1
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Zhang Y, Zhang C, Peng C, Jia J. Unraveling the crosstalk: circRNAs and the wnt signaling pathway in cancers of the digestive system. Noncoding RNA Res 2024; 9:853-864. [PMID: 38586314 PMCID: PMC10995981 DOI: 10.1016/j.ncrna.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/02/2024] [Accepted: 03/03/2024] [Indexed: 04/09/2024] Open
Abstract
Circular RNA (circRNA) is a unique type of noncoding RNA molecule characterized by its closed-loop structure. Functionally versatile, circRNAs play pivotal roles in gene expression regulation, protein activity modulation, and participation in cell signaling processes. In the context of cancers of the digestive system, the Wnt signaling pathway holds particular significance. Anomalous activation of the Wnt pathway serves as a primary catalyst for the development of colorectal cancer. Extensive research underscores the notable participation of circRNAs associated with the Wnt pathway in the progression of digestive system tumors. These circRNAs exhibit pronounced dysregulation across esophageal cancer, gastric cancer, liver cancer, colorectal cancer, pancreatic cancer, and cholangiocarcinoma. Furthermore, the altered expression of circRNAs linked to the Wnt pathway correlates with prognostic factors in digestive system tumors. Additionally, circRNAs related to the Wnt pathway showcase potential as diagnostic, therapeutic, and prognostic markers within the realm of digestive system tumors. This comprehensive review outlines the interplay between circRNAs and the Wnt signaling pathway in cancers of the digestive system. It seeks to provide a comprehensive perspective on their association while delving into ongoing research that explores the clinical applications of circRNAs associated with the Wnt pathway.
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Affiliation(s)
- Yu Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Cheng Zhang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Chuanhui Peng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Junjun Jia
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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2
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Sadhukhan S, Sinha T, Dey S, Panda AC. Subcellular localization of circular RNAs: Where and why. Biochem Biophys Res Commun 2024; 715:149937. [PMID: 38701688 DOI: 10.1016/j.bbrc.2024.149937] [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: 12/22/2023] [Revised: 04/02/2024] [Accepted: 04/11/2024] [Indexed: 05/05/2024]
Abstract
Localization of RNAs at specific subcellular locations regulating various local cellular events has gained much attention recently. Like most other classes of RNAs, the function of newly discovered circular RNAs (circRNAs) is predominantly determined by their association with different cellular factors in the cell. CircRNAs function as transcriptional and posttranscriptional regulators of gene expression by interacting with transcription factors, splicing regulators, RNA-binding proteins, and microRNAs or by translating into functional polypeptides. Hence, studying their subcellular localization to assess their function is essential. The discovery of more than a million circRNA and increasing evidence of their involvement in development and diseases require a thorough analysis of their subcellular localization linking to their biological functions. Here, we summarize current knowledge of circRNA localization in cells and extracellular vesicles, factors regulating their subcellular localization, and the implications of circRNA localization on their cellular functions. Given the discovery of many circRNAs in all life forms and their implications in pathophysiology, we discuss the challenges in studying circRNA localization and the opportunities for unlocking the mystery of circRNA functions.
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Affiliation(s)
- Susovan Sadhukhan
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Tanvi Sinha
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Suchanda Dey
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India.
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3
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Cao SM, Wu H, Yuan GH, Pan YH, Zhang J, Liu YX, Li S, Xu YF, Wei MY, Yang L, Chen LL. Altered nucleocytoplasmic export of adenosine-rich circRNAs by PABPC1 contributes to neuronal function. Mol Cell 2024; 84:2304-2319.e8. [PMID: 38838666 DOI: 10.1016/j.molcel.2024.05.011] [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: 11/16/2023] [Revised: 04/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
Circular RNAs (circRNAs) are upregulated during neurogenesis. Where and how circRNAs are localized and what roles they play during this process have remained elusive. Comparing the nuclear and cytoplasmic circRNAs between H9 cells and H9-derived forebrain (FB) neurons, we identify that a subset of adenosine (A)-rich circRNAs are restricted in H9 nuclei but exported to cytosols upon differentiation. Such a subcellular relocation of circRNAs is modulated by the poly(A)-binding protein PABPC1. In the H9 nucleus, newly produced (A)-rich circRNAs are bound by PABPC1 and trapped by the nuclear basket protein TPR to prevent their export. Modulating (A)-rich motifs in circRNAs alters their subcellular localization, and introducing (A)-rich circRNAs in H9 cytosols results in mRNA translation suppression. Moreover, decreased nuclear PABPC1 upon neuronal differentiation enables the export of (A)-rich circRNAs, including circRTN4(2,3), which is required for neurite outgrowth. These findings uncover subcellular localization features of circRNAs, linking their processing and function during neurogenesis.
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Affiliation(s)
- Shi-Meng Cao
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hao Wu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Hua Yuan
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yu-Hang Pan
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jun Zhang
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yu-Xin Liu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Siqi Li
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi-Feng Xu
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Meng-Yuan Wei
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ling-Ling Chen
- Key Laboratory of RNA Innovation, Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; New Cornerstone Science Laboratory, Shenzhen 518054, China.
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4
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Yellamaty R, Sharma S. Critical Cellular Functions and Mechanisms of Action of the RNA Helicase UAP56. J Mol Biol 2024; 436:168604. [PMID: 38729260 PMCID: PMC11168752 DOI: 10.1016/j.jmb.2024.168604] [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: 03/06/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Posttranscriptional maturation and export from the nucleus to the cytoplasm are essential steps in the normal processing of many cellular RNAs. The RNA helicase UAP56 (U2AF associated protein 56; also known as DDX39B) has emerged as a critical player in facilitating and co-transcriptionally linking these steps. Originally identified as a helicase involved in pre-mRNA splicing, UAP56 has been shown to facilitate formation of the A complex during spliceosome assembly. Additionally, it has been found to be critical for interactions between components of the exon junction and transcription and export complexes to promote the loading of export receptors. Although it appears to be structurally similar to other helicase superfamily 2 members, UAP56's ability to interact with multiple different protein partners allows it to perform its various cellular functions. Herein, we describe the structure-activity relationship studies that identified protein interactions of UAP56 and its human paralog URH49 (UAP56-related helicase 49; also known as DDX39A) and are beginning to reveal molecular mechanisms by which interacting proteins and substrate RNAs may regulate these helicases. We also provide an overview of reports that have demonstrated less well-characterized roles for UAP56, including R-loop resolution and telomere maintenance. Finally, we discuss studies that indicate a potential pathogenic effect of UAP56 in the development of autoimmune diseases and cancer, and identify the association of somatic and genetic mutations in UAP56 with neurodevelopmental disorders.
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Affiliation(s)
- Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA.
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5
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Choi SW, Nam JW. Optimal design of synthetic circular RNAs. Exp Mol Med 2024:10.1038/s12276-024-01251-w. [PMID: 38871815 DOI: 10.1038/s12276-024-01251-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/20/2024] [Accepted: 04/03/2024] [Indexed: 06/15/2024] Open
Abstract
Circular RNAs are an unusual class of single-stranded RNAs whose ends are covalently linked via back-splicing. Due to their versatility, the need to express circular RNAs in vivo and in vitro has increased. Efforts have been made to efficiently and precisely synthesize circular RNAs. However, a review on the optimization of the processes of circular RNA design, synthesis, and delivery is lacking. Our review highlights the multifaceted aspects considered when producing optimal circular RNAs and summarizes the available options for each step of exogenous circular RNA design and synthesis, including circularization strategies. Additionally, this review describes several potential applications of circular RNAs.
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Affiliation(s)
- Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Bio-BigData Center, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul, 04763, Republic of Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, Republic of Korea.
- Hanyang Institute of Advanced BioConvergence, Hanyang University, Seoul, 04763, Republic of Korea.
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6
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Liu X, Yao X, Chen L. Expanding roles of circRNAs in cardiovascular diseases. Noncoding RNA Res 2024; 9:429-436. [PMID: 38511061 PMCID: PMC10950605 DOI: 10.1016/j.ncrna.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/01/2024] [Accepted: 02/04/2024] [Indexed: 03/22/2024] Open
Abstract
CircRNAs are a class of single-stranded RNAs characterized by covalently looped structures. Emerging advances have promoted our understanding of circRNA biogenesis, nuclear export, biological functions, and functional mechanisms. Roles of circRNAs in diverse diseases have been increasingly recognized in the past decade, with novel approaches in bioinformatics analysis and new strategies in modulating circRNA levels, which have made circRNAs the hot spot for therapeutic applications. Moreover, due to the intrinsic features of circRNAs such as high stability, conservation, and tissue-/stage-specific expression, circRNAs are believed to be promising prognostic and diagnostic markers for diseases. Aiming cardiovascular disease (CVD), one of the leading causes of mortality worldwide, we briefly summarize the current understanding of circRNAs, provide the recent progress in circRNA functions and functional mechanisms in CVD, and discuss the future perspectives both in circRNA research and therapeutics based on existing knowledge.
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Affiliation(s)
- Xu Liu
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Xuelin Yao
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Liang Chen
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
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7
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Banerjee S, Nagasawa CK, Widen SG, Garcia-Blanco MA. Parsing the roles of DExD-box proteins DDX39A and DDX39B in alternative RNA splicing. Nucleic Acids Res 2024:gkae431. [PMID: 38801080 DOI: 10.1093/nar/gkae431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 05/01/2024] [Accepted: 05/12/2024] [Indexed: 05/29/2024] Open
Abstract
DExD-box RNA proteins DDX39A and DDX39B are highly homologous paralogs that are conserved in vertebrates. They are required for energy-driven reactions involved in RNA processing. Although we have some understanding of how their functions overlap in RNA nuclear export, our knowledge of whether or not these proteins have specific or redundant functions in RNA splicing is limited. Our previous work has shown that DDX39B is responsible for regulating the splicing of important immune transcripts IL7R and FOXP3. In this study, we aimed to investigate whether DDX39A, a highly homologous paralog of DDX39B, plays a similar role in regulating alternative RNA splicing. We find that DDX39A and DDX39B have significant redundancy in their gene targets, but there are targets that uniquely require one or the other paralog. For instance, DDX39A is incapable of complementing defective splicing of IL7R exon 6 when DDX39B is depleted. This exon and other cassette exons that specifically depend on DDX39B have U-poor/C-rich polypyrimidine tracts in the upstream intron and this variant polypyrimidine tract is required for DDX39B dependency. This study provides evidence that despite a high degree of functional redundancy, DDX39A and DDX39B are selectively required for the splicing of specific pre-mRNAs.
