes. However, aberrant circRNA expression patterns and their biological functions in prostate cancer (PCa) warrant further studies. Our research sought to shed further light on the possible role and molecular mechanism of circEPHA3 action in controlling the growth and metastasis of PCa cells. MATERIALS AND METHODS circEPHA3 (has_circ_0066596) was initially screened from a previous circRNA microarray and identified following Actinomycin D and RNase R assays. Fluorescence in situ hybridization, biotin-coupled probe RNA pulldown, and dual-luciferase reporter gene assays were performed to examine the relationship between circEPHA3 and miR-513a-3p. The biological role of circEPHA3 in PCa was assessed by CCK8, wound healing, Transwell assays, and animal experiments. RESULTS We identified a novel circular RNA, circEPHA3 (has_circ_0066596), which was down-regulated in high-grade PCa tissues and cell lines. The outcomes of CCK8, wound healing, Transwell assays, and animal experiments revealed that circEPHA3 prohibited the progression and metastasis of PCa in vivo and in vitro. Mechanistically, circEPHA3 was directly bound to miR-513a-3p and regulated the downstream gene, BMP2, thereby serving as a tumor suppressor in PCa. CONCLUSIONS As a tumor suppressor, circEPHA3 inhibited the proliferation and metastasis of PCa cells through the miR-513a-3p/BMP2 axis, suggesting that circEPHA3 might be a potential therapeutic target for PCa.
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Affiliation(s)
- Huan Feng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China
| | - Zhiyao Deng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China
| | - Wei Peng
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xian Wei
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tao Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, China.
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Al-Hawary SIS, Jasim SA, Romero-Parra RM, Bustani GS, Hjazi A, Alghamdi MI, Kareem AK, Alwaily ER, Zabibah RS, Gupta J, Mahmoudi R, Hosseini-Fard S. NLRP3 inflammasome pathway in atherosclerosis: Focusing on the therapeutic potential of non-coding RNAs. Pathol Res Pract 2023; 246:154490. [PMID: 37141699 DOI: 10.1016/j.prp.2023.154490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/06/2023]
Abstract
NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3) inflammasome pathway has a critical role in the pathogenesis of atherosclerosis. Activation of this pathway is implicated in the subendothelial inflammation and atherosclerosis progression. The NLRP3 inflammasome are cytoplasmic sensors with the distinct capacity to identify a wide range of inflammation-related signals, which enhance NLRP3 inflammasome assembly and allow it to trigger inflammation. This pathway is triggered by a variety of intrinsic signals which exist in atherosclerotic plaques, like cholesterol crystals and oxidized LDL. Further pharmacological findings indicated that NLRP3 inflammasome enhanced caspase-1-mediated secretion of pro-inflammatory mediators like interleukin (IL)- 1β/18. Newly published cutting-edge studies suggested that non-coding RNAs (ncRNAs) including microRNAs (miRNAs, miRs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs) are major modulators of NLRP3 inflammasome in atherosclerosis. Therefore, in this review, we aimed to discuss the NLRP3 inflammasome pathway, biogenesis of ncRNAs as well as the modulatory role of ncRNAs in regulating the various mediators of NLRP3 inflammasome pathway including TLR4, NF-kB, NLRP3, and caspase 1. We also discussed the importance of NLRP3 inflammasome pathway-related ncRNAs as a diagnostic biomarker in atherosclerosis and current therapeutics in the modulation of NLRP3 inflammasome in atherosclerosis. Finally, we speak about the limitations and future prospects of ncRNAs in regulating inflammatory atherosclerosis via the NLRP3 inflammasome pathway.