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Affiliation(s)
- Shefali Banerjee
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Chloe K Nagasawa
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
- Human Pathophysiology and Translational Medicine Program, Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX 77555-5302, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Mariano A Garcia-Blanco
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA 22903, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
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8
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Benitez MBM, Navarro YP, Azuara-Liceaga E, Cruz AT, Flores JV, Lopez-Canovas L. Circular RNAs and the regulation of gene expression in diabetic nephropathy (Review). Int J Mol Med 2024; 53:44. [PMID: 38516776 PMCID: PMC10998718 DOI: 10.3892/ijmm.2024.5368] [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: 10/06/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024] Open
Abstract
Circular RNAs (circRNAs) are non‑coding single‑stranded covalently closed RNA molecules that are considered important as regulators of gene expression at the transcriptional and post‑transcriptional levels. These molecules have been implicated in the initiation and progression of multiple human diseases, ranging from cancer to inflammatory and metabolic diseases, including diabetes mellitus and its vascular complications. The present article aimed to review the current knowledge on the biogenesis and functions of circRNAs, as well as their role in cell processes associated with diabetic nephropathy. In addition, novel potential interactions between circRNAs expressed in renal cells exposed to high‑glucose concentrations and the transcription factors c‑Jun and c‑Fos are reported.
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Affiliation(s)
- Maximo Berto Martinez Benitez
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Yussel Pérez Navarro
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Elisa Azuara-Liceaga
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Angeles Tecalco Cruz
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
| | - Jesús Valdés Flores
- Biochemistry Department, Center for Research and Advanced Studies, National Polytechnic Institute of Mexico, Mexico City, CP 07360, Mexico
| | - Lilia Lopez-Canovas
- Postgraduate Program in Genomic Sciences, Science and Technology School, Autonomous University of Mexico City, Mexico City, CP 03100, Mexico
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9
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Su R, Zhou M, Lin J, Shan G, Huang C. A circular RNA-gawky-chromatin regulatory axis modulates stress-induced transcription. Nucleic Acids Res 2024; 52:3702-3721. [PMID: 38416578 PMCID: PMC11039993 DOI: 10.1093/nar/gkae157] [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: 11/22/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
In response to heavy metal stress, the RNA-binding protein (RBP) gawky translocates into the nucleus and acts as a chromatin-interacting factor to activate the transcription of many stress-responsive genes. However, the upstream regulators of gawky-mediated transcription and their mechanistic details remain unknown. Here, we identified a class of metal-responsive element-containing circRNAs (MRE circRNAs) which specifically interact with gawky during copper stress. Using classic stress-responsive genes as a readout (Drosophila MT), we found that overexpression of MRE circRNAs led to a significant repression in stress-induced transcription. Mechanistically, MRE circRNAs promote the dissociation of gawky from chromatin and increase its aberrant cytoplasmic accumulation, which ultimately impedes the loading of RNA polymerase II to the active gene loci. The MRE motif serves as an important RNA regulon for maintaining the circRNA-gawky interaction, loss of which impaired the inhibitory effects of MRE circRNAs on gawky. Through RNA-seq analyses, we then identified over 500 additional stress-responsive genes whose induced transcription was attenuated upon MRE circRNA overexpression. Finally, we uncovered the physiological relevance of MRE circRNA-mediated regulation in cellular defense against copper overloading. Taken together, this study proposes that the circRNA-RBP-chromatin axis may represent a fundamental regulatory network for gene expression in eukaryotic cells.
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Affiliation(s)
- Rui Su
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Min Zhou
- Department of Obstetrics and Gynecology, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, China
- Department of Obstetrics and Gynecology, Chongqing Health Center for Women and Children, Chongqing 401147, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
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Li H, Tang Y, Ruan X, Zhang J, Liu H, Yu S, Chen H, Yang H, Zhang K, Chen K. N6-methyladenosine-modified circTEAD1 stabilizes Yap1 mRNA to promote chordoma tumorigenesis. Clin Transl Med 2024; 14:e1658. [PMID: 38659080 PMCID: PMC11043093 DOI: 10.1002/ctm2.1658] [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: 10/21/2023] [Revised: 03/26/2024] [Accepted: 03/30/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Chordoma, a rare bone tumour with aggressive local invasion and high recurrence rate with limited understanding of its molecular mechanisms. Circular RNAs (circRNAs) have been extensively implicated in tumorigenesis, yet their involvement in chordoma remains largely unexplored. N6-methyladenosine (m6A) modification holds a crucial function in regulating protein translation, RNA degradation and transcription. METHODS Initially, screening and validation of circTEAD1 in chordoma were conducted by high-throughput sequencing. Subsequently, sh-circTEAD1 and an overexpression plasmid were constructed. Colony formation assays, cell counting kit-8, Transwell and wound healing assays were utilized to validate the function of circTEAD1 in vitro. RNA pull-down assays identified the binding proteins of circTEAD1, which underwent verification through RNA immunoprecipitation (RIP). Methylated RIP assays were conducted to detect the m6A binding sites. Following this, luciferase assay, RT-qPCR, RIP and Western blotting analyses were conducted, revealing that Yap1 was the direct target of circTEAD1. Afterwards, the same methods were utilized for the validation of the function of Yap1 in chordoma in vitro. Finally, the regulatory relationship between circTEAD1 and Yap1 in chordoma was verified by an in vivo tumour formation assay. RESULTS CircTEAD1 was identified as an upregulated circRNA in chordoma specimens, with heightened circTEAD1 expression emerging as a prognostic indicator. In vitro experiments convincingly demonstrated that circTEAD1 significantly promoted chordoma cell invasion, migration and aggressiveness. Furthermore, the analysis revealed that methyltransferase-like 3-mediated m6A modification facilitated the cytoplasmic export of circTEAD1. The circTEAD1/IGF2BP3/Yap1 mRNA RNA-protein ternary complex not only bolstered the stability of Yap1 mRNA but also exerted a pivotal role in driving chordoma tumorigenesis. CONCLUSIONS In this study, the role of m6A-modified circTEAD1 in chordoma was identified. The findings offer novel insights into the potential molecular targets for chordoma therapy, shedding light on the intricate interplay between circRNAs, m6A modification and Yap1 mRNA in chordoma pathogenesis.
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Affiliation(s)
- Hanwen Li
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
| | - Yingchuang Tang
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
| | - Xingbang Ruan
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
| | - Junxin Zhang
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
| | - Hao Liu
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
| | - Shiyu Yu
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
| | - Hao Chen
- Institute of Translational Medicine, Medical CollegeYangzhou UniversityYangzhouPeople's Republic of China
| | - Huilin Yang
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
| | - Kai Zhang
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
| | - Kangwu Chen
- Department of Orthopedic SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouPeople's Republic of China
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11
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Ding W, Ding L, Lu Y, Sun W, Wang Y, Wang J, Gao Y, Li M. Circular RNA-circLRP6 protects cardiomyocyte from hypoxia-induced apoptosis by facilitating hnRNPM-mediated expression of FGF-9. FEBS J 2024; 291:1246-1263. [PMID: 38105623 DOI: 10.1111/febs.17038] [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: 04/18/2023] [Revised: 09/30/2023] [Accepted: 12/15/2023] [Indexed: 12/19/2023]
Abstract
Coronary atherosclerosis-induced myocardial ischemia leads to cardiomyocyte apoptosis. The regulatory mechanisms for cardiomyocyte apoptosis have not been fully understood. Circular RNAs are non-coding RNAs which play important roles in heart function maintenance and progression of heart diseases by regulating gene transcription and protein translation. Here, we reported a conserved cardiac circular RNA, which is generated from the second exon of LRP6 and named circLRP62-2 . CircLRP62-2 can protect cardiomyocyte from hypoxia-induced apoptosis. The expression of circLRP62-2 in cardiomyocytes was down-regulated under hypoxia, while forced expression of circLRP62-2 inhibited cell apoptosis. Normally, circLRP62-2 was mainly localized in the nucleus. Under hypoxia, circLRP62-2 is associated with heterogeneous nuclear ribonucleoprotein M (hnRNPM) to be translocated into the cytoplasm. It recruited hnRNPM to fibroblast growth factor 9 (FGF9) mRNA to enhance the expression of FGF9 protein, promoting hypoxia-adaption and viability of cardiomyocytes. In summary, this study uncovers a new inhibitor of apoptosis and reveals a novel anti-apoptotic pathway composed of circLRP62-2 , hnRNPM, and FGF9, which may provide therapeutic targets for coronary heart disease and ischemic myocardial injury.
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Affiliation(s)
- Wei Ding
- The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, China
| | - Lin Ding
- School of Basic Medical Sciences, Qingdao University, China
| | - Yijian Lu
- School of Basic Medical Sciences, Qingdao University, China
| | - Weihan Sun
- School of Basic Medical Sciences, Qingdao University, China
| | - Yu Wang
- School of Basic Medical Sciences, Qingdao University, China
| | - Jianxun Wang
- School of Basic Medical Sciences, Qingdao University, China
| | - Yufang Gao
- The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, China
| | - Mengyang Li
- School of Basic Medical Sciences, Qingdao University, China
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12
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Jin T, Wang H, Liu Y, Wang H. Circular RNAs: Regulators of endothelial cell dysfunction in atherosclerosis. J Mol Med (Berl) 2024; 102:313-335. [PMID: 38265445 DOI: 10.1007/s00109-023-02413-5] [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: 08/03/2023] [Revised: 12/09/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024]
Abstract
Endothelial cell (EC) dysfunction is associated with atherosclerosis. Circular RNAs (circRNAs) are covalently closed loops formed by back-splicing, are highly expressed in a tissue-specific or cell-specific manner, and regulate ECs mainly through miRNAs (mircoRNAs) or protein sponges. This review describes the regulatory mechanisms and physiological functions of circRNAs, as well as the differential expression of circRNAs in aberrant ECs. This review focuses on their roles in inflammation, proliferation, migration, angiogenesis, apoptosis, senescence, and autophagy in ECs from the perspective of signaling pathways, such as nuclear factor κB (NF-κB), nucleotide-binding domain, leucine-rich-repeat family, pyrin-domain-containing 3 (NLRP3)/caspase-1, Janus kinase/signal transducer and activator of transcription (JAK/STAT), and phosphoinositide-3 kinase/protein kinase B (PI3K/Akt). Finally, we address the issues and recent advances in circRNAs as well as circRNA-mediated regulation of ECs to improve our understanding of the molecular mechanisms underlying the progression of atherosclerosis and provide a reference for studies on circRNAs that regulate EC dysfunction and thus affect atherosclerosis.
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Affiliation(s)
- Tengyu Jin
- Hebei Medical University, Shijiazhuang 050011, Hebei, China
- Hebei General Hospital, Affiliated to Hebei Medical University, Shijiazhuang 050051, Hebei, China
| | - Haoyuan Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Yuelin Liu
- Hebei Medical University, Shijiazhuang 050011, Hebei, China
| | - Hebo Wang
- Hebei Medical University, Shijiazhuang 050011, Hebei, China.
- Hebei General Hospital, Affiliated to Hebei Medical University, Shijiazhuang 050051, Hebei, China.
- Hebei Provincial Key Laboratory of Cerebral Networks and Cognitive Disorders, Shijiazhuang 050051, Hebei, China.
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13
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Ngo LH, Bert AG, Dredge BK, Williams T, Murphy V, Li W, Hamilton WB, Carey KT, Toubia J, Pillman KA, Liu D, Desogus J, Chao JA, Deans AJ, Goodall GJ, Wickramasinghe VO. Nuclear export of circular RNA. Nature 2024; 627:212-220. [PMID: 38355801 DOI: 10.1038/s41586-024-07060-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
Circular RNAs (circRNAs), which are increasingly being implicated in a variety of functions in normal and cancerous cells1-5, are formed by back-splicing of precursor mRNAs in the nucleus6-10. circRNAs are predominantly localized in the cytoplasm, indicating that they must be exported from the nucleus. Here we identify a pathway that is specific for the nuclear export of circular RNA. This pathway requires Ran-GTP, exportin-2 and IGF2BP1. Enhancing the nuclear Ran-GTP gradient by depletion or chemical inhibition of the major protein exporter CRM1 selectively increases the nuclear export of circRNAs, while reducing the nuclear Ran-GTP gradient selectively blocks circRNA export. Depletion or knockout of exportin-2 specifically inhibits nuclear export of circRNA. Analysis of nuclear circRNA-binding proteins reveals that interaction between IGF2BP1 and circRNA is enhanced by Ran-GTP. The formation of circRNA export complexes in the nucleus is promoted by Ran-GTP through its interactions with exportin-2, circRNA and IGF2BP1. Our findings demonstrate that adaptors such as IGF2BP1 that bind directly to circular RNAs recruit Ran-GTP and exportin-2 to export circRNAs in a mechanism that is analogous to protein export, rather than mRNA export.
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Affiliation(s)
- Linh H Ngo
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew G Bert
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Adelaide Centre for Epigenetics, School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Tobias Williams
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Vincent Murphy
- Genome Stability Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Wanqiu Li
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine and Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - William B Hamilton
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kirstyn T Carey
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - John Toubia
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia
| | - Dawei Liu
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Jessica Desogus
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andrew J Deans
- Genome Stability Unit, St Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia.
- Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, Australia.
- Department of Medicine, University of Adelaide, Adelaide, South Australia, Australia.
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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14
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Marijan D, Momchilova EA, Burns D, Chandhok S, Zapf R, Wille H, Potoyan DA, Audas TE. Protein thermal sensing regulates physiological amyloid aggregation. Nat Commun 2024; 15:1222. [PMID: 38336721 PMCID: PMC10858206 DOI: 10.1038/s41467-024-45536-0] [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: 05/24/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
To survive, cells must respond to changing environmental conditions. One way that eukaryotic cells react to harsh stimuli is by forming physiological, RNA-seeded subnuclear condensates, termed amyloid bodies (A-bodies). The molecular constituents of A-bodies induced by different stressors vary significantly, suggesting this pathway can tailor the cellular response by selectively aggregating a subset of proteins under a given condition. Here, we identify critical structural elements that regulate heat shock-specific amyloid aggregation. Our data demonstrates that manipulating structural pockets in constituent proteins can either induce or restrict their A-body targeting at elevated temperatures. We propose a model where selective aggregation within A-bodies is mediated by the thermal stability of a protein, with temperature-sensitive structural regions acting as an intrinsic form of post-translational regulation. This system would provide cells with a rapid and stress-specific response mechanism, to tightly control physiological amyloid aggregation or other cellular stress response pathways.
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Affiliation(s)
- Dane Marijan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Evgenia A Momchilova
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Daniel Burns
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Sahil Chandhok
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Richard Zapf
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta, T6G 2M8, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Alberta, T6G 2E1, Canada
| | - Davit A Potoyan
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Chemistry, Iowa State University, Ames, IA, 50011, USA
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
- Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
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15
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Surendran A, Huang C, Liu L. Circular RNAs and their roles in idiopathic pulmonary fibrosis. Respir Res 2024; 25:77. [PMID: 38321530 PMCID: PMC10848557 DOI: 10.1186/s12931-024-02716-2] [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] [Received: 10/11/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with limited treatment options. Circular RNAs (circRNAs) have emerged as a novel class of non-coding RNAs with diverse functions in cellular processes. This review paper aims to explore the potential involvement of circRNAs in the pathogenesis of IPF and their diagnostic and therapeutic implications. We begin by providing an overview of the epidemiology and risk factors associated with IPF, followed by a discussion of the pathophysiology underlying this complex disease. Subsequently, we delve into the history, types, biogenesis, and functions of circRNAs and then emphasize their regulatory roles in the pathogenesis of IPF. Furthermore, we examine the current methodologies for detecting circRNAs and explore their diagnostic applications in IPF. Finally, we discuss the potential utility of circRNAs in the treatment of IPF. In conclusion, circRNAs hold great promise as novel biomarkers and therapeutic targets in the management of IPF.
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Affiliation(s)
- Akshaya Surendran
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Chaoqun Huang
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lin Liu
- The Lundberg-Kienlen Lung Biology and Toxicology Laboratory, Department of Physiological Sciences, Oklahoma State University, 264 McElroy Hall, Stillwater, OK, 74078, USA.
- Oklahoma Center for Respiratory and Infectious Diseases, Oklahoma State University, Stillwater, Oklahoma, USA.
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16
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Xie Q, Ma Y, Ren Z, Gu T, Jiang Z. Circular RNA: A new expectation for cardiovascular diseases. J Cell Biochem 2024; 125:e30512. [PMID: 38098251 DOI: 10.1002/jcb.30512] [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: 07/18/2023] [Revised: 11/14/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024]
Abstract
Circular RNA (circRNA) is a class of RNA with the 5' and 3' ends connected covalently to form a closed loop structure and characterized by high stability, conserved sequences and tissue specificity, which is caused by special reverse splicing methods. Currently, it has become a hot spot for research. With the discovery of its powerful regulatory functions and roles, the molecular mechanisms and future value of circRNA in participating in and regulating biological and pathological processes are becoming increasingly apparent. Among them is the increasing prevalence of cardiovascular diseases (CVDs). Many studies have elucidated that circRNA plays a crucial role in the development and progression of CVDs. Therefore, circRNA shows its advantages and brilliant expectations in the field of CVDs. In this review, we describe the biogenesis, bioinformatics detection and function of circRNA and discuss the role of circRNA and its effects on CVDs, including atherosclerosis, myocardial infarction, cardiac hypertrophy and heart failure, myocardial fibrosis, cardiac senescence, pulmonary hypertension, and diabetic cardiomyopathy by different mechanisms. That shows circRNA advantages and brilliant expectations in the field of CVDs.
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Affiliation(s)
- Qiao Xie
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Yun Ma
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Zhong Ren
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Tianhe Gu
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Zhisheng Jiang
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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17
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Zhou M, Li S, Huang C. Physiological and pathological functions of circular RNAs in the nervous system. Neural Regen Res 2024; 19:342-349. [PMID: 37488888 PMCID: PMC10503630 DOI: 10.4103/1673-5374.379017] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/20/2023] [Accepted: 05/29/2023] [Indexed: 07/26/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of covalently closed single-stranded RNAs that are expressed during the development of specific cells and tissues. CircRNAs play crucial roles in physiological and pathological processes by sponging microRNAs, modulating gene transcription, controlling the activity of certain RNA-binding proteins, and producing functional peptides. A key focus of research at present is the functionality of circRNAs in the nervous system and several advances have emerged over the last 2 years. However, the precise role of circRNAs in the nervous system has yet to be comprehensively reviewed. In this review, we first summarize the recently described roles of circRNAs in brain development, maturity, and aging. Then, we focus on the involvement of circRNAs in various diseases of the central nervous system, such as brain cancer, chronic neurodegenerative diseases, acute injuries of the nervous system, and neuropathic pain. A better understanding of the functionality of circRNAs will help us to develop potential diagnostic, prognostic, and therapeutic strategies to treat diseases of the nervous system.
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Affiliation(s)
- Min Zhou
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, China
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18
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Xie C, Hao X, Yuan H, Wang C, Sharif R, Yu H. Crosstalk Between circRNA and Tumor Microenvironment of Hepatocellular Carcinoma: Mechanism, Function and Applications. Onco Targets Ther 2024; 17:7-26. [PMID: 38283733 PMCID: PMC10812140 DOI: 10.2147/ott.s437536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common aggressive tumors in the world. Despite the availability of various treatments, its prognosis remains poor due to the lack of specific diagnostic indicators and the high heterogeneity of HCC cases. CircRNAs are noncoding RNAs with stable and highly specific expression. Extensive research evidence suggests that circRNAs mediate the pathogenesis and progression of HCC through acting as miRNA sponges, protein modulators, and translation templates. Tumor microenvironment (TME) has become a hotspot of immune-related research in recent years due to its effects on metabolism, secretion and immunity of HCC. Accordingly, understanding the role played by circRNAs in TME is important for the study of HCC. This review will discuss the crosstalk between circRNAs and TME in HCC. In addition, we will discuss the current deficiencies and controversies in research on circRNAs and predict future research directions.
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Affiliation(s)
- Chenxi Xie
- Hepatobiliary Center, Department of Hepatobiliary Surgery, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Xiaopei Hao
- The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, 450008, People’s Republic of China
| | - Hao Yuan
- Hepatobiliary Center, Department of Hepatobiliary Surgery, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Chongyu Wang
- The First Clinical Medical College of Xuzhou Medical University, Xuzhou, People’s Republic of China
| | - Razinah Sharif
- Center for Healthy Ageing & Wellness, Faculty of Health Sciences, University Kebangsaan Malaysia, Kuala Lumpur, 50300, Malaysia
- Biocompatibility Laboratory, Centre for Research and Instrumentation, University Kebangsaan Malaysia, UKM, Bangi, Selangor Darul Ehsan, 43600, Malaysia
| | - Haibo Yu
- Hepatobiliary Center, Department of Hepatobiliary Surgery, People’s Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
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19
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Fujita KI, Ito M, Irie M, Harada K, Fujiwara N, Ikeda Y, Yoshioka H, Yamazaki T, Kojima M, Mikami B, Mayeda A, Masuda S. Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes. Nat Commun 2024; 15:455. [PMID: 38225262 PMCID: PMC10789772 DOI: 10.1038/s41467-023-44217-8] [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: 04/23/2023] [Accepted: 12/05/2023] [Indexed: 01/17/2024] Open
Abstract
mRNA export is an essential pathway for the regulation of gene expression. In humans, closely related RNA helicases, UAP56 and URH49, shape selective mRNA export pathways through the formation of distinct complexes, known as apo-TREX and apo-AREX complexes, and their subsequent remodeling into similar ATP-bound complexes. Therefore, defining the unidentified components of the apo-AREX complex and elucidating the molecular mechanisms underlying the formation of distinct apo-complexes is key to understanding their functional divergence. In this study, we identify additional apo-AREX components physically and functionally associated with URH49. Furthermore, by comparing the structures of UAP56 and URH49 and performing an integrated analysis of their chimeric mutants, we exhibit unique structural features that would contribute to the formation of their respective complexes. This study provides insights into the specific structural and functional diversification of these two helicases that diverged from the common ancestral gene Sub2.