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Affiliation(s)
| | - Saade Abdalkareem Jasim
- Medical Laboratory Techniques Department, Al-maarif University College, Al-anbar-Ramadi, Iraq
| | | | | | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Kingdom of Saudi Arabia
| | | | - Ali Kamil Kareem
- Biomedical Engineering Department, Al-Mustaqbal University College, Hillah 51001, Iraq
| | - Enas R Alwaily
- Microbiology Research Group, College of Pharmacy, Al-Ayen University, Thi-Qar, Iraq
| | - Rahman S Zabibah
- Medical Laboratory Technology Department, College of Medical Technology, The Islamic University, Najaf, Iraq
| | - Jitendra Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura 281406, UP, India
| | - Reza Mahmoudi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Seyedreza Hosseini-Fard
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Abbas MN, Kausar S, Gul I, Li J, Yu H, Dong M, Cui H. The Potential Biological Roles of Circular RNAs in the Immune Systems of Insects to Pathogen Invasion. Genes (Basel) 2023; 14:genes14040895. [PMID: 37107653 PMCID: PMC10137924 DOI: 10.3390/genes14040895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Circular RNAs (circRNAs) are a newly discovered class of endogenously expressed non-coding RNAs (ncRNAs). They are highly stable, covalently closed molecules that frequently exhibit tissue-specific expression in eukaryotes. A small number of circRNAs are abundant and have been remarkably conserved throughout evolution. Numerous circRNAs are known to play important biological roles by acting as microRNAs (miRNAs) or protein inhibitors ('sponges'), by regulating the function of proteins, or by being translated themselves. CircRNAs have distinct cellular functions due to structural and production differences from mRNAs. Recent advances highlight the importance of characterizing circRNAs and their targets in a variety of insect species in order to fully understand how they contribute to the immune responses of these insects. Here, we focus on the recent advances in our understanding of the biogenesis of circRNAs, regulation of their abundance, and biological roles, such as serving as templates for translation and in the regulation of signaling pathways. We also discuss the emerging roles of circRNAs in regulating immune responses to various microbial pathogens. Furthermore, we describe the functions of circRNAs encoded by microbial pathogens that play in their hosts.
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Affiliation(s)
- Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Saima Kausar
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Isma Gul
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Jisheng Li
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Huijuan Yu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Mengyao Dong
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Southwest University, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing 400716, China
- Jinfeng Laboratory, Chongqing 401329, China
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Dinh P, Peng J, Tran T, Wu D, Tran C, Dinh T, Pan S. Identification of hsa_circ_0001445 of a novel circRNA-miRNA-mRNA regulatory network as potential biomarker for coronary heart disease. Front Cardiovasc Med 2023; 10:1104223. [PMID: 36998978 PMCID: PMC10043405 DOI: 10.3389/fcvm.2023.1104223] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/22/2023] [Indexed: 03/17/2023] Open
Abstract
ObjectsTo evaluate the hsa_circ_0001445 level in peripheral blood leukocytes of patients with coronary heart disease (CHD) and its related clinical factors, and predict its circRNA-miRNA-mRNA regulatory network in CHD pathogenesis via bioinformatics analysis.MethodsPeripheral blood leukocytes were isolated from the whole blood samples of 94 CHD patients (aged 65.96 ± 9.78 years old) and 126 healthy controls (aged 60.75 ± 8.81 years old). qRT-PCR was used to quantify the expression level of circRNA and subsequently analyze its association with CHD clinical parameters. Via bioinformatics algorithm and GEO datasets, differential miRNA expression was evaluated using the Limma package. A miRNA-mRNA regulatory network was predicted by cyTargetLinker. ClusterProfiler was employed to perform functional enrichment analysis of the circRNA network to investigate its role in CHD pathogenesis.ResultsThe expression of hsa_circ_0001445 in peripheral blood leukocytes of CHD patients was downregulated compared with that of healthy controls. Positive correlations were evident between hsa_circ_0001445 expression level and the levels of hemoglobin, triglycerides, high- and low-density lipoprotein cholesterol. A significant negative correlation was also found between hsa_circ_0001445 expression level and age and the neutrophil level. Low expression of hsa_circ_0001445 exhibited a discriminatory ability between CHD patients and healthy controls with a sensitivity of 67.5% and a specificity of 76.6% (p < 0.05). By bioinformatics analysis, 405 gene ontology terms were identified. The Kyoto Encyclopedia of Genes and Genomes terms focused principally on the PI3K-Akt signaling pathway. hsa_circ_0001445 was associated with the expression of three miRNAs that may regulate 18 genes involved in KEGG processes: hsa-miR-507, hsa-miR-375–3p, and hsa-miR-942–5p.ConclusionThe hsa_circ_0001445 level in peripheral blood leukocytes may serve as a biomarker for CHD diagnosis. Our work on circRNA-miRNA-mRNA networks suggests a potential role for hsa_circ_0001445 in CHD development.
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Affiliation(s)
- PhongSon Dinh
- Departments of Pathophysiology, Guangxi Medical University, Nanning, China
- College of Medicine and Pharmacy, Duy Tan University, Danang, Vietnam
| | - JunHua Peng
- Departments of Pathophysiology, Guangxi Medical University, Nanning, China
- Key Laboratory of Longevity and Ageing-Related Disease of Chinese Ministry of Education, Center for Translational Medicine and School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - ThanhLoan Tran
- Departments of Pathophysiology, Guangxi Medical University, Nanning, China
- Department of Immunology and Pathophysiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - DongFeng Wu
- Department of the Geriatric Cardiology, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - ChauMyThanh Tran
- College of Medicine and Pharmacy, Duy Tan University, Danang, Vietnam
| | - ThiPhuongHoai Dinh
- Department of Neurosurgery, Hue University Hospital, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - ShangLing Pan
- Departments of Pathophysiology, Guangxi Medical University, Nanning, China
- Key Laboratory of Longevity and Ageing-Related Disease of Chinese Ministry of Education, Center for Translational Medicine and School of Preclinical Medicine, Guangxi Medical University, Nanning, China
- Correspondence: ShangLing Pan
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Das A, Sinha T, Mishra SS, Das D, Panda AC. Identification of potential proteins translated from circular RNA splice variants. Eur J Cell Biol 2023; 102:151286. [PMID: 36645925 PMCID: PMC7614519 DOI: 10.1016/j.ejcb.2023.151286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 01/11/2023] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules generated from precursor RNAs by the head-to-tail backsplicing of exons. Hundreds of studies demonstrated that circRNAs are ubiquitously expressed and regulate cellular events by modulating microRNA (miRNA) and RNA-binding protein (RBP) activities. A few circRNAs are also known to translate into functional polypeptides regulating cellular physiology. All these functions primarily depend on the full-length sequence of the circRNAs. CircRNA backsplice junction sequence is the key to identifying circRNAs and their full-length mature sequence. However, some multi-exonic circRNAs exist in different isoforms sharing identical backsplice junction sequences and are termed circRNA splice variants. Here, we analyzed the previously published HeLa cell RNA-seq datasets to identify circRNA splice variants using the de novo module of the CIRCexplorer2 circRNA annotation pipeline. A subset of circRNAs with splice variants was validated by the circRNA-rolling circle amplification (circRNA-RCA) method. Interestingly, several validated circRNAs were predicted to translate into proteins by the riboCIRC database. Furthermore, polyribosome fractionation followed by quantitative PCR confirmed the association of a subset of circRNAs with polyribosome supporting their protein-coding potential. Finally, bioinformatics analysis of proteins derived from splice variants of circCORO1C and circASPH suggested altered protein sequences and structures that could affect their physiological functions. Together, our study identified novel circRNA splice variants and their potential translation into protein isoforms which may regulate various physiological processes.
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Affiliation(s)
- Aniruddha Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India; School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Tanvi Sinha
- Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
| | | | - Debojyoti Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar 751023, Odisha, India.
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Recent insights into the roles of circular RNAs in human brain development and neurologic diseases. Int J Biol Macromol 2023; 225:1038-1048. [PMID: 36410538 DOI: 10.1016/j.ijbiomac.2022.11.166] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022]
Abstract
Circular RNAs (circRNAs) are a novel class of non-coding RNAs. They are single-stranded RNA transcripts characterized with a closed loop structure making them resistant to degrading enzymes. Recently, circRNAs have been suggested with regulatory roles in gene expression involved in controlling various biological processes. Notably, they have demonstrated abundance, dynamic expression, back-splicing events, and spatiotemporally regulation in the human brain. Accordingly, they are expected to be involved in brain functions and related diseases. Studies in animals and human brain have revealed differential expression of circRNAs in brain compartments. Interestingly, contributing roles of circRNAs in the regulation of central nervous system (CNS) development have been demonstrated in a number of studies. It has been proposed that circRNAs play role in substantial neurological functions like neurotransmitter-associated tasks, neural cells maturation, and functions of synapses. Furthermore, 3 main pathways have been identified in association with circRNAs's host genes including axon guidance, Wnt signaling, and transforming growth factor beta (TGF-β) signaling pathways, which are known to be involved in substantial functions like migration and differentiation of neurons and specification of axons, and thus play role in brain development. In this review, we have an overview to the biogenesis, biological functions of circRNAs, and particularly their roles in human brain development and the pathogenesis of neurodegenerative diseases including Alzheimer's diseases, multiple sclerosis, Parkinson's disease and brain tumors.
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