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Affiliation(s)
- Ken-Ichi Fujita
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan.
- Division of Gene Expression Mechanism, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan.
- Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Misa Ito
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Midori Irie
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Kotaro Harada
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Naoko Fujiwara
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Yuya Ikeda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Hanae Yoshioka
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Tomohiro Yamazaki
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Masaki Kojima
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Bunzo Mikami
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, 611-0011, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, 611-0011, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Center for Medical Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto, Kyoto, 606-8502, Japan.
- Department of Food Science and Nutrition, Faculty of Agriculture Kindai University, Nara, Nara, 631-8505, Japan.
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Nara, 631-8505, Japan.
- Antiaging Center, Kindai University, Higashiosaka, Osaka, 577-8502, Japan.
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20
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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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21
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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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22
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Fu P, Yin S, Cheng H, Xu W, Jiang J. Engineered Exosomes for Drug Delivery in Cancer Therapy: A Promising Approach and Application. Curr Drug Deliv 2024; 21:817-827. [PMID: 37438904 DOI: 10.2174/1567201820666230712103942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/01/2023] [Accepted: 06/13/2023] [Indexed: 07/14/2023]
Abstract
A significant amount of research effort is currently focused on investigating the role of exosomes in various cancers. These tiny vesicles, apart from acting as biomarkers, also play a crucial role in tumor formation and development. Several studies have demonstrated that exosomes can be a drug delivery vehicle for cancer therapy. In this paper, we highlight the key advantages of exosomes as a drug delivery candidate, with a particular focus on their low immunogenicity, natural targeting ability and suitable mechanical properties. Furthermore, we propose that the selection of appropriate exosomes and drug loading methods based on therapeutic goals and product heterogeneity is essential for preparing engineered exosomes. We comprehensively analyzed the superiorities of current drug-loading methods to improve the creation of designed exosomes. Moreover, we systematically review the applications of engineered exosomes in various therapies such as immunotherapy, gene therapy, protein therapy, chemotherapy, indicating that engineered exosomes have the potential to be reliable and, safe drug carriers that can address the unmet needs in cancer clinical practice.
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Affiliation(s)
- Peiwen Fu
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China
- Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Siqi Yin
- Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Huiying Cheng
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China
- Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Wenrong Xu
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China
- Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jiajia Jiang
- Aoyang Cancer Institute, Affiliated Aoyang Hospital of Jiangsu University, Zhangjiagang, 215600, Jiangsu, China
- Jiangsu Province Key Laboratory of Medical Science and Laboratory Medicine, Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
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23
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Tang S, Cai L, Wang Z, Pan D, Wang Q, Shen Y, Zhou Y, Chen Q. Emerging roles of circular RNAs in the invasion and metastasis of head and neck cancer: Possible functions and mechanisms. CANCER INNOVATION 2023; 2:463-487. [PMID: 38125767 PMCID: PMC10730008 DOI: 10.1002/cai2.50] [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: 10/20/2022] [Revised: 11/27/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2023]
Abstract
Head and neck cancer (HNC) is the seventh most prevalent malignancy worldwide in 2020. Cancer metastasis is the main cause of poor prognosis in HNC patients. Recently, circular RNAs (circRNAs), initially thought to have no biological function, are attracting increasing attention, and their crucial roles in mediating HNC metastasis are being extensively investigated. Existing studies have shown that circRNAs primarily function through miRNA sponges, transcriptional regulation, interacting with RNA-binding proteins (RBPs) and as translation templates. Among these functions, the function of miRNA sponge is the most prominent. In this review, we summarized the reported circRNAs involved in HNC metastasis, aiming to elucidate the regulatory relationship between circRNAs and HNC metastasis. Furthermore, we summarized the latest advances in the epidemiological information of HNC metastasis and the tumor metastasis theories, the biogenesis, characterization and functional mechanisms of circRNAs, and their potential clinical applications. Although the research on circRNAs is still in its infancy, circRNAs are expected to serve as prognostic markers and effective therapeutic targets to inhibit HNC metastasis and significantly improve the prognosis of HNC patients.
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Affiliation(s)
- Shouyi Tang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Luyao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Zhen Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Dan Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Qing Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Yingqiang Shen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
| | - Yu Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
- State Institute of Drug/Medical Device Clinical TrialWest China Hospital of StomatologyChengduChina
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of StomatologySichuan UniversityChengduChina
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24
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Li Z, Ren Y, Lv Z, Li M, Li Y, Fan X, Xiong Y, Qian L. Decrypting the circular RNAs does a favor for us: Understanding, diagnosing and treating diabetes mellitus and its complications. Biomed Pharmacother 2023; 168:115744. [PMID: 37862970 DOI: 10.1016/j.biopha.2023.115744] [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: 07/11/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
Circular RNAs (circRNAs), a novel type of single-stranded noncoding RNAs with a covalently closed loop structure, are generated in a circular conformation via non-canonical splicing or back-splicing events. Functionally, circRNAs have been elucidated to soak up microRNAs (miRNAs) and RNA binding proteins (RBPs), serve as protein scaffolds, maintain mRNA stability, and regulate gene transcription and translation. Notably, circRNAs are strongly implicated in the regulation of β-cell functions, insulin resistance, adipocyte functions, inflammation as well as oxidative stress via acting as miRNA sponges and RBP sponges. Basic and clinical studies have demonstrated that aberrant alterations of circRNAs expressions are strongly associated with the initiation and progression of diabetes mellitus (DM) and its complications. Here in this review, we present a summary of the biogenesis, transportation, degradation and functions of circRNAs, and highlight the recent findings on circRNAs and their action mechanisms in DM and its complications. Overall, this review should contribute greatly to our understanding of circRNAs in DM pathogenesis, offering insights into the further perspectives of circRNAs for DM diagnosis and therapy.
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Affiliation(s)
- Zi Li
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, PR China
| | - Yuanyuan Ren
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, PR China
| | - Ziwei Lv
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, PR China
| | - Man Li
- Department of Endocrinology, Xi' an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China
| | - Yujia Li
- Department of Endocrinology, Xi' an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China
| | - Xiaobin Fan
- Department of Obstetrics and Gynecology, Xi' an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China
| | - Yuyan Xiong
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, PR China.
| | - Lu Qian
- Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China; Department of Endocrinology, Xi' an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi, PR China.
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25
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Wang S, Pan C, Sheng H, Yang M, Yang C, Feng X, Hu C, Ma Y. Construction of a molecular regulatory network related to fat deposition by multi-tissue transcriptome sequencing of Jiaxian red cattle. iScience 2023; 26:108346. [PMID: 38026203 PMCID: PMC10665818 DOI: 10.1016/j.isci.2023.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/26/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Intramuscular fat (IMF) refers to the fat that accumulates between muscle bundles or within muscle cells, whose content significantly impacts the taste, tenderness, and flavor of meat products, making it a crucial economic characteristic in livestock production. However, the intricate mechanisms governing IMF deposition, involving non-coding RNAs (ncRNAs), genes, and complex regulatory networks, remain largely enigmatic. Identifying adipose tissue-specific genes and ncRNAs is paramount to unravel these molecular mysteries. This study, conducted on Jiaxian red cattle, harnessed whole transcriptome sequencing to unearth the nuances of circRNAs and miRNAs across seven distinct tissues. The interplay of these ncRNAs was assessed through differential expression analysis and network analysis. These findings are not only pivotal in unveiling the intricacies of fat deposition mechanisms but also lay a robust foundation for future research, setting the stage for enhancing IMF content in Jiaxian red cattle breeding.
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Affiliation(s)
- Shuzhe Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Hui Sheng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Mengli Yang
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chaoyun Yang
- Xichang College, Liangshan Prefecture, Sichuan Province, China
| | - Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chunli Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
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26
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Tapescu I, Taschuk F, Pokharel SM, Zginnyk O, Ferretti M, Bailer PF, Whig K, Madden EA, Heise MT, Schultz DC, Cherry S. The RNA helicase DDX39A binds a conserved structure in chikungunya virus RNA to control infection. Mol Cell 2023; 83:4174-4189.e7. [PMID: 37949067 PMCID: PMC10722560 DOI: 10.1016/j.molcel.2023.10.008] [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: 10/17/2022] [Revised: 04/25/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
Alphaviruses are a large group of re-emerging arthropod-borne RNA viruses. The compact viral RNA genomes harbor diverse structures that facilitate replication. These structures can be recognized by antiviral cellular RNA-binding proteins, including DExD-box (DDX) helicases, that bind viral RNAs to control infection. The full spectrum of antiviral DDXs and the structures that are recognized remain unclear. Genetic screening identified DDX39A as antiviral against the alphavirus chikungunya virus (CHIKV) and other medically relevant alphaviruses. Upon infection, the predominantly nuclear DDX39A accumulates in the cytoplasm inhibiting alphavirus replication, independent of the canonical interferon pathway. Biochemically, DDX39A binds to CHIKV genomic RNA, interacting with the 5' conserved sequence element (5'CSE), which is essential for the antiviral activity of DDX39A. Altogether, DDX39A relocalization and binding to a conserved structural element in the alphavirus genomic RNA attenuates infection, revealing a previously unknown layer to the cellular control of infection.
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Affiliation(s)
- Iulia Tapescu
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Biochemistry and Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Frances Taschuk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Swechha M Pokharel
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oleksandr Zginnyk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Max Ferretti
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter F Bailer
- Biochemistry and Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, USA
| | - Kanupryia Whig
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily A Madden
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - Mark T Heise
- Department of Microbiology and Immunology, UNC-Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sara Cherry
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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27
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Li J, Cao H, Yang J, Wang B. CircCDK1 blocking IGF2BP2-mediated m6A modification of CPPED1 promotes laryngeal squamous cell carcinoma metastasis via the PI3K/AKT signal pathway. Gene 2023; 884:147686. [PMID: 37543219 DOI: 10.1016/j.gene.2023.147686] [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: 05/12/2023] [Revised: 07/05/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
BACKGROUND Circular RNA (circRNA) is a novel noncoding RNA (ncRNA) that plays a critical role in various cancers. However, the clinical significance, biological function, and molecular mechanisms of circRNAs in laryngeal squamous cell carcinoma (LSCC) remain unclear. METHODS A circRNA array was performed to identify the differentially expressed circRNAs. In vitro and in vivo assays were proceeded to verify the biological function of circCDK1 in LSCC. RNA pulldown assays and RNA immunoprecipitation (RIP) were used to confirm the binding between circCDK1 and insulin-like growth factor 2 mRNA binding protein 2(IGF2BP2). The MeRIP assay was then used to identified the N6-methyladenisine (m6A) methylation of calcineurin like phosphatase domain containing1 (CPPED1). RESULTS Hsa_circ_0005774 (circCDK1) was found upregulated in LSCC tissues compared to adjacent normal tissues. The level of circCDK1 was positively correlated with poor prognosisof LSCC patients. In vitro and in vivo, circCDK1 promoted migration and invasion of LSCC cells. Mechanistically, eukaryotic translation initiation factor4A3(EIF4A3) induced biogenesis of circCDK1 by binding to its flanking. By competitively binding to IGF2BP2, circCDK1 blocked the m6A modification of CPPED1 in IGF2BP2-dependent manner. Moreover, the circCDK1-mediated decrease of CPPED1 activated the PI3K/AKT signal pathway to facilitate progression of LSCC. CONCLUSIONS Our findings demonstrated that EIF4A3-induced upregulation of circCDK1 promoted LSCC metastasis via EIF4A3-circCDK1-IGF2BP2-CPPED1 to activate PI3K-AKT signal pathway. CircCDK1 might serve as a new diagnostic and prognostic marker or potential therapeutic target for LSCC.
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Affiliation(s)
- Jinling Li
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Huan Cao
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Jianwang Yang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Baoshan Wang
- Department of Otorhinolaryngology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
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28
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Singh S, Sinha T, Panda AC. Regulation of microRNA by circular RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1820. [PMID: 37783567 DOI: 10.1002/wrna.1820] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/04/2023]
Abstract
Circular (circ)RNAs have emerged as novel regulators of gene expression through various mechanisms. However, most publications focus on functional circRNAs regulating target gene expression by interacting with micro (mi)RNAs and acting as competing endogenous RNAs (ceRNAs). Although the theory of miRNA sponging by ceRNAs suggests the inhibition of miRNA activity, many studies are biased toward the selection of miRNAs showing a reverse expression pattern compared with circRNA expression. Although several computational tools and molecular assays have been used to predict and validate the interaction of miRNAs with circRNAs, the actual validation of functional in vivo interactions needs careful consideration of molecular experiments with specific controls. As extensive research is being performed on circRNA, many questions arise on the functional significance of circRNA-miRNA interactions. We hope the critical discussion on the criteria for selecting circRNA-miRNA pairs for functional analysis and providing standard methods for validating circRNA-miRNA interactions will advance our understanding of circRNAs as novel gene regulators. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Translation > Regulation RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Suman Singh
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Tanvi Sinha
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
| | - Amaresh C Panda
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha, India
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29
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Feng T, Li S, Zhao G, Li Q, Yuan H, Zhang J, Gu R, Ou D, Guo Y, Kou Q, Wang Q, Li K, Lin P. DDX39B facilitates the malignant progression of hepatocellular carcinoma via activation of SREBP1-mediated de novo lipid synthesis. Cell Oncol (Dordr) 2023; 46:1235-1252. [PMID: 37052853 DOI: 10.1007/s13402-023-00807-8] [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] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
PURPOSE The detailed molecular mechanisms of aberrant lipid metabolism in HCC remain unclear. Herein, we focused on the potential role of DDX39B in aberrant lipogenesis and malignant development in HCC. METHODS DDX39B expression in HCC and para-cancer tissues was measured by immunohistochemistry. CCK-8, colony formation and Transwell assays were utilized to detect HCC cell proliferation, migration and invasion in vitro. Oil red O and Nile red staining and triglyceride and cholesterol detection were used to measure lipogenesis. Coimmunoprecipitation was used to detect interactions between DDX39B and SREBP1. Immunofluorescence assays were performed to investigate the impact of DDX39B on SREBP1 nuclear translocation. A luciferase assay was used to explore the transcriptional activity of SREBP1. The subcutaneous and orthotopic xenograft models in nude mice were generated to verify the contribution of the DDX39B/SREBP1 axis to tumor growth, lung metastasis and lipid synthesis in vivo. RESULTS DDX39B is upregulated in HCC tissues and predicts a worse prognosis. Upregulated DDX39B contributes to the proliferation, metastasis and lipogenesis of HCC cells. Mechanistically, DDX39B directly interacts with SREBP1, and silencing DDX39B impairs the stabilization of the SREBP1 protein through FBXW7-mediated ubiquitination and degradation of SREBP1. Furthermore, DDX39B deficiency decreases the nuclear translocation and activation of SREBP1 and transcription of SREBP1 downstream genes, resulting in reduced lipid accumulation. CONCLUSIONS Our study reveals a novel mechanism by which DDX39B facilitates the malignant progression of HCC via activation of SREBP1-mediated de novo lipogenesis, implicating DDX39B as both a potential predictor of recurrence and prognosis and a promising therapeutic target.
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Affiliation(s)
- Tianyu Feng
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Siqi Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Gang Zhao
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Qin Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Hang Yuan
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Jie Zhang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Rui Gu
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Deqiong Ou
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Yafei Guo
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Qiming Kou
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Qijing Wang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Kai Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China.
- Hi-Tech Development, 1# Keyuan 4 Road, Gaopeng Avenue, Chengdu, Sichuan, 610041, People's Republic of China.
| | - Ping Lin
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center and Lab of Experimental Oncology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan Province, China.
- Hi-Tech Development, 1# Keyuan 4 Road, Gaopeng Avenue, Chengdu, Sichuan, 610041, People's Republic of China.
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30
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Abidin SZ, Mat Pauzi NA, Mansor NI, Mohd Isa NI, Hamid AA. A new perspective on Alzheimer's disease: microRNAs and circular RNAs. Front Genet 2023; 14:1231486. [PMID: 37790702 PMCID: PMC10542399 DOI: 10.3389/fgene.2023.1231486] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/25/2023] [Indexed: 10/05/2023] Open
Abstract
microRNAs (miRNAs) play a multifaceted role in the pathogenesis of Alzheimer's disease (AD). miRNAs regulate several aspects of the disease, such as Aβ metabolism, tau phosphorylation, neuroinflammation, and synaptic function. The dynamic interaction between miRNAs and their target genes depends upon various factors, including the subcellular localization of miRNAs, the relative abundance of miRNAs and target mRNAs, and the affinity of miRNA-mRNA interactions. The miRNAs are released into extracellular fluids and subsequently conveyed to specific target cells through various modes of transportation, such as exosomes. In comparison, circular RNAs (circRNAs) are non-coding RNA (ncRNA) characterized by their covalently closed continuous loops. In contrast to linear RNA, RNA molecules are circularized by forming covalent bonds between the 3'and 5'ends. CircRNA regulates gene expression through interaction with miRNAs at either the transcriptional or post-transcriptional level, even though their precise functions and mechanisms of gene regulation remain to be elucidated. The current stage of research on miRNA expression profiles for diagnostic purposes in complex disorders such as Alzheimer's disease is still in its early phase, primarily due to the intricate nature of the underlying pathological causes, which encompass a diverse range of pathways and targets. Hence, this review comprehensively addressed the alteration of miRNA expression across diverse sources such as peripheral blood, exosome, cerebrospinal fluid, and brain in AD patients. This review also addresses the nascent involvement of circRNAs in the pathogenesis of AD and their prospective utility as biomarkers and therapeutic targets for these conditions in future research.
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Affiliation(s)
- Shahidee Zainal Abidin
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Terengganu, Malaysia
- Biological Security and Sustainability (BIOSIS) Research Interest Group, Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Nurul Asykin Mat Pauzi
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Nur Izzati Mansor
- Department of Nursing, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Nurul Iffah Mohd Isa
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Adila A. Hamid
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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31
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Shao JL, Wang LJ, Xiao J, Yang JF. Non-coding RNAs: The potential biomarker or therapeutic target in hepatic ischemia-reperfusion injury. World J Gastroenterol 2023; 29:4927-4941. [PMID: 37731999 PMCID: PMC10507504 DOI: 10.3748/wjg.v29.i33.4927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/22/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023] Open
Abstract
Hepatic ischemia-reperfusion injury (HIRI) is the major complication of liver surgery and liver transplantation, that may increase the postoperative morbidity, mortality, tumor progression, and metastasis. The underlying mechanisms have been extensively investigated in recent years. Among these, oxidative stress, inflammatory responses, immunoreactions, and cell death are the most studied. Non-coding RNAs (ncRNAs) are defined as the RNAs that do not encode proteins, but can regulate gene expressions. In recent years, ncRNAs have emerged as research hotspots for various diseases. During the progression of HIRI, ncRNAs are differentially expressed, while these dysregulations of ncRNAs, in turn, have been verified to be related to the above pathological processes involved in HIRI. ncRNAs mainly contain microRNAs, long ncRNAs, and circular RNAs, some of which have been reported as biomarkers for early diagnosis or assessment of liver damage severity, and as therapeutic targets to attenuate HIRI. Here, we briefly summarize the common pathophysiology of HIRI, describe the current knowledge of ncRNAs involved in HIRI in animal and human studies, and discuss the potential of ncRNA-targeted therapeutic strategies. Given the scarcity of clinical trials, there is still a long way to go from pre-clinical to clinical application, and further studies are needed to uncover their potential as therapeutic targets.
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Affiliation(s)
- Jia-Li Shao
- Department of Anesthesiology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, China
| | - Li-Juan Wang
- Department of Anesthesiology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, China
| | - Ji Xiao
- Department of Anesthesiology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, China
| | - Jin-Feng Yang
- Department of Anesthesiology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, China
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Wang J, Zhang Y, Li Z. Advancements in Understanding the Role of Circular RNA in Osteosarcoma. Mol Biotechnol 2023:10.1007/s12033-023-00838-4. [PMID: 37661210 DOI: 10.1007/s12033-023-00838-4] [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: 02/06/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023]
Abstract
Osteosarcoma, the most prevalent primary malignant bone tumor and the third most frequent cancer in children and adolescents worldwide, still poses a significant therapeutic challenge. Even though combined chemotherapy and surgical resection have improved survival rates up to 60%, the prognosis for most patients with metastatic osteosarcoma continues to be dismal. The specific pathogenesis and key regulators of tumor invasion and metastasis remain largely elusive. Circular RNAs (circRNAs), novel endogenous non-coding RNA molecules that form covalently closed continuous loops through splicing, play a crucial role in the development, progression, clinical diagnosis, and treatment of various diseases. Recently, an escalating number of circular structures have been identified in osteosarcoma. Understanding their role in osteosarcoma is advantageous for early detection, diagnosis, and treatment of this disease. The primary function of circRNA involves its unique ability to bind specifically to miRNA, although their biological functions also extend to interacting with proteins, regulating gene transcription, and serving as translation templates. In this review, we explore the mechanisms and clinical applications of circRNAs in the pathogenesis and progression of osteosarcoma, with a particular emphasis on the regulatory mechanisms and functions of circRNAs as miRNA sponges in osteosarcoma development.
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Affiliation(s)
- Jin Wang
- Department of Orthopedics, Wuwei People's Hospital, Xuanwu Street, Liangzhou District, Wuwei, Gansu, 730030, People's Republic of China
| | - Yan Zhang
- Department of Outpatient, Liangzhou District Huangyang Hospital, Wuwei, Gansu, 733000, People's Republic of China
| | - Zicai Li
- Department of Orthopedics, Wuwei People's Hospital, Xuanwu Street, Liangzhou District, Wuwei, Gansu, 730030, People's Republic of China.
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Pisignano G, Michael DC, Visal TH, Pirlog R, Ladomery M, Calin GA. Going circular: history, present, and future of circRNAs in cancer. Oncogene 2023; 42:2783-2800. [PMID: 37587333 PMCID: PMC10504067 DOI: 10.1038/s41388-023-02780-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023]
Abstract
To date, thousands of highly abundant and conserved single-stranded RNA molecules shaped into ring structures (circRNAs) have been identified. CircRNAs are multifunctional molecules that have been shown to regulate gene expression transcriptionally and post-transcriptionally and exhibit distinct tissue- and development-specific expression patterns associated with a variety of normal and disease conditions, including cancer pathogenesis. Over the past years, due to their intrinsic stability and resistance to ribonucleases, particular attention has been drawn to their use as reliable diagnostic and prognostic biomarkers in cancer diagnosis, treatment, and prevention. However, there are some critical caveats to their utility in the clinic. Their circular shape limits their annotation and a complete functional elucidation is lacking. This makes their detection and biomedical application still challenging. Herein, we review the current knowledge of circRNA biogenesis and function, and of their involvement in tumorigenesis and potential utility in cancer-targeted therapy.
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Affiliation(s)
- Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - David C Michael
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tanvi H Visal
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Radu Pirlog
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol, BS16 1QY, UK
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Chen Z, Song J, Xie L, Xu G, Zheng C, Xia X, Lu F, Ma X, Zou F, Jiang J, Wang H. N6-methyladenosine hypomethylation of circGPATCH2L regulates DNA damage and apoptosis through TRIM28 in intervertebral disc degeneration. Cell Death Differ 2023; 30:1957-1972. [PMID: 37438603 PMCID: PMC10406905 DOI: 10.1038/s41418-023-01190-5] [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: 05/08/2022] [Revised: 05/31/2023] [Accepted: 06/29/2023] [Indexed: 07/14/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs that have been found to be involved in intervertebral disc degeneration (IVDD) progression, and N6-methyladenosine (m6A) broadly exists in circRNAs. Here, we identified circGPATCH2L with a low m6A methylation level to be upregulated in degenerative nucleus pulposus tissues. Mechanistically, as a protein decoy for tripartite motif containing 28 (TRIM28) within aa 402-452 region, circGPATCH2L abrogates the phosphorylation of TRIM28 and inhibits P53 degradation, which contributes to DNA damage accumulation and cellular apoptosis and leads to IVDD progression. Moreover, m6A-methylated circGPATCH2L is recognised and endoribonucleolytically cleaved by a YTHDF2-RPL10-RNase P/MRP complex to maintain the physiological state of nucleus pulposus cells. Thus, our data show the physiological significance of m6A modification in regulating circRNA abundance and provide a potentially effective therapeutic target for the treatment of IVDD.
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Affiliation(s)
- Zhenhao Chen
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China
| | - Jian Song
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China
| | - Lin Xie
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, China
| | - Guangyu Xu
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China
| | - Chaojun Zheng
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China
| | - Xinlei Xia
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China
| | - Feizhou Lu
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China
- Department of Orthopedics, Shanghai Fifth People's Hospital, Fudan University, Shanghai, 200000, China
| | - Xiaosheng Ma
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China
| | - Fei Zou
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China.
| | - Jianyuan Jiang
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China.
| | - Hongli Wang
- Department of Orthopedics, Huashan Hospital, Fudan University, Shanghai, 200000, China.
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Liu B, Shen H, He J, Jin B, Tian Y, Li W, Hou L, Zhao W, Nan J, Zhao J, Shen J, Yu H, Wang Y, Shan G, Shi L, Cai X. Cytoskeleton remodeling mediated by circRNA-YBX1 phase separation suppresses the metastasis of liver cancer. Proc Natl Acad Sci U S A 2023; 120:e2220296120. [PMID: 37459535 PMCID: PMC10372620 DOI: 10.1073/pnas.2220296120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/22/2023] [Indexed: 07/20/2023] Open
Abstract
Metastasis, especially intrahepatic, is a major challenge for hepatocellular carcinoma (HCC) treatment. Cytoskeleton remodeling has been identified as a vital process mediating intrahepatic spreading. Previously, we reported that HCC tumor adhesion and invasion were modulated by circular RNA (circRNA), which has emerged as an important regulator of various cellular processes and has been implicated in cancer progression. Here, we uncovered a nuclear circRNA, circASH2, which is preferentially lost in HCC tissues and inhibits HCC metastasis by altering tumor cytoskeleton structure. Tropomyosin 4 (TPM4), a critical binding protein of actin, turned out to be the major target of circASH2 and was posttranscriptionally suppressed. Such regulation is based on messenger RNA (mRNA)/precursormRNA splicing and degradation process. Furthermore, liquid-liquid phase separation of nuclear Y-box binding protein 1 (YBX1) enhanced by circASH2 augments TPM4 transcripts decay. Together, our data have revealed a tumor-suppressive circRNA and, more importantly, uncovered a fine regulation mechanism for HCC progression.
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Affiliation(s)
- Boqiang Liu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Hao Shen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Jing He
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Binghan Jin
- Department of Endocrinology, The Children's Hospital, School of Medicine, National Clinical Research Center for Child Health, Zhejiang University, Hangzhou310053, China
| | - Yuanshi Tian
- Department of Diagnostic Ultrasound & Echocardiography, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
| | - Weiqi Li
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Lidan Hou
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Weijun Zhao
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Junjie Nan
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Jia Zhao
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
| | - Jiliang Shen
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Hong Yu
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Yifan Wang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Ge Shan
- Zhejiang University Cancer Center, Zhejiang University, Hangzhou310030, China
- Department of Pulmonary and Critical Care Medicine, Regional medical center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Division of Life Science and Medicine, Department of Clinical Laboratory, First Affiliated Hospital of the University of Science and Technology of China, Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, University of Science and Technology of China, Hefei230027, China
| | - Liang Shi
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
| | - Xiujun Cai
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou310016, China
- Zhejiang Provincial Key Laboratory of Laparoscopic Technology, Zhejiang University, Hangzhou310016, China
- Zhejiang Minimal Invasive Diagnosis and Treatment Technology Research Center of Severe Hepatobiliary Disease, Hangzhou310016, China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and Equipment, Hangzhou310016, China
- Zhejiang University Cancer Center, Zhejiang University, Hangzhou310030, China
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36
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Wu S, Wu Y, Deng S, Lei X, Yang X. Emerging roles of noncoding RNAs in human cancers. Discov Oncol 2023; 14:128. [PMID: 37439905 DOI: 10.1007/s12672-023-00728-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/14/2023] [Indexed: 07/14/2023] Open
Abstract
Studies have found that RNA encoding proteins only account for a small part of the total number, most RNA is non-coding RNA, and non-coding RNA may affect the occurrence and development of human cancers by affecting gene expression, therefore play an important role in human pathology. At present, ncRNAs studied include miRNA, circRNA, lncRNA, piRNA, and snoRNA, etc. After decades of research, the basic role of these ncRNAs in many cancers has been clear. As far as we know, the role of miRNAs in cancer is one of the hottest research directions, however, it is also found that the imbalance of ncRNAs will affect the occurrence of gastric cancer, breast cancer, lung cancer, meanwhile, it may also affect the prognosis of these cancers. Therefore, the study of ncRNAs in cancers may help to find new cancer diagnostic and treatment methods. Here, we reviewed the biosynthesis and characteristics of miRNA, cricRNA, and lncRNA etc., their roles in human cancers, as well as the mechanism through which these ncRNAs affect human cancers.
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Affiliation(s)
- Shijie Wu
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Yiwen Wu
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Sijun Deng
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiaoyong Lei
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China
| | - Xiaoyan Yang
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, 28 Western Changsheng Road, Hengyang, 421001, Hunan, People's Republic of China.
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37
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Conn VM, Gabryelska M, Toubia J, Kirk K, Gantley L, Powell JA, Cildir G, Marri S, Liu R, Stringer BW, Townley S, Webb ST, Lin H, Samaraweera SE, Bailey S, Moore AS, Maybury M, Liu D, Colella AD, Chataway T, Wallington-Gates CT, Walters L, Sibbons J, Selth LA, Tergaonkar V, D'Andrea RJ, Pitson SM, Goodall GJ, Conn SJ. Circular RNAs drive oncogenic chromosomal translocations within the MLL recombinome in leukemia. Cancer Cell 2023; 41:1309-1326.e10. [PMID: 37295428 DOI: 10.1016/j.ccell.2023.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/03/2023] [Accepted: 05/03/2023] [Indexed: 06/12/2023]
Abstract
The first step of oncogenesis is the acquisition of a repertoire of genetic mutations to initiate and sustain the malignancy. An important example of this initiation phase in acute leukemias is the formation of a potent oncogene by chromosomal translocations between the mixed lineage leukemia (MLL) gene and one of 100 translocation partners, known as the MLL recombinome. Here, we show that circular RNAs (circRNAs)-a family of covalently closed, alternatively spliced RNA molecules-are enriched within the MLL recombinome and can bind DNA, forming circRNA:DNA hybrids (circR loops) at their cognate loci. These circR loops promote transcriptional pausing, proteasome inhibition, chromatin re-organization, and DNA breakage. Importantly, overexpressing circRNAs in mouse leukemia xenograft models results in co-localization of genomic loci, de novo generation of clinically relevant chromosomal translocations mimicking the MLL recombinome, and hastening of disease onset. Our findings provide fundamental insight into the acquisition of chromosomal translocations by endogenous RNA carcinogens in leukemia.
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Affiliation(s)
- Vanessa M Conn
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia; Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia
| | - Marta Gabryelska
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia; ACRF Cancer Genomics Facility, SA Pathology, Adelaide, SA 5000, Australia
| | - Kirsty Kirk
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Laura Gantley
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Jason A Powell
- Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Gökhan Cildir
- Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia
| | - Shashikanth Marri
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Ryan Liu
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Brett W Stringer
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Scott Townley
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Stuart T Webb
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - He Lin
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Saumya E Samaraweera
- Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia
| | - Sheree Bailey
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Andrew S Moore
- Child Health Research Centre, the University of Queensland, Brisbane, QLD 4101, Australia; Oncology Service, Children's Health Queensland Hospital and Health Service, Brisbane, QLD 4101, Australia
| | - Mellissa Maybury
- Child Health Research Centre, the University of Queensland, Brisbane, QLD 4101, Australia
| | - Dawei Liu
- Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia
| | - Alex D Colella
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia; Flinders Omics Facility, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Timothy Chataway
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia; Flinders Omics Facility, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Craig T Wallington-Gates
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia; Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, the University of Adelaide, Adelaide, SA 5000, Australia; Flinders Medical Centre, Bedford Park, SA 5042, Australia
| | - Lucie Walters
- Adelaide Rural Clinical School, Faculty of Health and Medical Sciences, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Jane Sibbons
- Adelaide Microscopy, Division of Research and Innovation, University of Adelaide, Adelaide, SA 5000, Australia
| | - Luke A Selth
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia; Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, SA 5042, Australia
| | - Vinay Tergaonkar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Richard J D'Andrea
- Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia
| | - Stuart M Pitson
- Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Gregory J Goodall
- Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia; Adelaide Medical School, Faculty of Health and Medical Sciences, the University of Adelaide, Adelaide, SA 5000, Australia
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine & Public Health, Flinders University, Bedford Park, SA 5042, Australia; Centre for Cancer Biology, SA Pathology & University of South Australia, Adelaide, SA 5000, Australia.
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38
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Sun P, Chen M, Sooranna SR, Shi D, Liu Q, Li H. The emerging roles of circRNAs in traits associated with livestock breeding. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1775. [PMID: 36631071 DOI: 10.1002/wrna.1775] [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: 08/16/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/13/2023]
Abstract
Many indicators can be used to evaluate the productivity and quality of livestock, such as meat and milk production as well as fat deposition. Meat and milk production are measures of livestock performance, while fat deposition affects the taste and flavor of the meat. The circRNAs, are non-coding RNAs, that are involved in the regulation of all these three traits. We review the functions and mechanisms of circRNAs in muscle and fat development as well as lactation to provide a theoretical basis for circRNA research in animal husbandry. Various phenotypic changes presented in livestock may be produced by different circRNAs. Our current concern is how to use the roles played by circRNAs to our advantage to produce the best possible livestock. Hence, we describe the advantages and disadvantages of knockout techniques for circRNAs. In addition, we also put forward our thoughts regarding the mechanism and network of circRNAs to provide researchers with novel ideas of how molecular biology can help us advance our goals in animal farming. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Ping Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Suren R Sooranna
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
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Fan YJ, Ding Z, Zhang Y, Su R, Yue JL, Liang AM, Huang QW, Meng YR, Li M, Xue Y, Xu YZ. Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs. Nucleic Acids Res 2023; 51:5228-5241. [PMID: 37070178 PMCID: PMC10250224 DOI: 10.1093/nar/gkad280] [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: 12/16/2022] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 04/19/2023] Open
Abstract
Conversely to canonical splicing, back-splicing connects the upstream 3' splice site (SS) with a downstream 5'SS and generates exonic circular RNAs (circRNAs) that are widely identified and have regulatory functions in eukaryotic gene expression. However, sex-specific back-splicing in Drosophila has not been investigated and its regulation remains unclear. Here, we performed multiple RNA analyses of a variety sex-specific Drosophila samples and identified over ten thousand circular RNAs, in which hundreds are sex-differentially and -specifically back-spliced. Intriguingly, we found that expression of SXL, an RNA-binding protein encoded by Sex-lethal (Sxl), the master Drosophila sex-determination gene that is only spliced into functional proteins in females, promoted back-splicing of many female-differential circRNAs in the male S2 cells, whereas expression of a SXL mutant (SXLRRM) did not promote those events. Using a monoclonal antibody, we further obtained the transcriptome-wide RNA-binding sites of SXL through PAR-CLIP. After splicing assay of mini-genes with mutations in the SXL-binding sites, we revealed that SXL-binding on flanking exons and introns of pre-mRNAs facilitates back-splicing, whereas SXL-binding on the circRNA exons inhibits back-splicing. This study provides strong evidence that SXL has a regulatory role in back-splicing to generate sex-specific and -differential circRNAs, as well as in the initiation of sex-determination cascade through canonical forward-splicing.
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Affiliation(s)
- Yu-Jie Fan
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Zhan Ding
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Yu Zhang
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Ruibao Su
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia-Le Yue
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - An-Min Liang
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Qi-Wei Huang
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Yan-Ran Meng
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Muwang Li
- College of Biotechnology, Jiangsu University of Science and Technology, Jiangsu 212018, China
| | - Yuanchao Xue
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Zhen Xu
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
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40
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Zhang Y, Luo J, Yang W, Ye WC. CircRNAs in colorectal cancer: potential biomarkers and therapeutic targets. Cell Death Dis 2023; 14:353. [PMID: 37296107 PMCID: PMC10250185 DOI: 10.1038/s41419-023-05881-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/09/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most prevalent cancer and the second leading cause of cancer-related deaths. Circular RNAs (circRNAs) are single-stranded RNA with covalently closed-loop structures and are highly stable, conserved, and abundantly expressed in various organs and tissues. Recent research found abnormal circRNA expression in CRC patients' blood/serum, cells, CRC tissues, and exosomes. Furthermore, mounting data demonstrated that circRNAs are crucial to the development of CRC. CircRNAs have been shown to exert biological functions by acting as microRNA sponges, RNA-binding protein sponges, regulators of gene splicing and transcription, and protein/peptide translators. These characteristics make circRNAs potential markers for CRC diagnosis and prognosis, potential therapeutic targets, and circRNA-based therapies. However, further studies are still necessary to improve the understanding of the roles and biological mechanisms of circRNAs in the development of CRC. In this review, up-to-date research on the role of circRNAs in CRC was examined, focusing on their potential application in CRC diagnosis and targeted therapy, which would advance the knowledge of the functions of circRNAs in the development and progression of CRC.
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Affiliation(s)
- Yuying Zhang
- Central Laboratory, Shenzhen Longhua Maternity and Child Healthcare Hospital, Shenzhen, 518109, China
| | - Jingyan Luo
- Forevergen Biosciences Centre, Guangzhou International Biotech Island, Guangzhou, 510300, China
| | - Weikang Yang
- Department of Prevention and Healthcare, Shenzhen Longhua Maternity and Child Healthcare Hospital, Shenzhen, 518109, China
| | - Wen-Chu Ye
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
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Chen X, Huang C. Chromatin-interacting RNA-binding proteins regulate transcription. Trends Cell Biol 2023:S0962-8924(23)00089-2. [PMID: 37270323 DOI: 10.1016/j.tcb.2023.05.006] [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: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/05/2023]
Abstract
RNA-binding proteins (RBPs) are essential regulators involved in the fate determination of diverse RNA species; however, emerging evidence indicates that a subset of RBPs may physically interact with chromatin and function at the transcriptional level. Here, we highlight the recently discovered mechanisms of chromatin-interacting RBPs (ChRBPs) in the regulation of chromatin/transcriptional activities.
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Affiliation(s)
- Xiaolan Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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Hirano M, Galarza-Muñoz G, Nagasawa C, Schott G, Wang L, Antonia AL, Jain V, Yu X, Widen SG, Briggs FBS, Gregory SG, Ko DC, Fagg WS, Bradrick S, Garcia-Blanco MA. The RNA helicase DDX39B activates FOXP3 RNA splicing to control T regulatory cell fate. eLife 2023; 12:e76927. [PMID: 37261960 PMCID: PMC10234631 DOI: 10.7554/elife.76927] [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: 01/10/2022] [Accepted: 05/09/2023] [Indexed: 06/03/2023] Open
Abstract
Genes associated with increased susceptibility to multiple sclerosis (MS) have been identified, but their functions are incompletely understood. One of these genes codes for the RNA helicase DExD/H-Box Polypeptide 39B (DDX39B), which shows genetic and functional epistasis with interleukin-7 receptor-α gene (IL7R) in MS-risk. Based on evolutionary and functional arguments, we postulated that DDX39B enhances immune tolerance thereby decreasing MS risk. Consistent with such a role we show that DDX39B controls the expression of many MS susceptibility genes and important immune-related genes. Among these we identified Forkhead Box P3 (FOXP3), which codes for the master transcriptional factor in CD4+/CD25+ T regulatory cells. DDX39B knockdown led to loss of immune-regulatory and gain of immune-effector expression signatures. Splicing of FOXP3 introns, which belong to a previously unrecognized type of introns with C-rich polypyrimidine tracts, was exquisitely sensitive to DDX39B levels. Given the importance of FOXP3 in autoimmunity, this work cements DDX39B as an important guardian of immune tolerance.
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Affiliation(s)
- Minato Hirano
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- National Research Center for the Control and Prevention of Infectious Disease, Nagasaki UniversityNagasakiJapan
| | - Gaddiel Galarza-Muñoz
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Autoimmunity Biological SolutionsGalvestonUnited States
| | - Chloe Nagasawa
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Human Pathophysiology and Translational Medicine Program, Institute for Translational Sciences, University of Texas Medical BranchGalvestonUnited States
| | - Geraldine Schott
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Duke UniversityDurhamUnited States
| | - Xiaoying Yu
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Department of Preventive Medicine and Population Health, University of Texas Medical BranchGalvestonUnited States
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
| | - Farren BS Briggs
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve UniversityClevelandUnited States
| | - Simon G Gregory
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
- Duke Molecular Physiology Institute, Duke UniversityDurhamUnited States
- Department of Neurology, Duke University School of MedicineDurhamUnited States
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, Duke UniversityDurhamUnited States
- Division of Infectious Diseases, Department of Medicine, Duke UniversityDurhamUnited States
| | - William S Fagg
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Transplant Division, Department of Surgery, University of Texas Medical BranchGalvestonUnited States
| | - Shelton Bradrick
- Institute of Human Infections and Immunity, University of Texas Medical BranchGalvestonUnited States
| | - Mariano A Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical BranchGalvestonUnited States
- Department of Internal Medicine, University of Texas Medical BranchGalvestonUnited States
- Department of Microbiology, Immunology and Cancer Biology, University of VirginiaCharlottesvilleUnited States
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Wei L, Liu L, Bai M, Ning X, Sun S. CircRNAs: versatile players and new targets in organ fibrosis. Cell Commun Signal 2023; 21:90. [PMID: 37131173 PMCID: PMC10152639 DOI: 10.1186/s12964-023-01051-1] [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: 11/28/2022] [Accepted: 01/15/2023] [Indexed: 05/04/2023] Open
Abstract
Organ fibrosis can occur in virtually all major organs with relentlessly progressive and irreversible progress, ultimately resulting in organ dysfunction and potentially death. Unfortunately, current clinical treatments cannot halt or reverse the progression of fibrosis to end-stage organ failure, and thus, advanced antifibrotic therapeutics are urgently needed. In recent years, a growing body of research has revealed that circular RNAs (circRNAs) play pivotal roles in the development and progression of organ fibrosis through highly diverse mechanisms of action. Thus, manipulating circRNAs has emerged as a promising strategy to mitigate fibrosis across different organ types. In this review, we systemically summarize the current state of knowledge about circRNA biological properties and the regulatory mechanisms of circRNAs. A comprehensive overview of major fibrotic signaling pathways and representative circRNAs that are known to modulate fibrotic signals are outlined. Then, we focus on the research progress of the versatile functional roles and underlying molecular mechanisms of circRNAs in various fibrotic diseases in different organs, including the heart, liver, lung, kidney and skin. Finally, we offer a glimpse into the prospects of circRNA-based interference and therapy, as well as their utilization as biomarkers in the diagnosis and prognosis of fibrotic diseases. Video abstract.
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Affiliation(s)
- Lei Wei
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, No. 127 Changle West Road, Xi'an, Shaanxi, China
| | - Limin Liu
- School of Medicine, Northwest University, 229 Taibai North Road, Xi'an, 710032, Shaanxi, China
| | - Ming Bai
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, No. 127 Changle West Road, Xi'an, Shaanxi, China
| | - Xiaoxuan Ning
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, No. 127 Changle West Road, Xi'an, 710032, Shaanxi, China.
| | - Shiren Sun
- Department of Nephrology, Xijing Hospital, The Fourth Military Medical University, No. 127 Changle West Road, Xi'an, Shaanxi, China.
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Khan M, Hou S, Chen M, Lei H. Mechanisms of RNA export and nuclear retention. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1755. [PMID: 35978483 DOI: 10.1002/wrna.1755] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/21/2022] [Accepted: 07/06/2022] [Indexed: 05/13/2023]
Abstract
With the identification of huge amount of noncoding RNAs in recent years, the concept of RNA localization has extended from traditional mRNA export to RNA export of mRNA and ncRNA as well as nuclear retention of ncRNA. This review aims to summarize the recent findings from studies on the mechanisms of export of different RNAs and nuclear retention of some lncRNAs in higher eukaryotes, with a focus on splicing-dependent TREX recruitment for the export of spliced mRNA and the sequence-dependent mechanism of mRNA export in the absence of splicing. In addition, evidence to support the involvement of m6 A modification in RNA export with the coordination between the methylase complex and TREX complex as well as sequence-dependent nuclear retention of lncRNA is recapitulated. Finally, a model of sequence-dependent RNA localization is proposed along with the many questions that remain to be answered. This article is categorized under: RNA Export and Localization > RNA Localization RNA Export and Localization > Nuclear Export/Import.
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Affiliation(s)
- Misbah Khan
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Shuai Hou
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Mo Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Haixin Lei
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
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45
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Dattilo D, Di Timoteo G, Setti A, Giuliani A, Peruzzi G, Beltran Nebot M, Centrón-Broco A, Mariani D, Mozzetta C, Bozzoni I. The m 6A reader YTHDC1 and the RNA helicase DDX5 control the production of rhabdomyosarcoma-enriched circRNAs. Nat Commun 2023; 14:1898. [PMID: 37019933 PMCID: PMC10076346 DOI: 10.1038/s41467-023-37578-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/22/2023] [Indexed: 04/07/2023] Open
Abstract
N6-Methyladenosine (m6A) is well-known for controlling different processes of linear RNA metabolism. Conversely, its role in the biogenesis and function of circular RNAs (circRNAs) is still poorly understood. Here, we characterize circRNA expression in the pathological context of rhabdomyosarcoma (RMS), observing a global increase when compared to wild-type myoblasts. For a set of circRNAs, such an increase is due to the raised expression of the m6A machinery, which we also find to control the proliferation activity of RMS cells. Furthermore, we identify the RNA helicase DDX5 as a mediator of the back-splicing reaction and as a co-factor of the m6A regulatory network. DDX5 and the m6A reader YTHDC1 are shown to interact and to promote the production of a common subset of circRNAs in RMS. In line with the observation that YTHDC1/DDX5 depletion reduces RMS proliferation, our results provide proteins and RNA candidates for the study of rhabdomyosarcoma tumorigenicity.
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Affiliation(s)
- Dario Dattilo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Gaia Di Timoteo
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Adriano Setti
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Andrea Giuliani
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Giovanna Peruzzi
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy
| | - Manuel Beltran Nebot
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Alvaro Centrón-Broco
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy
| | - Davide Mariani
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy
| | - Chiara Mozzetta
- Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) of Italy, Rome, Italy
| | - Irene Bozzoni
- Department of Biology and Biotechnology Charles Darwin, Sapienza University of Rome, Rome, 00185, Italy.
- Center for Life Nano- & Neuro-Science@Sapienza, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, 00161, Italy.
- Center for Human Technologies@Istituto Italiano di Tecnologia (IIT), Genoa, 16152, Italy.
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Ikeda Y, Morikawa S, Nakashima M, Yoshikawa S, Taniguchi K, Sawamura H, Suga N, Tsuji A, Matsuda S. CircRNAs and RNA-Binding Proteins Involved in the Pathogenesis of Cancers or Central Nervous System Disorders. Noncoding RNA 2023; 9:ncrna9020023. [PMID: 37104005 PMCID: PMC10142617 DOI: 10.3390/ncrna9020023] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Circular RNAs (circRNAs), a newly recognized group of noncoding RNA transcripts, have established widespread attention due to their regulatory role in cell signaling. They are covalently closed noncoding RNAs that form a loop, and are typically generated during the splicing of precursor RNAs. CircRNAs are key post-transcriptional and post-translational regulators of gene expression programs that might influence cellular response and/or function. In particular, circRNAs have been considered to function as sponges of specific miRNA, regulating cellular processes at the post-transcription stage. Accumulating evidence has shown that the aberrant expression of circRNAs could play a key role in the pathogenesis of several diseases. Notably, circRNAs, microRNAs, and several RNA-binding proteins, including the antiproliferative (APRO) family proteins, could be indispensable gene modulators, which might be strongly linked to the occurrence of diseases. In addition, circRNAs have attracted general interest for their stability, abundance in the brain, and their capability to cross the blood–brain barrier. Here, we present the current findings and theragnostic potentials of circRNAs in several diseases. With this, we aim to provide new insights to support the development of novel diagnostic and/or therapeutic strategies for these diseases.
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47
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Liu Y, Jiang C, Liu Q, Huang R, Wang M, Guo X. CircRNAs: emerging factors for regulating glucose metabolism in colorectal cancer. Clin Transl Oncol 2023:10.1007/s12094-023-03131-7. [PMID: 36944731 DOI: 10.1007/s12094-023-03131-7] [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: 10/21/2022] [Accepted: 02/19/2023] [Indexed: 03/23/2023]
Abstract
Colorectal cancer is a malignant disease with a high incidence and low survival rate, and the effectiveness of traditional treatments, such as surgery and radiotherapy, is very limited. CircRNAs, a kind of stable endogenous circular RNA, generally function by sponging miRNAs and binding or translating proteins. CircRNAs have been identified to play an important role in regulating the proliferation and metabolism of CRC. In recent years, many reports have indicated that by regulating the expression of glycolysis-related proteins, such as GLUT1 and HK2, or directly translating proteins, circRNAs can promote the Warburg effect in cancer cells, thereby driving CRC metabolism. Moreover, the Warburg effect increases lactate production in cancer cells and promotes acidification of the TME, which further drives cancer progression. In this review, we summarized the remarkable role of circRNAs in regulating glucose metabolism in CRC in recent years, which might be useful for finding new targets for the clinical treatment of CRC.
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Affiliation(s)
- Yulin Liu
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, The People's Republic of China
| | - Chenjun Jiang
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, The People's Republic of China
| | - Qianqian Liu
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, The People's Republic of China
| | - Runchun Huang
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, The People's Republic of China
| | - Mancai Wang
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, The People's Republic of China
- General Surgery Department, The Second Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Xiaohu Guo
- The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000, The People's Republic of China.
- General Surgery Department, The Second Hospital of Lanzhou University, Lanzhou, 730000, China.
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48
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Zhang Z, Huang Y, Guo AY, Yang L. Research progress of circular RNA molecules in aging and age-related diseases. Ageing Res Rev 2023; 87:101913. [PMID: 36934850 DOI: 10.1016/j.arr.2023.101913] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/05/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-chain endogenous closed circular RNAs that do not have a poly(A) tail at the 3' end and a cap structure at the 5' end and are connected end-to-end by covalent bonds. CircRNAs, which are pervasive, diverse, stable, and conversed, have functions in transcriptional control and protein translation and play vital roles in modulating cell senescence, individual aging, as well as the occurrence and development of age-related diseases. Studies in recent years were reviewed from aspects including the biosynthesis mechanisms, classification, expression, biomedical functions, associations with aging and age-related diseases, and potential clinical applications of circRNAs. It will provide the theoretic basis for exploring the molecular biological mechanisms of aging, using circRNA as the therapeutic target to delay aging, and finding therapeutic strategies to prevent and treat age-related diseases.
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Affiliation(s)
- Zhidan Zhang
- Departments of Infectious Disease, The First Hospital of China Medical University, Shenyang, PR China
| | - Yuling Huang
- Departments of Geriatrics, The First Hospital of China Medical University, Shenyang, PR China
| | - AYao Guo
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, PR China.
| | - Lina Yang
- Departments of Geriatrics, The First Hospital of China Medical University, Shenyang, PR China.
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49
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Wu C, Huang X, Li M, Wang Z, Zhang Y, Tian B. Crosstalk between circRNAs and the PI3K/AKT and/or MEK/ERK signaling pathways in digestive tract malignancy progression. Future Oncol 2023; 18:4525-4538. [PMID: 36891896 DOI: 10.2217/fon-2022-0429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Evidence indicates that circular RNAs (circRNAs) may play an important role in regulating gene expression by binding to miRNAs through miRNA response elements. circRNAs are formed by back-splicing and have a covalently closed structure. The biogenesis of circRNAs also appears to be regulated by certain cell-specific and/or gene-specific mechanisms, and thus some circRNAs are tissue specific and tumor-expression specific. Furthermore, the high stability and tissue specificity of circRNAs may be of value for early diagnosis, survival prediction and precision medicine. This review summarizes current knowledge regarding the classification and functions of circRNAs and the role of circRNAs in regulating the PI3K/AKT and/or MEK/ERK signaling pathways in digestive tract malignancy tumors.
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Affiliation(s)
- Chao Wu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Xing Huang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Mao Li
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Zihe Wang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Yi Zhang
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
| | - Bole Tian
- Department of Pancreatic Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu, Sichuan Province, China
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Yalamarty SSK, Filipczak N, Khan MM, Torchilin VP. Role of circular RNA and its delivery strategies to cancer - An overview. J Control Release 2023; 356:306-315. [PMID: 36878321 DOI: 10.1016/j.jconrel.2023.02.044] [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: 07/20/2022] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023]
Abstract
With the passage of years and the progress of research on ribonucleic acids, the range of forms in which these molecules have been observed grows. One of them, discovered relatively recently, is circular RNA - covalently closed circles (circRNA). In recent years, there has been a huge increase in the interest of researchers in this group of molecules. It entailed a significant increase in the state of knowledge about them, which in turn caused a dramatic change in their perception. Rather than seeing circular RNAs as curiosities that represent a minor information noise in a cell or a result of RNA misprocessing, they came to be regarded as a common, essential, and potentially extremely useful group of molecules. Nevertheless, the current state of the art of circRNA is full of white cards. A lot of valuable information has been obtained from high-throughput methods to study whole transcriptomes, but many issues related to circular RNAs still need to be clarified. Presumably, each answer obtained will raise several new questions. However, circRNAs have a wealth of potential applications, including therapeutic applications.
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Affiliation(s)
| | - Nina Filipczak
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA 02115, USA
| | | | - Vladimir P Torchilin
- Center for Pharmaceutical Biotechnology and Nanomedicine, Northeastern University, Boston, MA 02115, USA; Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA.
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